Vocalizations associated with anxiety and fear in the common marmoset (Callithrix jacchus).

PubMed

Kato, Yoko; Gokan, Hayato; Oh-Nishi, Arata; Suhara, Tetsuya; Watanabe, Shigeru; Minamimoto, Takafumi

2014-12-15

Vocalizations of common marmoset (Callithrix jacchus) were examined under experimental situations related to fear or anxiety. When marmosets were isolated in an unfamiliar environment, they frequently vocalized "tsik-egg" calls, which were the combination calls of 'tsik' followed by several 'egg'. Tsik-egg calls were also observed after treatment with the anxiogenic drug FG-7142 (20mg/kg, sc). In contrast, when marmosets were exposed to predatory stimuli as fear-evoking situations, they frequently vocalized tsik solo calls as well as tsik-egg calls. These results suggest that marmosets dissociate the vocalization of tsik-egg and tsik calls under conditions related to fear/anxiety; tsik-egg solo vocalizations were emitted under anxiety-related conditions (e.g., isolation and anxiogenic drug treatment), whereas a mixed vocalization of tsik-egg and tsik was emitted when confronted with fear-provoking stimuli (i.e., threatening predatory stimuli). Tsik-egg call with/without tsik can be used as a specific vocal index of fear/anxiety in marmosets, which allows us to understand the neural mechanism of negative emotions in primate. Copyright © 2014 Elsevier B.V. All rights reserved.

Object permanence in adult common marmosets (Callithrix jacchus): not everything is an "A-not-B" error that seems to be one.

PubMed

Kis, Anna; Gácsi, Márta; Range, Friederike; Virányi, Zsófia

2012-01-01

In this paper, we describe a behaviour pattern similar to the "A-not-B" error found in human infants and young apes in a monkey species, the common marmosets (Callithrix jacchus). In contrast to the classical explanation, recently it has been suggested that the "A-not-B" error committed by human infants is at least partially due to misinterpretation of the hider's ostensively communicated object hiding actions as potential 'teaching' demonstrations during the A trials. We tested whether this so-called Natural Pedagogy hypothesis would account for the A-not-B error that marmosets commit in a standard object permanence task, but found no support for the hypothesis in this species. Alternatively, we present evidence that lower level mechanisms, such as attention and motivation, play an important role in committing the "A-not-B" error in marmosets. We argue that these simple mechanisms might contribute to the effect of undeveloped object representational skills in other species including young non-human primates that commit the A-not-B error.

Abundant Occurrence of Basal Radial Glia in the Subventricular Zone of Embryonic Neocortex of a Lissencephalic Primate, the Common Marmoset Callithrix jacchus

PubMed Central

Kelava, Iva; Reillo, Isabel; Murayama, Ayako Y.; Kalinka, Alex T.; Stenzel, Denise; Tomancak, Pavel; Matsuzaki, Fumio; Lebrand, Cécile; Sasaki, Erika; Schwamborn, Jens C.; Okano, Hideyuki; Borrell, Víctor

2012-01-01

Subventricular zone (SVZ) progenitors are a hallmark of the developing neocortex. Recent studies described a novel type of SVZ progenitor that retains a basal process at mitosis, sustains expression of radial glial markers, and is capable of self-renewal. These progenitors, referred to here as basal radial glia (bRG), occur at high relative abundance in the SVZ of gyrencephalic primates (human) and nonprimates (ferret) but not lissencephalic rodents (mouse). Here, we analyzed the occurrence of bRG cells in the embryonic neocortex of the common marmoset Callithrix jacchus, a near-lissencephalic primate. bRG cells, expressing Pax6, Sox2 (but not Tbr2), glutamate aspartate transporter, and glial fibrillary acidic protein and retaining a basal process at mitosis, occur at similar relative abundance in the marmoset SVZ as in human and ferret. The proportion of progenitors in M-phase was lower in embryonic marmoset than developing ferret neocortex, raising the possibility of a longer cell cycle. Fitting the gyrification indices of 26 anthropoid species to an evolutionary model suggested that the marmoset evolved from a gyrencephalic ancestor. Our results suggest that a high relative abundance of bRG cells may be necessary, but is not sufficient, for gyrencephaly and that the marmoset's lissencephaly evolved secondarily by changing progenitor parameters other than progenitor type. PMID:22114084

Experimental respiratory Marburg virus haemorrhagic fever infection in the common marmoset (Callithrix jacchus).

PubMed

Smither, Sophie J; Nelson, Michelle; Eastaugh, Lin; Laws, Thomas R; Taylor, Christopher; Smith, Simon A; Salguero, Francisco J; Lever, Mark S

2013-04-01

Marburg virus causes a highly infectious and lethal haemorrhagic fever in primates and may be exploited as a potential biothreat pathogen. To combat the infection and threat of Marburg haemorrhagic fever, there is a need to develop and license appropriate medical countermeasures. To determine whether the common marmoset (Callithrix jacchus) would be an appropriate model to assess therapies against Marburg haemorrhagic fever, initial susceptibility, lethality and pathogenesis studies were performed. Low doses of virus, between 4 and 28 TCID50 , were sufficient to cause a lethal, reproducible infection. Animals became febrile between days 5 and 6, maintaining a high fever before succumbing to disease between 8 and 11 days postchallenge. Typical signs of Marburg virus infection were observed including haemorrhaging and a transient rash. In pathogenesis studies, virus was isolated from the animals' lungs from day 3 postchallenge and from the liver, spleen and blood from day 5 postchallenge. Early signs of histopathology were apparent in the kidney and liver from day 3. The most striking features were observed in animals exhibiting severe clinical signs, which included high viral titres in all organs, with the highest levels in the blood, increased levels in liver function enzymes and blood clotting times, decreased levels in platelets, multifocal moderate-to-severe hepatitis and perivascular oedema. © 2013 Crown copyright. International Journal of Experimental Pathology © 2013 International Journal of Experimental Pathology.

Comparative experimental subcutaneous glanders and melioidosis in the common marmoset (Callithrix jacchus)

PubMed Central

Nelson, Michelle; Salguero, Francisco J; Dean, Rachel E; Ngugi, Sarah A; Smither, Sophie J; Atkins, Timothy P; Lever, Mark S

2014-01-01

Glanders and melioidosis are caused by two distinct Burkholderia species and have generally been considered to have similar disease progression. While both of these pathogens are HHS/CDC Tier 1 agents, natural infection with both these pathogens is primarily through skin inoculation. The common marmoset (Callithrix jacchus) was used to compare disease following experimental subcutaneous challenge. Acute, lethal disease was observed in marmosets following challenge with between 26 and 1.2 × 108 cfu Burkholderia pseudomallei within 22–85 h. The reproducibility and progression of the disease were assessed following a challenge of 1 × 102 cfu of B. pseudomallei. Melioidosis was characterised by high levels of bacteraemia, focal microgranuloma progressing to non-necrotic multifocal solid lesions in the livers and spleens and multi-organ failure. Lethal disease was observed in 93% of animals challenged with Burkholderia mallei, occurring between 5 and 10.6 days. Following challenge with 1 × 102 cfu of B. mallei, glanders was characterised with lymphatic spread of the bacteria and non-necrotic, multifocal solid lesions progressing to a multifocal lesion with severe necrosis and pneumonia. The experimental results confirmed that the disease pathology and presentation is strikingly different between the two pathogens. The marmoset provides a model of the human syndrome for both diseases facilitating the development of medical countermeasures. PMID:25477002

Differential Virulence and Disease Progression following Mycobacterium tuberculosis Complex Infection of the Common Marmoset (Callithrix jacchus)

PubMed Central

Via, Laura E.; Weiner, Danielle M.; Schimel, Daniel; Lin, Philana Ling; Dayao, Emmanuel; Tankersley, Sarah L.; Cai, Ying; Coleman, M. Teresa; Tomko, Jaime; Paripati, Praveen; Orandle, Marlene; Kastenmayer, Robin J.; Tartakovsky, Michael; Rosenthal, Alexander; Portevin, Damien; Eum, Seok Yong; Lahouar, Saher; Gagneux, Sebastien; Young, Douglas B.; Flynn, JoAnne L.

2013-01-01

Existing small-animal models of tuberculosis (TB) rarely develop cavitary disease, limiting their value for assessing the biology and dynamics of this highly important feature of human disease. To develop a smaller primate model with pathology similar to that seen in humans, we experimentally infected the common marmoset (Callithrix jacchus) with diverse strains of Mycobacterium tuberculosis of various pathogenic potentials. These included recent isolates of the modern Beijing lineage, the Euro-American X lineage, and M. africanum. All three strains produced fulminant disease in this animal with a spectrum of progression rates and clinical sequelae that could be monitored in real time using 2-deoxy-2-[18F]fluoro-d-glucose (FDG) positron emission tomography (PET)/computed tomography (CT). Lesion pathology at sacrifice revealed the entire spectrum of lesions observed in human TB patients. The three strains produced different rates of progression to disease, various extents of extrapulmonary dissemination, and various degrees of cavitation. The majority of live births in this species are twins, and comparison of results from siblings with different infecting strains allowed us to establish that the infection was highly reproducible and that the differential virulence of strains was not simply host variation. Quantitative assessment of disease burden by FDG-PET/CT provided an accurate reflection of the pathology findings at necropsy. These results suggest that the marmoset offers an attractive small-animal model of human disease that recapitulates both the complex pathology and spectrum of disease observed in humans infected with various M. tuberculosis strain clades. PMID:23716617

An animal model that reflects human disease: the common marmoset (Callithrix jacchus).

PubMed

Carrion, Ricardo; Patterson, Jean L

2012-06-01

The common marmoset is a new world primate belonging to the Callitrichidae family weighing between 350 and 400 g. The marmoset has been shown to be an outstanding model for studying aging, reproduction, neuroscience, toxicology, and infectious disease. With regard to their susceptibility to infectious agents, they are exquisite NHP models for viral, protozoan and bacterial agents, as well as prions. The marmoset provides the advantages of a small animal model in high containment coupled with the immunological repertoire of a nonhuman primate and susceptibility to wild type, non-adapted viruses. Copyright © 2012 Elsevier B.V. All rights reserved.

Common Marmosets (Callithrix jacchus) as a Nonhuman Primate Model To Assess the Virulence of Eastern Equine Encephalitis Virus Strains▿

PubMed Central

Adams, A. Paige; Aronson, Judith F.; Tardif, Suzette D.; Patterson, Jean L.; Brasky, Kathleen M.; Geiger, Robert; de la Garza, Melissa; Carrion, Ricardo; Weaver, Scott C.

2008-01-01

Eastern equine encephalitis virus (EEEV) produces the most severe human arboviral disease in North America (NA) and is a potential biological weapon. However, genetically and antigenically distinct strains from South America (SA) have seldom been associated with human disease or mortality despite serological evidence of infection. Because mice and other small rodents do not respond differently to the NA versus SA viruses like humans, we tested common marmosets (Callithrix jacchus) by using intranasal infection and monitoring for weight loss, fever, anorexia, depression, and neurologic signs. The NA EEEV-infected animals either died or were euthanized on day 4 or 5 after infection due to anorexia and neurologic signs, but the SA EEEV-infected animals remained healthy and survived. The SA EEEV-infected animals developed peak viremia titers of 2.8 to 3.1 log10 PFU/ml on day 2 or 4 after infection, but there was no detectable viremia in the NA EEEV-infected animals. In contrast, virus was detected in the brain, liver, and muscle of the NA EEEV-infected animals at the time of euthanasia or death. Similar to the brain lesions described for human EEE, the NA EEEV-infected animals developed meningoencephalitis in the cerebral cortex with some perivascular hemorrhages. The findings of this study identify the common marmoset as a useful model of human EEE for testing antiviral drugs and vaccine candidates and highlight their potential for corroborating epidemiological evidence that some, if not all, SA EEEV strains are attenuated for humans. PMID:18614636

Natural and Anthropogenic Hybridization in Two Species of Eastern Brazilian Marmosets (Callithrix jacchus and C. penicillata)

PubMed Central

Malukiewicz, Joanna; Boere, Vanner; Fuzessy, Lisieux F.; Grativol, Adriana D.; de Oliveira e Silva, Ita; Pereira, Luiz C. M.; Ruiz-Miranda, Carlos R.; Valença, Yuri M.; Stone, Anne C.

2015-01-01

Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the São Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that São Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between “natural” and “man-made.” PMID:26061111

Comparative experimental subcutaneous glanders and melioidosis in the common marmoset (Callithrix jacchus).

PubMed

Nelson, Michelle; Salguero, Francisco J; Dean, Rachel E; Ngugi, Sarah A; Smither, Sophie J; Atkins, Timothy P; Lever, Mark S

2014-12-01

Glanders and melioidosis are caused by two distinct Burkholderia species and have generally been considered to have similar disease progression. While both of these pathogens are HHS/CDC Tier 1 agents, natural infection with both these pathogens is primarily through skin inoculation. The common marmoset (Callithrix jacchus) was used to compare disease following experimental subcutaneous challenge. Acute, lethal disease was observed in marmosets following challenge with between 26 and 1.2 × 10(8) cfu Burkholderia pseudomallei within 22-85 h. The reproducibility and progression of the disease were assessed following a challenge of 1 × 10(2) cfu of B. pseudomallei. Melioidosis was characterised by high levels of bacteraemia, focal microgranuloma progressing to non-necrotic multifocal solid lesions in the livers and spleens and multi-organ failure. Lethal disease was observed in 93% of animals challenged with Burkholderia mallei, occurring between 5 and 10.6 days. Following challenge with 1 × 10(2) cfu of B. mallei, glanders was characterised with lymphatic spread of the bacteria and non-necrotic, multifocal solid lesions progressing to a multifocal lesion with severe necrosis and pneumonia. The experimental results confirmed that the disease pathology and presentation is strikingly different between the two pathogens. The marmoset provides a model of the human syndrome for both diseases facilitating the development of medical countermeasures. © 2014 Crown copyright. International Journal of Experimental Pathology © 2014 Company of the International Journal of Experimental Pathology (CIJEP).

Metabolic Characterization of the Common Marmoset (Callithrix jacchus)

PubMed Central

Go, Young-Mi; Liang, Yongliang; Uppal, Karan; Soltow, Quinlyn A.; Promislow, Daniel E. L.; Wachtman, Lynn M.; Jones, Dean P.

2015-01-01

High-resolution metabolomics has created opportunity to integrate nutrition and metabolism into genetic studies to improve understanding of the diverse radiation of primate species. At present, however, there is very little information to help guide experimental design for study of wild populations. In a previous non-targeted metabolomics study of common marmosets (Callithrix jacchus), Rhesus macaques, humans, and four non-primate mammalian species, we found that essential amino acids (AA) and other central metabolites had interspecies variation similar to intraspecies variation while non-essential AA, environmental chemicals and catabolic waste products had greater interspecies variation. The present study was designed to test whether 55 plasma metabolites, including both nutritionally essential and non-essential metabolites and catabolic products, differ in concentration in common marmosets and humans. Significant differences were present for more than half of the metabolites analyzed and included AA, vitamins and central lipid metabolites, as well as for catabolic products of AA, nucleotides, energy metabolism and heme. Three environmental chemicals were present at low nanomolar concentrations but did not differ between species. Sex and age differences in marmosets were present for AA and nucleotide metabolism and warrant additional study. Overall, the results suggest that quantitative, targeted metabolomics can provide a useful complement to non-targeted metabolomics for studies of diet and environment interactions in primate evolution. PMID:26581102

Consistent inter-individual differences in common marmosets (Callithrix jacchus) in Boldness-Shyness, Stress-Activity, and Exploration-Avoidance.

PubMed

Šlipogor, Vedrana; Gunhold-de Oliveira, Tina; Tadić, Zoran; Massen, Jorg J M; Bugnyar, Thomas

2016-09-01

The study of animal personality, defined as consistent inter-individual differences in correlated behavioral traits stable throughout time and/or contexts, has recently become one of the fastest growing areas in animal biology, with study species ranging from insects to non-human primates. The latter have, however, only occasionally been tested with standardized experiments. Instead their personality has usually been assessed using questionnaires. Therefore, this study aimed to test 21 common marmosets (Callithrix jacchus) living in three family groups, in five different experiments, and their corresponding controls. We found that behavioral differences between our animals were not only consistent over time, but also across different contexts. Moreover, the consistent behaviors formed a construct of four major non-social personality components: Boldness-Shyness in Foraging, Boldness-Shyness in Predation, Stress-Activity, and Exploration-Avoidance. We found no sex or age differences in these components, but our results did reveal differences in Exploration-Avoidance between the three family groups. As social environment can have a large influence on behavior of individuals, our results may suggest group-level similarity in personality (i.e., "group personality") in common marmosets, a species living in highly cohesive social groups. Am. J. Primatol. 78:961-973, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Molecular Cloning of Ghrelin and Characteristics of Ghrelin-Producing Cells in the Gastrointestinal Tract of the Common Marmoset (Callithrix jacchus).

PubMed

Takemi, Shota; Sakata, Ichiro; Apu, Auvijit Saha; Tsukahara, Shinji; Yahashi, Satowa; Katsuura, Goro; Iwashige, Fumihiro; Akune, Atsushi; Inui, Akio; Sakai, Takafumi

2016-10-01

Ghrelin was first isolated from human and rat as an endogenous ligand for the growth hormone secretagogue receptor (GHS-R). In the present study, we determined the ghrelin cDNA sequence of the common marmoset (Callithrix jacchus), a small-bodied New World monkey, and investigated the distribution of ghrelin-producing cells in the gastrointestinal tract and localization profiles with somatostatin-producing cells. The marmoset ghrelin cDNA coding region was 354 base pairs, and showed high homology to that in human, rhesus monkey, and mouse. Marmoset ghrelin consists of 28 amino acids, and the N-terminal region is highly conserved as found in other mammalian species. Marmoset preproghrelin and mature ghrelin have 86.3% and 92.9% homology, respectively, to their human counterparts. Quantitative RT-PCR analysis showed that marmoset ghrelin mRNA is highly expressed in the stomach, but it is not detected in other tissues of the gastrointestinal tract. In addition, a large number of ghrelin mRNA-expressing cells and ghrelin-immunopositive cells were detected in the mucosal layer of the stomach, but not in the myenteric plexus. Moreover, all the ghrelin cells examined in the stomach were observed to be closed-type. Double staining showed that somatostatin-immunopositive cells were not co-localized with ghrelin-producing cells; however, a subset of somatostatin-immunopositive cells is directly adjacent to ghrelin-immunopositive cells. These findings suggest that the distribution of ghrelin cells in marmoset differs from that in rodents, and thus the marmoset may be a more useful model for the translational study of ghrelin in primates. In conclusion, we have clarified the expression and cell distribution of ghrelin in marmoset, which may represent a useful model in translational study.

A longitudinal analysis of the effects of age on the blood plasma metabolome in the common marmoset, Callithrix jacchus

PubMed Central

Hoffman, Jessica M.; Tran, ViLinh; Wachtman, Lynn M.; Green, Cara L.; Jones, Dean P.; Promislow, Daniel E.L.

2016-01-01

Primates tend to be long-lived for their size with humans being the longest lived of all primates. There are compelling reasons to understand the underlying age-related processes that shape human lifespan. But the very fact of our long lifespan that makes it so compelling, also makes it especially difficult to study. Thus, in studies of aging, researchers have turned to non-human primate models, including chimpanzees, baboons, and rhesus macaques. More recently, the common marmoset, Callithrix jacchus, has been recognized as a particularly valuable model in studies of aging, given its small size, ease of housing in captivity, and relatively short lifespan. However, little is known about the physiological changes that occur as marmosets age. To begin to fill in this gap, we utilized high sensitivity metabolomics to define the longitudinal biochemical changes associated with age in the common marmoset. We measured 2104 metabolites from blood plasma at three separate time points over a 17-month period, and we completed both a cross-sectional and longitudinal analysis of the metabolome. We discovered hundreds of metabolites associated with age and body weight in both male and female animals. Our longitudinal analysis identified age-associated metabolic pathways that were not found in our cross-sectional analysis. Pathways enriched for age-associated metabolites included tryptophan, nucleotide, and xenobiotic metabolism, suggesting these biochemical pathways might play an important role in the basic mechanisms of aging in primates. Moreover, we found that many metabolic pathways associated with age were sex specific. Our work illustrates the power of longitudinal approaches, even in a short time frame, to discover novel biochemical changes that occur with age. PMID:26805607

Developmental origins of pregnancy loss in the adult female common marmoset monkey (Callithrix jacchus).

PubMed

Rutherford, Julienne N; deMartelly, Victoria A; Layne Colon, Donna G; Ross, Corinna N; Tardif, Suzette D

2014-01-01

The impact of the intrauterine environment on the developmental programming of adult female reproductive success is still poorly understood and potentially underestimated. Litter size variation in a nonhuman primate, the common marmoset monkey (Callithrix jacchus), allows us to model the effects of varying intrauterine environments (e.g. nutrient restriction, exposure to male womb-mates) on the risk of losing fetuses in adulthood. Our previous work has characterized the fetuses of triplet pregnancies as experiencing intrauterine nutritional restriction. We used over a decade of demographic data from the Southwest National Primate Research Center common marmoset colony. We evaluated differences between twin and triplet females in the number of pregnancies they produce and the proportion of those pregnancies that ended in fetal loss. We found that triplet females produced the same number of total offspring as twin females, but lost offspring during pregnancy at a significantly higher rate than did twins (38% vs. 13%, p = 0.02). Regardless of their own birth weight or the sex ratio of the litter the experienced as fetuses, triplet females lost more fetuses than did twins. Females with a male littermate experienced a significant increase in the proportion of stillbirths. These striking findings anchor pregnancy loss in the mother's own fetal environment and development, underscoring a "Womb to Womb" view of the lifecourse and the intergenerational consequences of development. This has important translational implications for understanding the large proportion of human stillbirths that are unexplained. Our findings provide strong evidence that a full understanding of mammalian life history and reproductive biology requires a developmental foundation.

Cross-protection in nonhuman primates against Argentine hemorrhagic fever.

PubMed Central

Weissenbacher, M C; Coto, C E; Calello, M A; Rondinone, S N; Damonte, E B; Frigerio, M J

1982-01-01

The susceptibility of the marmoset Callithrix jacchus to Tacaribe virus infection was investigated to perform cross-protection studies between Junin and Tacaribe viruses. Five marmosets inoculated with Tacaribe virus failed to show any signs of disease, any alterations in erythrocyte, leukocyte, reticulocyte, and platelet counts or any changes in hematocrit or hemoglobin values. No Tacaribe virus could be recovered from blood at any time postinfection. Anti-Tacaribe neutralizing antibodies appeared 3 weeks postinfection. The five Tacaribe-infected marmosets and four noninfected controls were challenged with the pathogenic strain of Junin virus on day 60 post-Tacaribe infection. The former group showed no signs of disease, no viremia, and no challenge virus replication, whereas the control group exhibited the typical symptoms of Argentine hemorrhagic fever, high viremia, and viral titers in organs. Soon after challenge, the Tacaribe-protected marmosets synthesized neutralizing antibodies against Junin virus. These results indicate that the marmoset C. jacchus can be considered an experimental model for protection studies with arenaviruses and that the Tacaribe virus could be considered as a potential vaccine against Junin virus. PMID:6276301

Developmental Origins of Pregnancy Loss in the Adult Female Common Marmoset Monkey (Callithrix jacchus)

PubMed Central

Rutherford, Julienne N.; deMartelly, Victoria A.; Layne Colon, Donna G.; Ross, Corinna N.; Tardif, Suzette D.

2014-01-01

Background The impact of the intrauterine environment on the developmental programming of adult female reproductive success is still poorly understood and potentially underestimated. Litter size variation in a nonhuman primate, the common marmoset monkey (Callithrix jacchus), allows us to model the effects of varying intrauterine environments (e.g. nutrient restriction, exposure to male womb-mates) on the risk of losing fetuses in adulthood. Our previous work has characterized the fetuses of triplet pregnancies as experiencing intrauterine nutritional restriction. Methodology/Principal Findings We used over a decade of demographic data from the Southwest National Primate Research Center common marmoset colony. We evaluated differences between twin and triplet females in the number of pregnancies they produce and the proportion of those pregnancies that ended in fetal loss. We found that triplet females produced the same number of total offspring as twin females, but lost offspring during pregnancy at a significantly higher rate than did twins (38% vs. 13%, p = 0.02). Regardless of their own birth weight or the sex ratio of the litter the experienced as fetuses, triplet females lost more fetuses than did twins. Females with a male littermate experienced a significant increase in the proportion of stillbirths. Conclusions/Significance These striking findings anchor pregnancy loss in the mother’s own fetal environment and development, underscoring a "Womb to Womb" view of the lifecourse and the intergenerational consequences of development. This has important translational implications for understanding the large proportion of human stillbirths that are unexplained. Our findings provide strong evidence that a full understanding of mammalian life history and reproductive biology requires a developmental foundation. PMID:24871614

Characterization and Pathogenesis of Aerosolized Eastern Equine Encephalitis in the Common Marmoset (Callithrix jacchus)

DTIC Science & Technology

2016-08-10

9 Affiliations: 10 1United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Virology 11 Division; 2Pathology Division...balance. Fever was evident as 27 early as day 2-3 post exposure in the highest dose groups and hypothermia was observed in 28 several cases as animals...considered to consist of four genetic lineages 55 (Arrigo, 2010). Lineage I was considered to be the North American (NA) variant of EEEV, 56 while lineages

Patterns on serpentine shapes elicit visual attention in marmosets (Callithrix jacchus).

PubMed

Wombolt, Jessica R; Caine, Nancy G

2016-09-01

Given the prevalence of threatening snakes in the evolutionary history, and modern-day environments of human and nonhuman primates, sensory, and perceptual abilities that allow for quick detection of, and appropriate response to snakes are likely to have evolved. Many studies have demonstrated that primates recognize snakes faster than other stimuli, and it is suggested that the unique serpentine shape is responsible for its quick detection. However, there are many nonthreatening serpentine shapes in the environment (e.g., vines) that are not threatening; therefore, other cues must be used to distinguish threatening from benign serpentine objects. In two experiments, we systematically evaluated how common marmosets (Callithrix jacchus) visually attend to specific snake-like features. In the first experiment, we examined if skin pattern is a cue that elicits increased visual inspection of serpentine shapes by measuring the amount of time the marmosets looked into a blind before, during, and after presentation of clay models with and without patterns. The marmosets spent the most time looking at the objects, both serpentine and triangle, that were etched with scales, suggesting that something may be uniquely salient about scales in evoking attention. In contrast, they showed relatively little interest in the unpatterned serpentine and control (a triangle) stimuli. In experiment 2, we replicated and extended the results of experiment 1 by adding additional stimulus conditions. We found that patterns on a serpentine shape generated more inspection than those same patterns on a triangle shape. We were unable to confirm that a scaled pattern is unique in its ability to elicit visual interest; the scaled models elicited similar looking times as line and star patterns. Our data provide a foundation for future research to examine how snakes are detected and identified by primates. Am. J. Primatol. 78:928-936, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Quantification of hair cortisol concentration in common marmosets (Callithrix jacchus) and tufted capuchins (Cebus apella).

PubMed

Phillips, Kimberley A; Tukan, Alyson N; Rigodanzo, Anna D; Reusch, Ryan T; Brasky, Kathleen M; Meyer, Jerrold S

2018-06-04

Quantifying cortisol concentration in hair is a non-invasive biomarker of long-term hypothalamic-pituitary-adrenal (HPA) activation, and thus can provide important information on laboratory animal health. Marmosets (Callithrix jacchus) and capuchins (Cebus apella) are New World primates increasingly used in biomedical and neuroscience research, yet published hair cortisol concentrations for these species are limited. Review of the existing published hair cortisol values from marmosets reveals highly discrepant values and the use of variable techniques for hair collection, processing, and cortisol extraction. In this investigation we utilized a well-established, standardized protocol to extract and quantify cortisol from marmoset (n = 12) and capuchin (n = 4) hair. Shaved hair samples were collected from the upper thigh during scheduled exams and analyzed via methanol extraction and enzyme immunoassay. In marmosets, hair cortisol concentration ranged from 2,710 to 6,267 pg/mg and averaged 4,070 ± 304 pg/mg. In capuchins, hair cortisol concentration ranged from 621 to 2,089 pg/mg and averaged 1,092 ± 338 pg/mg. Hair cortisol concentration was significantly different between marmosets and capuchins, with marmosets having higher concentrations than capuchins. The incorporation of hair cortisol analysis into research protocols provides a non-invasive measure of HPA axis activity over time, which offers insight into animal health. Utilization of standard protocols across laboratories is essential to obtaining valid measurements and allowing for valuable future cross-species comparisons. © 2018 Wiley Periodicals, Inc.

Advantages and Risks of Husbandry and Housing Changes to Improve Animal Wellbeing in a Breeding Colony of Common Marmosets (Callithrix jacchus)

PubMed Central

Bakker, Jaco; Ouwerling, Boudewijn; Heidt, Peter J; Kondova, Ivanela; Langermans, Jan AM

2015-01-01

Between 1975 and 2014, housing conditions for laboratory-housed marmosets changed dramatically after the introduction of new guidelines designed to improve their care and wellbeing. According to these guidelines, our facility provided marmosets with outside enclosures, switched to deep litter as bedding material, and discontinued the use of disinfectant agents in animal enclosures. However, both deep litter and access to outside enclosures hypothetically increase the risk of potential exposure to pathogenic microorganisms. We evaluated whether these housing and husbandry modifications constituted an increased veterinary risk for laboratory-housed common marmosets (Callithrix jacchus). After the animals had been exposed to these new housing conditions for 2.5 y, we examined their intestinal bacterial flora and feces, the deep litter, and insects present in the housing. In addition, we assessed the marmosets’ general health and the effect of outdoor housing on, for example, vitamin D levels. Although numerous bacterial strains—from nonpathogenic to potentially pathogenic—were cultured, we noted no increase in illness, mortality, or breeding problems related to this environmental microflora. Housing laboratory marmosets in large enriched cages, with both indoor and outdoor enclosures, providing them with deep litter, and eliminating the use of disinfectants present an increased veterinary risk. However, after evaluating all of the collected data, we estimate that the veterinary risk of the new housing conditions is minimal to none in terms of clinical disease, disease outbreaks, abnormal behavior, and negative effects on reproduction. PMID:26045452

Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).

PubMed

Endo, Akihito; Futagawa-Endo, Yuka; Schumann, Peter; Pukall, Rüdiger; Dicks, Leon M T

2012-03-01

Five strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic group of the genus Bifidobacterium but did not show high sequence similarities between the isolates and to known species in the genus by phylogenetic analysis based on 16S rRNA gene sequences. Sequence analyses of dnaJ1 and hsp60 also indicated their independent phylogenetic positions to each other in the Bifidobacterium cluster. DNA G+C contents of the species ranged from 57.3 to 66.3 mol%, which is within the values recorded for Bifidobacterium species. All isolates showed fructose-6-phosphate phosphoketolase activity. Based on the data provided, the five isolates represent five novel species, for which the names Bifidobacterium reuteri sp. nov. (type strain: AFB22-1(T) = JCM 17295(T) = DSM 23975(T)), Bifidobacterium callitrichos sp. nov. (type strain: AFB22-5(T) = JCM 17296(T) = DSM 23973(T)), Bifidobacterium saguini sp. nov. (type strain: AFB23-1(T) = JCM 17297(T) = DSM 23967(T)), Bifidobacterium stellenboschense sp. nov. (type strain: AFB23-3(T) = JCM 17298(T) = DSM 23968(T)) and Bifidobacterium biavatii sp. nov. (type strain: AFB23-4(T) = JCM 17299(T) = DSM 23969(T)) are proposed. Copyright © 2011 Elsevier GmbH. All rights reserved.

Prolactin's Mediative Role in Male Parenting in Parentally Experienced Marmosets (Callithrix jacchus)

PubMed Central

Ziegler, Toni E.; Prudom, Shelley L.; Zahed, Sofia Refetoff; Parlow, A. F.; Wegner, Fredrick

2009-01-01

Prolactin has been implicated in promoting paternal care behaviors but little evidence of causality has been found to date except for birds and fish. This study was designed to examine the possible causal relationships between prolactin and male parenting behaviors, reproductive hormones, and physical changes in cooperatively breeding common marmosets, Callithrix jacchus. Fifteen parentally experienced fathers were studied over three consecutive infant care periods during two weeks prior and three weeks following their mates' parturition under three treatment conditions: normal control pregnancy, decreased prolactin and elevated prolactin. The treatments significantly altered the serum prolactin levels in the fathers. Using three methods of determining a father's level of parental care: infant carrying, family effort and responsiveness to infant stimulus tests, we found that only the male response to infant stimuli was altered by the hormone treatments. Lowering prolactin significantly reduced male responsiveness to infant stimuli but elevating prolactin showed the same effect. Hormonal sampling indicated that testosterone levels showed an inverse relationship to prolactin levels during a normal peripartum period and prolactin treatment reduced this relationship. Prepartum estradiol levels were significantly elevated during the lowered prolactin treatment and estradiol was significantly lowered postpartum with the elevated prolactin treatment. Father's weight decreased significantly by the third week of infant care during the normal treatment. Males in the elevated prolactin treatment lost little or no weight from prepartum while in the lowered prolactin treatment showed the most weight loss. The present findings did not distinguish a direct causal relationship of prolactin on behavior in experienced fathers but did find an interaction with other hormones and weight gain. PMID:19664636

Characterization and pathogenesis of aerosolized eastern equine encephalitis in the common marmoset (Callithrix jacchus).

PubMed

Porter, Aimee I; Erwin-Cohen, Rebecca A; Twenhafel, Nancy; Chance, Taylor; Yee, Steven B; Kern, Steven J; Norwood, David; Hartman, Laurie J; Parker, Michael D; Glass, Pamela J; DaSilva, Luis

2017-02-07

Licensed antiviral therapeutics and vaccines to protect against eastern equine encephalitis virus (EEEV) in humans currently do not exist. Animal models that faithfully recapitulate the clinical characteristics of human EEEV encephalitic disease, including fever, drowsiness, anorexia, and neurological signs such as seizures, are needed to satisfy requirements of the Food and Drug Administration (FDA) for clinical product licensing under the Animal Rule. In an effort to meet this requirement, we estimated the median lethal dose and described the pathogenesis of aerosolized EEEV in the common marmoset (Callithrix jacchus). Five marmosets were exposed to aerosolized EEEV FL93-939 in doses ranging from 2.4 × 10 1 PFU to 7.95 × 10 5 PFU. The median lethal dose was estimated to be 2.05 × 10 2 PFU. Lethality was observed as early as day 4 post-exposure in the highest-dosed marmoset but animals at lower inhaled doses had a protracted disease course where humane study endpoint was not met until as late as day 19 post-exposure. Clinical signs were observed as early as 3 to 4 days post-exposure, including fever, ruffled fur, decreased grooming, and leukocytosis. Clinical signs increased in severity as disease progressed to include decreased body weight, subdued behavior, tremors, and lack of balance. Fever was observed as early as day 2-3 post-exposure in the highest dose groups and hypothermia was observed in several cases as animals became moribund. Infectious virus was found in several key tissues, including brain, liver, kidney, and several lymph nodes. Clinical hematology results included early neutrophilia, lymphopenia, and thrombocytopenia. Key pathological changes included meningoencephalitis and retinitis. Immunohistochemical staining for viral antigen was positive in the brain, retina, and lymph nodes. More intense and widespread IHC labeling occurred with increased aerosol dose. We have estimated the medial lethal dose of aerosolized EEEV and described the pathology of clinical disease in the marmoset model. The results demonstrate that the marmoset is an animal model suitable for emulation of human EEEV disease in the development of medical countermeasures.

An Epstein–Barr-related herpesvirus from marmoset lymphomas

PubMed Central

Cho, Young-Gyu; Ramer, Jan; Rivailler, Pierre; Quink, Carol; Garber, Richard L.; Beier, David R.; Wang, Fred

2001-01-01

Epstein–Barr virus (EBV) is implicated in the development of human B cell lymphomas and carcinomas. Although related oncogenic herpesviruses were believed to be endemic only in Old World primate species, we now find these viruses to be endemic in New World primates. We have isolated a transforming, EBV-related virus from spontaneous B cell lymphomas of common marmosets (Callithrix jacchus). Sequencing of two-thirds of the genome reveals considerable divergence from the genomes of EBV and Old World primate EBV-related viruses, including differences in genes important for virus-induced cell growth transformation and pathogenesis. DNA related to the C. jacchus herpesvirus is frequently detected in squirrel monkey peripheral blood lymphocytes, indicating that persistent infection with EBV-related viruses is prevalent in both New World primate families. Understanding how these more divergent EBV-related viruses achieve similar biologic outcomes in their natural host is likely to provide important insights into EBV infection, B cell growth transformation, and oncogenesis. PMID:11158621

Ocular wavefront aberrations in the common marmoset Callithrix jacchus: effects of age and refractive error

PubMed Central

Coletta, Nancy J.; Marcos, Susana; Troilo, David

2012-01-01

The common marmoset, Callithrix jacchus, is a primate model for emmetropization studies. The refractive development of the marmoset eye depends on visual experience, so knowledge of the optical quality of the eye is valuable. We report on the wavefront aberrations of the marmoset eye, measured with a clinical Hartmann-Shack aberrometer (COAS, AMO Wavefront Sciences). Aberrations were measured on both eyes of 23 marmosets whose ages ranged from 18 to 452 days. Twenty-one of the subjects were members of studies of emmetropization and accommodation, and two were untreated normal subjects. Eleven of the 21 experimental subjects had worn monocular diffusers or occluders and ten had worn binocular spectacle lenses of equal power. Monocular deprivation or lens rearing began at about 45 days of age and ended at about 108 days of age. All refractions and aberration measures were performed while the eyes were cyclopleged; most aberration measures were made while subjects were awake, but some control measurements were performed under anesthesia. Wavefront error was expressed as a seventh-order Zernike polynomial expansion, using the Optical Society of America’s naming convention. Aberrations in young marmosets decreased up to about 100 days of age, after which the higher-order RMS aberration leveled off to about 0.10 micron over a 3 mm diameter pupil. Higher-order aberrations were 1.8 times greater when the subjects were under general anesthesia than when they were awake. Young marmoset eyes were characterized by negative spherical aberration. Visually deprived eyes of the monocular deprivation animals had greater wavefront aberrations than their fellow untreated eyes, particularly for asymmetric aberrations in the odd-numbered Zernike orders. Both lens-treated and deprived eyes showed similar significant increases in Z3-3 trefoil aberration, suggesting the increase in trefoil may be related to factors that do not involve visual feedback. PMID:20800078

A small nonhuman primate model for filovirus-induced disease.

PubMed

Carrion, Ricardo; Ro, Youngtae; Hoosien, Kareema; Ticer, Anysha; Brasky, Kathy; de la Garza, Melissa; Mansfield, Keith; Patterson, Jean L

2011-11-25

Ebolavirus and Marburgvirus are members of the filovirus family and induce a fatal hemorrhagic disease in humans and nonhuman primates with 90% case fatality. To develop a small nonhuman primate model for filovirus disease, common marmosets (Callithrix jacchus) were intramuscularly inoculated with wild type Marburgvirus Musoke or Ebolavirus Zaire. The infection resulted in a systemic fatal disease with clinical and morphological features closely resembling human infection. Animals experienced weight loss, fever, high virus titers in tissue, thrombocytopenia, neutrophilia, high liver transaminases and phosphatases and disseminated intravascular coagulation. Evidence of a severe disseminated viral infection characterized principally by multifocal to coalescing hepatic necrosis was seen in EBOV animals. MARV-infected animals displayed only moderate fibrin deposition in the spleen. Lymphoid necrosis and lymphocytic depletion observed in spleen. These findings provide support for the use of the common marmoset as a small nonhuman primate model for filovirus induced hemorrhagic fever. Copyright © 2011 Elsevier Inc. All rights reserved.

A case of nontraumatic gas gangrene in a common marmoset (Callithrix jacchus).

PubMed

Yasuda, Masahiko; Inoue, Takashi; Ueno, Masami; Morita, Hanako; Hayashimoto, Nobuhito; Kawai, Kenji; Itoh, Toshio

2016-01-01

The common marmoset is widely used in neuroscience and regenerative medicine research. However, information concerning common marmoset disorders, particularly infectious diseases, is scarce. Here, we report a case of a female common marmoset that died suddenly due to gas gangrene. The animal presented with gaseous abdominal distention at postmortem, and Clostridium perfringens type A was isolated from several tissues. Vacuoles, a Gram-positive bacteremia and intravascular hemolysis were observed microscopically in the muscles, liver and lungs. On the basis of these findings, we diagnosed nontraumatic gas gangrene caused by Clostridium perfringens type A in this common marmoset.

A case of nontraumatic gas gangrene in a common marmoset (Callithrix jacchus)

PubMed Central

YASUDA, Masahiko; INOUE, Takashi; UENO, Masami; MORITA, Hanako; HAYASHIMOTO, Nobuhito; KAWAI, Kenji; ITOH, Toshio

2015-01-01

The common marmoset is widely used in neuroscience and regenerative medicine research. However, information concerning common marmoset disorders, particularly infectious diseases, is scarce. Here, we report a case of a female common marmoset that died suddenly due to gas gangrene. The animal presented with gaseous abdominal distention at postmortem, and Clostridium perfringens type A was isolated from several tissues. Vacuoles, a Gram-positive bacteremia and intravascular hemolysis were observed microscopically in the muscles, liver and lungs. On the basis of these findings, we diagnosed nontraumatic gas gangrene caused by Clostridium perfringens type A in this common marmoset. PMID:26156080

Survey and Experimental Infection of Enteropathogenic Escherichia coli in Common Marmosets (Callithrix jacchus).

PubMed

Hayashimoto, Nobuhito; Inoue, Takashi; Morita, Hanako; Yasuda, Masahiko; Ueno, Masami; Kawai, Kenji; Itoh, Toshio

2016-01-01

Common marmosets (Callithrix jacchus) are frequently used for biomedical research but can be afflicted with diarrhea-a serious and potentially lethal health problem. Enteropathogenic Escherichia coli (EPEC) is thought to be the causative pathogen of hemorrhagic typhlocolitis in common marmosets, but the actual incidence of the disease and the relationship between EPEC and hematochezia are unknown. This study investigated the prevalence of EPEC infection in common marmosets and the association between EPEC and hematochezia. A total of 230 stool or rectal swab samples were collected from 230 common marmosets (98 clinically healthy, 85 diarrhea, and 47 bloody stool samples) and tested by culture-based detection and PCR amplification of VT1, VT2, LT, ST, eae, and bfp genes. Healthy animals were divided into three groups (n = 4 each for high and low concentration groups and n = 2 as negative control), and those in the experimental groups were perorally inoculated with a 2-ml of suspension of EPEC R811 strain adjusted to 5 × 108 (high concentration) and 5 × 104 (low concentration) CFU/ ml. Two animals in each group were examined 3 and 14 days post-inoculation (DPI). EPEC was detected in 10 of 98 clinically healthy samples (10.2%), 17 of 85 diarrhea samples (20%), and all 47 bloody stool samples (100%), with a significant difference detected between presence of EPEC and sample status (P < 0.01). Acute hematochezia was observed in all animals of the high-concentration group but not in other groups at 1 or 2 DPI. A histopathological examination revealed the attachment of gram-negative bacilli to epithelial apical membranes and desquamated epithelial cells in the cecum of animals in the high-concentration group at 3 DPI. These findings suggest that EPEC is a causative agent of hemorrhagic typhlocolitis in common marmosets.

Effect of luminosity on color discrimination of dichromatic marmosets (Callithrix jacchus).

PubMed

Freitag, Fabio Batista; Pessoa, Daniel Marques Almeida

2012-02-01

Psychophysical data have shown that under mesopic conditions cones and rods can interact, improving color vision. Since electrophysiological data have suggested that rods of dichromatic marmosets appear to be active at higher luminance, we aimed to investigate the effect of different levels of sunlight on the foraging abilities of male dichromatic marmosets. Captive marmosets were observed under three different conditions, with respect to their performance in detecting colored food items against a green background. Compared to high and low light intensities, intermediate luminosities significantly increased detection of orange targets by male dichromats, an indication of rod intrusion. © 2012 Optical Society of America

Primate Short-Wavelength Cones Share Molecular Markers with Rods

PubMed Central

Craft, Cheryl M.; Huang, Jing; Possin, Daniel E.; Hendrickson, Anita

2015-01-01

Macaca, Callithrix jacchus marmoset monkey, Pan troglodytes chim- panzee and human retinas were examined to define if short wavelength (S) cones share molecular markers with L&M cone or rod photoreceptors. S cones showed consistent differences in their immunohistochemical staining and expression levels compared to L&M cones for “rod” Arrestin1 (S-Antigen), “cone” Arrestin4, cone alpha transducin, and Calbindin. Our data verify a similar pattern of expression in these primate retinas and provide clues to the structural divergence of rods and S cones versus L&M cones, suggesting S cone retinal function is “intermediate” between them. PMID:24664680

The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information

PubMed Central

Bendor, Daniel

2015-01-01

In auditory cortex, temporal information within a sound is represented by two complementary neural codes: a temporal representation based on stimulus-locked firing and a rate representation, where discharge rate co-varies with the timing between acoustic events but lacks a stimulus-synchronized response. Using a computational neuronal model, we find that stimulus-locked responses are generated when sound-evoked excitation is combined with strong, delayed inhibition. In contrast to this, a non-synchronized rate representation is generated when the net excitation evoked by the sound is weak, which occurs when excitation is coincident and balanced with inhibition. Using single-unit recordings from awake marmosets (Callithrix jacchus), we validate several model predictions, including differences in the temporal fidelity, discharge rates and temporal dynamics of stimulus-evoked responses between neurons with rate and temporal representations. Together these data suggest that feedforward inhibition provides a parsimonious explanation of the neural coding dichotomy observed in auditory cortex. PMID:25879843

Susceptibility of Marmosets (Callithrix jacchus) to Monkeypox Virus: A Low Dose Prospective Model for Monkeypox and Smallpox Disease.

PubMed

Mucker, Eric M; Chapman, Jennifer; Huzella, Louis M; Huggins, John W; Shamblin, Joshua; Robinson, Camenzind G; Hensley, Lisa E

2015-01-01

Although current nonhuman primate models of monkeypox and smallpox diseases provide some insight into disease pathogenesis, they require a high titer inoculum, use an unnatural route of infection, and/or do not accurately represent the entire disease course. This is a concern when developing smallpox and/or monkeypox countermeasures or trying to understand host pathogen relationships. In our studies, we altered half of the test system by using a New World nonhuman primate host, the common marmoset. Based on dose finding studies, we found that marmosets are susceptible to monkeypox virus infection, produce a high viremia, and have pathological features consistent with smallpox and monkeypox in humans. The low dose (48 plaque forming units) required to elicit a uniformly lethal disease and the extended incubation (preclinical signs) are unique features among nonhuman primate models utilizing monkeypox virus. The uniform lethality, hemorrhagic rash, high viremia, decrease in platelets, pathology, and abbreviated acute phase are reflective of early-type hemorrhagic smallpox.

Susceptibility of Marmosets (Callithrix jacchus) to Monkeypox Virus: A Low Dose Prospective Model for Monkeypox and Smallpox Disease

PubMed Central

Mucker, Eric M.; Chapman, Jennifer; Huzella, Louis M.; Huggins, John W.; Shamblin, Joshua; Robinson, Camenzind G.; Hensley, Lisa E.

2015-01-01

Although current nonhuman primate models of monkeypox and smallpox diseases provide some insight into disease pathogenesis, they require a high titer inoculum, use an unnatural route of infection, and/or do not accurately represent the entire disease course. This is a concern when developing smallpox and/or monkeypox countermeasures or trying to understand host pathogen relationships. In our studies, we altered half of the test system by using a New World nonhuman primate host, the common marmoset. Based on dose finding studies, we found that marmosets are susceptible to monkeypox virus infection, produce a high viremia, and have pathological features consistent with smallpox and monkeypox in humans. The low dose (48 plaque forming units) required to elicit a uniformly lethal disease and the extended incubation (preclinical signs) are unique features among nonhuman primate models utilizing monkeypox virus. The uniform lethality, hemorrhagic rash, high viremia, decrease in platelets, pathology, and abbreviated acute phase are reflective of early-type hemorrhagic smallpox. PMID:26147658

Brain-mapping projects using the common marmoset.

PubMed

Okano, Hideyuki; Mitra, Partha

2015-04-01

Globally, there is an increasing interest in brain-mapping projects, including the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative project in the USA, the Human Brain Project (HBP) in Europe, and the Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS) project in Japan. These projects aim to map the structure and function of neuronal circuits to ultimately understand the vast complexity of the human brain. Brain/MINDS is focused on structural and functional mapping of the common marmoset (Callithrix jacchus) brain. This non-human primate has numerous advantages for brain mapping, including a well-developed frontal cortex and a compact brain size, as well as the availability of transgenic technologies. In the present review article, we discuss strategies for structural and functional mapping of the marmoset brain and the relation of the common marmoset to other animals models. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Distribution of olfactory epithelium in the primate nasal cavity: are microsmia and macrosmia valid morphological concepts?

PubMed

Smith, Timothy D; Bhatnagar, Kunwar P; Tuladhar, Praphul; Burrows, Annie M

2004-11-01

The terms "microsmatic" and "macrosmatic" are used to compare species with greater versus lesser olfactory capabilities, such as carnivores compared to certain primates. These categories have been morphologically defined based on the size of olfactory bulb and surface area of olfactory epithelium in the nasal fossa. The present study examines assumptions regarding the morphological relationship of bony elements to the olfactory mucosa, the utility of olfactory epithelial surface area as a comparative measurement, and the utility of the microsmatic concept. We examined the distribution of olfactory neuroepithelium (OE) across the anteroposterior length of the nasal fossa (from the first completely enclosed cross-section of the nasal fossa to the choanae) in the microsmatic marmoset (Callithrix jacchus) compared to four species of nocturnal strepsirrhines (Otolemur crassicaudatus, O. garnetti, Microcebus murinus, and Cheirogaleus medius). Adults of all species were examined and infant C. jacchus, O. crassicaudatus, M. murinus, and C. medius were also examined. All specimens were serially sectioned in the coronal plane and prepared for light microscopic study. Distribution of OE across all the turbinals, nasal septal surfaces, and accessory spaces of the nasal chamber was recorded for each specimen. The right nasal fossae of one adult C. jacchus and one neonatal M. murinus were also three-dimensionally reconstructed using Scion Image software to reveal OE distribution. Findings showed OE to be distributed relatively more anteriorly in adult C. jacchus compared to strepsirrhines. It was also distributed more anteriorly along the nasal septal walls and recesses in neonates than adults. Our findings also showed that OE surface area was not a reliable proxy for receptor neuron numbers due to differing OE thickness among species. Such results indicate that nasal cavity morphology must be carefully reconsidered regarding traditional functional roles (olfaction versus air conditioning) assigned to various nasal cavity structures. At present, the microsmatic concept itself lacks a basis in nasal chamber morphology, since OE may have varying patterns of distribution among different primates. (c) 2004 Wiley-Liss, Inc.

Neurobehavioral Development of Common Marmoset Monkeys

PubMed Central

Schultz-Darken, Nancy; Braun, Katarina M.; Emborg, Marina E.

2016-01-01

Common marmoset (Callithrix jacchus) monkeys are a resource for biomedical research and their use is predicted to increase due to the suitability of this species for transgenic approaches. Identification of abnormal neurodevelopment due to genetic modification relies upon the comparison with validated patterns of normal behavior defined by unbiased methods. As scientists unfamiliar with nonhuman primate development are interested to apply genomic editing techniques in marmosets, it would be beneficial to the field that the investigators use validated methods of postnatal evaluation that are age and species appropriate. This review aims to analyze current available data on marmoset physical and behavioral postnatal development, describe the methods used and discuss next steps to better understand and evaluate marmoset normal and abnormal postnatal neurodevelopment PMID:26502294

Grooming as a reward? Social function of grooming between females in cooperatively breeding marmosets

PubMed Central

LAZARO-PEREA, CRISTINA; DE FÁTIMA ARRUDA, MARIA; SNOWDON, CHARLES T.

2006-01-01

Classical models of grooming predict that subordinate primates will direct grooming towards dominants to receive coalitionary support from them. In contrast, recent reviews suggest that grooming asymmetries can change with social system and ecological conditions and should reflect asymmetries in services provided by different members of the dyad. We studied grooming patterns between females in six wild groups of common marmosets, Callithrix jacchus, to investigate the relation between social structure and grooming between females in a cooperatively breeding species. We observed grooming frequently and consistently in all study groups. Breeding females groomed nonbreeding females more than vice versa, and grooming between breeding and nonbreeding females was not related to agonistic behaviour. Our results provide some support to the hypothesis that grooming asymmetries are related to differences in services provided by different group members. We suggest that, in cooperatively breeding systems, breeding females may use grooming as an incentive for helper females to stay in the group. PMID:17237884

Brain/MINDS: brain-mapping project in Japan

PubMed Central

Okano, Hideyuki; Miyawaki, Atsushi; Kasai, Kiyoto

2015-01-01

There is an emerging interest in brain-mapping projects in countries across the world, including the USA, Europe, Australia and China. In 2014, Japan started a brain-mapping project called Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS). Brain/MINDS aims to map the structure and function of neuronal circuits to ultimately understand the vast complexity of the human brain, and takes advantage of a unique non-human primate animal model, the common marmoset (Callithrix jacchus). In Brain/MINDS, the RIKEN Brain Science Institute acts as a central institute. The objectives of Brain/MINDS can be categorized into the following three major subject areas: (i) structure and functional mapping of a non-human primate brain (the marmoset brain); (ii) development of innovative neurotechnologies for brain mapping; and (iii) human brain mapping; and clinical research. Brain/MINDS researchers are highly motivated to identify the neuronal circuits responsible for the phenotype of neurological and psychiatric disorders, and to understand the development of these devastating disorders through the integration of these three subject areas. PMID:25823872

The conclusiveness of less-invasive imaging techniques (computer tomography, X-ray) with regard to their identification of bone diseases in a primate model (Callithrix jacchus).

PubMed

Grohmann, J; Taetzner, S; Theuss, T; Kuehnel, F; Buchwald, U; Einspanier, A

2012-04-01

Although common marmosets seem to be appropriate animal models to examine bone diseases, no data about the conclusiveness of less-invasive techniques are available. Therefore, the aim was to combine different techniques to analyse changes in bone metabolism of common marmosets with bone diseases. Five monkeys were examined by X-ray, computer tomography (CT), histology and immunohistochemistry (IHC). Monkeys with lowest bone mineral density (BMD) showed increased bone marrow, decreased cancellous bone and decreased contrast in X-ray. Highest alkaline phosphatase (AP)-levels were detected in bones with low elastic modulus. Expression of osteopontin (OPN), osteocalcin (OC) and runt-related transcriptions factor 2 (RUNX 2) was detected in bones with high modulus. No expression was present in bones with lower modulus. Collagen type I and V were found in every bone. In conclusion, CT, X-ray and AP are useful techniques to detect bone diseases in common marmosets. These observations could be confirmed by IHC. © 2012 John Wiley & Sons A/S.

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

PubMed

Sato, Kengo; Kuroki, Yoko; Kumita, Wakako; Fujiyama, Asao; Toyoda, Atsushi; Kawai, Jun; Iriki, Atsushi; Sasaki, Erika; Okano, Hideyuki; Sakakibara, Yasubumi

2015-11-20

The first draft of the common marmoset (Callithrix jacchus) genome was published by the Marmoset Genome Sequencing and Analysis Consortium. The draft was based on whole-genome shotgun sequencing, and the current assembly version is Callithrix_jacches-3.2.1, but there still exist 187,214 undetermined gap regions and supercontigs and relatively short contigs that are unmapped to chromosomes in the draft genome. We performed resequencing and assembly of the genome of common marmoset by deep sequencing with high-throughput sequencing technology. Several different sequence runs using Illumina sequencing platforms were executed, and 181 Gbp of high-quality bases including mate-pairs with long insert lengths of 3, 8, 20, and 40 Kbp were obtained, that is, approximately 60× coverage. The resequencing significantly improved the MGSAC draft genome sequence. The N50 of the contigs, which is a statistical measure used to evaluate assembly quality, doubled. As a result, 51% of the contigs (total length: 299 Mbp) that were unmapped to chromosomes in the MGSAC draft were merged with chromosomal contigs, and the improved genome sequence helped to detect 5,288 new genes that are homologous to human cDNAs and the gaps in 5,187 transcripts of the Ensembl gene annotations were completely filled.

The common marmoset monkey: avenues for exploring the prenatal, placental, and postnatal mechanisms in developmental programming of pediatric obesity.

PubMed

Riesche, Laren; Tardif, Suzette D; Ross, Corinna N; deMartelly, Victoria A; Ziegler, Toni; Rutherford, Julienne N

2018-05-01

Animal models have been critical in building evidence that the prenatal experience and intrauterine environment are capable of exerting profound and permanent effects on metabolic health through developmental programming of obesity. However, despite physiological and evolutionary similarities, nonhuman primate models are relatively rare. The common marmoset monkey ( Callithrix jacchus) is a New World monkey that has been used as a biomedical model for well more than 50 years and has recently been framed as an appropriate model for exploring early-life impacts on later health and disease. The spontaneous, multifactorial, and early-life development of obesity in the common marmoset make it a valuable research model for advancing our knowledge about the role of the prenatal and placental mechanisms involved in developmental programming of obesity. This paper provides a brief overview of obesity in the common marmoset, followed by a discussion of marmoset reproduction and placental characteristics. We then discuss the occurrence and utility of variable intrauterine environments in developmental programming in marmosets. Evidence of developmental programming of obesity will be given, and finally, we put forward future directions and innovations for including the placenta in developmental programming of obesity in the common marmoset.

The marmoset monkey as a model for visual neuroscience

PubMed Central

Mitchell, Jude F.; Leopold, David A.

2015-01-01

The common marmoset (Callithrix jacchus) has been valuable as a primate model in biomedical research. Interest in this species has grown recently, in part due to the successful demonstration of transgenic marmosets. Here we examine the prospects of the marmoset model for visual neuroscience research, adopting a comparative framework to place the marmoset within a broader evolutionary context. The marmoset’s small brain bears most of the organizational features of other primates, and its smooth surface offers practical advantages over the macaque for areal mapping, laminar electrode penetration, and two-photon and optical imaging. Behaviorally, marmosets are more limited at performing regimented psychophysical tasks, but do readily accept the head restraint that is necessary for accurate eye tracking and neurophysiology, and can perform simple discriminations. Their natural gaze behavior closely resembles that of other primates, with a tendency to focus on objects of social interest including faces. Their immaturity at birth and routine twinning also makes them ideal for the study of postnatal visual development. These experimental factors, together with the theoretical advantages inherent in comparing anatomy, physiology, and behavior across related species, make the marmoset an excellent model for visual neuroscience. PMID:25683292

A B Cell-Driven Autoimmune Pathway Leading to Pathological Hallmarks of Progressive Multiple Sclerosis in the Marmoset Experimental Autoimmune Encephalomyelitis Model

PubMed Central

’t Hart, Bert A.; Dunham, Jordon; Faber, Bart W.; Laman, Jon D.; van Horssen, Jack; Bauer, Jan; Kap, Yolanda S.

2017-01-01

The absence of pathological hallmarks of progressive multiple sclerosis (MS) in commonly used rodent models of experimental autoimmune encephalomyelitis (EAE) hinders the development of adequate treatments for progressive disease. Work reviewed here shows that such hallmarks are present in the EAE model in marmoset monkeys (Callithrix jacchus). The minimal requirement for induction of progressive MS pathology is immunization with a synthetic peptide representing residues 34–56 from human myelin oligodendrocyte glycoprotein (MOG) formulated with a mineral oil [incomplete Freund’s adjuvant (IFA)]. Pathological aspects include demyelination of cortical gray matter with microglia activation, oxidative stress, and redistribution of iron. When the peptide is formulated in complete Freund’s adjuvant, which contains mycobacteria that relay strong activation signals to myeloid cells, oxidative damage pathways are strongly boosted leading to more intensive pathology. The proven absence of immune potentiating danger signals in the MOG34–56/IFA formulation implies that a narrow population of antigen-experienced T cells present in the monkey’s immune repertoire is activated. This novel pathway involves the interplay of lymphocryptovirus-infected B cells with MHC class Ib/Caja-E restricted CD8+ CD56+ cytotoxic T lymphocytes. PMID:28744286

Merits and complexities of modeling multiple sclerosis in non-human primates: implications for drug discovery.

PubMed

't Hart, Bert A; Laman, Jon D; Kap, Yolanda S

2018-05-01

The translation of scientific discoveries made in animal models into effective treatments for patients often fails, indicating that currently used disease models in preclinical research are insufficiently predictive for clinical success. An often-used model in the preclinical research of autoimmune neurological diseases, multiple sclerosis in particular, is experimental autoimmune encephalomyelitis (EAE). Most EAE models are based on genetically susceptible inbred/SPF mouse strains used at adolescent age (10-12 weeks), which lack exposure to genetic and microbial factors which shape the human immune system. Areas covered: Herein, the authors ask whether an EAE model in adult non-human primates from an outbred conventionally-housed colony could help bridge the translational gap between rodent EAE models and MS patients. Particularly, the authors discuss a novel and translationally relevant EAE model in common marmosets (Callithrix jacchus) that shares remarkable pathological similarity with MS. Expert opinion: The MS-like pathology in this model is caused by the interaction of effector memory T cells with B cells infected with the γ1-herpesvirus (CalHV3), both present in the pathogen-educated marmoset immune repertoire. The authors postulate that depletion of only the small subset (<0.05%) of CalHV3-infected B cells may be sufficient to limit chronic inflammatory demyelination.

The 14/15 association as a paradigmatic example of tracing karyotype evolution in New World monkeys.

PubMed

Capozzi, Oronzo; Archidiacono, Nicoletta; Lorusso, Nicola; Stanyon, Roscoe; Rocchi, Mariano

2016-09-01

Fluorescence in situ hybridization (FISH), especially chromosome painting, has been extensively exploited in the phylogenetic reconstruction of primate evolution. Although chromosome painting is a key method to map translocations, it is not effective in detecting chromosome inversions, which may be up to four times more frequent than other chromosomal rearrangements. BAC-FISH instead can economically delineate marker order and reveal intrachromosomal rearrangements. However, up to now, BAC-FISH was rarely used to study the chromosomes of New World monkeys partly due to technical difficulties. In this paper, we used BAC-FISH to disentangle the complex evolutionary history of the ancestral 14/15 association in NWMs, beginning from the squirrel monkey (Saimiri boliviensis). To improve the hybridization efficiency of BAC-FISH in NWMs, we "translated" the human BACs into Callithrix jacchus (CJA) BACs, which yielded much higher hybridization efficiencies on other NWM species than human BACs. Our results disclosed 14 synteny blocks in squirrel monkeys, 7 more than with chromosome painting. We then applied a subset of CJA BACs on six other NWM species. The comparison of the hybridization pattern of these species contained phylogenetic information to discriminate evolutionary relationships. Notably Aotus was found to share an inversion with Callithrix, thus definitely assigning the genus Aotus to Cebidae. The present study can be seen as a paradigmatic approach to investigate the phylogenetics of NWMs by molecular cytogenetics.

Evidence of Tau Hyperphosphorylation and Dystrophic Microglia in the Common Marmoset.

PubMed

Rodriguez-Callejas, Juan D; Fuchs, Eberhard; Perez-Cruz, Claudia

2016-01-01

Common marmosets ( Callithrix jacchus ) have recently gained popularity in biomedical research as models of aging research. Basically, they confer advantages from other non-human primates due to their shorter lifespan with onset of appearance of aging at 8 years. Old marmosets present some markers linked to neurodegeneration in the brain such as amyloid beta (Aβ) 1-42 and Aβ 1-40 . However, there are no studies exploring other cellular markers associated with neurodegenerative diseases in this non-human primate. Using immunohistochemistry, we analyzed brains of male adolescent, adult, old, and aged marmosets. We observed accumulation of Aβ 1-40 and Aβ 1-42 in the cortex of aged subjects. Tau hyperphosphorylation was already detected in the brain of adolescent animals and increased with aging in a more fibrillary form. Microglia activation was also observed in the aging process, while a dystrophic phenotype accumulates in aged subjects. Interestingly, dystrophic microglia contained hyperphosphorylated tau, but active microglia did not. These results support previous findings regarding microglia dysfunctionality in aging and neurodegenerative diseases as Alzheimer's disease. Further studies should explore the functional consequences of these findings to position this non-human primate as animal model of aging and neurodegeneration.

Evidence of Tau Hyperphosphorylation and Dystrophic Microglia in the Common Marmoset

PubMed Central

Rodriguez-Callejas, Juan D.; Fuchs, Eberhard; Perez-Cruz, Claudia

2016-01-01

Common marmosets (Callithrix jacchus) have recently gained popularity in biomedical research as models of aging research. Basically, they confer advantages from other non-human primates due to their shorter lifespan with onset of appearance of aging at 8 years. Old marmosets present some markers linked to neurodegeneration in the brain such as amyloid beta (Aβ)1-42 and Aβ1-40. However, there are no studies exploring other cellular markers associated with neurodegenerative diseases in this non-human primate. Using immunohistochemistry, we analyzed brains of male adolescent, adult, old, and aged marmosets. We observed accumulation of Aβ1-40 and Aβ1-42 in the cortex of aged subjects. Tau hyperphosphorylation was already detected in the brain of adolescent animals and increased with aging in a more fibrillary form. Microglia activation was also observed in the aging process, while a dystrophic phenotype accumulates in aged subjects. Interestingly, dystrophic microglia contained hyperphosphorylated tau, but active microglia did not. These results support previous findings regarding microglia dysfunctionality in aging and neurodegenerative diseases as Alzheimer’s disease. Further studies should explore the functional consequences of these findings to position this non-human primate as animal model of aging and neurodegeneration. PMID:28066237

Other-regarding preferences in a non-human primate: Common marmosets provision food altruistically

PubMed Central

Burkart, Judith M.; Fehr, Ernst; Efferson, Charles; van Schaik, Carel P.

2007-01-01

Human cooperation is unparalleled in the animal world and rests on an altruistic concern for the welfare of genetically unrelated strangers. The evolutionary roots of human altruism, however, remain poorly understood. Recent evidence suggests a discontinuity between humans and other primates because individual chimpanzees do not spontaneously provide food to other group members, indicating a lack of concern for their welfare. Here, we demonstrate that common marmoset monkeys (Callithrix jacchus) do spontaneously provide food to nonreciprocating and genetically unrelated individuals, indicating that other-regarding preferences are not unique to humans and that their evolution did not require advanced cognitive abilities such as theory of mind. Because humans and marmosets are cooperative breeders and the only two primate taxa in which such unsolicited prosociality has been found, we conclude that these prosocial predispositions may emanate from cooperative breeding. PMID:18077409

The fate of paternal mitochondria in marmoset pre-implantation embryos.

PubMed

Luetjens, C M; Wesselmann, R

2008-06-01

Sperm-derived mitochondria are integrated into the oocyte at fertilization but seem to vanish during the early cleavage phase. The developmental potential of pre-implantation embryos seems to be closely related to their ability to induce degeneration of these mitochondria, but the mechanisms underlying their loss of function are not yet understood. This study focuses on the fate of paternal mitochondria in pre-implantation embryos. Stimulation, collection and in vitro culture of oocytes from Callithrix jacchus, allows the study of the destiny of paternal mitochondria by utilizing immunostaining of pre-implantation embryos, fluorescence and laserscanning microscopy. Live pre-implantation embryos were stained with a fluorescence indicator reflecting mitochondrial membrane potential. Evidence indicating the loss of mitochondrial function was not found nor that apoptosis pathways were involved in the disappearance of paternally derived mitochondria. These findings may have implications for mitochondrially inherited diseases and could lead to new strategies for improving assisted reproduction.

Describing Ovarian Cycles, Pregnancy Characteristics, and the Use of Contraception in Female White-faced Marmosets, Callithrix geoffroyi

PubMed Central

MUSTOE, AARYN C.; JENSEN, HEATHER A.; FRENCH, JEFFREY A.

2012-01-01

Endocrine data and characteristics of nonconceptive ovarian cycling and pregnancy are limited within the genus Callithrix to the common marmoset (C. jacchus) and Wied's black tufted-ear marmoset (C. kuhlii). This paper presents patterns of urinary pregnandiol-3-glucuronide (PdG) excretion, as determined by enzyme immunoassay, throughout the course of ovarian cycling and pregnancy in white-faced marmosets (C. geoffroyi). Furthermore, characteristics of reproductive parameters including litter size, duration of gestation, maternal age, and information about ovarian cycling following administration of contraceptives are also described. A steep increase in PdG, an indication of ovulation, characterizes normative ovarian cycles, with peak-to-peak intervals between cycles being 27.82 ± 1.49 days in length. PdG excretion (μg/mg Cr) across pregnancy peaked during the 1st and 2nd trimesters (1st = 20.71 ± 2.98, 2nd = 21.16 ± 2.60) and declined gradually to near preconception levels over the 3rd trimester until parturition (3rd = 5.74 ± 1.60). Gestation lasted 148.55 ± 1.89 days. Most pregnancies (82.8%) resulted in an immediate postpartum ovulation (PPO) of 17.45 ± 2.22 days with 58.3% of PPOs resulting in conception. No differences in PdG excretion during the 1st trimester between full pregnancies and miscarriages were found, and pregnancy characteristics such as litter size, duration of gestation, and maternal age were not associated with PdG concentrations. Administration of cloprostenol resulted in shorter cycle durations, but ovulation was detectable with similar concentrations of peak PdG to a normal non-conceptive cycle. Conversely, medroxyprogesterone acetate (DMPA) injections resulted in little to no PdG excretion across the ovarian cycle, with both methods of contraception providing effective prevention of conception. Overall, these results show that strong similarities in reproductive parameters persist within the genus Callithrix and to a lesser extent across the Callitrichidae family. PMID:22865351

Optogenetic manipulation of neural circuits in awake marmosets

PubMed Central

MacDougall, Matthew; Nummela, Samuel U.; Coop, Shanna; Disney, Anita; Mitchell, Jude F.

2016-01-01

Optogenetics has revolutionized the study of functional neuronal circuitry (Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K. Nat Neurosci 8: 1263–1268, 2005; Deisseroth K. Nat Methods 8: 26–29, 2011). Although these techniques have been most successfully implemented in rodent models, they have the potential to be similarly impactful in studies of nonhuman primate brains. Common marmosets (Callithrix jacchus) have recently emerged as a candidate primate model for gene editing, providing a potentially powerful model for studies of neural circuitry and disease in primates. The application of viral transduction methods in marmosets for identifying and manipulating neuronal circuitry is a crucial step in developing this species for neuroscience research. In the present study we developed a novel, chronic method to successfully induce rapid photostimulation in individual cortical neurons transduced by adeno-associated virus to express channelrhodopsin (ChR2) in awake marmosets. We found that large proportions of neurons could be effectively photoactivated following viral transduction and that this procedure could be repeated for several months. These data suggest that techniques for viral transduction and optical manipulation of neuronal populations are suitable for marmosets and can be combined with existing behavioral preparations in the species to elucidate the functional neural circuitry underlying perceptual and cognitive processes. PMID:27334951

Mobbing vocalizations as a coping response in the common marmoset.

PubMed

Cross, N; Rogers, L J

2006-02-01

Using a non-invasive method of sampling saliva followed by assay for cortisol levels, we found that common marmosets (Callithrix jacchus) show a decrease in cortisol levels after seeing a snake-model stimulus that reliably elicits mobbing (tsik) calls. In fact, there was a significant positive correlation between the number of tsik vocalizations made and the magnitude of the decrease in the cortisol concentrations. Furthermore, marmosets with higher levels of cortisol prior to being exposed to the stimulus produce more tsik calls than those with lower levels of cortisol. Subsequent experiments showed that, in response to 15 min of isolation with no visual or auditory contact with conspecifics (a traditional stressor), cortisol levels increased significantly. However, playback of the mobbing calls of a familiar conspecific to individual isolated marmosets not only prevented the rise in cortisol, but also actually caused a decrease in the levels of this hormone. This suggests that the mobbing calls serve to calm the marmoset after experiencing a stressful situation. This finding results in a greater understanding as to the role of physiological responses during communication in this species and could have implications for the welfare of marmosets in captivity.

Bone Disease in the Common Marmoset: Radiographic and Histological Findings.

PubMed

Olson, E J; Shaw, G C; Hutchinson, E K; Schultz-Darken, N; Bolton, I D; Parker, J B; Morrison, J M; Baxter, V K; Pate, K A Metcalf; Mankowski, J L; Carlson, C S

2015-09-01

The common marmoset (Callithrix jacchus) is a New World primate that is used in biomedical research due to its small size and relative ease of handling compared with larger primates. Although bone disease in common marmosets is well recognized, there are very few detailed descriptions in the literature that cover the range of lesions seen in these animals. For all animals used to model human disease, it is important to be aware of background lesions that may affect the interpretation of study findings. This retrospective study details bone diseases encountered in marmoset breeding colonies at 2 different institutions. Affected marmosets at Johns Hopkins University had lesions compatible with diagnoses of rickets, fibrous osteodystrophy and osteopenia. Affected marmosets at the Wisconsin National Primate Research Center exhibited severe lesions of osteoclastic bone resorption and remodeling that had an unusual distribution and were not easily categorized into a known disease entity. The purpose of this report is to document these naturally occurring skeletal lesions of common marmosets and suggest an approach to evaluating skeletal disease in prospective studies of these animals that will allow the most accurate diagnoses. © The Author(s) 2015.

Hunger enhances consistent economic choices in non-human primates.

PubMed

Yamada, Hiroshi

2017-05-24

Hunger and thirst are fundamental biological processes that drive consumption behavior in humans and non-human animals. While the existing literature in neuroscience suggests that these satiety states change how consumable rewards are represented in the brain, it remains unclear as to how they change animal choice behavior and the underlying economic preferences. Here, I used combined techniques from experimental economics, psychology, and neuroscience to measure food preferences of marmoset monkeys (Callithrix jacchus), a recently developed primate model for neuroscience. Hunger states of animals were manipulated by scheduling feeding intervals, resulting in three different conditions: sated, non-sated, and hungry. During these hunger states, animals performed pairwise choices of food items, which included all possible pairwise combinations of five different food items except for same-food pairs. Results showed that hunger enhanced economic rationality, evident as a decrease of transitivity violations (item A was preferred to item B, and B to C, but C was preferred to A). Further analysis demonstrated that hungry monkeys chose more-preferred items over less-preferred items in a more deterministic manner, while the individual food preferences appeared to remain stable across hunger states. These results suggest that hunger enhances consistent choice behavior and shifts animals towards efficient outcome maximization.

Intertemporal choice in lemurs.

PubMed

Stevens, Jeffrey R; Mühlhoff, Nelly

2012-02-01

Different species vary in their ability to wait for delayed rewards in intertemporal choice tasks. Models of rate maximization account for part of this variation, but other factors such as social structure and feeding ecology seem to underly some species differences. Though studies have evaluated intertemporal choice in several primate species, including Old World monkeys, New World monkeys, and apes, prosimians have not been tested. This study investigated intertemporal choices in three species of lemur (black-and-white ruffed lemurs, Varecia variegata, red ruffed lemurs, Varecia rubra, and black lemurs, Eulemur macaco) to assess how they compare to other primate species and whether their choices are consistent with rate maximization. We offered lemurs a choice between two food items available immediately and six food items available after a delay. We found that by adjusting the delay to the larger reward, the lemurs were indifferent between the two options at a mean delay of 17 s, ranging from 9 to 25 s. These data are comparable to data collected from common marmosets (Callithrix jacchus). The lemur data were not consistent with models of rate maximization. The addition of lemurs to the list of species tested in these tasks will help uncover the role of life history and socio-ecological factors influencing intertemporal choices. Copyright © 2011 Elsevier B.V. All rights reserved.

Characterization of mammary epithelial stem/progenitor cells and their changes with aging in common marmosets.

PubMed

Wu, Anqi; Dong, Qiaoxiang; Gao, Hui; Shi, Yuanshuo; Chen, Yuanhong; Zhang, Fuchuang; Bandyopadhyay, Abhik; Wang, Danhan; Gorena, Karla M; Huang, Changjiang; Tardif, Suzette; Nathanielsz, Peter W; Sun, Lu-Zhe

2016-08-25

Age is the number one risk factor for breast cancer, yet the underlying mechanisms are unexplored. Age-associated mammary stem cell (MaSC) dysfunction is thought to play an important role in breast cancer carcinogenesis. Non-human primates with their close phylogenetic relationship to humans provide a powerful model system to study the effects of aging on human MaSC. In particular, the common marmoset monkey (Callithrix jacchus) with a relatively short life span is an ideal model for aging research. In the present study, we characterized for the first time the mammary epithelial stem/progenitor cells in the common marmoset. The MaSC-enriched cells formed four major types of morphologically distinct colonies when cultured on plates pre-seeded with irradiated NIH3T3 fibroblasts, and were also capable of forming mammospheres in suspension culture and subsequent formation of 3D organoids in Matrigel culture. Most importantly, these 3D organoids were found to contain stem/progenitor cells that can undergo self-renewal and multi-lineage differentiation both in vitro and in vivo. We also observed a significant decrease of luminal-restricted progenitors with age. Our findings demonstrate that common marmoset mammary stem/progenitor cells can be isolated and quantified with established in vitro and in vivo assays used for mouse and human studies.

Simultaneous pharmacokinetics evaluation of human cytochrome P450 probes, caffeine, warfarin, omeprazole, metoprolol and midazolam, in common marmosets (Callithrix jacchus).

PubMed

Uehara, Shotaro; Inoue, Takashi; Utoh, Masahiro; Toda, Akiko; Shimizu, Makiko; Uno, Yasuhiro; Sasaki, Erika; Yamazaki, Hiroshi

2016-01-01

1. Pharmacokinetics of human cytochrome P450 probes (caffeine, racemic warfarin, omeprazole, metoprolol and midazolam) composite, after single intravenous and oral administrations at doses of 0.20 and 1.0 mg kg(-1), respectively, to four male common marmosets were investigated. 2. The plasma concentrations of caffeine and warfarin decreased slowly in a monophasic manner but those of omeprazole, metoprolol and midazolam decreased extensively after intravenous and oral administrations, in a manner that approximated those as reported for pharmacokinetics in humans. 3. Bioavailabilities were ∼100% for caffeine and warfarin, but <25% for omeprazole and metoprolol. Bioavailability of midazolam was 4% in marmosets, presumably because of contribution of marmoset P450 3A4 expressed in small intestine and liver, with a high catalytic efficiency for midazolam 1'-hydroxylation as evident in the recombinant system. 4. These results suggest that common marmosets, despite their rapid clearance of some human P450 probe substrates, could be an experimental model for humans and that marmoset P450s have functional characteristics that differ from those of human and/or cynomolgus monkey P450s in some aspects, indicating their importance in modeling in P450-dependent drug metabolism studies in marmosets and of further studies.

The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features

PubMed Central

Debowski, Katharina; Drummer, Charis; Lentes, Jana; Cors, Maren; Dressel, Ralf; Lingner, Thomas; Salinas-Riester, Gabriela; Fuchs, Sigrid; Sasaki, Erika; Behr, Rüdiger

2016-01-01

Embryonic stem cells (ESCs) are useful for the study of embryonic development. However, since research on naturally conceived human embryos is limited, non-human primate (NHP) embryos and NHP ESCs represent an excellent alternative to the corresponding human entities. Though, ESC lines derived from naturally conceived NHP embryos are still very rare. Here, we report the generation and characterization of four novel ESC lines derived from natural preimplantation embryos of the common marmoset monkey (Callithrix jacchus). For the first time we document derivation of NHP ESCs derived from morula stages. We show that quantitative chromosome-wise transcriptome analyses precisely reflect trisomies present in both morula-derived ESC lines. We also demonstrate that the female ESC lines exhibit different states of X-inactivation which is impressively reflected by the abundance of the lncRNA X inactive-specific transcript (XIST). The novel marmoset ESC lines will promote basic primate embryo and ESC studies as well as preclinical testing of ESC-based regenerative approaches in NHP. PMID:27385131

The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features.

PubMed

Debowski, Katharina; Drummer, Charis; Lentes, Jana; Cors, Maren; Dressel, Ralf; Lingner, Thomas; Salinas-Riester, Gabriela; Fuchs, Sigrid; Sasaki, Erika; Behr, Rüdiger

2016-07-07

Embryonic stem cells (ESCs) are useful for the study of embryonic development. However, since research on naturally conceived human embryos is limited, non-human primate (NHP) embryos and NHP ESCs represent an excellent alternative to the corresponding human entities. Though, ESC lines derived from naturally conceived NHP embryos are still very rare. Here, we report the generation and characterization of four novel ESC lines derived from natural preimplantation embryos of the common marmoset monkey (Callithrix jacchus). For the first time we document derivation of NHP ESCs derived from morula stages. We show that quantitative chromosome-wise transcriptome analyses precisely reflect trisomies present in both morula-derived ESC lines. We also demonstrate that the female ESC lines exhibit different states of X-inactivation which is impressively reflected by the abundance of the lncRNA X inactive-specific transcript (XIST). The novel marmoset ESC lines will promote basic primate embryo and ESC studies as well as preclinical testing of ESC-based regenerative approaches in NHP.

The Brain/MINDS 3D digital marmoset brain atlas

PubMed Central

Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko

2018-01-01

We present a new 3D digital brain atlas of the non-human primate, common marmoset monkey (Callithrix jacchus), with MRI and coregistered Nissl histology data. To the best of our knowledge this is the first comprehensive digital 3D brain atlas of the common marmoset having normalized multi-modal data, cortical and sub-cortical segmentation, and in a common file format (NIfTI). The atlas can be registered to new data, is useful for connectomics, functional studies, simulation and as a reference. The atlas was based on previously published work but we provide several critical improvements to make this release valuable for researchers. Nissl histology images were processed to remove illumination and shape artifacts and then normalized to the MRI data. Brain region segmentation is provided for both hemispheres. The data is in the NIfTI format making it easy to integrate into neuroscience pipelines, whereas the previous atlas was in an inaccessible file format. We also provide cortical, mid-cortical and white matter boundary segmentations useful for visualization and analysis. PMID:29437168

Distinct Neural Activities in Premotor Cortex during Natural Vocal Behaviors in a New World Primate, the Common Marmoset (Callithrix jacchus).

PubMed

Roy, Sabyasachi; Zhao, Lingyun; Wang, Xiaoqin

2016-11-30

Although evidence from human studies has long indicated the crucial role of the frontal cortex in speech production, it has remained uncertain whether the frontal cortex in nonhuman primates plays a similar role in vocal communication. Previous studies of prefrontal and premotor cortices of macaque monkeys have found neural signals associated with cue- and reward-conditioned vocal production, but not with self-initiated or spontaneous vocalizations (Coudé et al., 2011; Hage and Nieder, 2013), which casts doubt on the role of the frontal cortex of the Old World monkeys in vocal communication. A recent study of marmoset frontal cortex observed modulated neural activities associated with self-initiated vocal production (Miller et al., 2015), but it did not delineate whether these neural activities were specifically attributed to vocal production or if they may result from other nonvocal motor activity such as orofacial motor movement. In the present study, we attempted to resolve these issues and examined single neuron activities in premotor cortex during natural vocal exchanges in the common marmoset (Callithrix jacchus), a highly vocal New World primate. Neural activation and suppression were observed both before and during self-initiated vocal production. Furthermore, by comparing neural activities between self-initiated vocal production and nonvocal orofacial motor movement, we identified a subpopulation of neurons in marmoset premotor cortex that was activated or suppressed by vocal production, but not by orofacial movement. These findings provide clear evidence of the premotor cortex's involvement in self-initiated vocal production in natural vocal behaviors of a New World primate. Human frontal cortex plays a crucial role in speech production. However, it has remained unclear whether the frontal cortex of nonhuman primates is involved in the production of self-initiated vocalizations during natural vocal communication. Using a wireless multichannel neural recording technique, we observed in the premotor cortex neural activation and suppression both before and during self-initiated vocalizations when marmosets, a highly vocal New World primate species, engaged in vocal exchanges with conspecifics. A novel finding of the present study is the discovery of a subpopulation of premotor cortex neurons that was activated by vocal production, but not by orofacial movement. These observations provide clear evidence of the premotor cortex's involvement in vocal production in a New World primate species. Copyright © 2016 the authors 0270-6474/16/3612168-12$15.00/0.

Large-scale brain networks in the awake, truly resting marmoset monkey.

PubMed

Belcher, Annabelle M; Yen, Cecil C; Stepp, Haley; Gu, Hong; Lu, Hanbing; Yang, Yihong; Silva, Afonso C; Stein, Elliot A

2013-10-16

Resting-state functional MRI is a powerful tool that is increasingly used as a noninvasive method for investigating whole-brain circuitry and holds great potential as a possible diagnostic for disease. Despite this potential, few resting-state studies have used animal models (of which nonhuman primates represent our best opportunity of understanding complex human neuropsychiatric disease), and no work has characterized networks in awake, truly resting animals. Here we present results from a small New World monkey that allows for the characterization of resting-state networks in the awake state. Six adult common marmosets (Callithrix jacchus) were acclimated to light, comfortable restraint using individualized helmets. Following behavioral training, resting BOLD data were acquired during eight consecutive 10 min scans for each conscious subject. Group independent component analysis revealed 12 brain networks that overlap substantially with known anatomically constrained circuits seen in the awake human. Specifically, we found eight sensory and "lower-order" networks (four visual, two somatomotor, one cerebellar, and one caudate-putamen network), and four "higher-order" association networks (one default mode-like network, one orbitofrontal, one frontopolar, and one network resembling the human salience network). In addition to their functional relevance, these network patterns bear great correspondence to those previously described in awake humans. This first-of-its-kind report in an awake New World nonhuman primate provides a platform for mechanistic neurobiological examination for existing disease models established in the marmoset.

Marmosets: A Neuroscientific Model of Human Social Behavior

PubMed Central

Freiwald, Winrich A; Leopold, David A; Mitchell, Jude F; Silva, Afonso C; Wang, Xiaoqin

2016-01-01

The common marmoset (Callithrix jacchus) has garnered interest recently as a powerful model for the future of neuroscience research. Much of this excitement has centered on the species’ reproductive biology and compatibility with gene editing techniques, which together have provided a path for transgenic marmosets to contribute to the study of disease as well as basic brain mechanisms. In step with technical advances is the need to establish experimental paradigms that optimally tap into the marmosets’ behavioral and cognitive capacities. While conditioned task performance of a marmoset can compare unfavorably with rhesus monkey performance on conventional testing paradigms, marmosets’ social cognition and communication are more similar to that of humans. For example, marmosets are amongst only a handful of primates that, like humans, routinely pair bond and care cooperatively for their young. They are also notably pro-social and exhibit social cognitive abilities, such as imitation, that are rare outside of the Apes. In this review, we describe key facets of marmoset natural social behavior and demonstrate that emerging behavioral paradigms are well suited to isolate components of marmoset cognition that are highly relevant to humans. These approaches generally embrace natural behavior and communication, which has been rare in conventional primate testing, and thus allow for a new consideration of neural mechanisms underlying primate social cognition and communication. We anticipate that through parallel technical and paradigmatic advances, marmosets will become an essential model of human social behavior, including its dysfunction in nearly all neuropsychiatric disorders. PMID:27100195

Utah optrode array customization using stereotactic brain atlases and 3-D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates.

PubMed

Boutte, Ronald W; Merlin, Sam; Yona, Guy; Griffiths, Brandon; Angelucci, Alessandra; Kahn, Itamar; Shoham, Shy; Blair, Steve

2017-10-01

As the optogenetic field expands, the need for precise targeting of neocortical circuits only grows more crucial. This work demonstrates a technique for using Solidworks ® computer-aided design (CAD) and readily available stereotactic brain atlases to create a three-dimensional (3-D) model of the dorsal region of area visual cortex 4 (V4D) of the macaque monkey ( Macaca fascicularis ) visual cortex. The 3-D CAD model of the brain was used to customize an [Formula: see text] Utah optrode array (UOA) after it was determined that a high-density ([Formula: see text]) UOA caused extensive damage to marmoset ( Callithrix jacchus ) primary visual cortex as assessed by electrophysiological recording of spiking activity through a 1.5-mm-diameter through glass via. The [Formula: see text] UOA was customized for optrode length ([Formula: see text]), optrode width ([Formula: see text]), optrode pitch ([Formula: see text]), backplane thickness ([Formula: see text]), and overall form factor ([Formula: see text]). Two [Formula: see text] UOAs were inserted into layer VI of macaque V4D cortices with minimal damage as assessed in fixed tissue cytochrome oxidase staining in nonrecoverable surgeries. Additionally, two [Formula: see text] arrays were implanted in mice ( Mus musculus ) motor cortices, providing early evidence for long-term tolerability (over 6 months), and for the ability to integrate the UOA with a Holobundle light delivery system toward patterned optogenetic stimulation of cortical networks.

Larger cages with housing unit environment enrichment improve the welfare of marmosets.

PubMed

Yoshimoto, Takuro; Takahashi, Eiki; Yamashita, Shunji; Ohara, Kiichi; Niimi, Kimie

2018-02-09

The provision of adequate space for laboratory animals is essential not only for good welfare but accurate studies. For example, housing conditions for primates used in biomedical research may negatively affect welfare and thus the reliability of findings. In common marmosets (Callithrix jacchus), an appropriate cage size enables a socially harmonious family environment and optimizes reproductive potential. In this study, we investigated the effects of cage size on body weight (BW), behavior, and nursing succession in the common marmoset. Large cages (LCs) with environment enrichment led to an increase in BW while small cages (SCs) caused stereotypic behaviors that were not observed in LCs. In addition, the BW of infants increased with aging in LCs. Our findings indicate that the welfare of marmosets was enhanced by living in LCs. Research on non-human primates is essential for understanding the human brain and developing knowledge-based strategies for the diagnosis and treatment of psychiatric and neurological disorders. Thus, the present findings are important because they indicate that different cages may influence emotional and behavioral phenotypes.

Cognitive impairment in a young marmoset reveals lateral ventriculomegaly and a mild hippocampal atrophy: a case report

PubMed Central

Sadoun, A.; Strelnikov, K.; Bonté, E.; Fonta, C.; Girard, P.

2015-01-01

The number of studies that use the common marmoset (Callithrix jacchus) in various fields of neurosciences is increasing dramatically. In general, animals enter the study when their health status is considered satisfactory on the basis of classical clinical investigations. In behavioral studies, variations of score between individuals are frequently observed, some of them being considered as poor performers or outliers. Experimenters rarely consider the fact that it could be related to some brain anomaly. This raises the important issue of the reliability of such classical behavioral approaches without using complementary imaging, especially in animals lacking striking external clinical signs. Here we report the case of a young marmoset which presented a set of cognitive impairments in two different tasks compared to other age-matched animals. Brain imaging revealed a patent right lateral ventricular enlargement with a mild hippocampal atrophy. This abnormality could explain the cognitive impairments of this animal. Such a case points to the importance of complementing behavioral studies by imaging explorations to avoid experimental bias. PMID:26527211

Dual-Pitch Processing Mechanisms in Primate Auditory Cortex

PubMed Central

Bendor, Daniel; Osmanski, Michael S.

2012-01-01

Pitch, our perception of how high or low a sound is on a musical scale, is a fundamental perceptual attribute of sounds and is important for both music and speech. After more than a century of research, the exact mechanisms used by the auditory system to extract pitch are still being debated. Theoretically, pitch can be computed using either spectral or temporal acoustic features of a sound. We have investigated how cues derived from the temporal envelope and spectrum of an acoustic signal are used for pitch extraction in the common marmoset (Callithrix jacchus), a vocal primate species, by measuring pitch discrimination behaviorally and examining pitch-selective neuronal responses in auditory cortex. We find that pitch is extracted by marmosets using temporal envelope cues for lower pitch sounds composed of higher-order harmonics, whereas spectral cues are used for higher pitch sounds with lower-order harmonics. Our data support dual-pitch processing mechanisms, originally proposed by psychophysicists based on human studies, whereby pitch is extracted using a combination of temporal envelope and spectral cues. PMID:23152599

Harmonic template neurons in primate auditory cortex underlying complex sound processing

PubMed Central

Feng, Lei

2017-01-01

Harmonicity is a fundamental element of music, speech, and animal vocalizations. How the auditory system extracts harmonic structures embedded in complex sounds and uses them to form a coherent unitary entity is not fully understood. Despite the prevalence of sounds rich in harmonic structures in our everyday hearing environment, it has remained largely unknown what neural mechanisms are used by the primate auditory cortex to extract these biologically important acoustic structures. In this study, we discovered a unique class of harmonic template neurons in the core region of auditory cortex of a highly vocal New World primate, the common marmoset (Callithrix jacchus), across the entire hearing frequency range. Marmosets have a rich vocal repertoire and a similar hearing range to that of humans. Responses of these neurons show nonlinear facilitation to harmonic complex sounds over inharmonic sounds, selectivity for particular harmonic structures beyond two-tone combinations, and sensitivity to harmonic number and spectral regularity. Our findings suggest that the harmonic template neurons in auditory cortex may play an important role in processing sounds with harmonic structures, such as animal vocalizations, human speech, and music. PMID:28096341

Occurrence of hemotropic mycoplasmas in non-human primates (Alouatta caraya, Sapajus nigritus and Callithrix jacchus) of southern Brazil.

PubMed

Cubilla, Michelle P; Santos, Leonilda C; de Moraes, Wanderlei; Cubas, Zalmir S; Leutenegger, Christian M; Estrada, Marko; Vieira, Rafael F C; Soares, Maurilio J; Lindsay, LeAnn L; Sykes, Jane E; Biondo, Alexander W

2017-06-01

Hemoplasmas, the erythrocyte-associated mycoplasmas, have been detected in several primates, causing mostly subclinical infection. This study aimed to determine the prevalence of hemoplasma infection in captive and free-ranging monkeys from southern Brazil, as well as factors and hematological abnormalities associated with infection. Blood samples from 40 non-human primates (NHP) were tested for hemoplasmas and coinfections. An overall of 10/40 (25.0%) NHP tested positive for hemoplasmas using PCR-based assays, including 9/14 (64.3%) black howler monkeys (Alouatta caraya) and 1/24 (4.2%) black-horned capuchin (Sapajus nigritus). Infection was not statistically associated with anemia, but wild-born monkeys and male black howler monkeys were more likely to be positive when compared with captive-born animals and female black howler monkeys, respectively. The sequences from the black howler monkey hemoplasma were similar (94% identity) to the squirrel monkey hemoplasma ("Candidatus Mycoplasma kahanei") and were phylogenetically located in a different cluster when compared to the human hemoplasma ("Candidatus Mycoplasma haemohominis"). Copyright © 2017 Elsevier Ltd. All rights reserved.

Complex pitch perception mechanisms are shared by humans and a New World monkey.

PubMed

Song, Xindong; Osmanski, Michael S; Guo, Yueqi; Wang, Xiaoqin

2016-01-19

The perception of the pitch of harmonic complex sounds is a crucial function of human audition, especially in music and speech processing. Whether the underlying mechanisms of pitch perception are unique to humans, however, is unknown. Based on estimates of frequency resolution at the level of the auditory periphery, psychoacoustic studies in humans have revealed several primary features of central pitch mechanisms. It has been shown that (i) pitch strength of a harmonic tone is dominated by resolved harmonics; (ii) pitch of resolved harmonics is sensitive to the quality of spectral harmonicity; and (iii) pitch of unresolved harmonics is sensitive to the salience of temporal envelope cues. Here we show, for a standard musical tuning fundamental frequency of 440 Hz, that the common marmoset (Callithrix jacchus), a New World monkey with a hearing range similar to that of humans, exhibits all of the primary features of central pitch mechanisms demonstrated in humans. Thus, marmosets and humans may share similar pitch perception mechanisms, suggesting that these mechanisms may have emerged early in primate evolution.

An Embedded 4-Channel Receive-Only RF Coil Array for fMRI Experiments of the Somatosensory Pathway in Conscious Awake Marmosets at 7T

PubMed Central

Papoti, Daniel; Yen, Cecil Chern-Chyi; Mackel, Julie B.; Merkle, Hellmut; Silva, Afonso C.

2014-01-01

Functional Magnetic Resonance Imaging (fMRI) has established itself as the main research tool in neuroscience and brain cognitive research. The common marmoset (Callithrix jacchus) is a non-human primate model of increasing interest in biomedical research. However, commercial MRI coils for marmosets are not generally available. The present work describes the design and construction of a 4-channel receive-only surface RF coil array with excellent signal-to-noise ratio (SNR) specifically optimized for fMRI experiments in awake marmosets in response to somatosensory stimulation. The array was designed as part of a helmet-based head restraint system used to prevent motion during the scans. High SNR was obtained by building the coil array using a thin and flexible substrate glued to the inner surface of the restraint helmet, so as to minimize the distance between the array elements and the somatosensory cortex. Decoupling between coil elements was achieved by partial geometrical overlapping and by connecting them to home-built low input impedance preamplifiers. In vivo images show excellent coverage of the brain cortical surface with high sensitivity near the somatosensory cortex. Embedding the coil elements within the restraint helmet allowed fMRI data in response to somatosensory stimulation to be collected with high sensitivity and reproducibility in conscious, awake marmosets. PMID:23696219

Inhibition of allergic encephalomyelitis in marmosets by vaccination with recombinant vaccinia virus encoding for myelin basic protein.

PubMed

Genain, C P; Gritz, L; Joshi, N; Panicali, D; Davis, R L; Whitaker, J N; Letvin, N L; Hauser, S L

1997-11-01

A primary demyelinating form of experimental allergic encephalomyelitis (EAE) resembling human multiple sclerosis (MS) occurs in Callithrix jacchus marmosets following immunization with human white matter. Participation of a T-cell immune response against myelin basic protein (MBP) in this disease model is supported by observations of increased reactivity against MBP in PBMC and of adoptive transfer of an inflammatory form of EAE by MBP-reactive T-cells. To evaluate the effects of ectopic presentation of MBP on marmoset EAE, animals were vaccinated prior to induction of EAE by subcutaneous injection of attenuated strains of vaccinia virus genetically engineered to contain either the entire coding sequence for human MBP (vT15) or the equine herpes virus glycoprotein gH gene (vAbT249). Vaccination with vT15 was followed by transient cytoplasmic and surface membrane expression of MBP in circulating PBMC (15-45 days). The onset of clinical EAE after immunization (pi) was markedly delayed in vT15-vaccinated animals (37-97 days pi, n = 4) compared to vAbT249-vaccinated controls (14-18 days pi, n = 3). Proliferative responses against MBP but not against vaccinia antigens or phytohemagglutinin were suppressed in protected animals. Thus, development of attenuated live viruses carrying genes for myelin antigens could be useful for induction of immunologic tolerance and for modulation of autoimmune demyelination.

Differential cadherin expression in the developing postnatal telencephalon of a New World monkey.

PubMed

Matsunaga, Eiji; Nambu, Sanae; Oka, Mariko; Iriki, Atsushi

2013-12-01

Cadherins are cell adhesion molecules widely expressed in the nervous system, where they play various roles in neural patterning, nuclei formation, axon guidance, and synapse formation and function. Although many published articles have reported on cadherin expression in rodents and ferrets, there are limited data on their expression in primate brains. In this study, in situ hybridization analysis was performed for 10 cadherins [nine classic cadherins (Cdh4, -6, -7, -8, -9, -10, -11, -12, and -20) and T-cadherin (Cdh13)] in the developing postnatal telencephalon of the common marmoset (Callithrix jacchus). Each cadherin showed broad expression in the cerebral cortex, basal ganglia, amygdala, and hippocampus, as previously shown in the rodent brain. However, detailed expression patterns differed between rodents and marmosets. In contrast to rodents, cadherin expression was reduced overall and localized to restricted areas of the brain during the developmental process, suggesting that cadherins are more crucially involved in developmental or maturation processes rather than in neural functioning. These results also highlight the possibility that restricted/less redundant cadherin expression allows primate brains to generate functional diversity among neurons, allowing morphological and functional differences between rodents and primates. Copyright © 2013 Wiley Periodicals, Inc.

Male and female breeding strategies in a cooperative primate.

PubMed

Yamamoto, Maria Emilia; Araujo, Arrilton; Arruda, Maria de Fatima; Lima, Ana Karinne Moreira; Siqueira, Jose de Oliveira; Hattori, Wallisen Tadashi

2014-11-01

Marmosets are cooperative breeders organized as extended family groups, but breeding is generally restricted to a single pair. Breeding competition is fierce in female marmosets; males, on the other hand, show low levels of intragroup aggression. We investigated male and female breeding strategies and the resulting reproductive output in 9 wild groups. Reproductive output, tenure of breeding animals, identification of the breeding system, breeding position replacements, migration and infanticide were recorded; also, we recorded grooming and aggression. Replacement of the breeding male or female was observed on nine occasions. On four occasions, the son of the breeding male inherited the breeding post, but we never observed inheritance of a breeding post by a daughter. Mostly, females attained a breeding post by immigrating to a group that had a breeding vacancy. Our results showed that Callithrix jacchus males and females use different strategies to attain a breeding position and maintain it for as long as possible. These strategies prolong the tenure of the breeding position, which is the best way to produce a large number of offspring. This article is part of a Special Issue entitled: Neotropical Behaviour. Copyright © 2014 Elsevier B.V. All rights reserved.

Glutamine/glutamate (Glx) concentration in prefrontal cortex predicts reversal learning performance in the marmoset.

PubMed

Lacreuse, Agnès; Moore, Constance M; LaClair, Matthew; Payne, Laurellee; King, Jean A

2018-07-02

This study used Magnetic Resonance Spectroscopy (MRS) to identify potential neurometabolitic markers of cognitive performance in male (n = 7) and female (n = 8) middle-aged (∼5 years old) common marmosets (Callithrix jacchus). Anesthetized marmosets were scanned with a 4.7 T/40 cm horizontal magnet equipped with 450 mT/m magnetic field gradients and a 20 G/cm magnetic field gradient insert, within 3 months of completing the CANTAB serial Reversal Learning task. Neurometabolite concentrations of N-Acetyl Asparate, Myo-Inositol, Choline, Phosphocreatine + creatine, Glutamate and Glutamine were acquired from a 3 mm 3 voxel positioned in the Prefrontal Cortex (PFC). Males acquired the reversals (but not simple discriminations) faster than the females. Higher PFC Glx (glutamate + glutamine) concentration was associated with faster acquisition of the reversals. Interestingly, the correlation between cognitive performance and Glx was significant in males, but not in females. These results suggest that MRS is a useful tool to identify biochemical markers of cognitive performance in the healthy nonhuman primate brain and that biological sex modulates the relationship between neurochemical composition and cognition. Copyright © 2018 Elsevier B.V. All rights reserved.

The neonatal marmoset monkey ovary is very primitive exhibiting many oogonia

PubMed Central

Fereydouni, B; Drummer, C; Aeckerle, N; Schlatt, S; Behr, R

2014-01-01

Oogonia are characterized by diploidy and mitotic proliferation. Human and mouse oogonia express several factors such as OCT4, which are characteristic of pluripotent cells. In human, almost all oogonia enter meiosis between weeks 9 and 22 of prenatal development or undergo mitotic arrest and subsequent elimination from the ovary. As a consequence, neonatal human ovaries generally lack oogonia. The same was found in neonatal ovaries of the rhesus monkey, a representative of the old world monkeys (Catarrhini). By contrast, proliferating oogonia were found in adult prosimians (now called Strepsirrhini), which is a group of ‘lower’ primates. The common marmoset monkey (Callithrix jacchus) belongs to the new world monkeys (Platyrrhini) and is increasingly used in reproductive biology and stem cell research. However, ovarian development in the marmoset monkey has not been widely investigated. Herein, we show that the neonatal marmoset ovary has an extremely immature histological appearance compared with the human ovary. It contains numerous oogonia expressing the pluripotency factors OCT4A, SALL4, and LIN28A (LIN28). The pluripotency factor-positive germ cells also express the proliferation marker MKI67 (Ki-67), which has previously been shown in the human ovary to be restricted to premeiotic germ cells. Together, the data demonstrate the primitiveness of the neonatal marmoset ovary compared with human. This study may introduce the marmoset monkey as a non-human primate model to experimentally study the aspects of primate primitive gonad development, follicle assembly, and germ cell biology in vivo. PMID:24840529

Behavioral phenotypes associated with MPTP induction of partial lesions in common marmosets (Callithrix jacchus).

PubMed

Phillips, Kimberley A; Ross, Corinna N; Spross, Jennifer; Cheng, Catherine J; Izquierdo, Alyssa; Biju, K C; Chen, Cang; Li, Senlin; Tardif, Suzette D

2017-05-15

Parkinson's disease is a chronic neurodegenerative disorder with the core motor features of resting tremor, bradykinesia, rigidity, and postural instability. Non-motor symptoms also occur, and include cognitive dysfunction, mood disorders, anosmia (loss of smell), and REM sleep disturbances. As the development of medications and other therapies for treatment of non-motor symptoms is ongoing, it is essential to have animal models that aid in understanding the neural changes underlying non-motor PD symptoms and serve as a testing ground for potential therapeutics. We investigated several non-motor symptoms in 10 adult male marmosets using the MPTP model, with both the full (n=5) and partial (n=5) MPTP dosing regimens. Baseline data in numerous domains were collected prior to dosing; assessments in these same domains occurred post-dosing for 12 weeks. Marmosets given the partial MPTP dose (designed to mimic the early stages of the disease) differed significantly from marmosets given the full MPTP dose in several ways, including behavior, olfactory discrimination, cognitive performance, and social responses. Importantly, while spontaneous recovery of PD motor symptoms has been previously reported in studies of MPTP monkeys and cats, we did not observe recovery of any non-motor symptoms. This suggests that the neurochemical mechanisms behind the non-motor symptoms of PD, which appear years before the onset of symptoms, are independent of the striatal dopaminergic transmission. We demonstrate the value of assessing a broad range of behavioral change to detect non-motor impairment, anosmia, and differences in socially appropriate responses, in the marmoset MPTP model of early PD. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel highly reproducible and lethal nonhuman primate model for orthopox virus infection.

PubMed

Kramski, Marit; Mätz-Rensing, Kerstin; Stahl-Hennig, Christiane; Kaup, Franz-Josef; Nitsche, Andreas; Pauli, Georg; Ellerbrok, Heinz

2010-04-29

The intentional re-introduction of Variola virus (VARV), the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV) and Monkeypox virus (MPXV) cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus).A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV) outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1-3 days after onset of symptoms, even when very low infectious viral doses of 5x10(2) pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed.We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID(50) (minimal monkey infectious dose 50%) of 8.3x10(2) pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis.

A Novel Highly Reproducible and Lethal Nonhuman Primate Model for Orthopox Virus Infection

PubMed Central

Kramski, Marit; Mätz-Rensing, Kerstin; Stahl-Hennig, Christiane; Kaup, Franz-Josef; Nitsche, Andreas; Pauli, Georg; Ellerbrok, Heinz

2010-01-01

The intentional re-introduction of Variola virus (VARV), the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV) and Monkeypox virus (MPXV) cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus). A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV) outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1–3 days after onset of symptoms, even when very low infectious viral doses of 5×102 pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed. We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID50 (minimal monkey infectious dose 50%) of 8.3×102 pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis. PMID:20454688

Bisphenol A-induced ultrastructural changes in the testes of common marmoset.

PubMed

Vijaykumar, Tushara; Singh, Dipty; Vanage, Geeta R; Dhumal, Rohit V; Dighe, Vikas D

2017-07-01

Bisphenol A (BPA) is an endocrine disruptor that is widely used in the manufacture of polycarbonate plastics, epoxy resins and dental sealants. It is known to have adverse effects on spermatogenesis in rodents. This study was aimed to evaluate the effects of BPA in adult common marmoset owing to its similarities with human spermatogenesis. Sixteen marmosets were divided into four groups (n=4 per group) and given oral doses of BPA (2.5, 12.5 and 25 μg/kg BW/day) for 70 days to cover two spermatogenic cycles, and the control group received only vehicle (honey). Testes were processed for histological and transmission electron microscopy studies. Histology of the testis showed sloughing of germ cells into the lumen, increase in interstitial space and vacuolation of Sertoli cell cytoplasm. Ultrastructural analysis of the testis revealed several degenerative effects on the basement membrane, Sertoli cells, Leydig cells and other developing germ cells in the 12.5 and 25 μg/kg BW/day groups as compared to control. The observed ultrastructural changes caused by BPA in testicular morphology might be indicative of a perturbed sperm production. Considering the genetic and spermatogenic similarities of common marmoset (Callithrix jacchus) and humans, the study findings are of significance. Further studies are, however, needed to elucidate the mechanism of action.

Inflammatory fibroid polyp in the duodenum of a common marmoset (Callithrix jacchus).

PubMed

Yokouchi, Yusuke; Imaoka, Masako; Sayama, Ayako; Jindo, Toshimasa; Sanbuissho, Atsushi

2013-01-01

A 32-month-old male common marmoset had a firm and white-colored mass in the duodenal wall. The cut surface was smooth and grayish white in color. Histologically, the mass consisted of a proliferation of spindle cells with an oval to spindle-shaped nucleus and scant eosinophilic cytoplasm in a loose myxoid or fibrotic background. Most of the lesion displayed no specific growth pattern whereas some of the cells concentrated around the vessels and created an onion-bulb structure. Additionally, marked inflammatory cellular infiltration, mainly eosinophils, was observed throughout the lesion. Immunohistochemically, the spindle cells were positive for vimentin, α-smooth muscle actin, fascin, and cyclin D1, and negative for S-100, factor VIII-related antigen, and c-kit. These histological and immunohistochemical features did not meet any differential diagnoses such as gastrointestinal stromal tumor, inflammatory myofibroblastic tumor, solitary fibrous tumor/hemangiopericytoma, smooth muscle tumor, schwannoma, and hemangiosarcoma. Collectively, the authors diagnosed the mass as a lesion that corresponded to an inflammatory fibroid polyp (IFP) in humans. IFP is defined as a mesenchymal proliferation composed of spindle stromal cells, small blood vessels, and inflammatory cells, particularly eosinophils, and is currently classified as a nonneoplastic lesion. To the best of our knowledge, this is the first case of spontaneous IFP in nonhuman primates.

Cognitive bias, hand preference and welfare of common marmosets.

PubMed

Gordon, Dianne J; Rogers, Lesley J

2015-01-01

Common marmosets (Callithrix jacchus) have hand preferences for grasping pieces of food and holding them while eating and these are stable throughout adult life. We report here that left-handed marmosets have negative cognitive bias compared to right-handed marmosets. Twelve marmosets were trained to expect a food reward from a bowl with a black lid and not from one with a white lid, or vice versa. In probe tests with ambiguous, grey-lidded bowls a left-handed group (N=7) were less likely to remove the lid to inspect the bowl than a right-handed group (N=5). This difference between left- and right-handed marmosets was not dependent on rate of learning, sex or age. In fact, hand-preference was not associated with rate of learning the task. Furthermore, retrospective examination of colony records of 39 marmosets revealed that more aggression was directed towards left- than right-handed marmosets. Hence, hand preference, which can be measured easily, could serve as an indicator of cognitive bias and may signal a need for particular care in laboratory environments. We explain the results by arguing that hand preference reflects more frequent (or dominant) use of the opposite hemisphere and this predisposes individuals to behave differently. Copyright © 2015 Elsevier B.V. All rights reserved.

Formation of infectious dengue virus-antibody immune complex in vivo in marmosets (Callithrix jacchus) after passive transfer of anti-dengue virus monoclonal antibodies and infection with dengue virus.

PubMed

Moi, Meng Ling; Ami, Yasushi; Shirai, Kenji; Lim, Chang-Kweng; Suzaki, Yuriko; Saito, Yuka; Kitaura, Kazutaka; Saijo, Masayuki; Suzuki, Ryuji; Kurane, Ichiro; Takasaki, Tomohiko

2015-02-01

Infection with a dengue virus (DENV) serotype induces cross-reactive, weakly neutralizing antibodies to different dengue serotypes. It has been postulated that cross-reactive antibodies form a virus-antibody immune complex and enhance DENV infection of Fc gamma receptor (FcγR)-bearing cells. We determined whether infectious DENV-antibody immune complex is formed in vivo in marmosets after passive transfer of DENV-specific monoclonal antibody (mAb) and DENV inoculation and whether infectious DENV-antibody immune complex is detectable using FcγR-expressing cells. Marmosets showed that DENV-antibody immune complex was exclusively infectious to FcγR-expressing cells on days 2, 4, and 7 after passive transfer of each of the mAbs (mAb 4G2 and mAb 6B6C) and DENV inoculation. Although DENV-antibody immune complex was detected, contribution of the passively transferred antibody to overall viremia levels was limited in this study. The results indicate that DENV cross-reactive antibodies form DENV-antibody immune complex in vivo, which is infectious to FcγR-bearing cells but not FcγR-negative cells. © The American Society of Tropical Medicine and Hygiene.

When play is a family business: adult play, hierarchy, and possible stress reduction in common marmosets.

PubMed

Norscia, Ivan; Palagi, Elisabetta

2011-04-01

Easy to recognize but not easy to define, animal play is a baffling behavior because it has no obvious immediate benefits for the performers. However, the absence of immediate advantages, if true, would leave adult play (costly but maintained by evolution, spanning lemurs to Homo sapiens) unexplained. Although a commonly held view maintains that play is limited by stress, an emergent hypothesis states that play can regulate stress in the short term. Here we explored this hypothesis in a captive family group of New World monkeys, Callithrix jacchus (common marmoset). We observed six subjects and gathered data on aggressive, play, and scratching behavior via focal (6 h/individual) and all occurrences sampling (115 h). We found that play levels were highest during pre-feeding, the period of maximum anxiety due to the forthcoming competition over food. Scratching (the most reliable indicator of stress in primates) and play showed opposite trends along hierarchy, with dominants scratching more and playing less than subordinates. Finally, scratching decreased after play, whereas play appeared to be unrelated to previous scratching events, symptoms of a potential stressful state. In conclusion, both play timing and hierarchical distribution indicate that play limits stress, more than vice versa, at least in the short term.

A conveyor belt task for assessing visuo-motor coordination in the marmoset (Callithrix jacchus): effects of diazepam, chlorpromazine, pentobarbital and d-amphetamine.

PubMed

D'Mello, G D; Duffy, E A; Miles, S S

1985-01-01

A conveyor belt task for assessing visuo-motor coordination in the marmoset is described. Animals are motivated by apple, a preferred food, under a state of minimal food deprivation. The apparatus used was designed to test animals within their home cages and not restrained in any way, thus avoiding possible confounding factors associated with restraint stress. Stable baseline levels of performance were reached by all animals in a median of 24 sessions. Performance was shown to be differentially sensitive to the effects of four psychoactive drugs. Moderate doses of diazepam, chlorpromazine and pentobarbital disrupted visuo-motor coordination in a dose-related manner. The possibility that disruption of performance observed at higher doses may have resulted from non-specific actions of these drugs such as decreases in feeding motivation were not supported by results from ancillary experiments. Changes in performance characteristic of high dose effects were similar in nature to changes observed when the degree of task difficulty was increased. Doses of d-amphetamine up to and including those reported to produce signs of stereotypy failed to influence performance. The potential of the conveyor belt task for measuring visuo-motor coordination in both primate and rodent species is discussed.

Antisera against Neisseria gonorrhoeae cross-react with specific brain proteins of the common marmoset monkey and other nonhuman primate species.

PubMed

Reuss, Bernhard; Asif, Abdul R; Almamy, Abdullah; Schwerk, Christian; Schroten, Horst; Ishikawa, Hiroshi; Drummer, Charis; Behr, Rüdiger

2016-12-15

Prenatal maternal infections with Neisseria gonorrhoeae (NG) correlate with an increased lifetime probability for the offspring to develop psychosis. We could previously demonstrate that in human choroid plexus papilloma cells, anti-NG antibodies (α-NG) bind to mitochondrial proteins HSP60 and ATPB, and interfere with cellular energy metabolism. To assess the in vivo relevance for this, especially during prenatal neural development, we investigated here interactions of NG-specific antisera (α-NG1, α-NG2) with brain, choroid plexus and other non-neural tissues in pre- and perinatal samples of the nonhuman primate (NHP) Callithrix jacchus (CJ), a NHP model for preclinical research. In histological sections at embryonic day E75, immunohistochemistry revealed α-NG1 and -2-staining in choroid plexus, ganglionic hill, optic cup, heart, and liver. Within the cells, organelle-like structures were labeled, which could be identified by immunohistochemical double-labeling as mitochondria. Both one- and two-dimensional Western blot analysis revealed tissue specific patterns of α-NG1 immunoreactive bands and spots, respectively, which were subsequently characterized by mass spectrometry. Thereby we could confirm the interactions of α-NG1 with human HSP60 and ATPB also in CJ choroid plexus and liver. Even more important, in the CJ brain, several new targets, including NCAM1, CRMP2, and SYT1, were identified, which by unrelated studies have been previously suggested to correlate with an increased schizophrenia risk. These findings support the idea that the marmoset monkey is a useful NHP model to investigate the role of maternal bacterial infections during prenatal brain development, and thereby might improve the understanding of this important aspect of schizophrenia pathology. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of methods to measure humoral immune responses against selected antigens in the common marmoset (Callithrix jacchus) and the effect of pyridostigmine bromide administration.

PubMed

Griffiths, Gareth D; Hornby, Rebecca J; Jagger, Christopher P; Brown, Alan P; Stoten, Adam; Pearce, Peter C; Scott, Leah; Pritchard, David I

2006-12-05

This methodological study was carried out in preparation for a major long term study, also reported in this volume, which was designed to investigate whether the combination of vaccines and pyridostigmine bromide (PB) could have been responsible for adverse signs and symptoms reported by a number of veterans of the 1990/1991 Gulf conflict. In this context, the marmoset has been used to model aspects of the human immune system. The purposes of this methodological study were to select appropriate immunochemical reagents to measure humoral responses induced in marmosets in response to selected health and hygiene and biological warfare vaccines and to initially assess the effects of PB on the responses recorded. Vaccines were administered at 1/5th of a human dose, and also investigated in combination with the nerve agent pretreatment compound PB. PB dosing was selected to induce an inhibition of erythrocyte acetylcholinesterase by 30%. In order to assess the functionality of the immune system, antibody responses to a neo-antigen (keyhole limpet haemocyanin--KLH), administered some 2 months following the completion of the vaccination schedule, were measured. The present study identified appropriate isotyping reporter reagents which cross-reacted with equivalent marmoset immunoglobulins. Robust antibody responses were identified against anthrax protective antigen (PA), whole cell pertussis vaccine and KLH, while weaker responses were measured against cholera and typhoid vaccines. The killed whole cell plague vaccine induced a response which was at the limit of detection of the assay. Coadministered PB had no discernable effect on immunological responses in this study.

A geometrically adjustable receive array for imaging marmoset cohorts.

PubMed

Gilbert, Kyle M; Gati, Joseph S; Klassen, L Martyn; Zeman, Peter; Schaeffer, David J; Everling, Stefan; Menon, Ravi S

2017-08-01

The common marmoset (Callithrix jacchus) is an increasingly popular animal model for translational neuroscience studies, during which anatomical and functional MRI can be useful investigative tools. To attain the requisite SNR for high-resolution acquisitions, the radiofrequency coil must be optimized for the marmoset; however, relatively few custom coils have been developed that maximize SNR and are compatible with accelerated acquisitions. For the study of large populations of animals, the heterogeneity in animal size reduces the effectiveness of a "one size fits all" approach to coil sizing and makes coils tailored to individual animals cost and time prohibitive. The approach taken in this study was to create an 8-channel phased-array receive coil that was adjustable to the width of the marmoset head, thereby negating the need for tailored coils while still maintaining high SNR. Two marmosets of different size were imaged on a 9.4-T small-animal scanner. Consistent SNR was achieved in the periphery of the brain between head sizes. When compared to a 15-channel, "one size fits all" receive coil, the adjustable coil achieved 57% higher SNR in the superior frontal and parietal cortices and 29% higher SNR in the centre of the brain. The mean geometry factor of the adjustable coil was less than 1.2 for a 2-fold reduction factor in the left-right and anterior-posterior directions. Geometry factors were compared to the 15-channel coil to guide future designs. The adjustable coil was shown to be a practical means for anatomical and echo-planar imaging of marmoset cohorts. Copyright © 2017 Elsevier Inc. All rights reserved.

Can vocal conditioning trigger a semiotic ratchet in marmosets?

PubMed

Turesson, Hjalmar K; Ribeiro, Sidarta

2015-01-01

The complexity of human communication has often been taken as evidence that our language reflects a true evolutionary leap, bearing little resemblance to any other animal communication system. The putative uniqueness of the human language poses serious evolutionary and ethological challenges to a rational explanation of human communication. Here we review ethological, anatomical, molecular, and computational results across several species to set boundaries for these challenges. Results from animal behavior, cognitive psychology, neurobiology, and semiotics indicate that human language shares multiple features with other primate communication systems, such as specialized brain circuits for sensorimotor processing, the capability for indexical (pointing) and symbolic (referential) signaling, the importance of shared intentionality for associative learning, affective conditioning and parental scaffolding of vocal production. The most substantial differences lie in the higher human capacity for symbolic compositionality, fast vertical transmission of new symbols across generations, and irreversible accumulation of novel adaptive behaviors (cultural ratchet). We hypothesize that increasingly-complex vocal conditioning of an appropriate animal model may be sufficient to trigger a semiotic ratchet, evidenced by progressive sign complexification, as spontaneous contact calls become indexes, then symbols and finally arguments (strings of symbols). To test this hypothesis, we outline a series of conditioning experiments in the common marmoset (Callithrix jacchus). The experiments are designed to probe the limits of vocal communication in a prosocial, highly vocal primate 35 million years far from the human lineage, so as to shed light on the mechanisms of semiotic complexification and cultural transmission, and serve as a naturalistic behavioral setting for the investigation of language disorders.

Experimental Cross-Species Infection of Common Marmosets by Titi Monkey Adenovirus

PubMed Central

Chen, Eunice C.; Liu, Maria; Brasky, Kathleen M.; Lanford, Robert E.; Kelly, Kristi R.; Bales, Karen L.; Schnurr, David P.; Canfield, Don R.; Patterson, Jean L.; Chiu, Charles Y.

2013-01-01

Adenoviruses are DNA viruses that infect a number of vertebrate hosts and are associated with both sporadic and epidemic disease in humans. We previously identified a novel adenovirus, titi monkey adenovirus (TMAdV), as the cause of a fulminant pneumonia outbreak in a colony of titi monkeys (Callicebus cupreus) at a national primate center in 2009. Serological evidence of infection by TMAdV was also found in a human researcher at the facility and household family member, raising concerns for potential cross-species transmission of the virus. Here we present experimental evidence of cross-species TMAdV infection in common marmosets (Callithrix jacchus). Nasal inoculation of a cell cultured-adapted TMAdV strain into three marmosets produced an acute, mild respiratory illness characterized by low-grade fever, reduced activity, anorexia, and sneezing. An increase in virus-specific neutralization antibody titers accompanied the development of clinical signs. Although serially collected nasal swabs were positive for TMAdV for at least 8 days, all 3 infected marmosets spontaneously recovered by day 12 post-inoculation, and persistence of the virus in tissues could not be established. Thus, the pathogenesis of experimental inoculation of TMAdV in common marmosets resembled the mild, self-limiting respiratory infection typically seen in immunocompetent human hosts rather than the rapidly progressive, fatal pneumonia observed in 19 of 23 titi monkeys during the prior 2009 outbreak. These findings further establish the potential for adenovirus cross-species transmission and provide the basis for development of a monkey model useful for assessing the zoonotic potential of adenoviruses. PMID:23894316

Can vocal conditioning trigger a semiotic ratchet in marmosets?

PubMed Central

Turesson, Hjalmar K.; Ribeiro, Sidarta

2015-01-01

The complexity of human communication has often been taken as evidence that our language reflects a true evolutionary leap, bearing little resemblance to any other animal communication system. The putative uniqueness of the human language poses serious evolutionary and ethological challenges to a rational explanation of human communication. Here we review ethological, anatomical, molecular, and computational results across several species to set boundaries for these challenges. Results from animal behavior, cognitive psychology, neurobiology, and semiotics indicate that human language shares multiple features with other primate communication systems, such as specialized brain circuits for sensorimotor processing, the capability for indexical (pointing) and symbolic (referential) signaling, the importance of shared intentionality for associative learning, affective conditioning and parental scaffolding of vocal production. The most substantial differences lie in the higher human capacity for symbolic compositionality, fast vertical transmission of new symbols across generations, and irreversible accumulation of novel adaptive behaviors (cultural ratchet). We hypothesize that increasingly-complex vocal conditioning of an appropriate animal model may be sufficient to trigger a semiotic ratchet, evidenced by progressive sign complexification, as spontaneous contact calls become indexes, then symbols and finally arguments (strings of symbols). To test this hypothesis, we outline a series of conditioning experiments in the common marmoset (Callithrix jacchus). The experiments are designed to probe the limits of vocal communication in a prosocial, highly vocal primate 35 million years far from the human lineage, so as to shed light on the mechanisms of semiotic complexification and cultural transmission, and serve as a naturalistic behavioral setting for the investigation of language disorders. PMID:26500583

Gene targeting and subsequent site-specific transgenesis at the β-actin (ACTB) locus in common marmoset embryonic stem cells.

PubMed

Shiozawa, Seiji; Kawai, Kenji; Okada, Yohei; Tomioka, Ikuo; Maeda, Takuji; Kanda, Akifumi; Shinohara, Haruka; Suemizu, Hiroshi; James Okano, Hirotaka; Sotomaru, Yusuke; Sasaki, Erika; Okano, Hideyuki

2011-09-01

Nonhuman primate embryonic stem (ES) cells have vast promise for preclinical studies. Genetic modification in nonhuman primate ES cells is an essential technique for maximizing the potential of these cells. The common marmoset (Callithrix jacchus), a nonhuman primate, is expected to be a useful transgenic model for preclinical studies. However, genetic modification in common marmoset ES (cmES) cells has not yet been adequately developed. To establish efficient and stable genetic modifications in cmES cells, we inserted the enhanced green fluorescent protein (EGFP) gene with heterotypic lox sites into the β-actin (ACTB) locus of the cmES cells using gene targeting. The resulting knock-in ES cells expressed EGFP ubiquitously under the control of the endogenous ACTB promoter. Using inserted heterotypic lox sites, we demonstrated Cre recombinase-mediated cassette exchange (RMCE) and successfully established a monomeric red fluorescent protein (mRFP) knock-in cmES cell line. Further, a herpes simplex virus-thymidine kinase (HSV-tk) knock-in cmES cell line was established using RMCE. The growth of tumor cells originating from the cell line was significantly suppressed by the administration of ganciclovir. Therefore, the HSV-tk/ganciclovir system is promising as a safeguard for stem cell therapy. The stable and ubiquitous expression of EGFP before RMCE enables cell fate to be tracked when the cells are transplanted into an animal. Moreover, the creation of a transgene acceptor locus for site-specific transgenesis will be a powerful tool, similar to the ROSA26 locus in mice.

Protection by pyridostigmine bromide of marmoset hemi-diaphragm acetylcholinesterase activity after soman exposure.

PubMed

Haigh, Julian R; Adler, Michael; Apland, James P; Deshpande, Sharad S; Barham, Charles B; Desmond, Patrick; Koplovitz, Irwin; Lenz, David E; Gordon, Richard K

2010-09-06

Pyridostigmine bromide (PB) was approved by the U.S. Food and Drug Administration (FDA) in 2003 as a pretreatment in humans against the lethal effects of the irreversible nerve agent soman (GD). Organophosphate (OP) chemical warfare agents such as GD exert their toxic effects by inhibiting acetylcholinesterase (AChE) from terminating the action of acetylcholine at postsynaptic sites in cholinergic nerve terminals (including crucial peripheral muscle such as diaphragm). As part of the post-marketing approval of PB, the FDA required (under 21CFR314, the "two animal rule") the study of a non-human primate model (the common marmoset Callithrix jacchus jacchus) to demonstrate increased survival against lethal GD poisoning, and protection of physiological hemi-diaphragm function after PB pretreatment and subsequent GD exposure. Marmosets (male and female) were placed in the following experimental groups: (i) control (saline pretreatment only), (ii) low dose PB (12.5 microg/kg), or (iii) high dose (39.5 microg/kg) PB. Thirty minutes after the PB dose, animals were challenged with either saline (control) or soman (GD, 45 microg/kg), followed 1 min later by atropine (2mg/kg) and 2-PAM (25mg/kg). After a further 16 min, animals were euthanized and the complete diaphragm removed; the right hemi-diaphragm was frozen immediately at -80 degrees C, and the left hemi-diaphragm was placed in a tissue bath for 4h (to allow for decarbamylation to occur), then frozen. AChE activities were determined using the automated WRAIR cholinesterase assay. Blood samples were collected for AChE activities prior to PB, before GD challenge, and after sacrifice. RBC-AChE was inhibited by approximately 18% and 50% at the low and high doses of PB, respectively, compared to control (baseline) activity. In the absence of PB pretreatment, the inhibition of RBC-AChE by GD was 98%. The recovery of hemi-diaphragm AChE activity after the 4h wash period (decarbamylation) was approximately 8% and 17%, at the low and high PB doses, respectively, compared with the baseline (control) AChE activity prior to PB pretreatment or soman exposure. The results suggest that PB pretreatment protects a critical fraction of AChE activity in the marmoset diaphragm, which is sufficient to allow the animal to breathe despite exposure to a dose of soman that is lethal in unprotected animals. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Bisphenol A-induced ultrastructural changes in the testes of common marmoset

PubMed Central

Vijaykumar, Tushara; Singh, Dipty; Vanage, Geeta R.; Dhumal, Rohit V.; Dighe, Vikas D.

2017-01-01

Background & objectives: Bisphenol A (BPA) is an endocrine disruptor that is widely used in the manufacture of polycarbonate plastics, epoxy resins and dental sealants. It is known to have adverse effects on spermatogenesis in rodents. This study was aimed to evaluate the effects of BPA in adult common marmoset owing to its similarities with human spermatogenesis. Methods: Sixteen marmosets were divided into four groups (n=4 per group) and given oral doses of BPA (2.5, 12.5 and 25 μg/kg BW/day) for 70 days to cover two spermatogenic cycles, and the control group received only vehicle (honey). Testes were processed for histological and transmission electron microscopy studies. Results: Histology of the testis showed sloughing of germ cells into the lumen, increase in interstitial space and vacuolation of Sertoli cell cytoplasm. Ultrastructural analysis of the testis revealed several degenerative effects on the basement membrane, Sertoli cells, Leydig cells and other developing germ cells in the 12.5 and 25 μg/kg BW/day groups as compared to control. Interpretation & conclusions: The observed ultrastructural changes caused by BPA in testicular morphology might be indicative of a perturbed sperm production. Considering the genetic and spermatogenic similarities of common marmoset (Callithrix jacchus) and humans, the study findings are of significance. Further studies are, however, needed to elucidate the mechanism of action. PMID:29168469

An Observational Investigation of Behavioral Contagion in Common Marmosets (Callithrix jacchus): Indications for Contagious Scent-Marking

PubMed Central

Massen, Jorg J. M.; Šlipogor, Vedrana; Gallup, Andrew C.

2016-01-01

Behavioral contagion is suggested to promote group coordination that may facilitate activity transitions, increased vigilance, and state matching. Apart from contagious yawning, however, very little attention has been given to this phenomenon, and studies on contagious yawning in primates have so far only focused on Old World monkeys and apes. Here we studied behavioral contagion in common marmosets, a species for which group coordination and vigilance are paramount. In particular, we investigated the contagiousness of yawning, stretching, scratching, tongue protrusion, gnawing, and scent-marking. We coded these behaviors from 14 adult marmosets, from two different social groups. During testing sessions, animals were separated into groups of four individuals for 20-min observation periods, across three distinct diurnal time points (morning, midday, and afternoon) to test for circadian patterns. We observed almost no yawning (0.12 yawns/h) and very little stretching behavior. For all other behaviors, which were more common, we found several temporal and inter-individual differences (i.e., sex, age, dominance status) predictive of these responses. Moreover, we found that gnawing and scent-marking, which almost always co-occurred as a fixed-action pattern, were highly temporally clustered within observation sessions. We discuss the relative absence of yawning in marmosets as well as the possible function of contagious scent-marking, and provide suggestions for future research into the proximate and ultimate functions of these behaviors in marmosets. PMID:27563294

Touchscreen assays of learning, response inhibition, and motivation in the marmoset (Callithrix jacchus).

PubMed

Kangas, Brian D; Bergman, Jack; Coyle, Joseph T

2016-05-01

Recent developments in precision gene editing have led to the emergence of the marmoset as an experimental subject of considerable interest and translational value. A better understanding of behavioral phenotypes of the common marmoset will inform the extent to which forthcoming transgenic mutants are cognitively intact. Therefore, additional information regarding their learning, inhibitory control, and motivational abilities is needed. The present studies used touchscreen-based repeated acquisition and discrimination reversal tasks to examine basic dimensions of learning and response inhibition. Marmosets were trained daily to respond to one of the two simultaneously presented novel stimuli. Subjects learned to discriminate the two stimuli (acquisition) and, subsequently, with the contingencies switched (reversal). In addition, progressive ratio performance was used to measure the effort expended to obtain a highly palatable reinforcer varying in magnitude and, thereby, provide an index of relative motivational value. Results indicate that rates of both acquisition and reversal of novel discriminations increased across successive sessions, but that rate of reversal learning remained slower than acquisition learning, i.e., more trials were needed for mastery. A positive correlation was observed between progressive ratio break point and reinforcement magnitude. These results closely replicate previous findings with squirrel monkeys, thus providing evidence of similarity in learning processes across nonhuman primate species. Moreover, these data provide key information about the normative phenotype of wild-type marmosets using three relevant behavioral endpoints.

Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens.

PubMed

Fan, Xiaobo; Supiwong, Weerayuth; Weise, Anja; Mrasek, Kristin; Kosyakova, Nadezda; Tanomtong, Alongkoad; Pinthong, Krit; Trifonov, Vladimir A; Cioffi, Marcelo de Bello; Grothmann, Pierre; Liehr, Thomas; Oliveira, Edivaldo H C de

2015-11-01

Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

Computed Tomography of the Abdomen in Eight Clinically Normal Common Marmosets (Callithrix jacchus).

PubMed

du Plessis, W M; Groenewald, H B; Elliott, D

2017-08-01

The aim of this study was to provide a detailed anatomical description of the abdomen in the clinically normal common marmoset by means of computed tomography (CT). Eight clinically healthy mature common marmosets ranging from 12 to 48 months and 235 to 365 g bodyweight were anesthetized and pre- and post-contrast CT examinations were performed using different CT settings in dorsal recumbency. Abdominal organs were identified and visibility noted. Diagnostic quality abdominal images could be obtained of the common marmoset despite its small size using a dual-slice CT scanner. Representative cross-sectional images were chosen from different animals illustrating the abdominal CT anatomy of clinically normal common marmosets. Identification or delineation of abdominal organs greatly improved with i.v. contrast. A modified high-frequency algorithm with edge enhancement added valuable information for identification of small structures such as the ureters. The Hounsfield unit (HU) of major abdominal organs differed from that of small animals (domestic dogs and cats). Due to their size and different anatomy, standard small animal CT protocols need to be critically assessed and adapted for exotics, such as the common marmoset. The established normal reference range of HU of major abdominal organs and adapted settings for a CT protocol will aid clinical assessment of the common marmoset. © 2017 Blackwell Verlag GmbH.

Representation of Glossy Material Surface in Ventral Superior Temporal Sulcal Area of Common Marmosets

PubMed Central

Miyakawa, Naohisa; Banno, Taku; Abe, Hiroshi; Tani, Toshiki; Suzuki, Wataru; Ichinohe, Noritaka

2017-01-01

The common marmoset (Callithrix jacchus) is one of the smallest species of primates, with high visual recognition abilities that allow them to judge the identity and quality of food and objects in their environment. To address the cortical processing of visual information related to material surface features in marmosets, we presented a set of stimuli that have identical three-dimensional shapes (bone, torus or amorphous) but different material appearances (ceramic, glass, fur, leather, metal, stone, wood, or matte) to anesthetized marmoset, and recorded multiunit activities from an area ventral to the superior temporal sulcus (STS) using multi-shanked, and depth resolved multi-electrode array. Out of 143 visually responsive multiunits recorded from four animals, 29% had significant main effect only of the material, 3% only of the shape and 43% of both the material and the shape. Furthermore, we found neuronal cluster(s), in which most cells: (1) showed a significant main effect in material appearance; (2) the best stimulus was a glossy material (glass or metal); and (3) had reduced response to the pixel-shuffled version of the glossy material images. The location of the gloss-selective area was in agreement with previous macaque studies, showing activation in the ventral bank of STS. Our results suggest that perception of gloss is an important ability preserved across wide range of primate species. PMID:28367117

Representation of Glossy Material Surface in Ventral Superior Temporal Sulcal Area of Common Marmosets.

PubMed

Miyakawa, Naohisa; Banno, Taku; Abe, Hiroshi; Tani, Toshiki; Suzuki, Wataru; Ichinohe, Noritaka

2017-01-01

The common marmoset ( Callithrix jacchus ) is one of the smallest species of primates, with high visual recognition abilities that allow them to judge the identity and quality of food and objects in their environment. To address the cortical processing of visual information related to material surface features in marmosets, we presented a set of stimuli that have identical three-dimensional shapes (bone, torus or amorphous) but different material appearances (ceramic, glass, fur, leather, metal, stone, wood, or matte) to anesthetized marmoset, and recorded multiunit activities from an area ventral to the superior temporal sulcus (STS) using multi-shanked, and depth resolved multi-electrode array. Out of 143 visually responsive multiunits recorded from four animals, 29% had significant main effect only of the material, 3% only of the shape and 43% of both the material and the shape. Furthermore, we found neuronal cluster(s), in which most cells: (1) showed a significant main effect in material appearance; (2) the best stimulus was a glossy material (glass or metal); and (3) had reduced response to the pixel-shuffled version of the glossy material images. The location of the gloss-selective area was in agreement with previous macaque studies, showing activation in the ventral bank of STS. Our results suggest that perception of gloss is an important ability preserved across wide range of primate species.

Mirror Neurons in a New World Monkey, Common Marmoset

PubMed Central

Suzuki, Wataru; Banno, Taku; Miyakawa, Naohisa; Abe, Hiroshi; Goda, Naokazu; Ichinohe, Noritaka

2015-01-01

Mirror neurons respond when executing a motor act and when observing others' similar act. So far, mirror neurons have been found only in macaques, humans, and songbirds. To investigate the degree of phylogenetic specialization of mirror neurons during the course of their evolution, we determined whether mirror neurons with similar properties to macaques occur in a New World monkey, the common marmoset (Callithrix jacchus). The ventral premotor cortex (PMv), where mirror neurons have been reported in macaques, is difficult to identify in marmosets, since no sulcal landmarks exist in the frontal cortex. We addressed this problem using “in vivo” connection imaging methods. That is, we first identified cells responsive to others' grasping action in a clear landmark, the superior temporal sulcus (STS), under anesthesia, and injected fluorescent tracers into the region. By fluorescence stereomicroscopy, we identified clusters of labeled cells in the ventrolateral frontal cortex, which were confirmed to be within the ventrolateral frontal cortex including PMv after sacrifice. We next implanted electrodes into the ventrolateral frontal cortex and STS and recorded single/multi-units under an awake condition. As a result, we found neurons in the ventrolateral frontal cortex with characteristic “mirror” properties quite similar to those in macaques. This finding suggests that mirror neurons occur in a common ancestor of New and Old World monkeys and its common properties are preserved during the course of primate evolution. PMID:26696817

Comparative analysis of Meissner's corpuscles in the fingertips of primates.

PubMed

Verendeev, Andrey; Thomas, Christian; McFarlin, Shannon C; Hopkins, William D; Phillips, Kimberley A; Sherwood, Chet C

2015-07-01

Meissner's corpuscles (MCs) are tactile mechanoreceptors found in the glabrous skin of primates, including fingertips. These receptors are characterized by sensitivity to light touch, and therefore might be associated with the evolution of manipulative abilities of the hands in primates. We examined MCs in different primate species, including common marmoset (Callithrix jacchus, n = 5), baboon (Papio anubis, n = 2), rhesus macaque (Macaca mulatta, n = 3), chimpanzee (Pan troglodytes, n = 3), bonobo (Pan paniscus, n = 1) and human (Homo sapiens, n = 8). Fingertips of the first, second and fourth digits were collected from both hands of specimens, dissected and histologically stained using hematoxylin and eosin. The density (MCs per 1 mm(2) ) and the size (cross-sectional diameter of MCs) were quantified. Overall, there were no differences in the densities of MCs or their size among the digits or between the hands for any species examined. However, MCs varied across species. We found a trend for higher densities of MCs in macaques and humans compared with chimpanzees and bonobos; moreover, apes had larger MCs than monkeys. We further examined whether the density or size of MCs varied as a function of body mass, measures of dexterity and dietary frugivory. Among these variables, only body size accounted for a significant amount of variation in the size of MCs. © 2015 Anatomical Society.

Food Avoidance Learning in Squirrel Monkeys and Common Marmosets

PubMed Central

Laska, Matthias; Metzker, Karin

1998-01-01

Using a conditioned food avoidance learning paradigm, six squirrel monkeys (Saimiri sciureus) and six common marmosets (Callithrix jacchus) were tested for their ability to (1) reliably form associations between visual or olfactory cues of a potential food and its palatability and (2) remember such associations over prolonged periods of time. We found (1) that at the group level both species showed one-trial learning with the visual cues color and shape, whereas only the marmosets were able to do so with the olfactory cue, (2) that all individuals from both species learned to reliably avoid the unpalatable food items within 10 trials, (3) a tendency in both species for quicker acquisition of the association with the visual cues compared with the olfactory cue, (4) a tendency for quicker acquisition and higher reliability of the aversion by the marmosets compared with the squirrel monkeys, and (5) that all individuals from both species were able to reliably remember the significance of the visual cues, color and shape, even after 4 months, whereas only the marmosets showed retention of the significance of the olfactory cues for up to 4 weeks. Furthermore, the results suggest that in both species tested, illness is not a necessary prerequisite for food avoidance learning but that the presumably innate rejection responses toward highly concentrated but nontoxic bitter and sour tastants are sufficient to induce robust learning and retention. PMID:10454364

Novel method of extracting motion from natural movies.

PubMed

Suzuki, Wataru; Ichinohe, Noritaka; Tani, Toshiki; Hayami, Taku; Miyakawa, Naohisa; Watanabe, Satoshi; Takeichi, Hiroshige

2017-11-01

The visual system in primates can be segregated into motion and shape pathways. Interaction occurs at multiple stages along these pathways. Processing of shape-from-motion and biological motion is considered to be a higher-order integration process involving motion and shape information. However, relatively limited types of stimuli have been used in previous studies on these integration processes. We propose a new algorithm to extract object motion information from natural movies and to move random dots in accordance with the information. The object motion information is extracted by estimating the dynamics of local normal vectors of the image intensity projected onto the x-y plane of the movie. An electrophysiological experiment on two adult common marmoset monkeys (Callithrix jacchus) showed that the natural and random dot movies generated with this new algorithm yielded comparable neural responses in the middle temporal visual area. In principle, this algorithm provided random dot motion stimuli containing shape information for arbitrary natural movies. This new method is expected to expand the neurophysiological and psychophysical experimental protocols to elucidate the integration processing of motion and shape information in biological systems. The novel algorithm proposed here was effective in extracting object motion information from natural movies and provided new motion stimuli to investigate higher-order motion information processing. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Corticospinal Tract Tracing in the Marmoset with a Clinical Whole-Body 3T Scanner Using Manganese-Enhanced MRI

PubMed Central

Plas, Benjamin; Bolan, Faye; Boulanouar, Kader; Renaud, Luc; Darmana, Robert; Vaysse, Laurence; Vieu, Christophe; Loubinoux, Isabelle

2015-01-01

Manganese-enhanced MRI (MEMRI) has been described as a powerful tool to depict the architecture of neuronal circuits. In this study we investigated the potential use of in vivo MRI detection of manganese for tracing neuronal projections from the primary motor cortex (M1) in healthy marmosets (Callithrix Jacchus). We determined the optimal dose of manganese chloride (MnCl2) among 800, 400, 40 and 8nmol that led to manganese-induced hyperintensity furthest from the injection site, as specific to the corticospinal tract as possible, and that would not induce motor deficit. A commonly available 3T human clinical MRI scanner and human knee coil were used to follow hyperintensity in the corticospinal tract 24h after injection. A statistical parametric map of seven marmosets injected with the chosen dose, 8 nmol, showed the corticospinal tract and M1 connectivity with the basal ganglia, substantia nigra and thalamus. Safety was determined for the lowest dose that did not induce dexterity and grip strength deficit, and no behavioral effects could be seen in marmosets who received multiple injections of manganese one month apart. In conclusion, our study shows for the first time in marmosets, a reliable and reproducible way to perform longitudinal ME-MRI experiments to observe the integrity of the marmoset corticospinal tract on a clinical 3T MRI scanner. PMID:26398500

The different clinical effects of anti-BLyS, anti-APRIL and anti-CD20 antibodies point at a critical pathogenic role of γ-herpesvirus infected B cells in the marmoset EAE model.

PubMed

Anwar Jagessar, S; Fagrouch, Zahra; Heijmans, Nicole; Bauer, Jan; Laman, Jon D; Oh, Luke; Migone, Thi; Verschoor, Ernst J; 't Hart, Bert A

2013-06-01

The robust and rapid clinical effect of depleting anti-CD20 monoclonal antibodies (mAb) in multiple sclerosis (MS) demonstrates a critical pathogenic contribution of B cells. The clinical effect of anti-CD20 mAb has been replicated in a relevant preclinical MS model, experimental autoimmune encephalomyelitis (EAE) in marmoset monkeys (Callithrix jacchus). By contrast, treatment with mAbs against two essential cytokines in B cell activation growth and survival, i.e. BlyS/BAFF and APRIL, was only partially effective. All three mAbs induced depletion of CD20+ B cells from the circulation, albeit with different kinetics and based on distinct mechanisms of action. In the current study we analyzed whether the different clinical effect of anti-CD20 mAb or the anti-BLyS and anti-APRIL mAbs is due to different depletion of B cells infected with the EBV of marmosets, CalHV3. Employing a novel PCR-based assay, half of the colony of group-housed marmosets was tested positive for CalHV3 DNA in secondary lymphoid organs. The same prevalence was observed in placebo-treated monkeys. In marmosets treated with anti-CD20 mAb the load of CalHV3 DNA in lymphoid organs was substantially reduced, while this was not observed in the monkeys treated with anti-BLyS or anti-APRIL mAbs. To examine the pathogenic role of virus-transformed B cells, we infused EBV-transformed B lymphoblastic cell (BLC) lines presenting the immunodominant MOG34-56 peptide. We observed in the recipients of MOG34-56 pulsed BLC, but not in their fraternal siblings infused with non-pulsed BLC, activation of anti-MOG34-56 T cells and meningeal inflammation. Collectively, the data show that among CD20+ B cells, the herpesvirus-transformed subset has a particularly important pathogenic role in the marmoset EAE model.

Misleading and reliable markers to differentiate between primate testis-derived multipotent stromal cells and spermatogonia in culture

PubMed Central

Eildermann, K.; Gromoll, J.; Behr, R.

2012-01-01

BACKGROUND Several studies have reported the generation of spermatogonia-derived pluripotent stem cells from human testes. The initial aim of the present study was the derivation of equivalent stem cells from an established and experimentally accessible non-human primate model, the common marmoset monkey (Callithrix jacchus). However, an essential prerequisite in the absence of transgenic reporters in primates and man is the availability of validated endogenous markers for the identification of specific cell types in vitro. METHODS AND RESULTS We cultured marmoset testicular cells in a similar way to that described for human testis-derived pluripotent cells and set out to characterize these cultures under different conditions and in differentiation assays applying established marker panels. Importantly, the cells emerged as testicular multipotent stromal cells (TMSCs) instead of (pluripotent) germ cell-derived cells. TMSCs expressed many markers such as GFR-α, GPR125, THY-1 (CD90), ITGA6, SSEA4 and TRA-1-81, which were considered as spermatogonia specific and were previously used for the enrichment or characterization of spermatogonia. Proliferation of TMSCs was highly dependent on basic fibroblast growth factor, a growth factor routinely present in germ cell culture media. As reliable markers for the distinction between spermatogonia and TMSCs, we established VASA, in combination with the spermatogonia-expressed factors, MAGEA4, PLZF and SALL4. CONCLUSIONS Marmoset monkey TMSCs and spermatogonia exhibit an overlap of markers, which may cause erroneous interpretations of experiments with testis-derived stem cells in vitro. We provide a marker panel for the unequivocal identification of spermatogonia providing a better basis for future studies on primate, including human, testis-derived stem cells. PMID:22442249

Attenuation and efficacy of live-attenuated Rift Valley fever virus vaccine candidates in non-human primates.

PubMed

Smith, Darci R; Johnston, Sara C; Piper, Ashley; Botto, Miriam; Donnelly, Ginger; Shamblin, Joshua; Albariño, César G; Hensley, Lisa E; Schmaljohn, Connie; Nichol, Stuart T; Bird, Brian H

2018-05-09

Rift Valley fever virus (RVFV) is an important mosquito-borne veterinary and human pathogen that has caused large outbreaks of severe disease throughout Africa and the Arabian Peninsula. Currently, no licensed vaccine or therapeutics exists to treat this potentially deadly disease. The explosive nature of RVFV outbreaks and the severe consequences of its accidental or intentional introduction into RVFV-free areas provide the impetus for the development of novel vaccine candidates for use in both livestock and humans. Rationally designed vaccine candidates using reverse genetics have been used to develop deletion mutants of two known RVFV virulence factors, the NSs and NSm genes. These recombinant viruses were demonstrated to be protective and immunogenic in rats, mice, and sheep, without producing clinical illness in these animals. Here, we expand upon those findings and evaluate the single deletion mutant (ΔNSs rRVFV) and double deletion mutant (ΔNSs-ΔNSm rRVFV) vaccine candidates in the common marmoset (Callithrix jacchus), a non-human primate (NHP) model resembling severe human RVF disease. We demonstrate that both the ΔNSs and ΔNSs-ΔNSm rRVFV vaccine candidates were found to be safe and immunogenic in the current study. The vaccinated animals received a single dose of vaccine that led to the development of a robust antibody response. No vaccine-induced adverse reactions, signs of clinical illness or infectious virus were detected in the vaccinated marmosets. All vaccinated animals that were subsequently challenged with RVFV were protected against viremia and liver disease. In summary, our results provide the basis for further development of the ΔNSs and ΔNSs-ΔNSm rRVFV as safe and effective human RVFV vaccines for this significant public health threat.

Multiple vaccine and pyridostigmine bromide interactions in the common marmoset Callithrix jacchus: immunological and endocrinological effects.

PubMed

Hornby, Rebecca J; Pearce, Peter C; Bowditch, Andrew P; Scott, Leah; Griffiths, Gareth D

2006-12-05

Following active service during the 1990/1991 Gulf Conflict, a number of UK and US veterans presented with a diverse range of symptoms, collectively known as Gulf Veterans Illnesses (GVI). The administration of vaccines and/or the pretreatment against possible nerve agent poisoning, pyridostigmine bromide (PB), given to Armed Forces personnel during the Gulf Conflict has been implicated as a possible factor in the aetiology of these illnesses. The possibility that adverse health effects may result from the administration of these vaccines (anthrax, pertussis, plague, yellow fever, polio, typhoid, tetanus, hepatitis B, meningococcal meningitis and cholera) and/or PB, have been investigated over an eighteen month period, in a non-human primate model, the common marmoset. This study reports immunological indices, including leukocyte phenotypes, intracellular cytokines IFN-gamma and IL-4 and antibody responses against vaccine antigens. Using human isotyping reagents previously shown to cross react with marmoset immunoglobulins (ibid) it was shown that marmosets responded strongly against anthrax PA and pertussis and weakly against killed whole cell plague, cholera and typhoid. At the end of the study the immune response to a previously unseen T-cell dependent antigen, keyhole limpet haemocyanin (KLH), was examined in order to determine whether immune function had been compromised by the compounds administered. Statistically equivalent, robust antibody responses were measured against KLH in all treatment groups indicating that the immune system had not been compromised by any of the treatments. In addition, urinary cortisol was measured at key points throughout the study as an index of physiological stress which may have been induced by the treatments. There were no effects of treatment on urinary cortisol secretion. With respect to the other immunological indices measured, there were no statistical differences between the treatment groups during the period of the study.

Marmoset Cytochrome P450 3A4 Ortholog Expressed in Liver and Small-Intestine Tissues Efficiently Metabolizes Midazolam, Alprazolam, Nifedipine, and Testosterone.

PubMed

Uehara, Shotaro; Uno, Yasuhiro; Nakanishi, Kazuyuki; Ishii, Sakura; Inoue, Takashi; Sasaki, Erika; Yamazaki, Hiroshi

2017-05-01

Common marmosets ( Callithrix jacchus ), small New World primates, are increasingly attracting attention as potentially useful animal models for drug development. However, characterization of cytochrome P450 (P450) 3A enzymes involved in the metabolism of a wide variety of drugs has not investigated in marmosets. In this study, sequence homology, tissue distribution, and enzymatic properties of marmoset P450 3A4 ortholog, 3A5 ortholog, and 3A90 were investigated. Marmoset P450 3A forms exhibited high amino acid sequence identities (88-90%) to the human and cynomolgus monkey P450 3A orthologs and evolutionary closeness to human and cynomolgus monkey P450 3A orthologs compared with other P450 3A enzymes. Among the five marmoset tissues examined, P450 3A4 ortholog mRNA was abundant in livers and small intestines where P450 3A4 ortholog proteins were immunologically detected. Three marmoset P450 3A proteins heterologously expressed in Escherichia coli membranes catalyzed midazolam 1'- and 4-hydroxylation, alprazolam 4-hydroxylation, nifedipine oxidation, and testosterone 6 β -hydroxylation, similar to cynomolgus monkey and human P450 3A enzymes. Among the marmoset P450 3A enzymes, P450 3A4 ortholog effectively catalyzed midazolam 1'-hydroxylation, comparable to microsomes from marmoset livers and small intestines. Correlation analyses with 23 individual marmoset liver microsomes suggested contributions of P450 3A enzymes to 1'-hydroxylation of both midazolam (human P450 3A probe) and bufuralol (human P450 2D6 probe), similar to cynomolgus monkey P450 3A enzymes. These results indicated that marmoset P450 3A forms had functional characteristics roughly similar to cynomolgus monkeys and humans in terms of tissue expression patterns and catalytic activities, suggesting marmosets as suitable animal models for P450 3A-dependent drug metabolism. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Individual differences in choice (in)flexibility but not impulsivity in the common marmoset: an automated, operant-behavior choice task.

PubMed

Adriani, Walter; Romani, Chiara; Manciocco, Arianna; Vitale, Augusto; Laviola, Giovanni

2013-11-01

Individual differences in behavioural flexibility are a significant issue in human psychopathology as well as in its animal models. We aimed to investigate individual variations of operant-choice behaviour in the common marmoset (Callithrix jacchus), a small New World primate, using a new operant panel with two hand-poking holes. Experimental subjects (N=16) were presented with a choice between a Small & Soon (SS) vs a Large & Late (LL) food reward. After extensive training (31 daily sessions with no delay, during which a basal, large-reward preference developed), the delay before release of LL was progressively increased (from 0 to 60 s, during 16 daily sessions; indifferent point at delay=9 s). Subjects were classified as either "flexible" or "non-flexible", respectively, based on a decrease (or not) in the preference for LL with increasing delays. Each subject was also classified as "maximizer" (or "non-maximizer") based on capacity (or not) to maximize the food payoff as delay increased. Upon delays shorter than the indifferent point (<9s), none of the subjects showed a shift from LL to SS, denoting a lack of delay-induced, cognitive impulsivity. Individual differences only emerged upon delays longer than the indifferent point (>9 s), when a preference shift could be interpreted as economically-driven. In general, a profile of few unrewarded hand-pokes in reaction to initial delays (i.e., a low motor impulsivity) and of clear-cut basal LL preference seemed to predict elevated flexibility of choices and better food payoff, which was typical of subjects classified as both "flexible & maximizer". These results provide normative data on the marmosets, which can be used as a model for the investigation of 1) individual differences in behavioural flexibility, as well as 2) biological mechanisms rooted in our evolutionary history. Copyright © 2013 Elsevier B.V. All rights reserved.

Colonization of collagen scaffolds by adipocytes derived from mesenchymal stem cells of the common marmoset monkey

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernemann, Inga, E-mail: bernemann@imp.uni-hannover.de; Mueller, Thomas; Blasczyk, Rainer

Highlights: {yields} Marmoset bone marrow-derived MSCs differentiate in suspension into adipogenic, osteogenic and chondrogenic lineages. {yields} Marmoset MSCs integrate in collagen type I scaffolds and differentiate excellently into adipogenic cells. {yields} Common marmoset monkey is a suitable model for soft tissue engineering in human regenerative medicine. -- Abstract: In regenerative medicine, human cell replacement therapy offers great potential, especially by cell types differentiated from immunologically and ethically unproblematic mesenchymal stem cells (MSCs). In terms of an appropriate carrier material, collagen scaffolds with homogeneous pore size of 65 {mu}m were optimal for cell seeding and cultivating. However, before clinical application andmore » transplantation of MSC-derived cells in scaffolds, the safety and efficiency, but also possible interference in differentiation due to the material must be preclinically tested. The common marmoset monkey (Callithrix jacchus) is a preferable non-human primate animal model for this aim due to its genetic and physiological similarities to the human. Marmoset bone marrow-derived MSCs were successfully isolated, cultured and differentiated in suspension into adipogenic, osteogenic and chondrogenic lineages by defined factors. The differentiation capability could be determined by FACS. Specific marker genes for all three cell types could be detected by RT-PCR. Furthermore, MSCs seeded on collagen I scaffolds differentiated in adipogenic lineage showed after 28 days of differentiation high cell viability and homogenous distribution on the material which was validated by calcein AM and EthD staining. As proof of adipogenic cells, the intracellular lipid vesicles in the cells were stained with Oil Red O. The generation of fat vacuoles was visibly extensive distinguishable and furthermore determined on the molecular level by expression of specific marker genes. The results of the study proved both the differential potential of marmoset MSCs in adipogenic, osteogenic and chondrogenic lineages and the suitability of collagen scaffolds as carrier material undisturbing differentiation of primate mesenchymal stem cells.« less

Use of the Common Marmoset to Study Burkholderia mallei Infection

PubMed Central

Harvey, Stephen B.; Mead, Daniel G.; Shaffer, Teresa L.; Estes, D. Mark; Michel, Frank; Quinn, Frederick D.; Hogan, Robert J.; Lafontaine, Eric R.

2015-01-01

Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus) were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 104 to 2.5 X 105 bacteria developed acute lethal infection within 3–4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 103 bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 103 organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B. mallei. PMID:25860021

Use of the common marmoset to study Burkholderia mallei infection.

PubMed

Jelesijevic, Tomislav; Zimmerman, Shawn M; Harvey, Stephen B; Mead, Daniel G; Shaffer, Teresa L; Estes, D Mark; Michel, Frank; Quinn, Frederick D; Hogan, Robert J; Lafontaine, Eric R

2015-01-01

Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus) were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4) to 2.5 X 10(5) bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3) bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3) organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B. mallei.

Preimplantation development of somatic cell cloned embryos in the common marmoset (Callithrix jacchus).

PubMed

Sotomaru, Yusuke; Hirakawa, Reiko; Shimada, Akiko; Shiozawa, Seiji; Sugawara, Ayako; Oiwa, Ryo; Nobukiyo, Asako; Okano, Hideyuki; Tamaoki, Norikazu; Nomura, Tatsuji; Hiyama, Eiso; Sasaki, Erika

2009-12-01

The somatic cell nuclear transfer technique has been applied to various mammals to produce cloned animals; however, a standardized method is not applicable to all species. We aimed here to develop optimum procedures for somatic cell cloning in nonhuman primates, using common marmosets. First, we confirmed that parthenogenetic activation of in vitro matured oocytes was successfully induced by electrical stimulation (three cycles of 150 V/mm, 50 microsec x 2, 20 min intervals), and this condition was applied to the egg activation procedure in the subsequent experiments. Next, nuclear transfer to recipient enucleated oocytes was performed 1 h before, immediately after, or 1 h after egg activation treatment. The highest developmental rate was observed when nuclear transfer was performed 1 h before activation, but none of the cloned embryos developed beyond the eight-cell stage. To investigate the causes of the low developmental potential of cloned embryos, a study was performed to determine whether the presence of metaphase II (MII) chromosome in recipient ooplasm has an effect on developmental potential. As a result, only tetraploid cloned embryos produced by transferring a donor cell into a recipient bearing the MII chromosome developed into blastocysts (66.7%). In contrast, neither parthenogenetic embryos nor cloned embryos (whether diploid or tetraploid) produced using enucleated oocytes developed past the eight-cell stage. These results suggest that MII chromosome, or cytoplasm proximal to the MII chromosome, plays a major role in the development of cloned embryos in common marmosets.

Molecular evolution of the neurohypophysial hormone precursors in mammals: Comparative genomics reveals novel mammalian oxytocin and vasopressin analogues.

PubMed

Wallis, Michael

2012-11-01

Among vertebrates the neurohypophysial hormones show considerable variation. However, in eutherian mammals they have been considered rather conserved, with arginine vasopressin (AVP) and oxytocin (OT) in all species except pig and some relatives, where lysine vasopressin replaces AVP. The availability of genomic data for a wide range of mammals makes it possible to assess whether these peptides and their precursors may be more variable in Eutheria than previously suspected. A survey of these data confirms that AVP and OT occur in most eutherians, but with exceptions. In a New-World monkey (marmoset, Callithrix jacchus) and in tree shrew (Tupaia belangeri), Pro(8)OT replaces OT, confirming a recent report for these species. In armadillo (Dasypus novemcinctus) Leu(3)OT replaces OT, while in tenrec (Echinops telfairi) Thr(4)AVP replaces AVP. In these two species there is also evidence for additional genes/pseudogenes, encoding much-modified forms of AVP, but in most other eutherian species there is no evidence for additional neurohypophysial hormone genes. Evolutionary analysis shows that sequences of eutherian neurohypophysial hormone precursors are generally strongly conserved, particularly those regions encoding active peptide and neurophysin. The close association between OT and VP genes has led to frequent gene conversion of sequences encoding neurophysins. A monotreme, platypus (Ornithorhynchus anatinus) has genes for OT and AVP, organized tail-to-tail as in eutherians, but in marsupials 3-4 genes are present for neurohypophysial hormones, organized tail-to-head as in lower vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

Sound Frequency Representation in the Auditory Cortex of the Common Marmoset Visualized Using Optical Intrinsic Signal Imaging

PubMed Central

Tani, Toshiki; Abe, Hiroshi; Hayami, Taku; Banno, Taku; Kitamura, Naohito; Mashiko, Hiromi

2018-01-01

Abstract Natural sound is composed of various frequencies. Although the core region of the primate auditory cortex has functionally defined sound frequency preference maps, how the map is organized in the auditory areas of the belt and parabelt regions is not well known. In this study, we investigated the functional organizations of the core, belt, and parabelt regions encompassed by the lateral sulcus and the superior temporal sulcus in the common marmoset (Callithrix jacchus). Using optical intrinsic signal imaging, we obtained evoked responses to band-pass noise stimuli in a range of sound frequencies (0.5–16 kHz) in anesthetized adult animals and visualized the preferred sound frequency map on the cortical surface. We characterized the functionally defined organization using histologically defined brain areas in the same animals. We found tonotopic representation of a set of sound frequencies (low to high) within the primary (A1), rostral (R), and rostrotemporal (RT) areas of the core region. In the belt region, the tonotopic representation existed only in the mediolateral (ML) area. This representation was symmetric with that found in A1 along the border between areas A1 and ML. The functional structure was not very clear in the anterolateral (AL) area. Low frequencies were mainly preferred in the rostrotemplatal (RTL) area, while high frequencies were preferred in the caudolateral (CL) area. There was a portion of the parabelt region that strongly responded to higher sound frequencies (>5.8 kHz) along the border between the rostral parabelt (RPB) and caudal parabelt (CPB) regions. PMID:29736410

A digital 3D atlas of the marmoset brain based on multi-modal MRI.

PubMed

Liu, Cirong; Ye, Frank Q; Yen, Cecil Chern-Chyi; Newman, John D; Glen, Daniel; Leopold, David A; Silva, Afonso C

2018-04-01

The common marmoset (Callithrix jacchus) is a New-World monkey of growing interest in neuroscience. Magnetic resonance imaging (MRI) is an essential tool to unveil the anatomical and functional organization of the marmoset brain. To facilitate identification of regions of interest, it is desirable to register MR images to an atlas of the brain. However, currently available atlases of the marmoset brain are mainly based on 2D histological data, which are difficult to apply to 3D imaging techniques. Here, we constructed a 3D digital atlas based on high-resolution ex-vivo MRI images, including magnetization transfer ratio (a T1-like contrast), T2w images, and multi-shell diffusion MRI. Based on the multi-modal MRI images, we manually delineated 54 cortical areas and 16 subcortical regions on one hemisphere of the brain (the core version). The 54 cortical areas were merged into 13 larger cortical regions according to their locations to yield a coarse version of the atlas, and also parcellated into 106 sub-regions using a connectivity-based parcellation method to produce a refined atlas. Finally, we compared the new atlas set with existing histology atlases and demonstrated its applications in connectome studies, and in resting state and stimulus-based fMRI. The atlas set has been integrated into the widely-distributed neuroimaging data analysis software AFNI and SUMA, providing a readily usable multi-modal template space with multi-level anatomical labels (including labels from the Paxinos atlas) that can facilitate various neuroimaging studies of marmosets. Published by Elsevier Inc.

Wireless multi-channel single unit recording in freely moving and vocalizing primates

PubMed Central

Roy, Sabyasachi; Wang, Xiaoqin

2011-01-01

The ability to record well-isolated action potentials from individual neurons in naturally behaving animals is crucial for understanding neural mechanisms underlying natural behaviors. Traditional neurophysiology techniques, however, require the animal to be restrained which often restricts natural behavior. An example is the common marmoset (Callithrix jacchus), a highly vocal New World primate species, used in our laboratory to study the neural correlates of vocal production and sensory feedback. When restrained by traditional neurophysiological techniques marmoset vocal behavior is severely inhibited. Tethered recording systems, while proven effective in rodents pose limitations in arboreal animals such as the marmoset that typically roam in a three-dimensional environment. To overcome these obstacles, we have developed a wireless neural recording technique that is capable of collecting single-unit data from chronically implanted multi-electrodes in freely moving marmosets. A lightweight, low power and low noise wireless transmitter (headstage) is attached to a multi-electrode array placed in the premotor cortex of the marmoset. The wireless headstage is capable of transmitting 15 channels of neural data with signal-to-noise ratio (SNR) comparable to a tethered system. To minimize radio-frequency (RF) and electro-magnetic interference (EMI), the experiments were conducted within a custom designed RF/EMI and acoustically shielded chamber. The individual electrodes of the multi-electrode array were periodically advanced to densely sample the cortical layers. We recorded single-unit data over a period of several months from the frontal cortex of two marmosets. These recordings demonstrate the feasibility of using our wireless recording method to study single neuron activity in freely roaming primates. PMID:21933683

Effect of antiprogestin ZK 98. 734 on the ovarian cycle, early pregnancy, and on its binding to progesterone receptors in the myometrium of marmoset Callithrix jacchus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puri, C.P.; Kholkute, S.D.; Pongubala, J.M.

1988-04-01

The antiprogestin ZK 98.734 (11 beta-(4-dimethylaminophenyl-17 beta-hydroxy-17 alpha-(3-hydroxy-prop-1(Z)-enyl-4,9(10)-estradien-3-one) was administered i.m. (5 mg/day) for three consecutive days to two groups of common marmosets. In one group (nonpregnant, n = 6), it was injected during the luteal phase, and to the second group (pregnant, n = 7), it was injected during early pregnancy, on Days 24-26 of the mid-cycle estradiol peak. Administration of ZK 98.734 during the luteal phase caused a sharp drop in plasma progesterone levels. The luteal phase was shortened whether the drug was administered during the early or the late luteal phase. Similarly, administration of ZK 98.734 duringmore » early pregnancy caused a significant drop in progesterone levels, and pregnancy was terminated in all of the animals. The post-treatment cycles in both groups of animals were ovulatory and of normal duration. /sup 3/H-ZK 98.734 showed specific binding to myometrial cytosol fraction. ZK 98.734 also displaced the binding of /sup 3/H-progesterone to progesterone receptors. However, progesterone had higher binding affinity than did ZK 98.734. The antifertility action of ZK 98.734 could be a result either of its luteolytic action or of its blocking the progesterone receptors in the target tissue. This study, therefore, indicates that in the common marmoset ZK 98.734 is a progesterone antagonist with a potential to terminate early pregnancy.« less

The behavioral context of visual displays in common marmosets (Callithrix jacchus).

PubMed

de Boer, Raïssa A; Overduin-de Vries, Anne M; Louwerse, Annet L; Sterck, Elisabeth H M

2013-11-01

Communication is important in social species, and may occur with the use of visual, olfactory or auditory signals. However, visual communication may be hampered in species that are arboreal have elaborate facial coloring and live in small groups. The common marmoset fits these criteria and may have limited visual communication. Nonetheless, some (contradictive) propositions concerning visual displays in the common marmoset have been made, yet quantitative data are lacking. The aim of this study was to assign a behavioral context to different visual displays using pre-post-event-analyses. Focal observations were conducted on 16 captive adult and sub-adult marmosets in three different family groups. Based on behavioral elements with an unambiguous meaning, four different behavioral contexts were distinguished: aggression, fear, affiliation, and play behavior. Visual displays concerned behavior that included facial expressions, body postures, and pilo-erection of the fur. Visual displays related to aggression, fear, and play/affiliation were consistent with the literature. We propose that the visual display "pilo-erection tip of tail" is related to fear. Individuals receiving these fear signals showed a higher rate of affiliative behavior. This study indicates that several visual displays may provide cues or signals of particular social contexts. Since the three displays of fear elicited an affiliative response, they may communicate a request of anxiety reduction or signal an external referent. Concluding, common marmosets, despite being arboreal and living in small groups, use several visual displays to communicate with conspecifics and their facial coloration may not hamper, but actually promote the visibility of visual displays. © 2013 Wiley Periodicals, Inc.

Individual identity and affective valence in marmoset calls: in vivo brain imaging with vocal sound playback.

PubMed

Kato, Masaki; Yokoyama, Chihiro; Kawasaki, Akihiro; Takeda, Chiho; Koike, Taku; Onoe, Hirotaka; Iriki, Atsushi

2018-05-01

As with humans, vocal communication is an important social tool for nonhuman primates. Common marmosets (Callithrix jacchus) often produce whistle-like 'phee' calls when they are visually separated from conspecifics. The neural processes specific to phee call perception, however, are largely unknown, despite the possibility that these processes involve social information. Here, we examined behavioral and whole-brain mapping evidence regarding the detection of individual conspecific phee calls using an audio playback procedure. Phee calls evoked sound exploratory responses when the caller changed, indicating that marmosets can discriminate between caller identities. Positron emission tomography with [ 18 F] fluorodeoxyglucose revealed that perception of phee calls from a single subject was associated with activity in the dorsolateral prefrontal, medial prefrontal, orbitofrontal cortices, and the amygdala. These findings suggest that these regions are implicated in cognitive and affective processing of salient social information. However, phee calls from multiple subjects induced brain activation in only some of these regions, such as the dorsolateral prefrontal cortex. We also found distinctive brain deactivation and functional connectivity associated with phee call perception depending on the caller change. According to changes in pupillary size, phee calls from a single subject induced a higher arousal level compared with those from multiple subjects. These results suggest that marmoset phee calls convey information about individual identity and affective valence depending on the consistency or variability of the caller. Based on the flexible perception of the call based on individual recognition, humans and marmosets may share some neural mechanisms underlying conspecific vocal perception.

Regio- and Stereo-Selective Oxidation of a Cardiovascular Drug, Metoprolol, Mediated by Cytochrome P450 2D and 3A Enzymes in Marmoset Livers.

PubMed

Uehara, Shotaro; Ishii, Sakura; Uno, Yasuhiro; Inoue, Takashi; Sasaki, Erika; Yamazaki, Hiroshi

2017-08-01

A β -blocker, metoprolol, is one of the in vivo probes for human cytochrome P450 (P450) 2D6. Investigation of nonhuman primate P450 enzymes helps to improve the accuracy of the extrapolation of pharmacokinetic data from animals into humans. Common marmosets ( Callithrix jacchus ) are a potential primate model for preclinical research, but the detailed roles of marmoset P450 enzymes in metoprolol oxidation remain unknown. In this study, regio- and stereo-selectivity of metoprolol oxidations by a variety of P450 enzymes in marmoset and human livers were investigated in vitro. Although liver microsomes from cynomolgus monkeys and rats preferentially mediated S -metoprolol O -demethylation and R -metoprolol α -hydroxylation, respectively, those from humans, marmosets, minipigs, and dogs preferentially mediated R -metoprolol O -demethylation, in contrast to the slow rates of R - and S -metoprolol oxidation in mouse liver microsomes. R - and S -metoprolol O -demethylation activities in marmoset livers were strongly inhibited by quinidine and ketoconazole, and were significantly correlated with bufuralol 1'-hydroxylation and midazolam 1'-hydroxylation activities and also with P450 2D and 3A4 contents, which is different from the case in human livers that did not have any correlations with P450 3A-mediated midazolam 1'-hydroxylation. Recombinant human P450 2D6 enzyme and marmoset P450 2D6/3A4 enzymes effectively catalyzed R -metoprolol O -demethylation, comparable to the activities of human and marmoset liver microsomes, respectively. These results indicated that the major roles of P450 2D enzymes for the regio- and stereo-selectivity of metoprolol oxidation were similar between human and marmoset livers, but the minor roles of P450 3A enzymes were unique to marmosets. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Birth of Healthy Offspring following ICSI in In Vitro-Matured Common Marmoset (Callithrix jacchus) Oocytes

PubMed Central

Takahashi, Tsukasa; Hanazawa, Kisaburo; Inoue, Takashi; Sato, Kenya; Sedohara, Ayako; Okahara, Junko; Suemizu, Hiroshi; Yagihashi, Chie; Yamamoto, Masafumi; Eto, Tomoo; Konno, Yusuke; Okano, Hideyuki; Suematsu, Makoto; Sasaki, Erika

2014-01-01

Intracytoplasmic sperm injection (ICSI), an important method used to treat male subfertility, is applied in the transgenic technology of sperm-mediated gene transfer. However, no study has described successful generation of offspring using ICSI in the common marmoset, a small non-human primate used as a model for biomedical translational research. In this study, we investigated blastocyst development and the subsequent live offspring stages of marmoset oocytes matured in vitro and fertilized by ICSI. To investigate the optimal timing of performing ICSI, corrected immature oocytes were matured in vitro and ICSI was performed at various time points (1–2 h, 2–4 h, 4–6 h, 6–8 h, and 8–10 h after extrusion of the first polar body (PB)). Matured oocytes were then divided randomly into two groups: one was used for in vitro fertilization (IVF) and the other for ICSI. To investigate in vivo development of embryos followed by ICSI, 6-cell- to 8-cell-stage embryos and blastocysts were nonsurgically transferred into recipient marmosets. Although no significant differences were observed in the fertilization rate of blastocysts among ICSI timing after the first PB extrusion, the blastocyst rate at 1–2 h was lowest among groups at 2–4 h, 4–6 h, 6–8 h, and 8–10 h. Comparing ICSI to IVF, the fertilization rates obtained in ICSI were higher than in IVF (p>0.05). No significant difference was noted in the cleaved blastocyst rate between ICSI and IVF. Following the transfer of 37 ICSI blastocysts, 4 of 20 recipients became pregnant, while with the transfer of 21 6-cell- to 8-cell-stage ICSI embryos, 3 of 8 recipients became pregnant. Four healthy offspring were produced and grew normally. These are the first marmoset offspring produced by ICSI, making it an effective fertilization method for marmosets. PMID:24751978

Non-Viral Generation of Marmoset Monkey iPS Cells by a Six-Factor-in-One-Vector Approach

PubMed Central

Debowski, Katharina; Warthemann, Rita; Lentes, Jana; Salinas-Riester, Gabriela; Dressel, Ralf; Langenstroth, Daniel; Gromoll, Jörg; Sasaki, Erika; Behr, Rüdiger

2015-01-01

Groundbreaking studies showed that differentiated somatic cells of mouse and human origin could be reverted to a stable pluripotent state by the ectopic expression of only four proteins. The resulting pluripotent cells, called induced pluripotent stem (iPS) cells, could be an alternative to embryonic stem cells, which are under continuous ethical debate. Hence, iPS cell-derived functional cells such as neurons may become the key for an effective treatment of currently incurable degenerative diseases. However, besides the requirement of efficacy testing of the therapy also its long-term safety needs to be carefully evaluated in settings mirroring the clinical situation in an optimal way. In this context, we chose the long-lived common marmoset monkey (Callithrix jacchus) as a non-human primate species to generate iPS cells. The marmoset monkey is frequently used in biomedical research and is gaining more and more preclinical relevance due to the increasing number of disease models. Here, we describe, to our knowledge, the first-time generation of marmoset monkey iPS cells from postnatal skin fibroblasts by non-viral means. We used the transposon-based, fully reversible piggyback system. We cloned the marmoset monkey reprogramming factors and established robust and reproducible reprogramming protocols with a six-factor-in-one-construct approach. We generated six individual iPS cell lines and characterized them in comparison with marmoset monkey embryonic stem cells. The generated iPS cells are morphologically indistinguishable from marmoset ES cells. The iPS cells are fully reprogrammed as demonstrated by differentiation assays, pluripotency marker expression and transcriptome analysis. They are stable for numerous passages (more than 80) and exhibit euploidy. In summary, we have established efficient non-viral reprogramming protocols for the derivation of stable marmoset monkey iPS cells, which can be used to develop and test cell replacement therapies in preclinical settings. PMID:25785453

Non-viral generation of marmoset monkey iPS cells by a six-factor-in-one-vector approach.

PubMed

Debowski, Katharina; Warthemann, Rita; Lentes, Jana; Salinas-Riester, Gabriela; Dressel, Ralf; Langenstroth, Daniel; Gromoll, Jörg; Sasaki, Erika; Behr, Rüdiger

2015-01-01

Groundbreaking studies showed that differentiated somatic cells of mouse and human origin could be reverted to a stable pluripotent state by the ectopic expression of only four proteins. The resulting pluripotent cells, called induced pluripotent stem (iPS) cells, could be an alternative to embryonic stem cells, which are under continuous ethical debate. Hence, iPS cell-derived functional cells such as neurons may become the key for an effective treatment of currently incurable degenerative diseases. However, besides the requirement of efficacy testing of the therapy also its long-term safety needs to be carefully evaluated in settings mirroring the clinical situation in an optimal way. In this context, we chose the long-lived common marmoset monkey (Callithrix jacchus) as a non-human primate species to generate iPS cells. The marmoset monkey is frequently used in biomedical research and is gaining more and more preclinical relevance due to the increasing number of disease models. Here, we describe, to our knowledge, the first-time generation of marmoset monkey iPS cells from postnatal skin fibroblasts by non-viral means. We used the transposon-based, fully reversible piggyback system. We cloned the marmoset monkey reprogramming factors and established robust and reproducible reprogramming protocols with a six-factor-in-one-construct approach. We generated six individual iPS cell lines and characterized them in comparison with marmoset monkey embryonic stem cells. The generated iPS cells are morphologically indistinguishable from marmoset ES cells. The iPS cells are fully reprogrammed as demonstrated by differentiation assays, pluripotency marker expression and transcriptome analysis. They are stable for numerous passages (more than 80) and exhibit euploidy. In summary, we have established efficient non-viral reprogramming protocols for the derivation of stable marmoset monkey iPS cells, which can be used to develop and test cell replacement therapies in preclinical settings.

Characterization of a nonhuman primate model for the study of testicular peritubular cells - comparison with human testicular cells.

PubMed

Schmid, N; Stöckl, J B; Flenkenthaler, F; Dietrich, K-G; Schwarzer, J U; Köhn, F-M; Drummer, C; Fröhlich, T; Arnold, G J; Behr, R; Mayerhofer, A

2018-05-29

Are monkey testicular peritubular cells (MKTPCs) from the common marmoset monkey (Callithrix jacchus) a suitable translational model for the study of human testicular peritubular cells (HTPCs)? MKTPCs can be isolated and propagated in vitro, retain characteristic markers for testicular peritubular cells and their proteome strongly (correlation coefficient of 0.78) overlaps with the proteome of HTPCs. Smooth-muscle-like peritubular cells form the wall of seminiferous tubules, transport sperm, are immunologically active, secrete a plethora of factors and may contribute to the spermatogonial stem cell niche. Mechanistic studies are hampered by heterogeneity of human samples. We established a culture method for MKTPCs and characterized these cells from 6 young adult animals (2-3 years). To examine whether they qualify as a translational model we also examined HTPCs from 7 men and compared the proteomes of both groups. We used explant cultures to obtain MKTPCs, which express smooth muscle markers (calponin (CNN1), smooth muscle actin (ACTA2)), lack FSH-receptors (FSHR) and LH-receptors (LHCGR), but possess androgen receptors (AR). MKTPCs can be passaged at least up to 8 times, without discernable phenotypic changes. Mass-spectrometry-based analyses of the MKTPC and HTPC proteomes were performed. We established a method for isolation and cultivation of MKTPCs, and provide a comprehensive analysis of their protein repertoire. The results let us conclude that MKTPCs are suitable as a nonhuman primate model to study peritubular cell functions. List of identified proteins in MKTPCs by LC-MS/MS is accessible at the ProteomeXchange (identifier PXD009394). This is an in vitro cellular non-human primate model used to provide a window into the role of these cells in the human testis. Previous studies with HTPCs from patients revealed a degree of heterogeneity, possibly due to age, lifestyle and medical history of the individual human donors. We anticipate that the new translational model, derived from young health nonhuman primates, may allow us to circumvent these issues and may lead to a better understanding of the role of peritubular cells. This work was supported by grants from the DFG (MA 1080/27-1; AR 362/9-1; BE 2296/8-1). The authors declare no competing financial interests.

Dissecting the mechanisms of squirrel monkey (Saimiri boliviensis) social learning

PubMed Central

Holmes, AN; Williams, LE; Brosnan, SF

2013-01-01

Although the social learning abilities of monkeys have been well documented, this research has only focused on a few species. Furthermore, of those that also incorporated dissections of social learning mechanisms, the majority studied either capuchins (Cebus apella) or marmosets (Callithrix jacchus). To gain a broader understanding of how monkeys gain new skills, we tested squirrel monkeys (Saimiri boliviensis) which have never been studied in tests of social learning mechanisms. To determine whether S. boliviensis can socially learn, we ran “open diffusion” tests with monkeys housed in two social groups (N = 23). Over the course of 10 20-min sessions, the monkeys in each group observed a trained group member retrieving a mealworm from a bidirectional task (the “Slide-box”). Two thirds (67%) of these monkeys both learned how to operate the Slide-box and they also moved the door significantly more times in the direction modeled by the trained demonstrator than the alternative direction. To tease apart the underlying social learning mechanisms we ran a series of three control conditions with 35 squirrel monkeys that had no previous experience with the Slide-box. The first replicated the experimental open diffusion sessions but without the inclusion of a trained model, the second was a no-information control with dyads of monkeys, and the third was a ‘ghost’ display shown to individual monkeys. The first two controls tested for the importance of social support (mere presence effect) and the ghost display showed the affordances of the task to the monkeys. The monkeys showed a certain level of success in the group control (54% of subjects solved the task on one or more occasions) and paired controls (28% were successful) but none were successful in the ghost control. We propose that the squirrel monkeys’ learning, observed in the experimental open diffusion tests, can be best described by a combination of social learning mechanisms in concert; in this case, those mechanisms are most likely object movement reenactment and social facilitation. We discuss the interplay of these mechanisms and how they related to learning shown by other primate species. PMID:23638347

Different methods for volatile sampling in mammals

PubMed Central

Möller, Manfred; Marcillo, Andrea; Einspanier, Almuth; Weiß, Brigitte M.

2017-01-01

Previous studies showed that olfactory cues are important for mammalian communication. However, many specific compounds that convey information between conspecifics are still unknown. To understand mechanisms and functions of olfactory cues, olfactory signals such as volatile compounds emitted from individuals need to be assessed. Sampling of animals with and without scent glands was typically conducted using cotton swabs rubbed over the skin or fur and analysed by gas chromatography-mass spectrometry (GC-MS). However, this method has various drawbacks, including a high level of contaminations. Thus, we adapted two methods of volatile sampling from other research fields and compared them to sampling with cotton swabs. To do so we assessed the body odor of common marmosets (Callithrix jacchus) using cotton swabs, thermal desorption (TD) tubes and, alternatively, a mobile GC-MS device containing a thermal desorption trap. Overall, TD tubes comprised most compounds (N = 113), with half of those compounds being volatile (N = 52). The mobile GC-MS captured the fewest compounds (N = 35), of which all were volatile. Cotton swabs contained an intermediate number of compounds (N = 55), but very few volatiles (N = 10). Almost all compounds found with the mobile GC-MS were also captured with TD tubes (94%). Hence, we recommend TD tubes for state of the art sampling of body odor of mammals or other vertebrates, particularly for field studies, as they can be easily transported, stored and analysed with high performance instruments in the lab. Nevertheless, cotton swabs capture compounds which still may contribute to the body odor, e.g. after bacterial fermentation, while profiles from mobile GC-MS include only the most abundant volatiles of the body odor. PMID:28841690

Effects of prenatal dexamethasone treatment on physical growth, pituitary-adrenal hormones, and performance of motor, motivational, and cognitive tasks in juvenile and adolescent common marmoset monkeys.

PubMed

Hauser, Jonas; Knapman, Alana; Zürcher, Nicole R; Pilloud, Sonia; Maier, Claudia; Diaz-Heijtz, Rochellys; Forssberg, Hans; Dettling, Andrea; Feldon, Joram; Pryce, Christopher R

2008-12-01

Synthetic glucocorticoids such as dexamethasone (DEX) are commonly used to prevent respiratory distress syndrome in preterm infants, but there is emerging evidence of subsequent neurobehavioral abnormalities (e.g. problems with inattention/hyperactivity). In the present study, we exposed pregnant common marmosets (Callithrix jacchus, primates) to daily repeated DEX (5 mg/kg by mouth) during either early (d 42-48) or late (d 90-96) pregnancy (gestation period of 144 days). Relative to control, and with a longitudinal design, we investigated DEX effects in offspring in terms of physical growth, plasma ACTH and cortisol titers, social and maintenance behaviors, skilled motor reaching, motivation for palatable reward, and learning between infancy and adolescence. Early DEX resulted in reduced sociability in infants and increased motivation for palatable reward in adolescents. Late DEX resulted in a mild transient increase in knee-heel length in infants and enhanced reversal learning of stimulus-reward association in adolescents. There was no effect of either early or late DEX on basal plasma ACTH or cortisol titers. Both treatments resulted in impaired skilled motor reaching in juveniles, which attenuated in early DEX but persisted in late DEX across test sessions. The increased palatable-reward motivation and decreased social motivation observed in early DEX subjects provide experimental support for the clinical reports that prenatal glucocorticoid treatment impairs social development and predisposes to metabolic syndrome. These novel primate findings indicate that fetal glucocorticoid overexposure can lead to abnormal development of motor, affective, and cognitive behaviors. Importantly, the outcome is highly dependent upon the timing of glucocorticoid overexposure.

Serum Albumin and Body Weight as Biomarkers for the Antemortem Identification of Bone and Gastrointestinal Disease in the Common Marmoset

PubMed Central

Baxter, Victoria K.; Shaw, Gillian C.; Sotuyo, Nathaniel P.; Carlson, Cathy S.; Olson, Erik J.; Zink, M. Christine; Mankowski, Joseph L.; Adams, Robert J.

2013-01-01

The increasing use of the common marmoset (Callithrix jacchus) in research makes it important to diagnose spontaneous disease that may confound experimental studies. Bone disease and gastrointestinal disease are two major causes of morbidity and mortality in captive marmosets, but currently no effective antemortem tests are available to identify affected animals prior to the terminal stage of disease. In this study we propose that bone disease and gastrointestinal disease are associated disease entities in marmosets and aim to establish the efficacy of several economical antemortem tests in identifying and predicting disease. Tissues from marmosets were examined to define affected animals and unaffected controls. Complete blood count, serum chemistry values, body weight, quantitative radiographs, and tissue-specific biochemical markers were evaluated as candidate biomarkers for disease. Bone and gastrointestinal disease were associated, with marmosets being over seven times more likely to have either concurrent bone and gastrointestinal disease or neither disease as opposed to lesions in only one organ system. When used in tandem, serum albumin <3.5 g/dL and body weight <325 g identified 100% of the marmosets affected with concurrent bone and gastrointestinal disease. Progressive body weight loss of 0.05% of peak body weight per day predicted which marmosets would develop disease prior to the terminal stage. Bone tissue-specific tests, such as quantitative analysis of radiographs and serum parathyroid hormone levels, were effective for distinguishing between marmosets with bone disease and those without. These results provide an avenue for making informed decisions regarding the removal of affected marmosets from studies in a timely manner, preserving the integrity of research results. PMID:24324827

Small but wise: Common marmosets (Callithrix jacchus) use acoustic signals as cues to avoid interactions with blonde capuchin monkeys (Sapajus flavius).

PubMed

Bastos, Monique; Medeiros, Karolina; Jones, Gareth; Bezerra, Bruna

2018-03-01

Vocalizations are often used by animals to communicate and mediate social interactions. Animals may benefit from eavesdropping on calls from other species to avoid predation and thus increase their chances of survival. Here we use both observational and experimental evidence to investigate eavesdropping and how acoustic signals may mediate interactions between two sympatric and endemic primate species (common marmosets and blonde capuchin monkeys) in a fragment of Atlantic Rainforest in Northeastern Brazil. We observed 22 natural vocal encounters between the study species, but no evident visual or physical contact over the study period. These two species seem to use the same area throughout the day, but at different times. We broadcasted alarm and long distance calls to and from both species as well as two control stimuli (i.e., forest background noise and a loud call from an Amazonian primate) in our playback experiments. Common marmosets showed anti-predator behavior (i.e., vigilance and flight) when exposed to blonde capuchin calls both naturally and experimentally. However, blonde capuchin monkeys showed no anti-predator behavior in response to common marmoset calls. Blonde capuchins uttered long distance calls and looked in the direction of the speaker following exposure to their own long distance call, whereas they fled when exposed to their own alarm calls. Both blonde capuchin monkeys and common marmosets showed fear behaviors in response to the loud call from a primate species unknown to them, and showed no apparent response to the forest background noise. Common marmoset responses to blonde capuchin calls suggests that the latter is a potential predator. Furthermore, common marmosets appear to be eavesdropping on calls from blonde capuchin monkeys to avoid potentially costly encounters with them. © 2018 Wiley Periodicals, Inc.

The Effect of Habitat Acoustics on Common Marmoset Vocal Signal Transmission

PubMed Central

MORRILL, RYAN J.; THOMAS, A. WREN; SCHIEL, NICOLA; SOUTO, ANTONIO; MILLER, CORY T.

2013-01-01

Noisy acoustic environments present several challenges for the evolution of acoustic communication systems. Among the most significant is the need to limit degradation of spectro-temporal signal structure in order to maintain communicative efficacy. This can be achieved by selecting for several potentially complementary processes. Selection can act on behavioral mechanisms permitting signalers to control the timing and occurrence of signal production to avoid acoustic interference. Likewise, the signal itself may be the target of selection, biasing the evolution of its structure to comprise acoustic features that avoid interference from ambient noise or degrade minimally in the habitat. Here, we address the latter topic for common marmoset (Callithrix jacchus) long-distance contact vocalizations, known as phee calls. Our aim was to test whether this vocalization is specifically adapted for transmission in a species-typical forest habitat, the Atlantic forests of northeastern Brazil. We combined seasonal analyses of ambient habitat acoustics with experiments in which pure tones, clicks, and vocalizations were broadcast and rerecorded at different distances to characterize signal degradation in the habitat. Ambient sound was analyzed from intervals throughout the day and over rainy and dry seasons, showing temporal regularities across varied timescales. Broadcast experiment results indicated that the tone and click stimuli showed the typically inverse relationship between frequency and signaling efficacy. Although marmoset phee calls degraded over distance with marked predictability compared with artificial sounds, they did not otherwise appear to be specially designed for increased transmission efficacy or minimal interference in this habitat. We discuss these data in the context of other similar studies and evidence of potential behavioral mechanisms for avoiding acoustic interference in order to maintain effective vocal communication in common marmosets. PMID:23592313

Fetal sulcation and gyrification in common marmosets (Callithrix jacchus) obtained by ex vivo magnetic resonance imaging.

PubMed

Sawada, K; Hikishima, K; Murayama, A Y; Okano, H J; Sasaki, E; Okano, H

2014-01-17

The present study characterized fetal sulcation patterns and gyrification in the cerebrum of the New World monkey group, common marmosets, using a 3D T2-weighted high-resolution anatomical magnetic resonance imaging (MRI) sequence from the fixed brain at 7-tesla ex vivo. Fetal sulcation in the marmoset cerebrum began to indent the lateral fissure and hippocampal sulcus in gestational week (GW) 12, and then the following sulci emerged: the callosal and calcarine sulci on GW 15; the superior temporal sulcus on GW 17; and the circular and occipitotemporal sulci on GW 18. The degree of cortical convolution was evaluated quantitatively based on 2D MRI slices by the gyrification index (GI) and based on 3D MRI data by sulcation index (SI). Both the mean GI and SI increased from GW 16, and were closely correlated with the cortical volume and the cortical surface area during fetal periods (their correlation coefficients marked more than 0.95). After birth, both the mean GI and SI decreased slightly by 2years of age, whereas the cortical volume and surface area continuously increased. Notably, histological analysis showed that the outer subventricular zone (oSVZ) in non-sulcal regions was thicker than that in the presumptive calcarine sulcal region on GW 13, preceding the infolding of the calcarine sulcus. The present results showed definite sulcal infolding on the cerebral cortical surface of the marmosets, with similar pattern and sequence of their emergences to other higher-order primates such as macaques and humans. Differential expansion of the oSVZ may be involved in gyral convolution and sulcal infolding in the developing cerebrum. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

The effect of habitat acoustics on common marmoset vocal signal transmission.

PubMed

Morrill, Ryan J; Thomas, A Wren; Schiel, Nicola; Souto, Antonio; Miller, Cory T

2013-09-01

Noisy acoustic environments present several challenges for the evolution of acoustic communication systems. Among the most significant is the need to limit degradation of spectro-temporal signal structure in order to maintain communicative efficacy. This can be achieved by selecting for several potentially complementary processes. Selection can act on behavioral mechanisms permitting signalers to control the timing and occurrence of signal production to avoid acoustic interference. Likewise, the signal itself may be the target of selection, biasing the evolution of its structure to comprise acoustic features that avoid interference from ambient noise or degrade minimally in the habitat. Here, we address the latter topic for common marmoset (Callithrix jacchus) long-distance contact vocalizations, known as phee calls. Our aim was to test whether this vocalization is specifically adapted for transmission in a species-typical forest habitat, the Atlantic forests of northeastern Brazil. We combined seasonal analyses of ambient habitat acoustics with experiments in which pure tones, clicks, and vocalizations were broadcast and rerecorded at different distances to characterize signal degradation in the habitat. Ambient sound was analyzed from intervals throughout the day and over rainy and dry seasons, showing temporal regularities across varied timescales. Broadcast experiment results indicated that the tone and click stimuli showed the typically inverse relationship between frequency and signaling efficacy. Although marmoset phee calls degraded over distance with marked predictability compared with artificial sounds, they did not otherwise appear to be specially designed for increased transmission efficacy or minimal interference in this habitat. We discuss these data in the context of other similar studies and evidence of potential behavioral mechanisms for avoiding acoustic interference in order to maintain effective vocal communication in common marmosets. © 2013 Wiley Periodicals, Inc.

Representation of the visual field in the primary visual area of the marmoset monkey: magnification factors, point-image size, and proportionality to retinal ganglion cell density.

PubMed

Chaplin, Tristan A; Yu, Hsin-Hao; Rosa, Marcello G P

2013-04-01

The primary visual area (V1) forms a systematic map of the visual field, in which adjacent cell clusters represent adjacent points of visual space. A precise quantification of this map is key to understanding the anatomical relationships between neurons located in different stations of the visual pathway, as well as the neural bases of visual performance in different regions of the visual field. We used computational methods to quantify the visual topography of V1 in the marmoset (Callithrix jacchus), a small diurnal monkey. The receptive fields of neurons throughout V1 were mapped in two anesthetized animals using electrophysiological recordings. Following histological reconstruction, precise 3D reconstructions of the V1 surface and recording sites were generated. We found that the areal magnification factor (M(A) ) decreases with eccentricity following a function that has the same slope as that observed in larger diurnal primates, including macaque, squirrel, and capuchin monkeys, and humans. However, there was no systematic relationship between M(A) and polar angle. Despite individual variation in the shape of V1, the relationship between M(A) and eccentricity was preserved across cases. Comparison between V1 and the retinal ganglion cell density demonstrated preferential magnification of central space in the cortex. The size of the cortical compartment activated by a punctiform stimulus decreased from the foveal representation towards the peripheral representation. Nonetheless, the relationship between the receptive field sizes of V1 cells and the density of ganglion cells suggested that each V1 cell receives information from a similar number of retinal neurons, throughout the visual field. Copyright © 2012 Wiley Periodicals, Inc.

Reversal learning in gonadectomized marmosets with and without hormone replacement: are males more sensitive to punishment?

PubMed

LaClair, Matthew; Lacreuse, Agnès

2016-05-01

This study examined sex differences in executive function in middle-aged gonadectomized marmosets (Callithrix jacchus) with or without hormonal replacement. We tested ten castrated male (mean age 5.5 years) marmosets treated with testosterone cypionate (T, n = 5) or vehicle (n = 5) on Reversal Learning, which contributes to cognitive flexibility, and the Delayed Response task, measuring working memory. Their performance was compared to that of 11 ovariectomized females (mean age = 3.7 years) treated with Silastic capsules filled with 17-β estradiol (E2, n = 6) or empty capsules (n = 5), previously tested on the same tasks (Lacreuse et al. in J Neuroendocrinol 26:296-309, 2014. doi: 10.1111/jne.12147). Behavioral observations were conducted daily. Females exhibited more locomotor behaviors than males. Males and females did not differ in the number of trials taken to reach criterion on the reversals, but males had significantly longer response latencies, regardless of hormone replacement. They also had a greater number of refusals than females. Additionally, both control and T-treated males, but not females, had slower responses on incorrect trials, suggesting that males were making errors due to distraction, lack of motivation or uncertainty. Furthermore, although both males and females had slower responding following an incorrect compared to a correct trial, the sex difference in response latencies was disproportionally large following an incorrect trial. No sex difference was found in the Delayed Response task. Overall, slower response latencies in males than females during Reversal Learning, especially during and following an incorrect trial, may reflect greater sensitivity to punishment (omission of reward) and greater performance monitoring in males, compared to females. Because these differences occurred in gonadectomized animals and regardless of hormone replacement, they may be organized early in life.

Proteome profiling reveals regional protein alteration in cerebrum of common marmoset (Callithrix jacchus) exposed to methylmercury.

PubMed

Shao, Yueting; Yamamoto, Megumi; Figeys, Daniel; Ning, Zhibin; Chan, Hing Man

2016-03-10

Methylmercury (MeHg) is known to selectively damage the calcarine and precentral cortices along deep sulci and fissures in adult cases, but the detailed mechanism is still unclear. This study aims to identify and analyze the differential proteome expression in two regions of the cerebrum (the frontal lobe and the occipital lobe including the calcarine sulcus) of the common marmoset exposed to MeHg using a shot-gun proteomic approach. A total of 1045 and 1062 proteins were identified in the frontal lobe (FL) and occipital lobe (OL), of which, 62 and 89 proteins were found significantly changed with MeHg exposure. Functional enrichment/depletion analysis showed that the lipid metabolic process and proteolysis were affected in both two lobes. Functional changes in FL were characterized in cell cycle and cell division, sulfur compound metabolic process, microtubule-based process and glycerolipid metabolic process. In comparison, proteins were enriched in the functions of transport, carbohydrate metabolic process, chemical caused homeostasis and regulation of body fluid levels in OL. Pathway analysis predicted that vasopressin-regulated water reabsorption was disturbed in MeHg-treated FL. Our results showed that MeHg induced regional specific protein changes in FL and OL but with similar endpoint effects such as energy diminish and disruption of water transport. APOE and GPX1 were shown to be possible key proteins targeted by MeHg leading to multiple functional changes in OL. This is the first report of the whole proteome changes of primate cerebrum for MeHg neurotoxicity, and the results will contribute to the understanding of molecular basis of MeHg intoxication in humans. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Cellular Composition and Organization of the Subventricular Zone and Rostral Migratory Stream in the Adult and Neonatal Common Marmoset Brain

PubMed Central

Sawamoto, Kazunobu; Hirota, Yuki; Alfaro-Cervello, Clara; Soriano-Navarro, Mario; He, Xiaoping; Hayakawa-Yano, Yoshika; Yamada, Masayuki; Hikishima, Keigo; Tabata, Hidenori; Iwanami, Akio; Nakajima, Kazunori; Toyama, Yoshiaki; Itoh, Toshio; Alvarez-Buylla, Arturo; Garcia-Verdugo, Jose Manuel; Okano, Hideyuki

2014-01-01

The adult subventricular zone (SVZ) of the lateral ventricle contains neural stem cells. In rodents, these cells generate neuroblasts that migrate as chains toward the olfactory bulb along the rostral migratory stream (RMS). The neural-stem-cell niche at the ventricular wall is conserved in various animal species, including primates. However, it is unclear how the SVZ and RMS organization in nonhuman primates relates to that of rodents and humans. Here we studied the SVZ and RMS of the adult and neonatal common marmoset (Callithrix jacchus), a New World primate used widely in neuroscience, by electron microscopy, and immunohistochemical detection of cell-type-specific markers. The marmoset SVZ contained cells similar to type B, C, and A cells of the rodent SVZ in their marker expression and morphology. The adult marmoset SVZ had a three-layer organization, as in the human brain, with ependymal, hypocellular, and astro-cyte-ribbon layers. However, the hypocellular layer was very thin or absent in the adult-anterior and neonatal SVZ. Anti-PSA-NCAM staining of the anterior SVZ in whole-mount ventricular wall preparations of adult marmosets revealed an extensive network of elongated cell aggregates similar to the neuroblast chains in rodents. Time-lapse recordings of marmoset SVZ explants cultured in Matrigel showed the neuroblasts migrating in chains, like rodent type A cells. These results suggest that some features of neurogenesis and neuronal migration in the SVZ are common to marmosets, humans, and rodents. This basic description of the adult and neonatal marmoset SVZ will be useful for future studies on adult neurogenesis in primates. PMID:21246550

Report on primate supply for biomedical scientific work in the UK. EUPREN UK Working Party.

PubMed

Owen, S; Thomas, C; West, P; Wolfensohn, S; Wood, M

1997-10-01

A Working Party of the UK group of European Primate Resources Network (EUPREN) considered primate supply for scientific work in the UK. Through a questionnaire, which achieved a very good response, it obtained details of primate use, sources and breeding in the UK and it put forward options to ensure that animal welfare is the best possible whilst ensuring continued supply. The questionnaire showed that contract research laboratories and pharmaceutical companies use about 80% of the 4233 primates used annually at the moment, with the rest accounted for by academic establishments and public sector laboratories. Fifty-four per cent are cynomolgus macaques (Macaca fascicularis), of which nearly 90% are captive-bred outside the European Union (EU), the remainder being bred in the UK. Nearly 90% of cynomolgus macaques are used by only five institutions. Thirty-seven per cent of primates used are marmosets (Callithrix jacchus jacchus), all of which are bred in the UK. Most of the rest are rhesus macaques (Macaca mulatta), about half of which are captive-bred outside the EU, the other half being bred in the UK. Overall primate use has increased from about 3000 per year in 1990 and users predict that requirements for all species except baboons (Papio sp.) will be maintained or increase. Marmoset breeding in the UK is already closely matched to use, and it could be increased reasonably easily if necessary. Some of the existing breeding centres of macaques in the UK would be prepared to consider expanding to supply others, although investment and imported breeding stock would be needed and it is likely that a large investment would be needed to breed a significant fraction of the macaque use in the UK. A further problem is that the users of only about 10% of the cynomolgus macaques said that they could replace this species by rhesus macaques, which are easier to breed in the UK. The questionnaire showed that much of the use of macaques would be transferred to other countries equally remote from the natural source countries of the animals, if constraints on primate use became more severe in the UK. Users felt that it is unlikely that much of the work could be transferred to the natural source countries themselves. A review of the literature revealed a paucity of information on the effects of transport on primate welfare. The importance of obtaining this information before making decisions about alternative means of supply is stressed. Current schemes for the accreditation of primate breeders were reviewed. A list of options is presented for discussion. Users vary so much in their requirements that it is unlikely that one means of supply will be applicable to all. Animal welfare will benefit and supply will be more certain if cooperation between those concerned (preferably through the UK group of EUPREN) is maintained.

Spermatogonial behavior in marmoset: a new generation, their kinetics and niche.

PubMed

Caldeira-Brant, A L; Eras-Garcia, L; Alves-Freitas, D; Almeida, F R C L; Chiarini-Garcia, H

2018-06-01

Could a more detailed evaluation of marmoset spermatogonial morphology, kinetics and niches using high-resolution light microscopy (HRLM) lead to new findings? Three subtypes of marmoset undifferentiated spermatogonia, which were not evenly distributed in terms of number and position along the basal membrane, and an extra premeiotic cell division not present in humans were identified using HRLM. The seminiferous epithelium cycle (SEC) of marmosets is divided into nine stages when based on the acrosome system, and several spermatogenic stages can usually be recognized within the same tubular cross-section. Three spermatogonial generations have been previously described in marmosets: types Adark, Apale and B spermatogonia. Testes from five adult Callithrix penicillata were fixed by glutaraldehyde perfusion via the cardiac route and embedded in Araldite plastic resin for HRLM evaluation. Semi-thin sections (1 μm) were analyzed morphologically and morphometrically to evaluate spermatogonial morphology and kinetics (number, mitosis and apoptosis), spermatogenesis efficiency and the spermatogonial niche. Shape and nuclear diameter, the presence and distribution of heterochromatin, the granularity of the euchromatin, as well as the number, morphology and degree of nucleolar compaction were observed for morphological characterization. Kinetics analyses were performed for all spermatogonial subtypes and preleptotene spermatocytes, and their mitosis and apoptosis indexes determined across all SEC stages. Spermatogenesis parameters (mitotic, meiotic, Sertoli cell workload and general spermatogenesis efficiency) were determined through the counting of Adark and Apale spermatogonia, preleptotene and pachytene primary spermatocytes, round spermatids, and Sertoli cells at stage IV of the SEC. This is the first time that a study in marmosets demonstrates: the existence of a new spermatogonial generation (B2); the presence of two subtypes of Adark spermatogonia with (AdVac) and without (AdNoVac) nuclear rarefaction zones; the peculiar behavior of AdVac spermatogonia across the stages of the SEC, suggesting that they are quiescent stem spermatogonia; and that AdVac spermatogonia are located close to areas in which blood vessels, Leydig cells and macrophages are concentrated, suggesting a niche area for these cells. Not applicable. The C. penicillata spermatogonial kinetics evaluated here consider spermatogonial number across the SEC and their mitotic and apoptotic figures identified in HRLM sections. Therefore, caution is required when comparing absolute values between species. Although morphometric evaluation has suggested that AdVac spermatogonia are stem cells, a functional proof of this is still missing. It is known that parameters of the spermatogenic process in C. penicillata have similarities with those of the common marmoset C. jacchus, however, a detailed study of spermatogonial morphology, kinetics and niche has not yet been performed in C. jacchus, and a full comparison of the two species is not possible. Our findings in C. penicillata contribute to a better understanding of the spermatogonial behavior and spermatogenesis efficiency in non-human primates. Given the phylogenetic closeness of the marmoset to the human species, similar processes might occur in humans. Therefore, marmosets may be an excellent model for studies regarding human testicular biology, fertility and related disorders. Experiments were partially supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) and Conselho Nacional de Desenvolvimento Cientifico e Tecnológico (CNPq). The authors declare that there are no conflicts of interest.

Contextual effects of noise on vocalization encoding in primary auditory cortex

PubMed Central

Ni, Ruiye; Bender, David A.; Shanechi, Amirali M.; Gamble, Jeffrey R.

2016-01-01

Robust auditory perception plays a pivotal function for processing behaviorally relevant sounds, particularly with distractions from the environment. The neuronal coding enabling this ability, however, is still not well understood. In this study, we recorded single-unit activity from the primary auditory cortex (A1) of awake marmoset monkeys (Callithrix jacchus) while delivering conspecific vocalizations degraded by two different background noises: broadband white noise and vocalization babble. Noise effects on neural representation of target vocalizations were quantified by measuring the responses' similarity to those elicited by natural vocalizations as a function of signal-to-noise ratio. A clustering approach was used to describe the range of response profiles by reducing the population responses to a summary of four response classes (robust, balanced, insensitive, and brittle) under both noise conditions. This clustering approach revealed that, on average, approximately two-thirds of the neurons change their response class when encountering different noises. Therefore, the distortion induced by one particular masking background in single-unit responses is not necessarily predictable from that induced by another, suggesting the low likelihood of a unique group of noise-invariant neurons across different background conditions in A1. Regarding noise influence on neural activities, the brittle response group showed addition of spiking activity both within and between phrases of vocalizations relative to clean vocalizations, whereas the other groups generally showed spiking activity suppression within phrases, and the alteration between phrases was noise dependent. Overall, the variable single-unit responses, yet consistent response types, imply that primate A1 performs scene analysis through the collective activity of multiple neurons. NEW & NOTEWORTHY The understanding of where and how auditory scene analysis is accomplished is of broad interest to neuroscientists. In this paper, we systematically investigated neuronal coding of multiple vocalizations degraded by two distinct noises at various signal-to-noise ratios in nonhuman primates. In the process, we uncovered heterogeneity of single-unit representations for different auditory scenes yet homogeneity of responses across the population. PMID:27881720

Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3.

PubMed

Hirschi, Marscha; Herzik, Mark A; Wie, Jinhong; Suo, Yang; Borschel, William F; Ren, Dejian; Lander, Gabriel C; Lee, Seok-Yong

2017-10-19

The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signalling. The transient receptor potential mucolipin (TRPML) channel family belongs to the TRP superfamily and is composed of three members: TRPML1-TRPML3. TRPMLs are the major Ca 2+ -permeable channels on late endosomes and lysosomes (LEL). They regulate the release of Ca 2+ from organelles, which is important for various physiological processes, including organelle trafficking and fusion. Loss-of-function mutations in the MCOLN1 gene, which encodes TRPML1, cause the neurodegenerative lysosomal storage disorder mucolipidosis type IV, and a gain-of-function mutation (Ala419Pro) in TRPML3 gives rise to the varitint-waddler (Va) mouse phenotype. Notably, TRPML channels are activated by the low-abundance and LEL-enriched signalling lipid phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P 2 ), whereas other phosphoinositides such as PtdIns(4,5)P 2 , which is enriched in plasma membranes, inhibit TRPMLs. Conserved basic residues at the N terminus of the channel are important for activation by PtdIns(3,5)P 2 and inhibition by PtdIns(4,5)P 2 . However, owing to a lack of structural information, the mechanism by which TRPML channels recognize PtdIns(3,5)P 2 and increase their Ca 2+ conductance remains unclear. Here we present the cryo-electron microscopy (cryo-EM) structure of a full-length TRPML3 channel from the common marmoset (Callithrix jacchus) at an overall resolution of 2.9 Å. Our structure reveals not only the molecular basis of ion conduction but also the unique architecture of TRPMLs, wherein the voltage sensor-like domain is linked to the pore via a cytosolic domain that we term the mucolipin domain. Combined with functional studies, these data suggest that the mucolipin domain is responsible for PtdIns(3,5)P 2 binding and subsequent channel activation, and that it acts as a 'gating pulley' for lipid-dependent TRPML gating.

Contextual effects of noise on vocalization encoding in primary auditory cortex.

PubMed

Ni, Ruiye; Bender, David A; Shanechi, Amirali M; Gamble, Jeffrey R; Barbour, Dennis L

2017-02-01

Robust auditory perception plays a pivotal function for processing behaviorally relevant sounds, particularly with distractions from the environment. The neuronal coding enabling this ability, however, is still not well understood. In this study, we recorded single-unit activity from the primary auditory cortex (A1) of awake marmoset monkeys (Callithrix jacchus) while delivering conspecific vocalizations degraded by two different background noises: broadband white noise and vocalization babble. Noise effects on neural representation of target vocalizations were quantified by measuring the responses' similarity to those elicited by natural vocalizations as a function of signal-to-noise ratio. A clustering approach was used to describe the range of response profiles by reducing the population responses to a summary of four response classes (robust, balanced, insensitive, and brittle) under both noise conditions. This clustering approach revealed that, on average, approximately two-thirds of the neurons change their response class when encountering different noises. Therefore, the distortion induced by one particular masking background in single-unit responses is not necessarily predictable from that induced by another, suggesting the low likelihood of a unique group of noise-invariant neurons across different background conditions in A1. Regarding noise influence on neural activities, the brittle response group showed addition of spiking activity both within and between phrases of vocalizations relative to clean vocalizations, whereas the other groups generally showed spiking activity suppression within phrases, and the alteration between phrases was noise dependent. Overall, the variable single-unit responses, yet consistent response types, imply that primate A1 performs scene analysis through the collective activity of multiple neurons. The understanding of where and how auditory scene analysis is accomplished is of broad interest to neuroscientists. In this paper, we systematically investigated neuronal coding of multiple vocalizations degraded by two distinct noises at various signal-to-noise ratios in nonhuman primates. In the process, we uncovered heterogeneity of single-unit representations for different auditory scenes yet homogeneity of responses across the population. Copyright © 2017 the American Physiological Society.

Secondary pneumatization of the maxillary sinus in callitrichid primates: insights from immunohistochemistry and bone cell distribution.

PubMed

Smith, Timothy D; Rossie, James B; Cooper, Gregory M; Mooney, Mark P; Siegel, Michael I

2005-08-01

The paranasal sinuses remain elusive both in terms of function and in the proximate mechanism of their development. The present study sought to describe the maxillary sinuses (MSs) in three species of callitrichid primates at birth, a time when secondary pneumatization occurs rapidly in humans. The MSs were examined in serially sectioned and stained slides from the heads of two Callithrix jacchus, one Leontopithecus rosalia, and two Saguinus geoffroyi. Specimens were examined microscopically regarding the distribution of osteoclasts and osteoblasts along the osseous boundaries of the MS and other parts of the maxillary bone. Selected sections were immunohistochemically evaluated for the distribution of osteopontin (OPN), which facilitates osteoclast binding. Taken together, OPN immunoreactivity and bone cell distribution suggested trends of bone resorption/deposition that were consistent among species for the superior (roof) and inferior (floor) boundaries of the MS. Expansion at the roof and floor of the MS appeared to correspond to overall vertical midfacial growth in callitrichids. Much more variability was noted for the lateral (alveolar) and medial (nasal walls) of the MS. Unlike the other species, the nasal wall of Saguinus was static and mostly composed of inferior portions of the nasal capsule that were undergoing endochondral ossification. The variation seen in the alveolar walls may relate to the presence or absence of adjacent structures, although it was noted that adjacency of deciduous molars influenced medial drift of the alveolar wall in Saguinus but not Leontopithecus. The results of this study are largely consistent with the "structural" or "architectural" hypothesis of sinus formation with respect to vertical MS enlargement, and the variable cellular/OPN distribution found along the nasal and alveolar walls was evocative of Witmer's (J Vert Paleontol 1997;17:1-73) epithelial hypothesis in revealing that most expansion occurred in regions unopposed by adjacent structures. (c) 2005 Wiley-Liss, Inc.

Identification of Plasmodium spp. in Neotropical primates of Maranhense Amazon in Northeast Brazil.

PubMed

Figueiredo, Mayra Araguaia Pereira; Di Santi, Silvia Maria; Manrique, Wilson Gómez; André, Marcos Rogério; Machado, Rosangela Zacarias

2017-01-01

In the Brazilian Amazon region, malaria caused by Plasmodium malariae is considered to be a zoonosis because of cross-transfer of the parasite between humans and Neotropical primates. To contribute information on this issue, we investigated occurrences of natural infection with Plasmodium sp. among Neotropical primates in the Maranhense Amazon (Amazon region of the state of Maranhão), in the northeastern region of Brazil. Blood samples were collected from 161 Neotropical primates of six species that were caught in an environmental reserve (Sítio Aguahy) and from captive primates (CETAS-Wildlife Screening Center, municipality of São Luís), in Maranhão. Plasmodium sp. was diagnosed based on light microscopy, PCR, qPCR and LAMP for amplification of the 18S rRNA gene. Serum samples were also assayed by means of indirect immunofluorescence for IgG antibodies against P. malariae/P. brasilianum, P. falciparum and P. berghei. Parasites were detected through light microscopy on five slides from captive primates (four Sapajus spp. and one Callithrix jacchus). In the molecular tests, 34.16% (55/161) and 29.81% (48/161) of the animals sampled were positive in the qPCR and PCR assays, respectively. In the PCR, 47/48 animals were positive for P. malariae/P. brasilianum; of these, eight were free-living primates and 39 from CETAS, São Luís. One sample showed a band in the genus-specific reaction, but not in the second PCR reaction. Anti-P. malariae/P. brasilianum IgG antibodies were detected in four serum samples from Sapajus spp. in captivity. In this study, circulation of P. malariae/P. brasilianum in Neotropical primates was confirmed, with low levels of parasitemia and low levels of antibodies. The importance of these animals as reservoirs of human malaria in the region studied is still unknown. This scenario has an impact on control and elimination of malaria in this region.

Cutting costs in response to predatory threat by Geoffroy's marmosets (Callithrix geoffroyi).

PubMed

Caine, N G

1998-01-01

Ideally, prey should respond to their predators efficiently, without over- or underreacting to the threat. This may be particularly important for small-bodied species for whom metabolic demands are high and predatory risk is great. In the current study, two family groups of Callithrix geoffroyi living outside in a rural setting at the Center for Reproduction of Endangered Species, San Diego Wild Animal Park, were observed before, during, and after ten presentations of a great horned owl model. The owl was mounted on a post on a nearby hillside, simulating a situation in which a real but nonimminent threat is posed. As controls, a model of a crow and a cloth bag were also presented, each for ten trials. During the 10 min presentations of the owl, rates of play and foraging decreased, and rates of locomotion and vigilant looking increased from baseline rates. Data on occupation of the best viewing area suggest that the marmosets shared the job of monitoring a potential threat. After the owl was removed, behavior quickly returned to baseline rates, with the exception of looking at the place where the owl had been, and play. Neither the bag nor the crow generated significant differences from the baseline condition that preceded it. Marmosets may reduce the costs of antipredator behavior by appropriately assessing the degree of risk and by quickly resuming important activities once a potential threat has passed.

Serological Evidence of Infection by Leishmania (Leishmania) infantum (Synonym: Leishmania (Leishmania) chagasi) in Free-Ranging Wild Mammals in a Nonendemic Region of the State of São Paulo, Brazil.

PubMed

Paiz, Laís Moraes; Fornazari, Felipe; Menozzi, Benedito Donizete; Oliveira, Gabriela Capriogli; Coiro, Carla Janeiro; Teixeira, Carlos Roberto; da Silva, Valdinei Moraes Campanucci; Donalisio, Maria Rita; Langoni, Helio

2015-11-01

Concerns about the interface between wildlife, domestic animals, and humans in the transmission of visceral leishmaniasis (VL) have been growing due to natural or anthropogenic environmental changes. In this context, investigations of the infection in wild mammals are important to assess their exposure to the vector and the parasite. A study of anti-Leishmania (Leishmania) infantum antibodies was carried out using the direct agglutination test (DAT) on 528 free-ranging wild mammals of 38 species from the region of Botucatu, state of São Paulo, Brazil, a municipality that has no records of the vector or of human or canine autochthony. Antibodies were detected, with a cutoff of 1:320, in 9/528 (1.7%; 95% confidence interval [CI] 0.6-2.8%) mammals of the species Callithrix jacchus, Lepus europaeus, Sphiggurus villosus, Nasua nasua, Eira barbara, and Galictis cuja, with high titers (≥1280) for the last three. These three are little-studied species, and previous records of the detection of anti-Leishmania spp. antibodies in Brazil exist only for coatis (N. nasua), whereas worldwide, infection by L. (L.) infantum has been confirmed only in hares (Le. europaeus). On the other hand, opossums and canids, the species most commonly reported to be naturally infected by L. (L.) infantum, were not seropositive. Fifty-eight (58/528; 10.9%) mammals were found to have antibody titers ranging from 20 to 160 and were not included among the seropositive animals due to the adopted cutoff. However, the possibility of infection in these animals should not be discarded, because there is no standard cutoff point for the different wild species. Our findings indicate the need for investigations into the exact role of the seropositive species in the epidemiology of VL and for effective epidemiological surveillance to prevent its expansion, because even in regions where there are no records of canine or human autochthonous cases, there may be parasite circulation among wild mammals.

Positron emission tomography assessment of 8-OH-DPAT-mediated changes in an index of cerebral glucose metabolism in female marmosets

PubMed Central

Converse, Alexander K.; Aubert, Yves; Farhoud, Mohammed; Weichert, Jamey P.; Rowland, Ian J.; Ingrisano, Nicole M.; Allers, Kelly A.; Sommer, Bernd; Abbott, David H.

2013-01-01

As part of a larger experiment investigating serotonergic regulation of female marmoset sexual behavior, this study was designed to (1) advance methods for PET imaging of common marmoset monkey brain, (2) measure normalized FDG uptake as an index of local cerebral metabolic rates for glucose, and (3) study changes induced in this index of cerebral glucose metabolism by chronic treatment of female marmosets with a serotonin 1A receptor (5-HT1A) agonist. We hypothesized that chronic treatment with the 5-HT1A agonist 8-OH-DPAT would alter the glucose metabolism index in dorsal raphe (DR), medial prefrontal cortex (mPFC), medial preoptic area of hypothalamus (mPOA), ventromedial nucleus of hypothalamus (VMH), and field CA1 of hippocampus. Eight adult ovariectomized female common marmosets (Callithrix jacchus) were studied with and without estradiol replacement. In a crossover design, each subject was treated daily with 8-OH-DPAT (0.1 mg/kg SC daily) or saline. After 42–49 days of treatment, the glucose metabolism radiotracer FDG was administered to each female immediately prior to 30 min of interaction with her male pairmate, after which the subject was anesthetized and imaged by PET. Whole brain normalized PET images were analyzed with anatomically defined regions of interest (ROI). Whole brain voxelwise mapping was also used to explore treatment effects and correlations between alterations in the glucose metabolism index and pairmate interactions. The rank order of normalized FDG uptake was VMH/mPOA>DR>mPFC/CA1 in both conditions. 8-OH-DPAT did not induce alterations in the glucose metabolism index in ROIs. Voxelwise mapping showed a significant reduction in normalized FDG uptake in response to 8-OH-DPAT in a cluster in medial occipital cortex as well as a significant correlation between increased rejection of mount attempts and reduced normalized FDG uptake in an overlapping cluster. In conclusion, PET imaging has been used to measure FDG uptake relative to whole brain in marmoset monkeys. Voxelwise mapping shows that 8-OH-DPAT reduces this index of glucose metabolism in medial occipital cortex, consistent with alterations in female sexual behavior. PMID:22233732

Antibody-enhanced dengue disease generates a marked CNS inflammatory response in the black-tufted marmoset Callithrix penicillata.

PubMed

Vasconcelos, Barbara Cristina Baldez; Vieira, Juliana Almeida; Silva, Geane Oliveira; Fernandes, Taiany Nogueira; Rocha, Luciano Chaves; Viana, André Pereira; Serique, Cássio Diego Sá; Filho, Carlos Santos; Bringel, Raissa Aires Ribeiro; Teixeira, Francisco Fernando Dacier Lobato; Ferreira, Milene Silveira; Casseb, Samir Mansour Moraes; Carvalho, Valéria Lima; de Melo, Karla Fabiane Lopes; de Castro, Paulo Henrique Gomes; Araújo, Sanderson Corrêa; Diniz, José Antonio Picanço; Demachki, Samia; Anaissi, Ana Karyssa Mendes; Sosthenes, Marcia Consentino Kronka; Vasconcelos, Pedro Fernando da Costa; Anthony, Daniel Clive; Diniz, Cristovam Wanderley Picanço; Diniz, Daniel Guerreiro

2016-02-01

Severe dengue disease is often associated with long-term neurological impairments, but it is unclear what mechanisms are associated with neurological sequelae. Previously, we demonstrated antibody-enhanced dengue disease (ADE) dengue in an immunocompetent mouse model with a dengue virus 2 (DENV2) antibody injection followed by DENV3 virus infection. Here we migrated this ADE model to Callithrix penicillata. To mimic human multiple infections of endemic zones where abundant vectors and multiple serotypes co-exist, three animals received weekly subcutaneous injections of DENV3 (genotype III)-infected supernatant of C6/36 cell cultures, followed 24 h later by anti-DENV2 antibody for 12 weeks. There were six control animals, two of which received weekly anti-DENV2 antibodies, and four further animals received no injections. After multiple infections, brain, liver, and spleen samples were collected and tissue was immunolabeled for DENV3 antigens, ionized calcium binding adapter molecule 1, Ki-67, TNFα. There were marked morphological changes in the microglial population of ADE monkeys characterized by more highly ramified microglial processes, higher numbers of trees and larger surface areas. These changes were associated with intense TNFα-positive immunolabeling. It is unclear why ADE should generate such microglial activation given that IgG does not cross the blood-brain barrier, but this study reveals that in ADE dengue therapy targeting the CNS host response is likely to be important. © 2015 Japanese Society of Neuropathology.

Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates.

PubMed

Ghersi, Bruno M; Jia, Hongwei; Aiewsakun, Pakorn; Katzourakis, Aris; Mendoza, Patricia; Bausch, Daniel G; Kasper, Matthew R; Montgomery, Joel M; Switzer, William M

2015-10-29

Although simian foamy viruses (SFV) are the only exogenous retroviruses to infect New World monkeys (NWMs), little is known about their evolutionary history and epidemiology. Previous reports show distinct SFVs among NWMs but were limited to small numbers of captive or wild monkeys from five (Cebus, Saimiri, Ateles, Alouatta, and Callithrix) of the 15 NWM genera. Other studies also used only PCR testing or serological assays with limited validation and may have missed infection in some species. We developed and validated new serological and PCR assays to determine the prevalence of SFV in blood specimens from a large number of captive NWMs in the US (n = 274) and in captive and wild-caught NWMs (n = 236) in Peruvian zoos, rescue centers, and illegal trade markets. Phylogenetic and co-speciation reconciliation analyses of new SFV polymerase (pol) and host mitochondrial cytochrome B sequences, were performed to infer SFV and host co-evolutionary histories. 124/274 (45.2 %) of NWMs captive in the US and 59/157 (37.5 %) of captive and wild-caught NWMs in Peru were SFV WB-positive representing 11 different genera (Alouatta, Aotus, Ateles, Cacajao, Callithrix, Cebus, Lagothrix, Leontopithecus, Pithecia, Saguinus and Saimiri). Seroprevalences were lower at rescue centers (10/53, 18.9 %) compared to zoos (46/97, 47.4 %) and illegal trade markets (3/7, 8/19, 42.9 %) in Peru. Analyses showed that the trees of NWM hosts and SFVs have remarkably similar topologies at the level of species and sub-populations suggestive of co-speciation. Phylogenetic reconciliation confirmed 12 co-speciation events (p < 0.002) which was further supported by obtaining highly similar divergence dates for SFV and host genera and correlated SFV-host branch times. However, four ancient cross-genus transmission events were also inferred for Pitheciinae to Atelidae, Cacajao to ancestral Callithrix or Cebus monkeys, between Callithrix and Cebus monkeys, and Lagothrix to Alouatta. We demonstrate a broad distribution and stable co-speciation history of SFV in NWMs at the species level. Additional studies are necessary to further explore the epidemiology and natural history of SFV infection of NWMs and to determine the zoonotic potential for persons exposed to infected monkeys in captivity and in the wild.

Relationship between body temperature, weight, and hematological parameters of black tufted-ear marmosets (Callithrix penicillata).

PubMed

Pereira, Lucas Cardoso; Barros, Marilia

2016-06-01

Basal thermal values of captive adult black tufted-ear marmosets (Callithrix penicillata) in a thermoneutral environment were measured via different methods, along with body weight and hematological parameters. Body temperatures were recorded with rectal (RC), subcutaneous (SC) microchip transponder and infrared (left and right) tympanic membrane (TM) thermometries. Thermal values were correlated with body mass and some hematological data. Similar RC and SC temperatures were observed, these being significantly higher than the left and right TM values. SC temperature was positively correlated and in close agreement with RC measurements. Although body temperatures were not influenced by gender, capture time, or body weight, they were correlated with hematological parameters. Thus, body temperatures in this species seem to reflect some of the characteristics of the assessments' location, with SC microchip transponders being a less invasive method to assess body temperature in these small-bodied non-human primates. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Hierarchical equivalence of somatosensory areas I and II for tactile processing in the cerebral cortex of the marmoset monkey.

PubMed

Zhang, H Q; Zachariah, M K; Coleman, G T; Rowe, M J

2001-05-01

Responsiveness of the first somatosensory area (SI) of the cerebral cortex was investigated in the marmoset monkey (Callithrix jacchus) in association with cooling-induced, reversible inactivation of the second somatosensory area, SII. The aim was to determine whether SI responsiveness to peripheral tactile stimulation depends on SII and therefore whether SI and SII in the marmoset occupy hierarchically equivalent positions in a parallel organizational scheme for thalamocortical tactile processing as appears to be the case in nonprimate mammals. Inactivation of SII was achieved when the temperature over SII was lowered to < or =12 degrees C, as indicated by abolition of the SII-evoked potentials generated by brief tap stimuli to the hand or foot, and by abolition of tactile responses in single SII neurons located at the margin beneath the block. The effect of SII inactivation on SI-evoked potentials was examined in 16 experiments by simultaneous recording of the SI- and SII-evoked potentials. SI-evoked potentials were never abolished and remained unaffected in 11 cases. In three experiments there was a small reduction in amplitude and inconsistent effects in the remaining two. Responsiveness to controlled tactile stimuli was examined quantitatively in 31 individual SI neurons of different functional classes before, during, and after the inactivation of SII. Tactile responsiveness in individual SI neurons was never abolished by SII inactivation, remaining unchanged in 20 neurons (65%) while undergoing some reduction in the remaining 11 SI neurons (35%). This reduction of tactile responsiveness in one-third of SI neurons is most likely attributable to a removal of a facilitatory influence emanating from SII, based on the observation that background activity of the affected neurons was also reduced. Furthermore, phase locking of SI responses to vibrotactile stimulation was unchanged when SII was inactivated. The retention of responsiveness in SI neurons when SII was inactivated by cooling in the marmoset demonstrates that tactile inputs can reach SI without traversing an indirect, serially organized path through SII. The present results, together with our previous observations that responsiveness in the majority of SII neurons survived SI inactivation, demonstrate that there is a parallel organization of the SI and SII areas for tactile processing in the marmoset monkey and that SI and SII occupy hierarchically equivalent positions in a parallel processing network. There is therefore no longer justification for the view that there are fundamental differences in the organization of thalamocortical tactile processing for SI and SII between simian primates, in general, and other mammals.

Maternal Gestational Androgen Levels in Female Marmosets (Callithrix geoffroyi) Vary Across Trimesters but Do Not Vary With the Sex Ratio of Litters

PubMed Central

French, Jeffrey A.; Smith, Adam S.; Birnie, Andrew K.

2009-01-01

Maternal hormones can dramatically modify offspring phenotypes via organizational actions on morphological and behavioral development. In placental mammals, there is the possibility that some portion of hormones in maternal circulation may be derived from fetal origin. We tested the possibility that maternal androgens in pregnant female marmosets reflected, in part, contributions from male fetuses by comparing levels of urinary androgens across pregnancy in females carrying varying numbers of male offspring. We monitored urinary androgen excretion in 18 pregnancies from five female white-faced marmosets (Callithrix geoffroyi). Androgen levels rose significantly in the first trimester of pregnancy, reached a peak in the middle of the second trimester, and then declined gradually until parturition. At no point in pregnancy were levels of urinary androgens higher in females carrying litters that had 50% or more males than females carrying litters that were less than 50% male. Levels of maternal androgens were not associated with litter size, the number of males in the litter, or with the proportion of the litter that was male. The high levels of androgen in pregnant females are therefore likely of strictly maternal origin, and any modification of fetal growth and development can be considered a ‘maternal effect’. PMID:19646445

Treatment With CRH-1 Antagonist Antalarmin Reduces Behavioral and Endocrine Responses to Social Stressors in Marmosets (Callithrix kuhlii)

PubMed Central

FRENCH, JEFFREY A.; FITE, JEFFREY E.; JENSEN, HEATHER; OPAROWSKI, KATIE; RUKSTALIS, MICHAEL R.; FIX, HOLLY; JONES, BRENDA; MAXWELL, HEATHER; PACER, MOLLY; POWER, MICHAEL L.; SCHULKIN, JAY

2010-01-01

Corticotropin-releasing hormone (CRH) has multiple roles in coordinating the behavioral and endocrine responses to a host of environmental challenges, including social stressors. In the present study we evaluated the role of CRH in mediating responses to a moderate social stressor in Wied’s black tufted-eared marmosets (Callithrix kuhlii). Male and female marmosets (n = 14) were administered antalarmin (a selective CRH-1 receptor antagonist; 50μg/kg, p.o.) or vehicle in a blind, counterbalanced, crossover design. One hr after treatment, marmosets were separated from long-term pairmates and then housed alone in a novel enclosure for 7 hr. Behavior was recorded during separation and upon reunion with the partner, and urine samples for cortisol assay collected before, during, and after the intervention. Separation from partners elevated urinary cortisol concentrations over baseline for both conditions, but antalarmin treatment reduced the magnitude of the elevation. Antalarmin also lowered rates of behavioral patterns associated with arousal (alarm and ‘‘e-e’’ vocalizations, object manipulate/chew), but had no effect on contact calls, locomotory activity or alertness. Although most patterns of social behavior upon reunion with the partner were not affected by antalarmin, antalarmin-treated marmosets displayed more sexual behavior (mounts and copulations) upon reunion. These data indicate that antagonism of the CRH-1 receptor acts to reduce the magnitude of both endocrine and behavioral responses to a moderate social stressor without causing any overall reduction in alertness or general activity. This supports the hypothesis that CRH, acting through its type 1 receptor, is involved in coordinating the responses to anxiety-producing events. These results further suggest that the marmoset is a useful model for exploration of the role of CRH in mediating the behavioral and neuroendocrine responses to psychosocial stressors, particularly in the context of heterosexual social relationships. PMID:17397037

Fatal attack on black-tufted-ear marmosets (Callithrix penicillata) by a Boa constrictor: a simultaneous assault on two juvenile monkeys.

PubMed

Teixeira, Danilo Simonini; dos Santos, Edmilson; Leal, Silvana Gomes; de Jesus, Andrea Karla; Vargas, Waldemir Paixão; Dutra, Irapuan; Barros, Marilia

2016-01-01

Here we report the first witnessed attack on a marmoset by a constrictor snake. The incident occurred mid-morning in a gallery forest within an altered landscape of the Cerrado region of central Brazil and refers to a fatal attack by a Boa constrictor on two juvenile black-tufted-ear marmosets (Callithrix penicillata) simultaneously. The snake captured both individuals at a height of ~ 4 m while a group of eight marmosets traveled through the subcanopy. The actual strike was not seen. After 2 min, the boa fell to the ground with both marmosets in its coils and proceeded to kill one animal at a time through constriction. Two adult marmosets immediately descended to where the snake held its victims on the ground and attacked it. The snake showed no apparent reaction, and after ~ 1-2 min, the adults rejoined the remaining group members that were mobbing and vocalizing from 5 to 6 m above. The group left the scene ~ 7 min after the onset of the attack and was not seen again. The snake loosened its coils 10 min after its initial strike, left the two carcasses on the ground and stayed behind a nearby tree. Thus, we are not sure if the victims were in fact ingested. This report confirms that marmosets are vulnerable to boid snakes and capable of highly organized and cooperative antipredation behavior. It also suggests that snakes pose a greater threat to callitrichids than previously thought.

Separation of somatic and germ cells is required to establish primate spermatogonial cultures.

PubMed

Langenstroth, Daniel; Kossack, Nina; Westernströer, Birgit; Wistuba, Joachim; Behr, Rüdiger; Gromoll, Jörg; Schlatt, Stefan

2014-09-01

Can primate spermatogonial cultures be optimized by application of separation steps and well defined culture conditions? We identified the cell fraction which provides the best source for primate spermatogonia when prolonged culture is desired. Man and marmoset show similar characteristics in regard to germ cell development and function. Several protocols for isolation and culture of human testis-derived germline stem cells have been described. Subsequent analysis revealed doubts on the germline origin of these cells and characterized them as mesenchymal stem cells or fibroblasts. Studies using marmosets as preclinical model confirmed that the published isolation protocols did not lead to propagation of germline cells. Testicular cells derived from nine adult marmoset monkeys (Callithrix jacchus) were cultured for 1, 3, 6 and 11 days and consecutively analyzed for the presence of spermatogonia, differentiating germ cells and testicular somatic cells. Testicular tissue of nine adult marmoset monkeys was enzymatically dissociated and subjected to two different cell culture approaches. In the first approach all cells were kept in the same dish (non-separate culture, n = 5). In the second approach the supernatant cells were transferred into a new dish 24 h after seeding and subsequently supernatant and attached cells were cultured separately (separate culture, n = 4). Real-time quantitative PCR and immunofluorescence were used to analyze the expression of reliable germ cell and somatic markers throughout the culture period. Germ cell transplantation assays and subsequent wholemount analyses were performed to functionally evaluate the colonization of spermatogonial cells. This is the first report revealing an efficient isolation and culture of putative marmoset spermatogonial stem cells with colonization ability. Our results indicate that a separation of spermatogonia from testicular somatic cells is a crucial step during cell preparation. We identified the overgrowth of more rapidly expanding somatic cells to be a major problem when establishing spermatogonial cultures. Initiating germ cell cultures from the supernatant and maintaining germ cells in suspension cultures minimized the somatic cell contamination and provided enriched germ cell fractions which displayed after 11 days of culture a significantly higher expression of germ cell markers genes (DDX-4, MAGE A-4; P < 0.05) compared with separately cultured attached cells. Additionally, germ cell transplantation experiments demonstrated a significantly higher absolute number of cells with colonization ability (P < 0.001) in supernatant cells after 11 days of separate culture. This study presents a relevant aspect for the successful setup of spermatogonial cultures but provides limited data regarding the question of whether the long-term maintenance of spermatogonia can be achieved. Transfer of these preclinical data to man may require modifications of the protocol. Spermatogonial cultures from rodents have become important and innovative tools for basic and applied research in reproductive biology and veterinary medicine. It is expected that spermatogonia-based strategies will be transformed into clinical applications for the treatment of male infertility. Our data in the marmoset monkey may be highly relevant to establish spermatogonial cultures of human testes. Funding was provided by the DFG-Research Unit FOR 1041 Germ Cell Potential (SCHL394/11-2) and by the Graduate Program Cell Dynamics and Disease (CEDAD) together with the International Max Planck Research School - Molecular Biomedicine (IMPRS-MBM). The authors declare that there is no conflict of interest. Not applicable. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Manipulation of the oxytocin system alters social behavior and attraction in pair-bonding primates, Callithrix penicillata

PubMed Central

Smith, Adam S.; Ågmo, Anders; Birnie, Andrew K.; French, Jeffrey A.

2010-01-01

The establishment and maintenance of stable, long-term male-female relationships, or pair bonds, are marked by high levels of mutual attraction, selective preference for the partner, and high rates of sociosexual behavior. Central oxytocin (OT) affects social preference and partner-directed social behavior in rodents, but the role of this neuropeptide has yet to be studied in heterosexual primate relationships. The present study evaluated whether the OT system plays a role in the dynamics of social behavior and partner preference during the first three weeks of cohabitation in male and female marmosets, Callithrix penicillata. OT activity was stimulated by intranasal administration of OT, and inhibited by oral administration of a non-peptide OT-receptor antagonist (L-368,899; Merck). Social behavior throughout the pairing varied as a function of OT treatment. Compared to controls, marmosets initiated huddling with their social partner more often after OT treatments but reduced proximity and huddling after OT antagonist treatments. OT antagonist treatment also eliminated food sharing between partners. During the 24-h preference test, all marmosets interacted more with an opposite-sex stranger than with the partner. By the third-week preference test, marmosets interacted with the partner and stranger equally with the exception that intranasal-OT treatments facilitated initial partner-seeking behavior over initial contact with the stranger. Our findings demonstrate that pharmacological manipulations of OT activity alter partner-directed social behavior during pair interactions, suggesting that central OT may facilitate the process of pair-bond formation and social relationships in marmoset monkeys. PMID:20025881

Production and Perception of Sex Differences in Vocalizations of Wied’s Black-Tufted-Ear Marmosets (Callithrix kuhlii)

PubMed Central

Smith, Adam S.; Birnie, Andrew K.; Lane, Kent R.; French, Jeffrey A.

2010-01-01

Males and females from many species produce distinct acoustic variations of functionally identical call types. Social behavior may be primed by sex-specific variation in acoustic features of calls. We present a series of acoustic analyses and playback experiments as methods for investigating this subject. Acoustic parameters of phee calls produced by Wied’s black-tufted-ear marmosets (Callithrix kuhlii) were analyzed for sex differences. Discriminant function analyses showed that calls contained sufficient acoustic variation to predict the sex of the caller. Several frequency variables differed significantly between the sexes. Natural and synthesized calls were presented to male–female pairs. Calls elicited differential behavioral responses based on the sex of the caller. Marmosets became significantly more vigilant following the playback of male phee calls (both natural and synthetic) than following female phee calls. In a second playback experiment, synthesized calls were modified by independently manipulating three parameters that were known to differ between the sexes (low-, peak-, and end-frequency). When end-frequency-modified calls were presented, responsiveness was differentiable by sex of caller but did not differ from responses to natural calls. This suggests that marmosets did not use end-frequency to determine the sex of the caller. Manipulation of peak-and low-frequency parameters eliminated the discrete behavioral responses to male and female calls. Together, these parameters may be important features that encode for the sex-specific signal. Recognition of sex by acoustic cues seems to be a multivariate process that depends on the congruency of acoustic features. PMID:19090554

Manipulation of the oxytocin system alters social behavior and attraction in pair-bonding primates, Callithrix penicillata.

PubMed

Smith, Adam S; Agmo, Anders; Birnie, Andrew K; French, Jeffrey A

2010-02-01

The establishment and maintenance of stable, long-term male-female relationships, or pair-bonds, are marked by high levels of mutual attraction, selective preference for the partner, and high rates of sociosexual behavior. Central oxytocin (OT) affects social preference and partner-directed social behavior in rodents, but the role of this neuropeptide has yet to be studied in heterosexual primate relationships. The present study evaluated whether the OT system plays a role in the dynamics of social behavior and partner preference during the first 3 weeks of cohabitation in male and female marmosets, Callithrix penicillata. OT activity was stimulated by intranasal administration of OT, and inhibited by oral administration of a non-peptide OT-receptor antagonist (L-368,899; Merck). Social behavior throughout the pairing varied as a function of OT treatment. Compared to controls, marmosets initiated huddling with their social partner more often after OT treatments but reduced proximity and huddling after OT antagonist treatments. OT antagonist treatment also eliminated food sharing between partners. During the 24-h preference test, all marmosets interacted more with an opposite-sex stranger than with the partner. By the third-week preference test, marmosets interacted with the partner and stranger equally with the exception that intranasal-OT treatments facilitated initial partner-seeking behavior over initial contact with the stranger. Our findings demonstrate that pharmacological manipulations of OT activity alter partner-directed social behavior during pair interactions, suggesting that central OT may facilitate the process of pair-bond formation and social relationships in marmoset monkeys. Published by Elsevier Inc.

Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia.

PubMed

Pyritz, Lennart W; Büntge, Anna B S; Herzog, Sebastian K; Kessler, Michael

2010-10-01

Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures.

Quality of maternal and paternal care predicts later stress reactivity in the cooperatively-breeding marmoset (Callithrix geoffroyi).

PubMed

Birnie, Andrew K; Taylor, Jack H; Cavanaugh, Jon; French, Jeffrey A

2013-12-01

Variation in the early postnatal social environment can have lasting effects on hypothalamic-pituitary-adrenal (HPA) axis stress responses. Both rats and macaque monkeys subjected to low quality or abusive maternal care during the early postnatal period have more pronounced HPA responses to environmental stressors throughout development and into adulthood compared to animals reared in higher quality early maternal environments. However, little is known about the relative contributions to HPA stress response styles in developing offspring in species in which offspring care is routinely provided by group members other than the mother, such as in cooperatively breeding mammals. Marmoset monkeys exhibit cooperative offspring rearing, with fathers and older siblings providing care in addition to that provided by the mother. We evaluated the effects of early maternal, paternal, and older sibling care on HPA responses to social separation across development in captive white-faced marmoset offspring (Callithrix geoffroyi). We monitored offspring care by mothers, fathers, and older siblings in marmosets for the first 60 days of life. Later in development, each marmoset experienced three standardized social separation/novelty exposure stressors at 6, 12, and 18 months of age. During separation, we collected urine samples and analyzed them via enzyme immunoassay for cortisol levels. Infants that received higher rates of rejections from the entire family group showed higher cortisol responses to social separation. This relationship was found when mothers, fathers, and older siblings, were analyzed separately as well. No differences in cortisol responses were found between offspring that received high and low rates of carrying or high and low rates of licking and grooming by any group member. In the cooperatively breeding marmoset, early social cues from multiple classes of caregivers may influence HPA stress responses throughout the lifespan. Published by Elsevier Ltd.

Quality of Maternal and Paternal Care Predicts Later Stress Reactivity in the Cooperatively-Breeding Marmoset (Callithrix geoffroyi)

PubMed Central

Birnie, Andrew K.; Taylor, Jack H.; Cavanaugh, Jon; French, Jeffrey A.

2013-01-01

Variation in the early postnatal social environment can have lasting effects on hypothalamic-pituitary-adrenal (HPA) axis stress responses. Both rats and macaque monkeys subjected to low quality or abusive maternal care during the early postnatal period have more pronounced HPA responses to environmental stressors throughout development and into adulthood compared to animals reared in higher quality early maternal environments. However, little is known about the relative contributions to HPA stress response styles in developing offspring in species in which offspring care is routinely provided by group members other than the mother, such as in cooperatively breeding mammals. Marmoset monkeys exhibit cooperative offspring rearing, with fathers and older siblings providing care in addition to that provided by the mother. We evaluated the effects of early maternal, paternal, and older sibling care on HPA responses to social separation across development in captive white-faced marmoset offspring (Callithrix geoffroyi). We monitored offspring care by mothers, fathers, and older siblings in marmosets for the first 60 days of life. Later in development, each marmoset experienced three standardized social separation/novelty exposure stressors at 6, 12, and 18 months of age. During separation, we collected urine samples and analyzed them via enzyme immunoassay for cortisol levels. Infants that received higher rates of rejections from the entire family group showed higher cortisol responses to social separation. This relationship was found when mothers, fathers, and older siblings, were analyzed separately as well. No differences in cortisol responses were found between offspring that received high and low rates of carrying or high and low rates of licking and grooming by any group member. In the cooperatively breeding marmoset, early social cues from multiple classes of caregivers may influence HPA stress responses throughout the lifespan. PMID:24099861

Patch Size, Functional Isolation, Visibility and Matrix Permeability Influences Neotropical Primate Occurrence within Highly Fragmented Landscapes

PubMed Central

da Silva, Lucas Goulart; Ribeiro, Milton Cezar; Hasui, Érica; da Costa, Carla Aparecida; da Cunha, Rogério Grassetto Teixeira

2015-01-01

Forest fragmentation and habitat loss are among the major current extinction causes. Remaining fragments are mostly small, isolated and showing poor quality. Being primarily arboreal, Neotropical primates are generally sensitive to fragmentation effects. Furthermore, primates are involved in complex ecological process. Thus, landscape changes that negatively interfere with primate population dynamic affect the structure, composition, and ultimately the viability of the whole community. We evaluated if fragment size, isolation and visibility and matrix permeability are important for explaining the occurrence of three Neotropical primate species. Employing playback, we verified the presence of Callicebus nigrifrons, Callithrix aurita and Sapajus nigritus at 45 forest fragments around the municipality of Alfenas, Brazil. We classified the landscape and evaluated the metrics through predictive models of occurrence. We selected the best models through Akaike Selection Criterion. Aiming at validating our results, we applied the plausible models to another region (20 fragments at the neighboring municipality of Poço Fundo, Brazil). Twelve models were plausible, and three were validated, two for Sapajus nigritus (Area and Area+Visibility) and one for Callicebus nigrifrons (Area+Matrix). Our results reinforce the contribution of fragment size to maintain biodiversity within highly degraded habitats. At the same time, they stress the importance of including novel, biologically relevant metrics in landscape studies, such as visibility and matrix permeability, which can provide invaluable help for similar studies in the future and on conservation practices in the long run. PMID:25658108

Seasonality of the activity pattern of Callithrix penicillata (Primates, Callitrichidae) in the cerrado (scrub savanna vegetation).

PubMed

Vilela, S L; de Faria, D S

2004-05-01

Two wild groups of Callithrix penicillata, the Black Pincelled Marmoset, were observed from January to September 1998, in two areas, one an area of dense scrub savanna vegetation (cerrado) and the other, a semidecidual woodland (cerradão), both within the boundaries of the Ecological Reserve of IBGE (Brazilian Institute of Geography and Statistics), in an environmentally protected area, the APA (Portuguese abbreviation for "environmental protected area") Gama/Cabeça-de-Veado, Brasília, DF. The behavioral data collected during the rainy (January 15 to April 15) and dry season (June 1 to September 15) were compared. Because of the proximity to the Reserve facilities, the group from the dense scrub savanna vegetation (CD) was submitted to antropic impacts different from the group in the semidecidual woodland (CE), which was using as territory an area that had been suffering from man-made fires every two years as part of a long-term experimental project on fire impacts. The behavioral data was quantified by instantaneous cross-section ("scan sampling") every ten minutes with records of locomotion, rest, foraging for insects, use of exudate, and feeding. During the whole year, the greatest percentage of time spent by CE and CD was in foraging for insects, with 44% and 39%, respectively. It was evident when comparing the data for the two seasons that, for both groups, foraging for insects was more intense during the dry season, possibly to complement the shortage of food, and locomotion increased during the rainy season. The greater the availability and distribution of fruit in the areas, the greater the locomotion of the groups to obtain these resources. None of the other behavioral patterns, including the use of exudates, presented significant differences between the two seasons. Both groups foraged more frequently during the dry season and locomoted more during the rainy one.

Immediate, but no delayed, behavioral response to a snake model by captive black tufted-ear marmosets.

PubMed

Cagni, Priscila; Sampaio, Ana Cristhina; Ribeiro, Natália B; Barros, Marilia

2011-07-01

Whether callitrichids are naturally capable of detecting and responding to predators - or if such skills are learned - remains a controversial issue, with results differing in terms of species, predator and encounter conditions. Therefore, the behavioral response of naïve adult captive black tufted-ear marmosets (Callithrix penicillata) was assessed before, during, 0 and 4 h after a 5-min encounter with a snake and flower model. Using a two-phase cross-over design, marmosets (n = 16) were submitted to one trial for each stimulus, divided into four 5-min intervals: pre-exposure, exposure and post-exposure observations held 0 and 4h later. The snake exposure increased the number of gazes made towards the stimulus and the time cage-mates spent close to each other, as well as induced tsik-tsik alarm/mobbing calls, while inhibiting foraging and decreasing the time spent near the snake's location. After the snake was removed, all changes were immediately reversed. Mobbing was not observed. The flower stimulus only increased direct gazes and time spent in proximity during its presentation. All marmosets were captive-born and snake-naïve yet had recently been confronted with a cat stimulus in a previous experiment. Thus, previous experiences with snakes may be required for marmosets to fully develop appropriate immediate and long-term responses. Copyright © 2011 Elsevier B.V. All rights reserved.

Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting

PubMed Central

Dumas, Francesca; Stanyon, Roscoe; Sineo, Luca; Stone, Gary; Bigoni, Francesca

2007-01-01

Background The taxonomic and phylogenetic relationships of New World monkeys (Platyrrhini) are difficult to distinguish on the basis of morphology and because diagnostic fossils are rare. Recently, molecular data have led to a radical revision of the traditional taxonomy and phylogeny of these primates. Here we examine new hypotheses of platyrrhine evolutionary relationships by reciprocal chromosome painting after chromosome flow sorting of species belonging to four genera of platyrrhines included in the Cebidae family: Callithrix argentata (silvered-marmoset), Cebuella pygmaea (pygmy marmoset), Callimico goeldii (Goeldi's marmoset) and Saimiri sciureus (squirrel monkey). This is the first report of reciprocal painting in marmosets. Results The paints made from chromosome flow sorting of the four platyrrhine monkeys provided from 42 to 45 hybridization signals on human metaphases. The reciprocal painting of monkey probes on human chromosomes revealed that 21 breakpoints are common to all four studied species. There are only three additional breakpoints. A breakpoint on human chromosome 13 was found in Callithrix argentata, Cebuella pygmaea and Callimico goeldii, but not in Saimiri sciureus. There are two additional breakpoints on human chromosome 5: one is specific to squirrel monkeys, and the other to Goeldi's marmoset. Conclusion The reciprocal painting results support the molecular genomic assemblage of Cebidae. We demonstrated that the five chromosome associations previously hypothesized to phylogenetically link tamarins and marmosets are homologous and represent derived chromosome rearrangements. Four of these derived homologous associations tightly nest Callimico goeldii with marmosets. One derived association 2/15 may place squirrel monkeys within the Cebidae assemblage. An apparently common breakpoint on chromosome 5q33 found in both Saimiri and Aotus nancymae could be evidence of a phylogenetic link between these species. Comparison with previous reports shows that many syntenic associations found in platyrrhines have the same breakpoints and are homologous, derived rearrangements showing that the New World monkeys are a closely related group of species. Our data support the hypothesis that the ancestral karyotype of the Platyrrhini has a diploid number of 2n = 54 and is almost identical to that found today in capuchin monkeys; congruent with a basal position of the Cebidae among platyrrhine families. PMID:17767727

Can roads be used as transects for primate population surveys?.

PubMed

Hilário, Renato R; Rodrigues, Flávio H G; Chiarello, Adriano G; Mourthé, Italo

2012-01-01

Line transect distance sampling (LTDS) can be applied to either trails or roads. However, it is likely that sampling along roads might result in biased density estimates. In this paper, we compared the results obtained with LTDS applied on trails and roads for two primate species (Callithrix penicillata and Callicebus nigrifrons) to clarify whether roads are appropriate transects to estimate densities. We performed standard LTDS surveys in two nature reserves in south-eastern Brazil. Effective strip width and population density were different between trails and roads for C. penicillata, but not for C. nigrifrons. The results suggest that roads are not appropriate for use as transects in primate surveys, at least for some species. Further work is required to fully understand this issue, but in the meantime we recommend that researchers avoid using roads as transects or treat roads and trails as covariates when sampling on roads is unavoidable. Copyright © 2012 S. Karger AG, Basel.

THE SUSCEPTIBILITY OF MARMOSETS TO YELLOW FEVER VIRUS

PubMed Central

Davis, Nelson C.

1930-01-01

1. It has been possible to introduce yellow fever virus into the small Brazilian monkeys, Callithrix albicollis and Leontocebus ursulus, by the bites of infected mosquitoes and to carry the virus through a series of four passages in each species and back to rhesus monkeys by the bites of Stegomyia mosquitoes fed on the last marmoset of each series. 2. Five specimens of L. ursulus were used. Four developed fever, and all died during the experiments. At least two showed liver necroses comparable to those found in human beings and rhesus monkeys that died of yellow fever. 3. Twenty specimens of C. albicollis were used. Very few showed a temperature reaction following the introduction of virus. Of those that died, none had lesions typical of yellow fever as seen in certain other species of monkeys and in humans. 4. The convalescent serum from each of five C. albicollis protected a rhesus monkey against yellow fever virus, but the serum from a normal marmoset of the same species was found to be non-protective. PMID:19869773

Morphological, ultrastructural, and molecular characterization of intestinal tetratrichomonads isolated from non-human primates in southeastern Brazil.

PubMed

Dos Santos, Caroline Spitz; de Jesus, Vera Lúcia Teixeira; McIntosh, Douglas; Carreiro, Caroline Cunha; Batista, Lilian Cristina Oliveira; do Bomfim Lopes, Bruno; Neves, Daniel Marchesi; Lopes, Carlos Wilson Gomes

2017-09-01

Non-human primates are our closest relatives and represent an interesting model for comparative parasitological studies. However, research on this topic particularly in relation to intestinal parasites has been fragmentary and limited mainly to animals held in captivity. Thus, our knowledge of host-parasite relationships in this species-rich group of mammals could be considered rudimentary. The current study combined morphological, ultrastructural, and molecular analyses to characterize isolates of intestinal tetratrichomonads recovered from the feces of three species of South American, non-human primates. Fecal samples were collected from 16 animals, representing 12 distinct species. Parabasalid-like organisms were evident in five samples (31%) of feces: two from Alouatta sara, two from Callithrix penicillata, and one from Sapajus apella. The five samples presented morphologies consistent with the description of Tetratrichomonas sp., with four anterior flagella of unequal length, a well-developed undulating membrane, and a long recurrent flagellum. Sequencing of the ITS1-5.8S rRNA-ITS2 region demonstrated that the isolates from A. sara, and C. penicillata were closely related and highly similar to isolates of Tetratrichomonas brumpti, recovered previously from tortoises (Geochelone sp.). The flagellate recovered from S. apella demonstrated a similar morphology to those of the other isolates, however, sequence analysis showed it to be identical to an isolate of Tetratrichomonas sp. recovered from white-lipped peccaries (Tayassu pecari). The findings of this study extend and enhance our knowledge of parasitism of non-human primates by members of the genus Tetratrichomonas and indicate that the host range of these parasites is broader than previously believed.

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata

PubMed Central

Diniz, Daniel G.; Silva, Geane O.; Naves, Thaís B.; Fernandes, Taiany N.; Araújo, Sanderson C.; Diniz, José A. P.; de Farias, Luis H. S.; Sosthenes, Marcia C. K.; Diniz, Cristovam G.; Anthony, Daniel C.; da Costa Vasconcelos, Pedro F.; Picanço Diniz, Cristovam W.

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous. PMID:27047345

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata.

PubMed

Diniz, Daniel G; Silva, Geane O; Naves, Thaís B; Fernandes, Taiany N; Araújo, Sanderson C; Diniz, José A P; de Farias, Luis H S; Sosthenes, Marcia C K; Diniz, Cristovam G; Anthony, Daniel C; da Costa Vasconcelos, Pedro F; Picanço Diniz, Cristovam W

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous.

Synteny of human chromosomes 14 and 15 in the platyrrhines (Primates, Platyrrhini)

PubMed Central

2009-01-01

In order to study the intra- and interspecific variability of the 14/15 association in Platyrrhini, we analyzed 15 species from 13 genera, including species that had not been described yet. The DNA libraries of human chromosomes 14 and 15 were hybridized to metaphases of Alouatta guariba clamitans, A. caraya, A. sara, Ateles paniscus chamek, Lagothrix lagothricha, Brachyteles arachnoides, Saguinus midas midas, Leontopithecus chrysomelas, Callimico goeldii, Callithrix sp., Cebus apella, Aotus nigriceps, Cacajao melanocephalus,Chiropotes satanas and Callicebus caligatus. The 14/15 hybridization pattern was present in 13 species, but not in Alouatta sara that showed a 14/15/14 pattern and Aotus nigriceps that showed a 15/14/15/14 pattern. In the majority of the species, the HSA 14 homologue retained synteny for the entire chromosome, whereas the HSA 15 homologue displayed fragmented segments. Within primates, the New World monkeys represent the taxon with the highest variability in chromosome number (2n = 16 to 62). The presence of the HSA 14/15 association in all species and subspecies studied herein confirms that this association is the ancestral condition for platyrrhines and that this association has been retained in most platyrrhines, despite the occurrence of extensive inter- and intrachromosomal rearrangements in this infraorder of Primates. PMID:21637455

Pelage Variation and Distribution of the Black Lion Tamarin, Leontopithecus chrysopygus.

PubMed

Garbino, Guilherme Siniciato Terra; Rezende, Gabriela Cabral; Valladares-Padua, Claudio

2016-01-01

The black lion tamarin, Leontopithecus chrysopygus, is endemic to the Atlantic Forest of the interior of the state of São Paulo in Brazil. Since the discovery of the species, authors have described variations in the pelage of L. chrysopygus, but the nature of this variation has remained unknown. We examined museum specimens and living animals to see if the pelage of L. chrysopygus varies individually, geographically or ontogenetically. We reviewed all known locality records of the species, and concluded that the pelage of L. chrysopygus varies individually and ontogenetically, but not geographically. The extent of the golden chromogenetic fields is larger in younger individuals, and the pelage becomes darker after successive moults. We examined 2 juveniles that presented a pelage similar to adult L. caissara. Geographically, there is a clear break in the phenotypes attributed to L. caissara and L. chrysopygus, precluding clinal variation and corroborating the specific status of the former. The separation between these 2 species is coincident with a tectonic fault known as the 'Guapiara lineament', and may have been caused by a recent activation of this geological formation. We also suggest a historical contact zone between L. chrysopygus and the marmoset Callithrix aurita in the upper Rio Tietê region. © 2016 S. Karger AG, Basel.

Synteny of human chromosomes 14 and 15 in the platyrrhines (Primates, Platyrrhini).

PubMed

Gifalli-Iughetti, Cristiani; Koiffmann, Célia P

2009-10-01

In order to study the intra- and interspecific variability of the 14/15 association in Platyrrhini, we analyzed 15 species from 13 genera, including species that had not been described yet. The DNA libraries of human chromosomes 14 and 15 were hybridized to metaphases of Alouatta guariba clamitans, A. caraya, A. sara, Ateles paniscus chamek, Lagothrix lagothricha, Brachyteles arachnoides, Saguinus midas midas, Leontopithecus chrysomelas, Callimico goeldii, Callithrix sp., Cebus apella, Aotus nigriceps, Cacajao melanocephalus,Chiropotes satanas and Callicebus caligatus. The 14/15 hybridization pattern was present in 13 species, but not in Alouatta sara that showed a 14/15/14 pattern and Aotus nigriceps that showed a 15/14/15/14 pattern. In the majority of the species, the HSA 14 homologue retained synteny for the entire chromosome, whereas the HSA 15 homologue displayed fragmented segments. Within primates, the New World monkeys represent the taxon with the highest variability in chromosome number (2n = 16 to 62). The presence of the HSA 14/15 association in all species and subspecies studied herein confirms that this association is the ancestral condition for platyrrhines and that this association has been retained in most platyrrhines, despite the occurrence of extensive inter- and intrachromosomal rearrangements in this infraorder of Primates.

Pattern of maternal circulating CRH in laboratory-housed squirrel and owl monkeys

PubMed Central

Power, ML; Williams, LE; Gibson, SV; Schulkin, J; Helfers, J; Zorrilla, EP

2010-01-01

The anthropoid primate placenta appears to be unique in producing corticotropin-releasing hormone (CRH). Placental CRH is involved in an endocrine circuit key to the production of estrogens during pregnancy. CRH induces cortisol production by the maternal and fetal adrenal glands, leading to further placental CRH production. CRH also stimulates the fetal adrenal glands to produce dehydroepiandrostendione sulfate (DHEAS) which the placenta converts into estrogens. There are at least two patterns of maternal circulating CRH across gestation among anthropoids. Monkeys examined to date (Papio and Callithrix) have an early-to-mid gestational peak of circulating CRH, followed by a steady decline to a plateau level, with a possible rise near parturition. In contrast, humans and great apes have an exponential rise in circulating CRH peaking at parturition. To further document and compare patterns of maternal circulating CRH in anthropoid primates, we collected monthly blood samples on 14 squirrel monkeys (Saimiri boliviensis) and 10 owl monkeys (Aotus nancymaae) during pregnancy. CRH immunoreactivity was measured from extracted plasma by solid-phase RIA. Both squirrel and owl monkeys displayed a mid-gestational peak in circulating CRH: days 45–65 of the 152-day gestation for squirrel monkeys (mean±SEM CRH = 2694±276 pg/ml) and days 60–80 of the 133-day gestation for owl monkeys (9871±974 pg/ml). In squirrel monkeys, circulating CRH declined to 36% of mean peak value by two weeks before parturition and then appeared to increase; the best model for circulating CRH over gestation in squirrel monkeys was a cubic function, similar to previous results for baboons and marmosets. In owl monkeys, circulating CRH appeared to plateau with no subsequent significant decline approaching parturition, although a cubic function was the best fit. This study provides additional evidence for a mid-gestational peak of maternal circulating CRH in ancestral anthropoids that has been lost in the hominoid lineage. PMID:20872786

Conservation value of a native forest fragment in a region of extensive agriculture.

PubMed

Chiarello

2000-05-01

A survey of mammals and birds was carried out in a semi-deciduous forest fragment of 150 ha located in a zone of intensive agriculture in Ribeirão Preto, State of São Paulo, south-eastern Brazil. Line transect sampling was used to census mammals and birds during six days, totalling 27.8 km of trails and 27.8 hours of observation. Twenty mammal species were confirmed in the area (except bats and small mammals), including rare or endangered species, such as the mountain lion (Puma concolor), the maned wolf (Chrysocyon brachyurus), and the ocelot (Leopardus pardalis). The brown capuchin monkey (Cebus apella) and the black-tufted-ear marmoset (Callithrix penicillata) were found frequently, suggesting high population density in the fragment. Regarding the avifauna, 49 bird species were recorded, most of them typical of open areas or forest edges. Some confirmed species, however, are becoming increasingly rare in the region, as for example the muscovy duck (Cairina moschata) and the toco toucan (Ramphastos toco). The results demonstrate that forest fragment of this size are refuges for native fauna in a region dominated almost exclusively by sugar-cane plantations. Besides faunal aspects, the conservation of these fragments is of great importance for the establishment of studies related to species preservation in the long term, including reintroduction and translocation projects, as well as studies related to genetic health of isolated populations.

Comparative microcomputed tomography and histological study of maxillary pneumatization in four species of new world monkeys: the perinatal period.

PubMed

Smith, Timothy D; Rossie, James B; Cooper, Gregory M; Schmieg, Robin M; Bonar, Christopher J; Mooney, Mark P; Siegel, Michael I

2011-03-01

In anthropoid primates, it has been hypothesized that the magnitude of maxillary sinus growth is influenced by adjacent dental and soft tissue matrices. Relatively, little comparative evidence exists for the perinatal period when secondary pneumatization is at its earliest stages in some primates. Here, dental and midfacial variables were studied in a perinatal sample of four anthropoid primates, including three callitrichines (Leontopithecus, Saguinus, and Callithrix) and Saimiri boliviensis. In the latter species, the maxillary recess (the ontogenetic precursor to a "true" maxillary sinus) does not undergo secondary pneumatization. Using histological methods and micro-computed tomography, midfacial and dental dimensions and radiographic hydroxyapatite density of tooth cusps were measured. The distribution of osteoclasts and osteoblasts was also documented. Kruskal-Wallis's one-way analysis of variance tests indicates significant (P < 0.05) differences among groups for dental and midfacial measurements. In particular, the posterior maxillary dentition is relatively larger and more mineralized in Saimiri compared to the callitrichines. At posterior dental levels, Saimiri has the lowest palatonasal index [interdental (palatal) width/width of the nasal cavity] and highest bizygomatic-interorbital index. Distribution of osteoclasts indicates that the inferomedial surfaces of the orbits are resorptive in perinatal Saimiri, whereas, in all callitrichines, these surfaces are depository. Taken together, these findings suggest that pneumatization in Saimiri is suppressed by an inward growth trajectory of the orbits, relatively large posterior dentition, and a correspondingly compressed nasal region. Copyright © 2010 Wiley-Liss, Inc.

Nitric oxide fails to confer endogenous antiarrhythmic cardioprotection in the primate heart in vitro.

PubMed

Pabla, R; Curtis, M J

2007-04-01

The role of nitric oxide (NO) in cardiac pathophysiology remains controversial. According to data from several studies using rat and rabbit isolated hearts, NO is an endogenous cardioprotectant against reperfusion-induced ventricular fibrillation (VF). Thus, if cardiac NO production is abolished by perfusion with L-N(G)-nitro-L-arginine methylester (L-NAME) (100 microM) there is a concomittant increase in the incidence of reperfusion-induced VF, with L-NAME's effects on NO and VF prevented by L- (but not D-) arginine co-perfusion. To make a better estimate of the clinical relevance of these findings, 100 microM L-NAME was tested in primate hearts under similar conditions. Marmoset (Callithrix jaccus) hearts, isolated and perfused, were subjected to 60 min left regional ischaemia followed by 10 min reperfusion in vitro. The ECG was recorded and NO in coronary effluent measured by chemiluminescence. L-NAME (100 micro M) decreased NO in coronary effluent throughout ischaemia and reperfusion (e.g. from 3720+/-777 pmol min(-1) g(-1) in controls to 699+/-98 pmol min(-1) g(-1) after 5 min of ischaemia) and, during ischaemia, lowered coronary flow and reduced heart rate, actions identical to those seen in rat and rabbit hearts. However, the incidence of reperfusion-induced VF was unchanged (20%, with or without L-NAME). A species difference exists in the effectiveness of endogenous NO to protect hearts against reperfusion-induced VF. The present primate data, which presumably take precedence over rat and rabbit data, cast doubt on the clinical relevance of NO as an endogenous, antiarrhythmic, cardioprotectant.

Maternal gestational androgens are associated with decreased juvenile play in white-faced marmosets (Callithrix geoffroyi)

PubMed Central

Birnie, Andrew K.; Hendricks, Shelton E.; Smith, Adam S.; Milam, Ross; French, Jeffrey A.

2013-01-01

Exposure to androgens during prenatal development shapes both physiological and behavioral developmental trajectories. Notably, in rhesus macaques, prenatal androgen exposure has been shown to increase rough-and-tumble play, a prominent behavioral feature in males during the juvenile period in primates. While macaques are an Old World, polygamous species with marked sexually dimorphic behavior, New World callitrichine primates (marmosets and tamarins) live in cooperative breeding groups and are considered to be socially monogamous and exhibit minimal sexual dimorphism in social play, which suggests that androgen may affect this species in different ways compared to macaques. In addition, we previously described considerable variation in maternal androgen production during gestation in marmosets. Here we tested the association between this variation and variation in offspring rough-and-tumble play patterns in both males and females. We measured testosterone and androstenedione levels in urine samples collected from pregnant marmoset mothers and then observed their offspring's play behavior as juveniles (5–10 months of age). In contrast to findings in rhesus macaques, hierarchical regression analyses showed that higher gestational testosterone levels, primarily in the second semester, were associated with decreased rough-and-tumble play in juveniles, and this relationship appears to be driven more so by males than females. We found no reliable associations between gestational androstenedione and juvenile play behavior. Our findings provide evidence to suggest that normative variation in levels of maternal androgen during gestation may influence developmental behavioral trajectories in marmosets in a way that contradicts previous findings in Old World primates. PMID:22705955

Do marmosets care to share? Oxytocin treatment reduces prosocial behavior toward strangers.

PubMed

Mustoe, Aaryn C; Cavanaugh, Jon; Harnisch, April M; Thompson, Breanna E; French, Jeffrey A

2015-05-01

Cooperatively-breeding and socially-monogamous primates, like marmosets and humans, exhibit high levels of social tolerance and prosociality toward others. Oxytocin (OXT) generally facilitates prosocial behavior, but there is growing recognition that OXT modulation of prosocial behavior is shaped by the context of social interactions and by other motivational states such as arousal or anxiety. To determine whether prosociality varies based on social context, we evaluated whether marmoset donors (Callithrix penicillata) preferentially rewarded pairmates versus opposite-sex strangers in a prosocial food-sharing task. To examine potential links among OXT, stress systems, and prosociality, we evaluated whether pretrial cortisol levels in marmosets altered the impact of OXT on prosocial responses. Marmosets exhibited spontaneous prosociality toward others, but they did so preferentially toward strangers compared to their pairmates. When donor marmosets were treated with marmoset-specific Pro(8)-OXT, they exhibited reduced prosociality toward strangers compared to marmosets treated with saline or consensus-mammalian Leu(8)-OXT. When pretrial cortisol levels were lower, marmosets exhibited higher prosociality toward strangers. These findings demonstrate that while marmosets show spontaneous prosocial responses toward others, they do so preferentially toward opposite-sex strangers. Cooperative breeding may be associated with the expression of prosociality, but the existence of a pair-bond between marmoset partners appears to be neither necessary nor sufficient for the expression of spontaneous prosocial responses. Furthermore, high prosociality toward strangers is significantly reduced in marmosets treated with Pro(8)-OXT, suggesting that OXT does not universally enhance prosociality, but, rather OXT modulation of prosocial behavior varies depending on social context. Copyright © 2015 Elsevier Inc. All rights reserved.

Do marmosets care to share? Oxytocin treatment reduces prosocial behavior toward strangers

PubMed Central

Mustoe, Aaryn C.; Cavanaugh, Jon; Harnisch, April M.; Thompson, Breanna E.; French, Jeffrey A.

2015-01-01

Cooperatively-breeding and socially-monogamous primates, like marmosets and humans, exhibit high levels of social tolerance and prosociality toward others. Oxytocin (OXT) generally facilitates prosocial behavior, but there is growing recognition that OXT modulation of prosocial behavior is shaped by the context of social interactions and by other motivational states such as arousal or anxiety. To determine whether prosociality varies based on social context, we evaluated whether marmoset donors (Callithrix penicillata) preferentially rewarded pairmates versus opposite-sex strangers in a prosocial food-sharing task. To examine potential links among OXT, stress systems, and prosociality, we evaluated whether pretrial cortisol levels in marmosets altered the impact of OXT on prosocial responses. Marmosets exhibited spontaneous prosociality toward others, but they did so preferentially toward strangers compared to their pairmates. When donor marmosets were treated with marmoset-specific Pro8-OXT, they exhibited reduced prosociality toward strangers compared to marmosets treated with saline or consensus-mammalian Leu8-OXT. When pretrial cortisol levels were lower, marmosets exhibited higher prosociality toward strangers. These findings demonstrate that while marmosets show spontaneous prosocial responses toward others, they do so preferentially toward opposite-sex strangers. Cooperative breeding may be associated with the expression of prosociality, but the existence of a pair-bond between marmoset partners appears to be neither necessary nor sufficient for the expression of spontaneous prosocial responses. Further, high prosociality toward strangers is significantly reduced in marmosets treated with Pro8-OXT, suggesting that OXT does not universally enhance prosociality, but, rather OXT modulation of prosocial behavior varies depending on social context. PMID:25934057

Flibanserin stimulated partner grooming reflects brain metabolism changes in female marmosets

PubMed Central

Converse, Alexander K.; Aubert, Yves; Allers, Kelly A.; Sommer, Bernd; Abbott, David H.

2017-01-01

Introduction Female Sexual Interest and Arousal Disorder (FSIAD) is personally distressing for women. To better understand the mechanism of the candidate therapeutic, flibanserin, we determined its effects on an index of brain glucose metabolism. Aim We hypothesized that chronic treatment with flibanserin would alter metabolism in brain regions associated with serotonergic function and female sexual behavior. Methods In a crossover design, eight adult female common marmosets (Calithrix jacchus) received daily flibanserin or vehicle. After 7–12 weeks of treatment, the glucose metabolism radiotracer FDG was administered to each female immediately prior to 30 min of interaction with her male pairmate, after which females were anesthetized and imaged by PET. Whole-brain normalized images were analyzed with anatomically defined regions of interest. Whole brain voxelwise mapping was used to explore treatment effects. Correlations were examined between alterations in metabolism and pairmate social grooming. Main Outcome Measures Changes in metabolism associated with flibanserin were determined for dorsal raphe (DR), medial prefrontal cortex (mPFC), medial preoptic area of hypothalamus (mPOA), ventromedial nucleus of hypothalamus (VMH), and field CA1 of hippocampus. Results In response to chronic flibanserin, metabolism in mPOA declined, and this reduction correlated with increases in pairmate grooming. A cluster of voxels in frontal cortico-limbic regions exhibited reduced metabolism in response to flibanserin and overlapped with a voxel cluster in which reductions in metabolism correlated with increases in pairmate grooming. Finally, reductions in mPOA metabolism correlated with increases in metabolism in a cluster of voxels in somatosensory cortex. Conclusions Taken together, these results suggest that flibanserin-induced reductions in female mPOA neural activity increase intimate affiliative behavior with male pairmates. PMID:26635207

Different responses to reward comparisons by three primate species.

PubMed

Freeman, Hani D; Sullivan, Jennifer; Hopper, Lydia M; Talbot, Catherine F; Holmes, Andrea N; Schultz-Darken, Nancy; Williams, Lawrence E; Brosnan, Sarah F

2013-01-01

Recently, much attention has been paid to the role of cooperative breeding in the evolution of behavior. In many measures, cooperative breeders are more prosocial than non-cooperatively breeding species, including being more likely to actively share food. This is hypothesized to be due to selective pressures specific to the interdependency characteristic of cooperatively breeding species. Given the high costs of finding a new mate, it has been proposed that cooperative breeders, unlike primates that cooperate in other contexts, should not respond negatively to unequal outcomes between themselves and their partner. However, in this context such pressures may extend beyond cooperative breeders to other species with pair-bonding and bi-parental care. Here we test the response of two New World primate species with different parental strategies to unequal outcomes in both individual and social contrast conditions. One species tested was a cooperative breeder (Callithrix spp.) and the second practiced bi-parental care (Aotus spp.). Additionally, to verify our procedure, we tested a third confamilial species that shows no such interdependence but does respond to individual (but not social) contrast (Saimiri spp.). We tested all three genera using an established inequity paradigm in which individuals in a pair took turns to gain rewards that sometimes differed from those of their partners. None of the three species tested responded negatively to inequitable outcomes in this experimental context. Importantly, the Saimiri spp responded to individual contrast, as in earlier studies, validating our procedure. When these data are considered in relation to previous studies investigating responses to inequity in primates, they indicate that one aspect of cooperative breeding, pair-bonding or bi-parental care, may influence the evolution of these behaviors. These results emphasize the need to study a variety of species to gain insight in to how decision-making may vary across social structures.

The systematics and evolution of New World primates - A review.

PubMed

Schneider, Horacio; Sampaio, Iracilda

2015-01-01

This paper provides an overview of the taxonomy of New World primates from proposals of the 1980's based on morphology to the great number of studies based on molecular data aiming for the elucidation of the phylogeny of New World monkeys. The innovations of the first molecular phylogeny presented by Schneider et al. (1993) positioned Callimico as a sister group of Callithrix and Cebuella; Callicebus as a member of the pitheciids; Brachyteles as sister to Lagothrix; and the night monkeys (Aotus), capuchins (Cebus) and squirrel monkeys (Saimiri) in the same clade with the small callitrichines. These results were subsequently confirmed by dozens of subsequent studies using data from DNA sequences. Some issues difficult to resolve with the phylogenetic analyses of DNA sequences, such as the diversification of the oldest lineages (pitheciids, atelids and cebids), and the confirmation of Aotus as a member of the Cebinae clade (together with Cebus/Saimiri), were clarified with new molecular approaches based on the presence or absence of Alu insertions as well as through the use of phylogenomics. At this time, all relationships at the intergeneric level had been deciphered, with the exception of the definition of the sister group of callitrichines (whether Aotus or Cebus/Saimiri are sister to callitrichines, or if Aotus, Saimiri and Cebus form a clade together). Future studies should prioritize the alpha taxonomy of most Neotropical primate groups, and the use of phylogenetic and geographic data, combined with reliable estimates of divergence times, to clarify the taxonomic status at species and genus level, as well as to help understand the evolutionary history of this remarkable and highly diversified group. Copyright © 2013 Elsevier Inc. All rights reserved.

Vector-borne transmission of Trypanosoma cruzi among captive Neotropical primates in a Brazilian zoo.

PubMed

Minuzzi-Souza, Thaís Tâmara Castro; Nitz, Nadjar; Knox, Monique Britto; Reis, Filipe; Hagström, Luciana; Cuba, César A Cuba; Hecht, Mariana Machado; Gurgel-Gonçalves, Rodrigo

2016-01-26

Neotropical primates are important sylvatic hosts of Trypanosoma cruzi, the etiological agent of Chagas disease. Infection is often subclinical, but severe disease has been described in both free-ranging and captive primates. Panstrongylus megistus, a major T. cruzi vector, was found infesting a small-primate unit at Brasília zoo (ZooB), Brazil. ZooB lies close to a gallery-forest patch where T. cruzi circulates naturally. Here, we combine parasitological and molecular methods to investigate a focus of T. cruzi infection involving triatomine bugs and Neotropical primates at a zoo located in the Brazilian Savannah. We assessed T. cruzi infection in vectors using optical microscopy (n = 34) and nested PCR (n = 50). We used quantitative PCR (qPCR) to examine blood samples from 26 primates and necropsy samples from two primates that died during the study. We determined parasite lineages in five vectors and two primates by comparing glucose-6-phosphate isomerase (G6pi) gene sequences. Trypanosoma cruzi was found in 44 vectors and 17 primates (six genera and eight species); one Mico chrysoleucus and one Saguinus niger had high parasitaemias. Trypanosoma cruzi DNA was detected in three primates born to qPCR-negative mothers at ZooB and in the two dead specimens. One Callithrix geoffroyi became qPCR-positive over a two-year follow-up. All G6pi sequences matched T. cruzi lineage TcI. Our findings strongly suggest vector-borne T. cruzi transmission within a small-primate unit at ZooB - with vectors, and perhaps also parasites, presumably coming from nearby gallery forest. Periodic checks for vectors and parasites would help eliminate T. cruzi transmission foci in captive-animal facilities. This should be of special importance for captive-breeding programs involving endangered mammals, and would reduce the risk of accidental T. cruzi transmission to keepers and veterinarians.

Isolation and characterization of a novel Helicobacter species, Helicobacter jaachi sp. nov., from common marmosets (Callithrix jaachus)

PubMed Central

Shen, Zeli; Feng, Yan; Sheh, Alexander; Everitt, Jeffrey; Bertram, Frederick; Paster, Bruce J.

2015-01-01

Purpose-bred common marmosets from domestic sources housed in a US research facility, and used in multiple drug discovery programmes, were noted to have a high incidence of spontaneous inflammatory bowel disease and sporadic cholecystitis and cholangiohepatitis. Inflammatory infiltrates increased in incidence and severity with age. Because Helicobacter spp. have been linked to gastrointestinal diseases, samples from the gastrointestinal tracts of 39 marmosets were screened for Helicobacter spp. by culture and PCR. Helicobacter spp. were frequently detected in marmosets; 28.2 % of the marmosets were positive for a proposed novel species, Helicobacter jaachi sp. nov., by culture, and 48.7 % were positive by Helicobacter genus-specific PCR. Seventeen strains of Helicobacter sp. from 11 marmosets were cultured from various gastrointestinal sites. Older animals (age 6–11 years) had a higher helicobacter prevalence rate (57.1 %) compared with younger animals (age 3–5 years), which had a 27.2 % prevalence rate. Cells of H. jaachi sp. nov. were catalase, urease and oxidase positive and had fusiform morphology, with periplasmic fibres and multiple bipolar, sheathed flagella. All isolates had similar 16S and 23S rRNA sequences, which clustered as representatives of a novel Helicobacter species closely related to ‘Helicobacter sanguini’ (97 %), a species isolated from cotton-top tamarins and ‘Helicobacter callitrichis’ (96 %) isolated previously from the faeces of common marmosets. The whole genome sequence of one of the liver isolates, H. jaachi sp. nov. MIT 09-6949T, had a 1.9 Mb genome length with a 41 mol% DNA G+C content. The type strain of Helicobacter jaachi sp. nov., MIT 09-6949T, has been deposited in the BCCM/LMG Bacteria Collection as LMG 28613T. These findings add to the increasing number of animal species with gastrointestinal disease in which novel enterohepatic Helicobacter spp. have been isolated. PMID:26297446

Dental remains of cebid platyrrhines from the earliest late Miocene of Western Amazonia, Peru: Macroevolutionary implications on the extant capuchin and marmoset lineages.

PubMed

Marivaux, Laurent; Adnet, Sylvain; Altamirano-Sierra, Ali J; Pujos, François; Ramdarshan, Anusha; Salas-Gismondi, Rodolfo; Tejada-Lara, Julia V; Antoine, Pierre-Olivier

2016-11-01

Undoubted fossil Cebidae have so far been primarily documented from the late middle Miocene of Colombia, the late Miocene of Brazilian Amazonia, the early Miocene of Peruvian Amazonia, and very recently from the earliest Miocene of Panama. The evolutionary history of cebids is far from being well-documented, with notably a complete blank in the record of callitrichine stem lineages until and after the late middle Miocene (Laventan SALMA). Further documenting their evolutionary history is therefore of primary importance. Recent field efforts in Peruvian Amazonia (Contamana area, Loreto Department) have allowed for the discovery of an early late Miocene (ca. 11 Ma; Mayoan SALMA) fossil primate-bearing locality (CTA-43; Pebas Formation). In this study, we analyze the primate material, which consists of five isolated teeth documenting two distinct Cebidae: Cebus sp., a medium-sized capuchin (Cebinae), and Cebuella sp., a tiny marmoset (Callitrichinae). Although limited, this new fossil material of platyrrhines contributes to documenting the post-Laventan evolutionary history of cebids, and besides testifies to the earliest occurrences of the modern Cebuella and Cebus/Sapajus lineages in the Neotropics. Regarding the evolutionary history of callitrichine marmosets, the discovery of an 11 Ma-old fossil representative of the modern Cebuella pushes back by at least 6 Ma the age of the Mico/Cebuella divergence currently proposed by molecular biologists (i.e., ca. 4.5 Ma). This also extends back to > 11 Ma BP the divergence between Callithrix and the common ancestor (CA) of Mico/Cebuella, as well as the divergence between the CA of marmosets and Callimico (Goeldi's callitrichine). This discovery from Peruvian Amazonia implies a deep evolutionary root of the Cebuella lineage in the northwestern part of South America (the modern western Amazon basin), slightly before the recession of the Pebas mega-wetland system (PMWS), ca. 10.5 Ma, and well-before the subsequent establishment of the Amazon drainage system (ca. 9-7 Ma). During the late middle/early late Miocene interval, the PMWS was seemingly not a limiting factor for dispersals and widespread distribution of terrestrial mammals, but it was also likely a source of diversification via a complex patchwork of submerged/emerged lands varying through time. © 2016 Wiley Periodicals, Inc.

The sweet taste quality is linked to a cluster of taste fibers in primates: lactisole diminishes preference and responses to sweet in S fibers (sweet best) chorda tympani fibers of M. fascicularis monkey.

PubMed

Wang, Yiwen; Danilova, Vicktoria; Cragin, Tiffany; Roberts, Thomas W; Koposov, Alexey; Hellekant, Göran

2009-02-18

Psychophysically, sweet and bitter have long been considered separate taste qualities, evident already to the newborn human. The identification of different receptors for sweet and bitter located on separate cells of the taste buds substantiated this separation. However, this finding leads to the next question: is bitter and sweet also kept separated in the next link from the taste buds, the fibers of the taste nerves? Previous studies in non-human primates, P. troglodytes, C. aethiops, M. mulatta, M. fascicularis and C. jacchus, suggest that the sweet and bitter taste qualities are linked to specific groups of fibers called S and Q fibers. In this study we apply a new sweet taste modifier, lactisole, commercially available as a suppressor of the sweetness of sugars on the human tongue, to test our hypothesis that sweet taste is conveyed in S fibers. We first ascertained that lactisole exerted similar suppression of sweetness in M. fascicularis, as reported in humans, by recording their preference of sweeteners and non- sweeteners with and without lactisole in two-bottle tests. The addition of lactisole significantly diminished the preference for all sweeteners but had no effect on the intake of non-sweet compounds or the intake of water. We then recorded the response to the same taste stimuli in 40 single chorda tympani nerve fibers. Comparison between single fiber nerve responses to stimuli with and without lactisole showed that lactisole only suppressed the responses to sweeteners in S fibers. It had no effect on the responses to any other stimuli in all other taste fibers. In M. fascicularis, lactisole diminishes the attractiveness of compounds, which taste sweet to humans. This behavior is linked to activity of fibers in the S-cluster. Assuming that lactisole blocks the T1R3 monomer of the sweet taste receptor T1R2/R3, these results present further support for the hypothesis that S fibers convey taste from T1R2/R3 receptors, while the impulse activity in non-S fibers originates from other kinds of receptors. The absence of the effect of lactisole on the faint responses in some S fibers to other stimuli as well as the responses to sweet and non-sweet stimuli in non-S fibers suggest that these responses originate from other taste receptors.

Radiation Environment Modeling for Spacecraft Design: New Model Developments

NASA Technical Reports Server (NTRS)

Barth, Janet; Xapsos, Mike; Lauenstein, Jean-Marie; Ladbury, Ray

2006-01-01

A viewgraph presentation on various new space radiation environment models for spacecraft design is described. The topics include: 1) The Space Radiatio Environment; 2) Effects of Space Environments on Systems; 3) Space Radiatio Environment Model Use During Space Mission Development and Operations; 4) Space Radiation Hazards for Humans; 5) "Standard" Space Radiation Environment Models; 6) Concerns about Standard Models; 7) Inadequacies of Current Models; 8) Development of New Models; 9) New Model Developments: Proton Belt Models; 10) Coverage of New Proton Models; 11) Comparison of TPM-1, PSB97, AP-8; 12) New Model Developments: Electron Belt Models; 13) Coverage of New Electron Models; 14) Comparison of "Worst Case" POLE, CRESELE, and FLUMIC Models with the AE-8 Model; 15) New Model Developments: Galactic Cosmic Ray Model; 16) Comparison of NASA, MSU, CIT Models with ACE Instrument Data; 17) New Model Developmemts: Solar Proton Model; 18) Comparison of ESP, JPL91, KIng/Stassinopoulos, and PSYCHIC Models; 19) New Model Developments: Solar Heavy Ion Model; 20) Comparison of CREME96 to CREDO Measurements During 2000 and 2002; 21) PSYCHIC Heavy ion Model; 22) Model Standardization; 23) Working Group Meeting on New Standard Radiation Belt and Space Plasma Models; and 24) Summary.

Comparisons of Multilevel Modeling and Structural Equation Modeling Approaches to Actor-Partner Interdependence Model.

PubMed

Hong, Sehee; Kim, Soyoung

2018-01-01

There are basically two modeling approaches applicable to analyzing an actor-partner interdependence model: the multilevel modeling (hierarchical linear model) and the structural equation modeling. This article explains how to use these two models in analyzing an actor-partner interdependence model and how these two approaches work differently. As an empirical example, marital conflict data were used to analyze an actor-partner interdependence model. The multilevel modeling and the structural equation modeling produced virtually identical estimates for a basic model. However, the structural equation modeling approach allowed more realistic assumptions on measurement errors and factor loadings, rendering better model fit indices.

[Analysis of the stability and adaptability of near infrared spectra qualitative analysis model].

PubMed

Cao, Wu; Li, Wei-jun; Wang, Ping; Zhang, Li-ping

2014-06-01

The stability and adaptability of model of near infrared spectra qualitative analysis were studied. Method of separate modeling can significantly improve the stability and adaptability of model; but its ability of improving adaptability of model is limited. Method of joint modeling can not only improve the adaptability of the model, but also the stability of model, at the same time, compared to separate modeling, the method can shorten the modeling time, reduce the modeling workload; extend the term of validity of model, and improve the modeling efficiency. The experiment of model adaptability shows that, the correct recognition rate of separate modeling method is relatively low, which can not meet the requirements of application, and joint modeling method can reach the correct recognition rate of 90%, and significantly enhances the recognition effect. The experiment of model stability shows that, the identification results of model by joint modeling are better than the model by separate modeling, and has good application value.

Evaluating the Bias of Alternative Cost Progress Models: Tests Using Aerospace Industry Acquisition Programs

DTIC Science & Technology

1992-12-01

suspect :mat, -n2 extent predict:.on cas jas ccsiziveiv crrei:=e amonc e v:arious models, :he fandom *.;aik, learn ha r ur e, i;<ea- variable and Bemis...Functions, Production Rate Adjustment Model, Learning Curve Model. Random Walk Model. Bemis Model. Evaluating Model Bias, Cost Prediction Bias. Cost...of four cost progress models--a random walk model, the tradiuonai learning curve model, a production rate model Ifixed-variable model). and a model

Experience with turbulence interaction and turbulence-chemistry models at Fluent Inc.

NASA Technical Reports Server (NTRS)

Choudhury, D.; Kim, S. E.; Tselepidakis, D. P.; Missaghi, M.

1995-01-01

This viewgraph presentation discusses (1) turbulence modeling: challenges in turbulence modeling, desirable attributes of turbulence models, turbulence models in FLUENT, and examples using FLUENT; and (2) combustion modeling: turbulence-chemistry interaction and FLUENT equilibrium model. As of now, three turbulence models are provided: the conventional k-epsilon model, the renormalization group model, and the Reynolds-stress model. The renormalization group k-epsilon model has broadened the range of applicability of two-equation turbulence models. The Reynolds-stress model has proved useful for strongly anisotropic flows such as those encountered in cyclones, swirlers, and combustors. Issues remain, such as near-wall closure, with all classes of models.

Leadership Models.

ERIC Educational Resources Information Center

Freeman, Thomas J.

This paper discusses six different models of organizational structure and leadership, including the scalar chain or pyramid model, the continuum model, the grid model, the linking pin model, the contingency model, and the circle or democratic model. Each model is examined in a separate section that describes the model and its development, lists…

SUMMA and Model Mimicry: Understanding Differences Among Land Models

NASA Astrophysics Data System (ADS)

Nijssen, B.; Nearing, G. S.; Ou, G.; Clark, M. P.

2016-12-01

Model inter-comparison and model ensemble experiments suffer from an inability to explain the mechanisms behind differences in model outcomes. We can clearly demonstrate that the models are different, but we cannot necessarily identify the reasons why, because most models exhibit myriad differences in process representations, model parameterizations, model parameters and numerical solution methods. This inability to identify the reasons for differences in model performance hampers our understanding and limits model improvement, because we cannot easily identify the most promising paths forward. We have developed the Structure for Unifying Multiple Modeling Alternatives (SUMMA) to allow for controlled experimentation with model construction, numerical techniques, and parameter values and therefore isolate differences in model outcomes to specific choices during the model development process. In developing SUMMA, we recognized that hydrologic models can be thought of as individual instantiations of a master modeling template that is based on a common set of conservation equations for energy and water. Given this perspective, SUMMA provides a unified approach to hydrologic modeling that integrates different modeling methods into a consistent structure with the ability to instantiate alternative hydrologic models at runtime. Here we employ SUMMA to revisit a previous multi-model experiment and demonstrate its use for understanding differences in model performance. Specifically, we implement SUMMA to mimic the spread of behaviors exhibited by the land models that participated in the Protocol for the Analysis of Land Surface Models (PALS) Land Surface Model Benchmarking Evaluation Project (PLUMBER) and draw conclusions about the relative performance of specific model parameterizations for water and energy fluxes through the soil-vegetation continuum. SUMMA's ability to mimic the spread of model ensembles and the behavior of individual models can be an important tool in focusing model development and improvement efforts.

Seven Modeling Perspectives on Teaching and Learning: Some Interrelations and Cognitive Effects

ERIC Educational Resources Information Center

Easley, J. A., Jr.

1977-01-01

The categories of models associated with the seven perspectives are designated as combinatorial models, sampling models, cybernetic models, game models, critical thinking models, ordinary language analysis models, and dynamic structural models. (DAG)

Pursuing the method of multiple working hypotheses to understand differences in process-based snow models

NASA Astrophysics Data System (ADS)

Clark, Martyn; Essery, Richard

2017-04-01

When faced with the complex and interdisciplinary challenge of building process-based land models, different modelers make different decisions at different points in the model development process. These modeling decisions are generally based on several considerations, including fidelity (e.g., what approaches faithfully simulate observed processes), complexity (e.g., which processes should be represented explicitly), practicality (e.g., what is the computational cost of the model simulations; are there sufficient resources to implement the desired modeling concepts), and data availability (e.g., is there sufficient data to force and evaluate models). Consequently the research community, comprising modelers of diverse background, experience, and modeling philosophy, has amassed a wide range of models, which differ in almost every aspect of their conceptualization and implementation. Model comparison studies have been undertaken to explore model differences, but have not been able to meaningfully attribute inter-model differences in predictive ability to individual model components because there are often too many structural and implementation differences among the different models considered. As a consequence, model comparison studies to date have provided limited insight into the causes of differences in model behavior, and model development has often relied on the inspiration and experience of individual modelers rather than on a systematic analysis of model shortcomings. This presentation will summarize the use of "multiple-hypothesis" modeling frameworks to understand differences in process-based snow models. Multiple-hypothesis frameworks define a master modeling template, and include a a wide variety of process parameterizations and spatial configurations that are used in existing models. Such frameworks provide the capability to decompose complex models into the individual decisions that are made as part of model development, and evaluate each decision in isolation. It is hence possible to attribute differences in system-scale model predictions to individual modeling decisions, providing scope to mimic the behavior of existing models, understand why models differ, characterize model uncertainty, and identify productive pathways to model improvement. Results will be presented applying multiple hypothesis frameworks to snow model comparison projects, including PILPS, SnowMIP, and the upcoming ESM-SnowMIP project.

Research on Multi - Person Parallel Modeling Method Based on Integrated Model Persistent Storage

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Liu, Ying

2018-03-01

This paper mainly studies the multi-person parallel modeling method based on the integrated model persistence storage. The integrated model refers to a set of MDDT modeling graphics system, which can carry out multi-angle, multi-level and multi-stage description of aerospace general embedded software. Persistent storage refers to converting the data model in memory into a storage model and converting the storage model into a data model in memory, where the data model refers to the object model and the storage model is a binary stream. And multi-person parallel modeling refers to the need for multi-person collaboration, the role of separation, and even real-time remote synchronization modeling.

Constructive Epistemic Modeling: A Hierarchical Bayesian Model Averaging Method

NASA Astrophysics Data System (ADS)

Tsai, F. T. C.; Elshall, A. S.

2014-12-01

Constructive epistemic modeling is the idea that our understanding of a natural system through a scientific model is a mental construct that continually develops through learning about and from the model. Using the hierarchical Bayesian model averaging (HBMA) method [1], this study shows that segregating different uncertain model components through a BMA tree of posterior model probabilities, model prediction, within-model variance, between-model variance and total model variance serves as a learning tool [2]. First, the BMA tree of posterior model probabilities permits the comparative evaluation of the candidate propositions of each uncertain model component. Second, systemic model dissection is imperative for understanding the individual contribution of each uncertain model component to the model prediction and variance. Third, the hierarchical representation of the between-model variance facilitates the prioritization of the contribution of each uncertain model component to the overall model uncertainty. We illustrate these concepts using the groundwater modeling of a siliciclastic aquifer-fault system. The sources of uncertainty considered are from geological architecture, formation dip, boundary conditions and model parameters. The study shows that the HBMA analysis helps in advancing knowledge about the model rather than forcing the model to fit a particularly understanding or merely averaging several candidate models. [1] Tsai, F. T.-C., and A. S. Elshall (2013), Hierarchical Bayesian model averaging for hydrostratigraphic modeling: Uncertainty segregation and comparative evaluation. Water Resources Research, 49, 5520-5536, doi:10.1002/wrcr.20428. [2] Elshall, A.S., and F. T.-C. Tsai (2014). Constructive epistemic modeling of groundwater flow with geological architecture and boundary condition uncertainty under Bayesian paradigm, Journal of Hydrology, 517, 105-119, doi: 10.1016/j.jhydrol.2014.05.027.

The Influence of a Model's Reinforcement Contingency and Affective Response on Children's Perceptions of the Model

ERIC Educational Resources Information Center

Thelen, Mark H.; And Others

1977-01-01

Assesses the influence of model consequences on perceived model affect and, conversely, assesses the influence of model affect on perceived model consequences. Also appraises the influence of model consequences and model affect on perceived model attractiveness, perceived model competence, and perceived task attractiveness. (Author/RK)

Bayesian Model Averaging of Artificial Intelligence Models for Hydraulic Conductivity Estimation

NASA Astrophysics Data System (ADS)

Nadiri, A.; Chitsazan, N.; Tsai, F. T.; Asghari Moghaddam, A.

2012-12-01

This research presents a Bayesian artificial intelligence model averaging (BAIMA) method that incorporates multiple artificial intelligence (AI) models to estimate hydraulic conductivity and evaluate estimation uncertainties. Uncertainty in the AI model outputs stems from error in model input as well as non-uniqueness in selecting different AI methods. Using one single AI model tends to bias the estimation and underestimate uncertainty. BAIMA employs Bayesian model averaging (BMA) technique to address the issue of using one single AI model for estimation. BAIMA estimates hydraulic conductivity by averaging the outputs of AI models according to their model weights. In this study, the model weights were determined using the Bayesian information criterion (BIC) that follows the parsimony principle. BAIMA calculates the within-model variances to account for uncertainty propagation from input data to AI model output. Between-model variances are evaluated to account for uncertainty due to model non-uniqueness. We employed Takagi-Sugeno fuzzy logic (TS-FL), artificial neural network (ANN) and neurofuzzy (NF) to estimate hydraulic conductivity for the Tasuj plain aquifer, Iran. BAIMA combined three AI models and produced better fitting than individual models. While NF was expected to be the best AI model owing to its utilization of both TS-FL and ANN models, the NF model is nearly discarded by the parsimony principle. The TS-FL model and the ANN model showed equal importance although their hydraulic conductivity estimates were quite different. This resulted in significant between-model variances that are normally ignored by using one AI model.

A Smart Modeling Framework for Integrating BMI-enabled Models as Web Services

NASA Astrophysics Data System (ADS)

Jiang, P.; Elag, M.; Kumar, P.; Peckham, S. D.; Liu, R.; Marini, L.; Hsu, L.

2015-12-01

Serviced-oriented computing provides an opportunity to couple web service models using semantic web technology. Through this approach, models that are exposed as web services can be conserved in their own local environment, thus making it easy for modelers to maintain and update the models. In integrated modeling, the serviced-oriented loose-coupling approach requires (1) a set of models as web services, (2) the model metadata describing the external features of a model (e.g., variable name, unit, computational grid, etc.) and (3) a model integration framework. We present the architecture of coupling web service models that are self-describing by utilizing a smart modeling framework. We expose models that are encapsulated with CSDMS (Community Surface Dynamics Modeling System) Basic Model Interfaces (BMI) as web services. The BMI-enabled models are self-describing by uncovering models' metadata through BMI functions. After a BMI-enabled model is serviced, a client can initialize, execute and retrieve the meta-information of the model by calling its BMI functions over the web. Furthermore, a revised version of EMELI (Peckham, 2015), an Experimental Modeling Environment for Linking and Interoperability, is chosen as the framework for coupling BMI-enabled web service models. EMELI allows users to combine a set of component models into a complex model by standardizing model interface using BMI as well as providing a set of utilities smoothing the integration process (e.g., temporal interpolation). We modify the original EMELI so that the revised modeling framework is able to initialize, execute and find the dependencies of the BMI-enabled web service models. By using the revised EMELI, an example will be presented on integrating a set of topoflow model components that are BMI-enabled and exposed as web services. Reference: Peckham, S.D. (2014) EMELI 1.0: An experimental smart modeling framework for automatic coupling of self-describing models, Proceedings of HIC 2014, 11th International Conf. on Hydroinformatics, New York, NY.

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

USGS Publications Warehouse

Curtis, Gary P.; Lu, Dan; Ye, Ming

2015-01-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the synthetic study and future real-world modeling are discussed.

Automated model integration at source code level: An approach for implementing models into the NASA Land Information System

NASA Astrophysics Data System (ADS)

Wang, S.; Peters-Lidard, C. D.; Mocko, D. M.; Kumar, S.; Nearing, G. S.; Arsenault, K. R.; Geiger, J. V.

2014-12-01

Model integration bridges the data flow between modeling frameworks and models. However, models usually do not fit directly into a particular modeling environment, if not designed for it. An example includes implementing different types of models into the NASA Land Information System (LIS), a software framework for land-surface modeling and data assimilation. Model implementation requires scientific knowledge and software expertise and may take a developer months to learn LIS and model software structure. Debugging and testing of the model implementation is also time-consuming due to not fully understanding LIS or the model. This time spent is costly for research and operational projects. To address this issue, an approach has been developed to automate model integration into LIS. With this in mind, a general model interface was designed to retrieve forcing inputs, parameters, and state variables needed by the model and to provide as state variables and outputs to LIS. Every model can be wrapped to comply with the interface, usually with a FORTRAN 90 subroutine. Development efforts need only knowledge of the model and basic programming skills. With such wrappers, the logic is the same for implementing all models. Code templates defined for this general model interface could be re-used with any specific model. Therefore, the model implementation can be done automatically. An automated model implementation toolkit was developed with Microsoft Excel and its built-in VBA language. It allows model specifications in three worksheets and contains FORTRAN 90 code templates in VBA programs. According to the model specification, the toolkit generates data structures and procedures within FORTRAN modules and subroutines, which transfer data between LIS and the model wrapper. Model implementation is standardized, and about 80 - 90% of the development load is reduced. In this presentation, the automated model implementation approach is described along with LIS programming interfaces, the general model interface and five case studies, including a regression model, Noah-MP, FASST, SAC-HTET/SNOW-17, and FLake. These different models vary in complexity with software structure. Also, we will describe how these complexities were overcome through using this approach and results of model benchmarks within LIS.

Literature review of models on tire-pavement interaction noise

NASA Astrophysics Data System (ADS)

Li, Tan; Burdisso, Ricardo; Sandu, Corina

2018-04-01

Tire-pavement interaction noise (TPIN) becomes dominant at speeds above 40 km/h for passenger vehicles and 70 km/h for trucks. Several models have been developed to describe and predict the TPIN. However, these models do not fully reveal the physical mechanisms or predict TPIN accurately. It is well known that all the models have both strengths and weaknesses, and different models fit different investigation purposes or conditions. The numerous papers that present these models are widely scattered among thousands of journals, and it is difficult to get the complete picture of the status of research in this area. This review article aims at presenting the history and current state of TPIN models systematically, making it easier to identify and distribute the key knowledge and opinions, and providing insight into the future research trend in this field. In this work, over 2000 references related to TPIN were collected, and 74 models were reviewed from nearly 200 selected references; these were categorized into deterministic models (37), statistical models (18), and hybrid models (19). The sections explaining the models are self-contained with key principles, equations, and illustrations included. The deterministic models were divided into three sub-categories: conventional physics models, finite element and boundary element models, and computational fluid dynamics models; the statistical models were divided into three sub-categories: traditional regression models, principal component analysis models, and fuzzy curve-fitting models; the hybrid models were divided into three sub-categories: tire-pavement interface models, mechanism separation models, and noise propagation models. At the end of each category of models, a summary table is presented to compare these models with the key information extracted. Readers may refer to these tables to find models of their interest. The strengths and weaknesses of the models in different categories were then analyzed. Finally, the modeling trend and future direction in this area are given.

Multi-Model Combination techniques for Hydrological Forecasting: Application to Distributed Model Intercomparison Project Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ajami, N K; Duan, Q; Gao, X

2005-04-11

This paper examines several multi-model combination techniques: the Simple Multi-model Average (SMA), the Multi-Model Super Ensemble (MMSE), Modified Multi-Model Super Ensemble (M3SE) and the Weighted Average Method (WAM). These model combination techniques were evaluated using the results from the Distributed Model Intercomparison Project (DMIP), an international project sponsored by the National Weather Service (NWS) Office of Hydrologic Development (OHD). All of the multi-model combination results were obtained using uncalibrated DMIP model outputs and were compared against the best uncalibrated as well as the best calibrated individual model results. The purpose of this study is to understand how different combination techniquesmore » affect the skill levels of the multi-model predictions. This study revealed that the multi-model predictions obtained from uncalibrated single model predictions are generally better than any single member model predictions, even the best calibrated single model predictions. Furthermore, more sophisticated multi-model combination techniques that incorporated bias correction steps work better than simple multi-model average predictions or multi-model predictions without bias correction.« less

Expert models and modeling processes associated with a computer-modeling tool

NASA Astrophysics Data System (ADS)

Zhang, Baohui; Liu, Xiufeng; Krajcik, Joseph S.

2006-07-01

Holding the premise that the development of expertise is a continuous process, this study concerns expert models and modeling processes associated with a modeling tool called Model-It. Five advanced Ph.D. students in environmental engineering and public health used Model-It to create and test models of water quality. Using think aloud technique and video recording, we captured their computer screen modeling activities and thinking processes. We also interviewed them the day following their modeling sessions to further probe the rationale of their modeling practices. We analyzed both the audio-video transcripts and the experts' models. We found the experts' modeling processes followed the linear sequence built in the modeling program with few instances of moving back and forth. They specified their goals up front and spent a long time thinking through an entire model before acting. They specified relationships with accurate and convincing evidence. Factors (i.e., variables) in expert models were clustered, and represented by specialized technical terms. Based on the above findings, we made suggestions for improving model-based science teaching and learning using Model-It.

Illustrating a Model-Game-Model Paradigm for Using Human Wargames in Analysis

DTIC Science & Technology

2017-02-01

Working Paper Illustrating a Model- Game -Model Paradigm for Using Human Wargames in Analysis Paul K. Davis RAND National Security Research...paper proposes and illustrates an analysis-centric paradigm (model- game -model or what might be better called model-exercise-model in some cases) for...to involve stakehold- ers in model development from the outset. The model- game -model paradigm was illustrated in an application to crisis planning

Multi-model analysis of terrestrial carbon cycles in Japan: limitations and implications of model calibration using eddy flux observations

NASA Astrophysics Data System (ADS)

Ichii, K.; Suzuki, T.; Kato, T.; Ito, A.; Hajima, T.; Ueyama, M.; Sasai, T.; Hirata, R.; Saigusa, N.; Ohtani, Y.; Takagi, K.

2010-07-01

Terrestrial biosphere models show large differences when simulating carbon and water cycles, and reducing these differences is a priority for developing more accurate estimates of the condition of terrestrial ecosystems and future climate change. To reduce uncertainties and improve the understanding of their carbon budgets, we investigated the utility of the eddy flux datasets to improve model simulations and reduce variabilities among multi-model outputs of terrestrial biosphere models in Japan. Using 9 terrestrial biosphere models (Support Vector Machine - based regressions, TOPS, CASA, VISIT, Biome-BGC, DAYCENT, SEIB, LPJ, and TRIFFID), we conducted two simulations: (1) point simulations at four eddy flux sites in Japan and (2) spatial simulations for Japan with a default model (based on original settings) and a modified model (based on model parameter tuning using eddy flux data). Generally, models using default model settings showed large deviations in model outputs from observation with large model-by-model variability. However, after we calibrated the model parameters using eddy flux data (GPP, RE and NEP), most models successfully simulated seasonal variations in the carbon cycle, with less variability among models. We also found that interannual variations in the carbon cycle are mostly consistent among models and observations. Spatial analysis also showed a large reduction in the variability among model outputs. This study demonstrated that careful validation and calibration of models with available eddy flux data reduced model-by-model differences. Yet, site history, analysis of model structure changes, and more objective procedure of model calibration should be included in the further analysis.

Conceptual and logical level of database modeling

NASA Astrophysics Data System (ADS)

Hunka, Frantisek; Matula, Jiri

2016-06-01

Conceptual and logical levels form the top most levels of database modeling. Usually, ORM (Object Role Modeling) and ER diagrams are utilized to capture the corresponding schema. The final aim of business process modeling is to store its results in the form of database solution. For this reason, value oriented business process modeling which utilizes ER diagram to express the modeling entities and relationships between them are used. However, ER diagrams form the logical level of database schema. To extend possibilities of different business process modeling methodologies, the conceptual level of database modeling is needed. The paper deals with the REA value modeling approach to business process modeling using ER-diagrams, and derives conceptual model utilizing ORM modeling approach. Conceptual model extends possibilities for value modeling to other business modeling approaches.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

Service-oriented model-encapsulation strategy for sharing and integrating heterogeneous geo-analysis models in an open web environment

NASA Astrophysics Data System (ADS)

Yue, Songshan; Chen, Min; Wen, Yongning; Lu, Guonian

2016-04-01

Earth environment is extremely complicated and constantly changing; thus, it is widely accepted that the use of a single geo-analysis model cannot accurately represent all details when solving complex geo-problems. Over several years of research, numerous geo-analysis models have been developed. However, a collaborative barrier between model providers and model users still exists. The development of cloud computing has provided a new and promising approach for sharing and integrating geo-analysis models across an open web environment. To share and integrate these heterogeneous models, encapsulation studies should be conducted that are aimed at shielding original execution differences to create services which can be reused in the web environment. Although some model service standards (such as Web Processing Service (WPS) and Geo Processing Workflow (GPW)) have been designed and developed to help researchers construct model services, various problems regarding model encapsulation remain. (1) The descriptions of geo-analysis models are complicated and typically require rich-text descriptions and case-study illustrations, which are difficult to fully represent within a single web request (such as the GetCapabilities and DescribeProcess operations in the WPS standard). (2) Although Web Service technologies can be used to publish model services, model users who want to use a geo-analysis model and copy the model service into another computer still encounter problems (e.g., they cannot access the model deployment dependencies information). This study presents a strategy for encapsulating geo-analysis models to reduce problems encountered when sharing models between model providers and model users and supports the tasks with different web service standards (e.g., the WPS standard). A description method for heterogeneous geo-analysis models is studied. Based on the model description information, the methods for encapsulating the model-execution program to model services and for describing model-service deployment information are also included in the proposed strategy. Hence, the model-description interface, model-execution interface and model-deployment interface are studied to help model providers and model users more easily share, reuse and integrate geo-analysis models in an open web environment. Finally, a prototype system is established, and the WPS standard is employed as an example to verify the capability and practicability of the model-encapsulation strategy. The results show that it is more convenient for modellers to share and integrate heterogeneous geo-analysis models in cloud computing platforms.

Object-oriented biomedical system modelling--the language.

PubMed

Hakman, M; Groth, T

1999-11-01

The paper describes a new object-oriented biomedical continuous system modelling language (OOBSML). It is fully object-oriented and supports model inheritance, encapsulation, and model component instantiation and behaviour polymorphism. Besides the traditional differential and algebraic equation expressions the language includes also formal expressions for documenting models and defining model quantity types and quantity units. It supports explicit definition of model input-, output- and state quantities, model components and component connections. The OOBSML model compiler produces self-contained, independent, executable model components that can be instantiated and used within other OOBSML models and/or stored within model and model component libraries. In this way complex models can be structured as multilevel, multi-component model hierarchies. Technically the model components produced by the OOBSML compiler are executable computer code objects based on distributed object and object request broker technology. This paper includes both the language tutorial and the formal language syntax and semantic description.

Fitting IRT Models to Dichotomous and Polytomous Data: Assessing the Relative Model-Data Fit of Ideal Point and Dominance Models

ERIC Educational Resources Information Center

Tay, Louis; Ali, Usama S.; Drasgow, Fritz; Williams, Bruce

2011-01-01

This study investigated the relative model-data fit of an ideal point item response theory (IRT) model (the generalized graded unfolding model [GGUM]) and dominance IRT models (e.g., the two-parameter logistic model [2PLM] and Samejima's graded response model [GRM]) to simulated dichotomous and polytomous data generated from each of these models.…

Comparing and combining process-based crop models and statistical models with some implications for climate change

NASA Astrophysics Data System (ADS)

Roberts, Michael J.; Braun, Noah O.; Sinclair, Thomas R.; Lobell, David B.; Schlenker, Wolfram

2017-09-01

We compare predictions of a simple process-based crop model (Soltani and Sinclair 2012), a simple statistical model (Schlenker and Roberts 2009), and a combination of both models to actual maize yields on a large, representative sample of farmer-managed fields in the Corn Belt region of the United States. After statistical post-model calibration, the process model (Simple Simulation Model, or SSM) predicts actual outcomes slightly better than the statistical model, but the combined model performs significantly better than either model. The SSM, statistical model and combined model all show similar relationships with precipitation, while the SSM better accounts for temporal patterns of precipitation, vapor pressure deficit and solar radiation. The statistical and combined models show a more negative impact associated with extreme heat for which the process model does not account. Due to the extreme heat effect, predicted impacts under uniform climate change scenarios are considerably more severe for the statistical and combined models than for the process-based model.

An empirical model to forecast solar wind velocity through statistical modeling

NASA Astrophysics Data System (ADS)

Gao, Y.; Ridley, A. J.

2013-12-01

The accurate prediction of the solar wind velocity has been a major challenge in the space weather community. Previous studies proposed many empirical and semi-empirical models to forecast the solar wind velocity based on either the historical observations, e.g. the persistence model, or the instantaneous observations of the sun, e.g. the Wang-Sheeley-Arge model. In this study, we use the one-minute WIND data from January 1995 to August 2012 to investigate and compare the performances of 4 models often used in literature, here referred to as the null model, the persistence model, the one-solar-rotation-ago model, and the Wang-Sheeley-Arge model. It is found that, measured by root mean square error, the persistence model gives the most accurate predictions within two days. Beyond two days, the Wang-Sheeley-Arge model serves as the best model, though it only slightly outperforms the null model and the one-solar-rotation-ago model. Finally, we apply the least-square regression to linearly combine the null model, the persistence model, and the one-solar-rotation-ago model to propose a 'general persistence model'. By comparing its performance against the 4 aforementioned models, it is found that the accuracy of the general persistence model outperforms the other 4 models within five days. Due to its great simplicity and superb performance, we believe that the general persistence model can serve as a benchmark in the forecast of solar wind velocity and has the potential to be modified to arrive at better models.

A Primer for Model Selection: The Decisive Role of Model Complexity

NASA Astrophysics Data System (ADS)

Höge, Marvin; Wöhling, Thomas; Nowak, Wolfgang

2018-03-01

Selecting a "best" model among several competing candidate models poses an often encountered problem in water resources modeling (and other disciplines which employ models). For a modeler, the best model fulfills a certain purpose best (e.g., flood prediction), which is typically assessed by comparing model simulations to data (e.g., stream flow). Model selection methods find the "best" trade-off between good fit with data and model complexity. In this context, the interpretations of model complexity implied by different model selection methods are crucial, because they represent different underlying goals of modeling. Over the last decades, numerous model selection criteria have been proposed, but modelers who primarily want to apply a model selection criterion often face a lack of guidance for choosing the right criterion that matches their goal. We propose a classification scheme for model selection criteria that helps to find the right criterion for a specific goal, i.e., which employs the correct complexity interpretation. We identify four model selection classes which seek to achieve high predictive density, low predictive error, high model probability, or shortest compression of data. These goals can be achieved by following either nonconsistent or consistent model selection and by either incorporating a Bayesian parameter prior or not. We allocate commonly used criteria to these four classes, analyze how they represent model complexity and what this means for the model selection task. Finally, we provide guidance on choosing the right type of criteria for specific model selection tasks. (A quick guide through all key points is given at the end of the introduction.)

Women's Endorsement of Models of Sexual Response: Correlates and Predictors.

PubMed

Nowosielski, Krzysztof; Wróbel, Beata; Kowalczyk, Robert

2016-02-01

Few studies have investigated endorsement of female sexual response models, and no single model has been accepted as a normative description of women's sexual response. The aim of the study was to establish how women from a population-based sample endorse current theoretical models of the female sexual response--the linear models and circular model (partial and composite Basson models)--as well as predictors of endorsement. Accordingly, 174 heterosexual women aged 18-55 years were included in a cross-sectional study: 74 women diagnosed with female sexual dysfunction (FSD) based on DSM-5 criteria and 100 non-dysfunctional women. The description of sexual response models was used to divide subjects into four subgroups: linear (Masters-Johnson and Kaplan models), circular (partial Basson model), mixed (linear and circular models in similar proportions, reflective of the composite Basson model), and a different model. Women were asked to choose which of the models best described their pattern of sexual response and how frequently they engaged in each model. Results showed that 28.7% of women endorsed the linear models, 19.5% the partial Basson model, 40.8% the composite Basson model, and 10.9% a different model. Women with FSD endorsed the partial Basson model and a different model more frequently than did non-dysfunctional controls. Individuals who were dissatisfied with a partner as a lover were more likely to endorse a different model. Based on the results, we concluded that the majority of women endorsed a mixed model combining the circular response with the possibility of an innate desire triggering a linear response. Further, relationship difficulties, not FSD, predicted model endorsement.

The Use of Modeling-Based Text to Improve Students' Modeling Competencies

ERIC Educational Resources Information Center

Jong, Jing-Ping; Chiu, Mei-Hung; Chung, Shiao-Lan

2015-01-01

This study investigated the effects of a modeling-based text on 10th graders' modeling competencies. Fifteen 10th graders read a researcher-developed modeling-based science text on the ideal gas law that included explicit descriptions and representations of modeling processes (i.e., model selection, model construction, model validation, model…

Performance and Architecture Lab Modeling Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-06-19

Analytical application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult. Furthermore, models are frequently expressed in forms that are hard to distribute and validate. The Performance and Architecture Lab Modeling tool, or Palm, is a modeling tool designed to make application modeling easier. Palm provides a source code modeling annotation language. Not only does the modeling language divide the modeling task into sub problems, it formally links an application's source code with its model. This link is important because a model's purpose is to capture application behavior. Furthermore, this linkmore » makes it possible to define rules for generating models according to source code organization. Palm generates hierarchical models according to well-defined rules. Given an application, a set of annotations, and a representative execution environment, Palm will generate the same model. A generated model is a an executable program whose constituent parts directly correspond to the modeled application. Palm generates models by combining top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. A model's hierarchy is defined by static and dynamic source code structure. Because Palm coordinates models and source code, Palm's models are 'first-class' and reproducible. Palm automates common modeling tasks. For instance, Palm incorporates measurements to focus attention, represent constant behavior, and validate models. Palm's workflow is as follows. The workflow's input is source code annotated with Palm modeling annotations. The most important annotation models an instance of a block of code. Given annotated source code, the Palm Compiler produces executables and the Palm Monitor collects a representative performance profile. The Palm Generator synthesizes a model based on the static and dynamic mapping of annotations to program behavior. The model -- an executable program -- is a hierarchical composition of annotation functions, synthesized functions, statistics for runtime values, and performance measurements.« less

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

DOE PAGES

Lu, Dan; Ye, Ming; Curtis, Gary P.

2015-08-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict themore » reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally, limitations of applying MLBMA to the synthetic study and future real-world modeling are discussed.« less

Takagi-Sugeno-Kang fuzzy models of the rainfall-runoff transformation

NASA Astrophysics Data System (ADS)

Jacquin, A. P.; Shamseldin, A. Y.

2009-04-01

Fuzzy inference systems, or fuzzy models, are non-linear models that describe the relation between the inputs and the output of a real system using a set of fuzzy IF-THEN rules. This study deals with the application of Takagi-Sugeno-Kang type fuzzy models to the development of rainfall-runoff models operating on a daily basis, using a system based approach. The models proposed are classified in two types, each intended to account for different kinds of dominant non-linear effects in the rainfall-runoff relationship. Fuzzy models type 1 are intended to incorporate the effect of changes in the prevailing soil moisture content, while fuzzy models type 2 address the phenomenon of seasonality. Each model type consists of five fuzzy models of increasing complexity; the most complex fuzzy model of each model type includes all the model components found in the remaining fuzzy models of the respective type. The models developed are applied to data of six catchments from different geographical locations and sizes. Model performance is evaluated in terms of two measures of goodness of fit, namely the Nash-Sutcliffe criterion and the index of volumetric fit. The results of the fuzzy models are compared with those of the Simple Linear Model, the Linear Perturbation Model and the Nearest Neighbour Linear Perturbation Model, which use similar input information. Overall, the results of this study indicate that Takagi-Sugeno-Kang fuzzy models are a suitable alternative for modelling the rainfall-runoff relationship. However, it is also observed that increasing the complexity of the model structure does not necessarily produce an improvement in the performance of the fuzzy models. The relative importance of the different model components in determining the model performance is evaluated through sensitivity analysis of the model parameters in the accompanying study presented in this meeting. Acknowledgements: We would like to express our gratitude to Prof. Kieran M. O'Connor from the National University of Ireland, Galway, for providing the data used in this study.

A simple computational algorithm of model-based choice preference.

PubMed

Toyama, Asako; Katahira, Kentaro; Ohira, Hideki

2017-08-01

A broadly used computational framework posits that two learning systems operate in parallel during the learning of choice preferences-namely, the model-free and model-based reinforcement-learning systems. In this study, we examined another possibility, through which model-free learning is the basic system and model-based information is its modulator. Accordingly, we proposed several modified versions of a temporal-difference learning model to explain the choice-learning process. Using the two-stage decision task developed by Daw, Gershman, Seymour, Dayan, and Dolan (2011), we compared their original computational model, which assumes a parallel learning process, and our proposed models, which assume a sequential learning process. Choice data from 23 participants showed a better fit with the proposed models. More specifically, the proposed eligibility adjustment model, which assumes that the environmental model can weight the degree of the eligibility trace, can explain choices better under both model-free and model-based controls and has a simpler computational algorithm than the original model. In addition, the forgetting learning model and its variation, which assume changes in the values of unchosen actions, substantially improved the fits to the data. Overall, we show that a hybrid computational model best fits the data. The parameters used in this model succeed in capturing individual tendencies with respect to both model use in learning and exploration behavior. This computational model provides novel insights into learning with interacting model-free and model-based components.

Airborne Wireless Communication Modeling and Analysis with MATLAB

DTIC Science & Technology

2014-03-27

research develops a physical layer model that combines antenna modeling using computational electromagnetics and the two-ray propagation model to...predict the received signal strength. The antenna is modeled with triangular patches and analyzed by extending the antenna modeling algorithm by Sergey...7  2.7. Propagation Modeling : Statistical Models ............................................................8  2.8. Antenna Modeling

Marginal and Random Intercepts Models for Longitudinal Binary Data with Examples from Criminology

ERIC Educational Resources Information Center

Long, Jeffrey D.; Loeber, Rolf; Farrington, David P.

2009-01-01

Two models for the analysis of longitudinal binary data are discussed: the marginal model and the random intercepts model. In contrast to the linear mixed model (LMM), the two models for binary data are not subsumed under a single hierarchical model. The marginal model provides group-level information whereas the random intercepts model provides…

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

PubMed

Jenness, Samuel M; Goodreau, Steven M; Morris, Martina

2018-04-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel , designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel , designed to facilitate the exploration of novel research questions for advanced modelers.

EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks

PubMed Central

Jenness, Samuel M.; Goodreau, Steven M.; Morris, Martina

2018-01-01

Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers. PMID:29731699

Model compilation: An approach to automated model derivation

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Baudin, Catherine; Iwasaki, Yumi; Nayak, Pandurang; Tanaka, Kazuo

1990-01-01

An approach is introduced to automated model derivation for knowledge based systems. The approach, model compilation, involves procedurally generating the set of domain models used by a knowledge based system. With an implemented example, how this approach can be used to derive models of different precision and abstraction is illustrated, and models are tailored to different tasks, from a given set of base domain models. In particular, two implemented model compilers are described, each of which takes as input a base model that describes the structure and behavior of a simple electromechanical device, the Reaction Wheel Assembly of NASA's Hubble Space Telescope. The compilers transform this relatively general base model into simple task specific models for troubleshooting and redesign, respectively, by applying a sequence of model transformations. Each transformation in this sequence produces an increasingly more specialized model. The compilation approach lessens the burden of updating and maintaining consistency among models by enabling their automatic regeneration.

A composite computational model of liver glucose homeostasis. I. Building the composite model.

PubMed

Hetherington, J; Sumner, T; Seymour, R M; Li, L; Rey, M Varela; Yamaji, S; Saffrey, P; Margoninski, O; Bogle, I D L; Finkelstein, A; Warner, A

2012-04-07

A computational model of the glucagon/insulin-driven liver glucohomeostasis function, focusing on the buffering of glucose into glycogen, has been developed. The model exemplifies an 'engineering' approach to modelling in systems biology, and was produced by linking together seven component models of separate aspects of the physiology. The component models use a variety of modelling paradigms and degrees of simplification. Model parameters were determined by an iterative hybrid of fitting to high-scale physiological data, and determination from small-scale in vitro experiments or molecular biological techniques. The component models were not originally designed for inclusion within such a composite model, but were integrated, with modification, using our published modelling software and computational frameworks. This approach facilitates the development of large and complex composite models, although, inevitably, some compromises must be made when composing the individual models. Composite models of this form have not previously been demonstrated.

The applicability of turbulence models to aerodynamic and propulsion flowfields at McDonnell-Douglas Aerospace

NASA Technical Reports Server (NTRS)

Kral, Linda D.; Ladd, John A.; Mani, Mori

1995-01-01

The objective of this viewgraph presentation is to evaluate turbulence models for integrated aircraft components such as the forebody, wing, inlet, diffuser, nozzle, and afterbody. The one-equation models have replaced the algebraic models as the baseline turbulence models. The Spalart-Allmaras one-equation model consistently performs better than the Baldwin-Barth model, particularly in the log-layer and free shear layers. Also, the Sparlart-Allmaras model is not grid dependent like the Baldwin-Barth model. No general turbulence model exists for all engineering applications. The Spalart-Allmaras one-equation model and the Chien k-epsilon models are the preferred turbulence models. Although the two-equation models often better predict the flow field, they may take from two to five times the CPU time. Future directions are in further benchmarking the Menter blended k-w/k-epsilon and algorithmic improvements to reduce CPU time of the two-equation model.

The determination of third order linear models from a seventh order nonlinear jet engine model

NASA Technical Reports Server (NTRS)

Lalonde, Rick J.; Hartley, Tom T.; De Abreu-Garcia, J. Alex

1989-01-01

Results are presented that demonstrate how good reduced-order models can be obtained directly by recursive parameter identification using input/output (I/O) data of high-order nonlinear systems. Three different methods of obtaining a third-order linear model from a seventh-order nonlinear turbojet engine model are compared. The first method is to obtain a linear model from the original model and then reduce the linear model by standard reduction techniques such as residualization and balancing. The second method is to identify directly a third-order linear model by recursive least-squares parameter estimation using I/O data of the original model. The third method is to obtain a reduced-order model from the original model and then linearize the reduced model. Frequency responses are used as the performance measure to evaluate the reduced models. The reduced-order models along with their Bode plots are presented for comparison purposes.

BioModels: expanding horizons to include more modelling approaches and formats

PubMed Central

Nguyen, Tung V N; Graesslin, Martin; Hälke, Robert; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala M; Kothamachu, Varun B; Rodriguez, Nicolas; Swat, Maciej J; Eils, Jurgen; Eils, Roland; Laibe, Camille; Chelliah, Vijayalakshmi

2018-01-01

Abstract BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing. PMID:29106614

Modelling, teachers' views on the nature of modelling, and implications for the education of modellers

NASA Astrophysics Data System (ADS)

Justi, Rosária S.; Gilbert, John K.

2002-04-01

In this paper, the role of modelling in the teaching and learning of science is reviewed. In order to represent what is entailed in modelling, a 'model of modelling' framework is proposed. Five phases in moving towards a full capability in modelling are established by a review of the literature: learning models; learning to use models; learning how to revise models; learning to reconstruct models; learning to construct models de novo. In order to identify the knowledge and skills that science teachers think are needed to produce a model successfully, a semi-structured interview study was conducted with 39 Brazilian serving science teachers: 10 teaching at the 'fundamental' level (6-14 years); 10 teaching at the 'medium'-level (15-17 years); 10 undergraduate pre-service 'medium'-level teachers; 9 university teachers of chemistry. Their responses are used to establish what is entailed in implementing the 'model of modelling' framework. The implications for students, teachers, and for teacher education, of moving through the five phases of capability, are discussed.

Modelling land use change with generalized linear models--a multi-model analysis of change between 1860 and 2000 in Gallatin Valley, Montana.

PubMed

Aspinall, Richard

2004-08-01

This paper develops an approach to modelling land use change that links model selection and multi-model inference with empirical models and GIS. Land use change is frequently studied, and understanding gained, through a process of modelling that is an empirical analysis of documented changes in land cover or land use patterns. The approach here is based on analysis and comparison of multiple models of land use patterns using model selection and multi-model inference. The approach is illustrated with a case study of rural housing as it has developed for part of Gallatin County, Montana, USA. A GIS contains the location of rural housing on a yearly basis from 1860 to 2000. The database also documents a variety of environmental and socio-economic conditions. A general model of settlement development describes the evolution of drivers of land use change and their impacts in the region. This model is used to develop a series of different models reflecting drivers of change at different periods in the history of the study area. These period specific models represent a series of multiple working hypotheses describing (a) the effects of spatial variables as a representation of social, economic and environmental drivers of land use change, and (b) temporal changes in the effects of the spatial variables as the drivers of change evolve over time. Logistic regression is used to calibrate and interpret these models and the models are then compared and evaluated with model selection techniques. Results show that different models are 'best' for the different periods. The different models for different periods demonstrate that models are not invariant over time which presents challenges for validation and testing of empirical models. The research demonstrates (i) model selection as a mechanism for rating among many plausible models that describe land cover or land use patterns, (ii) inference from a set of models rather than from a single model, (iii) that models can be developed based on hypothesised relationships based on consideration of underlying and proximate causes of change, and (iv) that models are not invariant over time.

Investigation of prospective teachers' knowledge and understanding of models and modeling and their attitudes towards the use of models in science education

NASA Astrophysics Data System (ADS)

Aktan, Mustafa B.

The purpose of this study was to investigate prospective science teachers' knowledge and understanding of models and modeling, and their attitudes towards the use of models in science teaching through the following research questions: What knowledge do prospective science teachers have about models and modeling in science? What understandings about the nature of models do these teachers hold as a result of their educational training? What perceptions and attitudes do these teachers hold about the use of models in their teaching? Two main instruments, semi-structured in-depth interviewing and an open-item questionnaire, were used to obtain data from the participants. The data were analyzed from an interpretative phenomenological perspective and grounded theory methods. Earlier studies on in-service science teachers' understanding about the nature of models and modeling revealed that variations exist among teachers' limited yet diverse understanding of scientific models. The results of this study indicated that variations also existed among prospective science teachers' understanding of the concept of model and the nature of models. Apparently the participants' knowledge of models and modeling was limited and they viewed models as materialistic examples and representations. I found that the teachers believed the purpose of a model is to make phenomena more accessible and more understandable. They defined models by referring to an example, a representation, or a simplified version of the real thing. I found no evidence of negative attitudes towards use of models among the participants. Although the teachers valued the idea that scientific models are important aspects of science teaching and learning, and showed positive attitudes towards the use of models in their teaching, certain factors like level of learner, time, lack of modeling experience, and limited knowledge of models appeared to be affecting their perceptions negatively. Implications for the development of science teaching and teacher education programs are discussed. Directions for future research are suggested. Overall, based on the results, I suggest that prospective science teachers should engage in more modeling activities through their preparation programs, gain more modeling experience, and collaborate with their colleagues to better understand and implement scientific models in science teaching.

Validation of Groundwater Models: Meaningful or Meaningless?

NASA Astrophysics Data System (ADS)

Konikow, L. F.

2003-12-01

Although numerical simulation models are valuable tools for analyzing groundwater systems, their predictive accuracy is limited. People who apply groundwater flow or solute-transport models, as well as those who make decisions based on model results, naturally want assurance that a model is "valid." To many people, model validation implies some authentication of the truth or accuracy of the model. History matching is often presented as the basis for model validation. Although such model calibration is a necessary modeling step, it is simply insufficient for model validation. Because of parameter uncertainty and solution non-uniqueness, declarations of validation (or verification) of a model are not meaningful. Post-audits represent a useful means to assess the predictive accuracy of a site-specific model, but they require the existence of long-term monitoring data. Model testing may yield invalidation, but that is an opportunity to learn and to improve the conceptual and numerical models. Examples of post-audits and of the application of a solute-transport model to a radioactive waste disposal site illustrate deficiencies in model calibration, prediction, and validation.

Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

USGS Publications Warehouse

Royle, J. Andrew; Dorazio, Robert M.

2008-01-01

A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

Using the Model Coupling Toolkit to couple earth system models

USGS Publications Warehouse

Warner, J.C.; Perlin, N.; Skyllingstad, E.D.

2008-01-01

Continued advances in computational resources are providing the opportunity to operate more sophisticated numerical models. Additionally, there is an increasing demand for multidisciplinary studies that include interactions between different physical processes. Therefore there is a strong desire to develop coupled modeling systems that utilize existing models and allow efficient data exchange and model control. The basic system would entail model "1" running on "M" processors and model "2" running on "N" processors, with efficient exchange of model fields at predetermined synchronization intervals. Here we demonstrate two coupled systems: the coupling of the ocean circulation model Regional Ocean Modeling System (ROMS) to the surface wave model Simulating WAves Nearshore (SWAN), and the coupling of ROMS to the atmospheric model Coupled Ocean Atmosphere Prediction System (COAMPS). Both coupled systems use the Model Coupling Toolkit (MCT) as a mechanism for operation control and inter-model distributed memory transfer of model variables. In this paper we describe requirements and other options for model coupling, explain the MCT library, ROMS, SWAN and COAMPS models, methods for grid decomposition and sparse matrix interpolation, and provide an example from each coupled system. Methods presented in this paper are clearly applicable for coupling of other types of models. ?? 2008 Elsevier Ltd. All rights reserved.

Generalized Multilevel Structural Equation Modeling

ERIC Educational Resources Information Center

Rabe-Hesketh, Sophia; Skrondal, Anders; Pickles, Andrew

2004-01-01

A unifying framework for generalized multilevel structural equation modeling is introduced. The models in the framework, called generalized linear latent and mixed models (GLLAMM), combine features of generalized linear mixed models (GLMM) and structural equation models (SEM) and consist of a response model and a structural model for the latent…

Frequentist Model Averaging in Structural Equation Modelling.

PubMed

Jin, Shaobo; Ankargren, Sebastian

2018-06-04

Model selection from a set of candidate models plays an important role in many structural equation modelling applications. However, traditional model selection methods introduce extra randomness that is not accounted for by post-model selection inference. In the current study, we propose a model averaging technique within the frequentist statistical framework. Instead of selecting an optimal model, the contributions of all candidate models are acknowledged. Valid confidence intervals and a [Formula: see text] test statistic are proposed. A simulation study shows that the proposed method is able to produce a robust mean-squared error, a better coverage probability, and a better goodness-of-fit test compared to model selection. It is an interesting compromise between model selection and the full model.

Premium analysis for copula model: A case study for Malaysian motor insurance claims

NASA Astrophysics Data System (ADS)

Resti, Yulia; Ismail, Noriszura; Jaaman, Saiful Hafizah

2014-06-01

This study performs premium analysis for copula models with regression marginals. For illustration purpose, the copula models are fitted to the Malaysian motor insurance claims data. In this study, we consider copula models from Archimedean and Elliptical families, and marginal distributions of Gamma and Inverse Gaussian regression models. The simulated results from independent model, which is obtained from fitting regression models separately to each claim category, and dependent model, which is obtained from fitting copula models to all claim categories, are compared. The results show that the dependent model using Frank copula is the best model since the risk premiums estimated under this model are closely approximate to the actual claims experience relative to the other copula models.

Utilizing Biological Models to Determine the Recruitment of the IRA by Modeling the Voting Behavior of Sinn Fein

DTIC Science & Technology

2006-03-01

models, the thesis applies a biological model, the Lotka - Volterra predator- prey model, to a highly suggestive case study, that of the Irish Republican...Model, Irish Republican Army, Sinn Féin, Lotka - Volterra Predator Prey Model, Recruitment, British Army 16. PRICE CODE 17. SECURITY CLASSIFICATION OF...weaknesses of sociological and biological models, the thesis applies a biological model, the Lotka - Volterra predator-prey model, to a highly suggestive

Right-Sizing Statistical Models for Longitudinal Data

PubMed Central

Wood, Phillip K.; Steinley, Douglas; Jackson, Kristina M.

2015-01-01

Arguments are proposed that researchers using longitudinal data should consider more and less complex statistical model alternatives to their initially chosen techniques in an effort to “right-size” the model to the data at hand. Such model comparisons may alert researchers who use poorly fitting overly parsimonious models to more complex better fitting alternatives, and, alternatively, may identify more parsimonious alternatives to overly complex (and perhaps empirically under-identified and/or less powerful) statistical models. A general framework is proposed for considering (often nested) relationships between a variety of psychometric and growth curve models. A three-step approach is proposed in which models are evaluated based on the number and patterning of variance components prior to selection of better-fitting growth models that explain both mean and variation/covariation patterns. The orthogonal, free-curve slope-intercept (FCSI) growth model is considered as a general model which includes, as special cases, many models including the Factor Mean model (FM, McArdle & Epstein, 1987), McDonald's (1967) linearly constrained factor model, Hierarchical Linear Models (HLM), Repeated Measures MANOVA, and the Linear Slope Intercept (LinearSI) Growth Model. The FCSI model, in turn, is nested within the Tuckerized factor model. The approach is illustrated by comparing alternative models in a longitudinal study of children's vocabulary and by comparison of several candidate parametric growth and chronometric models in a Monte Carlo study. PMID:26237507

Right-sizing statistical models for longitudinal data.

PubMed

Wood, Phillip K; Steinley, Douglas; Jackson, Kristina M

2015-12-01

Arguments are proposed that researchers using longitudinal data should consider more and less complex statistical model alternatives to their initially chosen techniques in an effort to "right-size" the model to the data at hand. Such model comparisons may alert researchers who use poorly fitting, overly parsimonious models to more complex, better-fitting alternatives and, alternatively, may identify more parsimonious alternatives to overly complex (and perhaps empirically underidentified and/or less powerful) statistical models. A general framework is proposed for considering (often nested) relationships between a variety of psychometric and growth curve models. A 3-step approach is proposed in which models are evaluated based on the number and patterning of variance components prior to selection of better-fitting growth models that explain both mean and variation-covariation patterns. The orthogonal free curve slope intercept (FCSI) growth model is considered a general model that includes, as special cases, many models, including the factor mean (FM) model (McArdle & Epstein, 1987), McDonald's (1967) linearly constrained factor model, hierarchical linear models (HLMs), repeated-measures multivariate analysis of variance (MANOVA), and the linear slope intercept (linearSI) growth model. The FCSI model, in turn, is nested within the Tuckerized factor model. The approach is illustrated by comparing alternative models in a longitudinal study of children's vocabulary and by comparing several candidate parametric growth and chronometric models in a Monte Carlo study. (c) 2015 APA, all rights reserved).

Model averaging techniques for quantifying conceptual model uncertainty.

PubMed

Singh, Abhishek; Mishra, Srikanta; Ruskauff, Greg

2010-01-01

In recent years a growing understanding has emerged regarding the need to expand the modeling paradigm to include conceptual model uncertainty for groundwater models. Conceptual model uncertainty is typically addressed by formulating alternative model conceptualizations and assessing their relative likelihoods using statistical model averaging approaches. Several model averaging techniques and likelihood measures have been proposed in the recent literature for this purpose with two broad categories--Monte Carlo-based techniques such as Generalized Likelihood Uncertainty Estimation or GLUE (Beven and Binley 1992) and criterion-based techniques that use metrics such as the Bayesian and Kashyap Information Criteria (e.g., the Maximum Likelihood Bayesian Model Averaging or MLBMA approach proposed by Neuman 2003) and Akaike Information Criterion-based model averaging (AICMA) (Poeter and Anderson 2005). These different techniques can often lead to significantly different relative model weights and ranks because of differences in the underlying statistical assumptions about the nature of model uncertainty. This paper provides a comparative assessment of the four model averaging techniques (GLUE, MLBMA with KIC, MLBMA with BIC, and AIC-based model averaging) mentioned above for the purpose of quantifying the impacts of model uncertainty on groundwater model predictions. Pros and cons of each model averaging technique are examined from a practitioner's perspective using two groundwater modeling case studies. Recommendations are provided regarding the use of these techniques in groundwater modeling practice.

Examination of various turbulence models for application in liquid rocket thrust chambers

NASA Technical Reports Server (NTRS)

Hung, R. J.

1991-01-01

There is a large variety of turbulence models available. These models include direct numerical simulation, large eddy simulation, Reynolds stress/flux model, zero equation model, one equation model, two equation k-epsilon model, multiple-scale model, etc. Each turbulence model contains different physical assumptions and requirements. The natures of turbulence are randomness, irregularity, diffusivity and dissipation. The capabilities of the turbulence models, including physical strength, weakness, limitations, as well as numerical and computational considerations, are reviewed. Recommendations are made for the potential application of a turbulence model in thrust chamber and performance prediction programs. The full Reynolds stress model is recommended. In a workshop, specifically called for the assessment of turbulence models for applications in liquid rocket thrust chambers, most of the experts present were also in favor of the recommendation of the Reynolds stress model.

Comparative study of turbulence models in predicting hypersonic inlet flows

NASA Technical Reports Server (NTRS)

Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.

1992-01-01

A numerical study was conducted to analyze the performance of different turbulence models when applied to the hypersonic NASA P8 inlet. Computational results from the PARC2D code, which solves the full two-dimensional Reynolds-averaged Navier-Stokes equation, were compared with experimental data. The zero-equation models considered for the study were the Baldwin-Lomax model, the Thomas model, and a combination of the Baldwin-Lomax and Thomas models; the two-equation models considered were the Chien model, the Speziale model (both low Reynolds number), and the Launder and Spalding model (high Reynolds number). The Thomas model performed best among the zero-equation models, and predicted good pressure distributions. The Chien and Speziale models compared wery well with the experimental data, and performed better than the Thomas model near the walls.

Comparative study of turbulence models in predicting hypersonic inlet flows

NASA Technical Reports Server (NTRS)

Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.

1992-01-01

A numerical study was conducted to analyze the performance of different turbulence models when applied to the hypersonic NASA P8 inlet. Computational results from the PARC2D code, which solves the full two-dimensional Reynolds-averaged Navier-Stokes equation, were compared with experimental data. The zero-equation models considered for the study were the Baldwin-Lomax model, the Thomas model, and a combination of the Baldwin-Lomax and Thomas models; the two-equation models considered were the Chien model, the Speziale model (both low Reynolds number), and the Launder and Spalding model (high Reynolds number). The Thomas model performed best among the zero-equation models, and predicted good pressure distributions. The Chien and Speziale models compared very well with the experimental data, and performed better than the Thomas model near the walls.

[The reliability of dento-maxillary models created by cone-beam CT and rapid prototyping:a comparative study].

PubMed

Lv, Yan; Yan, Bin; Wang, Lin; Lou, Dong-hua

2012-04-01

To analyze the reliability of the dento-maxillary models created by cone-beam CT and rapid prototyping (RP). Plaster models were obtained from 20 orthodontic patients who had been scanned by cone-beam CT and 3-D models were formed after the calculation and reconstruction of software. Then, computerized composite models (RP models) were produced by rapid prototyping technique. The crown widths, dental arch widths and dental arch lengths on each plaster model, 3-D model and RP model were measured, followed by statistical analysis with SPSS17.0 software package. For crown widths, dental arch lengths and crowding, there were significant differences(P<0.05) among the 3 models, but the dental arch widths were on the contrary. Measurements on 3-D models were significantly smaller than those on other two models(P<0.05). Compared with 3-D models, RP models had more numbers which were not significantly different from those on plaster models(P>0.05). The regression coefficient among three models were significantly different(P<0.01), ranging from 0.8 to 0.9. But between RP and plaster models was bigger than that between 3-D and plaster models. There is high consistency within 3 models, while some differences were accepted in clinic. Therefore, it is possible to substitute 3-D and RP models for plaster models in order to save storage space and improve efficiency.

Smart Frameworks and Self-Describing Models: Model Metadata for Automated Coupling of Hydrologic Process Components (Invited)

NASA Astrophysics Data System (ADS)

Peckham, S. D.

2013-12-01

Model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System) and ESMF (Earth System Modeling Framework) have developed mechanisms that allow heterogeneous sets of process models to be assembled in a plug-and-play manner to create composite "system models". These mechanisms facilitate code reuse, but must simultaneously satisfy many different design criteria. They must be able to mediate or compensate for differences between the process models, such as their different programming languages, computational grids, time-stepping schemes, variable names and variable units. However, they must achieve this interoperability in a way that: (1) is noninvasive, requiring only relatively small and isolated changes to the original source code, (2) does not significantly reduce performance, (3) is not time-consuming or confusing for a model developer to implement, (4) can very easily be updated to accommodate new versions of a given process model and (5) does not shift the burden of providing model interoperability to the model developers, e.g. by requiring them to provide their output in specific forms that meet the input requirements of other models. In tackling these design challenges, model framework developers have learned that the best solution is to provide each model with a simple, standardized interface, i.e. a set of standardized functions that make the model: (1) fully-controllable by a caller (e.g. a model framework) and (2) self-describing. Model control functions are separate functions that allow a caller to initialize the model, advance the model's state variables in time and finalize the model. Model description functions allow a caller to retrieve detailed information on the model's input and output variables, its computational grid and its timestepping scheme. If the caller is a modeling framework, it can compare the answers to these queries with similar answers from other process models in a collection and then automatically call framework service components as necessary to mediate the differences between the coupled models. This talk will first review two key products of the CSDMS project, namely a standardized model interface called the Basic Model Interface (BMI) and the CSDMS Standard Names. The standard names are used in conjunction with BMI to provide a semantic matching mechanism that allows output variables from one process model to be reliably used as input variables to other process models in a collection. They include not just a standardized naming scheme for model variables, but also a standardized set of terms for describing the attributes and assumptions of a given model. To illustrate the power of standardized model interfaces and metadata, a smart, light-weight modeling framework written in Python will be introduced that can automatically (without user intervention) couple a set of BMI-enabled hydrologic process components together to create a spatial hydrologic model. The same mechanisms could also be used to provide seamless integration (import/export) of data and models.

A model-averaging method for assessing groundwater conceptual model uncertainty.

PubMed

Ye, Ming; Pohlmann, Karl F; Chapman, Jenny B; Pohll, Greg M; Reeves, Donald M

2010-01-01

This study evaluates alternative groundwater models with different recharge and geologic components at the northern Yucca Flat area of the Death Valley Regional Flow System (DVRFS), USA. Recharge over the DVRFS has been estimated using five methods, and five geological interpretations are available at the northern Yucca Flat area. Combining the recharge and geological components together with additional modeling components that represent other hydrogeological conditions yields a total of 25 groundwater flow models. As all the models are plausible given available data and information, evaluating model uncertainty becomes inevitable. On the other hand, hydraulic parameters (e.g., hydraulic conductivity) are uncertain in each model, giving rise to parametric uncertainty. Propagation of the uncertainty in the models and model parameters through groundwater modeling causes predictive uncertainty in model predictions (e.g., hydraulic head and flow). Parametric uncertainty within each model is assessed using Monte Carlo simulation, and model uncertainty is evaluated using the model averaging method. Two model-averaging techniques (on the basis of information criteria and GLUE) are discussed. This study shows that contribution of model uncertainty to predictive uncertainty is significantly larger than that of parametric uncertainty. For the recharge and geological components, uncertainty in the geological interpretations has more significant effect on model predictions than uncertainty in the recharge estimates. In addition, weighted residuals vary more for the different geological models than for different recharge models. Most of the calibrated observations are not important for discriminating between the alternative models, because their weighted residuals vary only slightly from one model to another.

Meta-Modeling: A Knowledge-Based Approach to Facilitating Model Construction and Reuse

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Dungan, Jennifer L.

1997-01-01

In this paper, we introduce a new modeling approach called meta-modeling and illustrate its practical applicability to the construction of physically-based ecosystem process models. As a critical adjunct to modeling codes meta-modeling requires explicit specification of certain background information related to the construction and conceptual underpinnings of a model. This information formalizes the heretofore tacit relationship between the mathematical modeling code and the underlying real-world phenomena being investigated, and gives insight into the process by which the model was constructed. We show how the explicit availability of such information can make models more understandable and reusable and less subject to misinterpretation. In particular, background information enables potential users to better interpret an implemented ecosystem model without direct assistance from the model author. Additionally, we show how the discipline involved in specifying background information leads to improved management of model complexity and fewer implementation errors. We illustrate the meta-modeling approach in the context of the Scientists' Intelligent Graphical Modeling Assistant (SIGMA) a new model construction environment. As the user constructs a model using SIGMA the system adds appropriate background information that ties the executable model to the underlying physical phenomena under investigation. Not only does this information improve the understandability of the final model it also serves to reduce the overall time and programming expertise necessary to initially build and subsequently modify models. Furthermore, SIGMA's use of background knowledge helps eliminate coding errors resulting from scientific and dimensional inconsistencies that are otherwise difficult to avoid when building complex models. As a. demonstration of SIGMA's utility, the system was used to reimplement and extend a well-known forest ecosystem dynamics model: Forest-BGC.

10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. MOVABLE BED SEDIMENTATION MODELS. DOGTOOTH BEND MODEL (MODEL SCALE: 1' = 400' HORIZONTAL, 1' = 100' VERTICAL), AND GREENVILLE BRIDGE MODEL (MODEL SCALE: 1' = 360' HORIZONTAL, 1' = 100' VERTICAL). - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

Bayesian Data-Model Fit Assessment for Structural Equation Modeling

ERIC Educational Resources Information Center

Levy, Roy

2011-01-01

Bayesian approaches to modeling are receiving an increasing amount of attention in the areas of model construction and estimation in factor analysis, structural equation modeling (SEM), and related latent variable models. However, model diagnostics and model criticism remain relatively understudied aspects of Bayesian SEM. This article describes…

Evolution of computational models in BioModels Database and the Physiome Model Repository.

PubMed

Scharm, Martin; Gebhardt, Tom; Touré, Vasundra; Bagnacani, Andrea; Salehzadeh-Yazdi, Ali; Wolkenhauer, Olaf; Waltemath, Dagmar

2018-04-12

A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present study is to identify changes in models and make them transparent and traceable. We analysed 13734 models from BioModels Database and the Physiome Model Repository. For each model, we studied the frequencies and types of updates between its first and latest release. To demonstrate the impact of changes, we explored the history of a Repressilator model in BioModels Database. We observed continuous updates in the majority of models. Surprisingly, even the early models are still being modified. We furthermore detected that many updates target annotations, which improves the information one can gain from models. To support the analysis of changes in model repositories we developed MoSt, an online tool for visualisations of changes in models. The scripts used to generate the data and figures for this study are available from GitHub https://github.com/binfalse/BiVeS-StatsGenerator and as a Docker image at https://hub.docker.com/r/binfalse/bives-statsgenerator/ . The website https://most.bio.informatik.uni-rostock.de/ provides interactive access to model versions and their evolutionary statistics. The reuse of models is still impeded by a lack of trust and documentation. A detailed and transparent documentation of all aspects of the model, including its provenance, will improve this situation. Knowledge about a model's provenance can avoid the repetition of mistakes that others already faced. More insights are gained into how the system evolves from initial findings to a profound understanding. We argue that it is the responsibility of the maintainers of model repositories to offer transparent model provenance to their users.

Large-watershed flood simulation and forecasting based on different-resolution distributed hydrological model

NASA Astrophysics Data System (ADS)

Li, J.

2017-12-01

Large-watershed flood simulation and forecasting is very important for a distributed hydrological model in the application. There are some challenges including the model's spatial resolution effect, model performance and accuracy and so on. To cope with the challenge of the model's spatial resolution effect, different model resolution including 1000m*1000m, 600m*600m, 500m*500m, 400m*400m, 200m*200m were used to build the distributed hydrological model—Liuxihe model respectively. The purpose is to find which one is the best resolution for Liuxihe model in Large-watershed flood simulation and forecasting. This study sets up a physically based distributed hydrological model for flood forecasting of the Liujiang River basin in south China. Terrain data digital elevation model (DEM), soil type and land use type are downloaded from the website freely. The model parameters are optimized by using an improved Particle Swarm Optimization(PSO) algorithm; And parameter optimization could reduce the parameter uncertainty that exists for physically deriving model parameters. The different model resolution (200m*200m—1000m*1000m ) are proposed for modeling the Liujiang River basin flood with the Liuxihe model in this study. The best model's spatial resolution effect for flood simulation and forecasting is 200m*200m.And with the model's spatial resolution reduction, the model performance and accuracy also become worse and worse. When the model resolution is 1000m*1000m, the flood simulation and forecasting result is the worst, also the river channel divided based on this resolution is differs from the actual one. To keep the model with an acceptable performance, minimum model spatial resolution is needed. The suggested threshold model spatial resolution for modeling the Liujiang River basin flood is a 500m*500m grid cell, but the model spatial resolution with a 200m*200m grid cell is recommended in this study to keep the model at a best performance.

Computational Models for Calcium-Mediated Astrocyte Functions.

PubMed

Manninen, Tiina; Havela, Riikka; Linne, Marja-Leena

2018-01-01

The computational neuroscience field has heavily concentrated on the modeling of neuronal functions, largely ignoring other brain cells, including one type of glial cell, the astrocytes. Despite the short history of modeling astrocytic functions, we were delighted about the hundreds of models developed so far to study the role of astrocytes, most often in calcium dynamics, synchronization, information transfer, and plasticity in vitro , but also in vascular events, hyperexcitability, and homeostasis. Our goal here is to present the state-of-the-art in computational modeling of astrocytes in order to facilitate better understanding of the functions and dynamics of astrocytes in the brain. Due to the large number of models, we concentrated on a hundred models that include biophysical descriptions for calcium signaling and dynamics in astrocytes. We categorized the models into four groups: single astrocyte models, astrocyte network models, neuron-astrocyte synapse models, and neuron-astrocyte network models to ease their use in future modeling projects. We characterized the models based on which earlier models were used for building the models and which type of biological entities were described in the astrocyte models. Features of the models were compared and contrasted so that similarities and differences were more readily apparent. We discovered that most of the models were basically generated from a small set of previously published models with small variations. However, neither citations to all the previous models with similar core structure nor explanations of what was built on top of the previous models were provided, which made it possible, in some cases, to have the same models published several times without an explicit intention to make new predictions about the roles of astrocytes in brain functions. Furthermore, only a few of the models are available online which makes it difficult to reproduce the simulation results and further develop the models. Thus, we would like to emphasize that only via reproducible research are we able to build better computational models for astrocytes, which truly advance science. Our study is the first to characterize in detail the biophysical and biochemical mechanisms that have been modeled for astrocytes.

Computational Models for Calcium-Mediated Astrocyte Functions

PubMed Central

Manninen, Tiina; Havela, Riikka; Linne, Marja-Leena

2018-01-01

The computational neuroscience field has heavily concentrated on the modeling of neuronal functions, largely ignoring other brain cells, including one type of glial cell, the astrocytes. Despite the short history of modeling astrocytic functions, we were delighted about the hundreds of models developed so far to study the role of astrocytes, most often in calcium dynamics, synchronization, information transfer, and plasticity in vitro, but also in vascular events, hyperexcitability, and homeostasis. Our goal here is to present the state-of-the-art in computational modeling of astrocytes in order to facilitate better understanding of the functions and dynamics of astrocytes in the brain. Due to the large number of models, we concentrated on a hundred models that include biophysical descriptions for calcium signaling and dynamics in astrocytes. We categorized the models into four groups: single astrocyte models, astrocyte network models, neuron-astrocyte synapse models, and neuron-astrocyte network models to ease their use in future modeling projects. We characterized the models based on which earlier models were used for building the models and which type of biological entities were described in the astrocyte models. Features of the models were compared and contrasted so that similarities and differences were more readily apparent. We discovered that most of the models were basically generated from a small set of previously published models with small variations. However, neither citations to all the previous models with similar core structure nor explanations of what was built on top of the previous models were provided, which made it possible, in some cases, to have the same models published several times without an explicit intention to make new predictions about the roles of astrocytes in brain functions. Furthermore, only a few of the models are available online which makes it difficult to reproduce the simulation results and further develop the models. Thus, we would like to emphasize that only via reproducible research are we able to build better computational models for astrocytes, which truly advance science. Our study is the first to characterize in detail the biophysical and biochemical mechanisms that have been modeled for astrocytes. PMID:29670517

Assessing the impact of land use change on hydrology by ensemble modeling (LUCHEM). I: Model intercomparison with current land use

USGS Publications Warehouse

Breuer, L.; Huisman, J.A.; Willems, P.; Bormann, H.; Bronstert, A.; Croke, B.F.W.; Frede, H.-G.; Graff, T.; Hubrechts, L.; Jakeman, A.J.; Kite, G.; Lanini, J.; Leavesley, G.; Lettenmaier, D.P.; Lindstrom, G.; Seibert, J.; Sivapalan, M.; Viney, N.R.

2009-01-01

This paper introduces the project on 'Assessing the impact of land use change on hydrology by ensemble modeling (LUCHEM)' that aims at investigating the envelope of predictions on changes in hydrological fluxes due to land use change. As part of a series of four papers, this paper outlines the motivation and setup of LUCHEM, and presents a model intercomparison for the present-day simulation results. Such an intercomparison provides a valuable basis to investigate the effects of different model structures on model predictions and paves the ground for the analysis of the performance of multi-model ensembles and the reliability of the scenario predictions in companion papers. In this study, we applied a set of 10 lumped, semi-lumped and fully distributed hydrological models that have been previously used in land use change studies to the low mountainous Dill catchment, Germany. Substantial differences in model performance were observed with Nash-Sutcliffe efficiencies ranging from 0.53 to 0.92. Differences in model performance were attributed to (1) model input data, (2) model calibration and (3) the physical basis of the models. The models were applied with two sets of input data: an original and a homogenized data set. This homogenization of precipitation, temperature and leaf area index was performed to reduce the variation between the models. Homogenization improved the comparability of model simulations and resulted in a reduced average bias, although some variation in model data input remained. The effect of the physical differences between models on the long-term water balance was mainly attributed to differences in how models represent evapotranspiration. Semi-lumped and lumped conceptual models slightly outperformed the fully distributed and physically based models. This was attributed to the automatic model calibration typically used for this type of models. Overall, however, we conclude that there was no superior model if several measures of model performance are considered and that all models are suitable to participate in further multi-model ensemble set-ups and land use change scenario investigations. ?? 2008 Elsevier Ltd. All rights reserved.

Benchmarking test of empirical root water uptake models

NASA Astrophysics Data System (ADS)

dos Santos, Marcos Alex; de Jong van Lier, Quirijn; van Dam, Jos C.; Freire Bezerra, Andre Herman

2017-01-01

Detailed physical models describing root water uptake (RWU) are an important tool for the prediction of RWU and crop transpiration, but the hydraulic parameters involved are hardly ever available, making them less attractive for many studies. Empirical models are more readily used because of their simplicity and the associated lower data requirements. The purpose of this study is to evaluate the capability of some empirical models to mimic the RWU distribution under varying environmental conditions predicted from numerical simulations with a detailed physical model. A review of some empirical models used as sub-models in ecohydrological models is presented, and alternative empirical RWU models are proposed. All these empirical models are analogous to the standard Feddes model, but differ in how RWU is partitioned over depth or how the transpiration reduction function is defined. The parameters of the empirical models are determined by inverse modelling of simulated depth-dependent RWU. The performance of the empirical models and their optimized empirical parameters depends on the scenario. The standard empirical Feddes model only performs well in scenarios with low root length density R, i.e. for scenarios with low RWU compensation. For medium and high R, the Feddes RWU model cannot mimic properly the root uptake dynamics as predicted by the physical model. The Jarvis RWU model in combination with the Feddes reduction function (JMf) only provides good predictions for low and medium R scenarios. For high R, it cannot mimic the uptake patterns predicted by the physical model. Incorporating a newly proposed reduction function into the Jarvis model improved RWU predictions. Regarding the ability of the models to predict plant transpiration, all models accounting for compensation show good performance. The Akaike information criterion (AIC) indicates that the Jarvis (2010) model (JMII), with no empirical parameters to be estimated, is the best model. The proposed models are better in predicting RWU patterns similar to the physical model. The statistical indices point to them as the best alternatives for mimicking RWU predictions of the physical model.

Modeling uncertainty: quicksand for water temperature modeling

USGS Publications Warehouse

Bartholow, John M.

2003-01-01

Uncertainty has been a hot topic relative to science generally, and modeling specifically. Modeling uncertainty comes in various forms: measured data, limited model domain, model parameter estimation, model structure, sensitivity to inputs, modelers themselves, and users of the results. This paper will address important components of uncertainty in modeling water temperatures, and discuss several areas that need attention as the modeling community grapples with how to incorporate uncertainty into modeling without getting stuck in the quicksand that prevents constructive contributions to policy making. The material, and in particular the reference, are meant to supplement the presentation given at this conference.

Energy modeling. Volume 2: Inventory and details of state energy models

NASA Astrophysics Data System (ADS)

Melcher, A. G.; Underwood, R. G.; Weber, J. C.; Gist, R. L.; Holman, R. P.; Donald, D. W.

1981-05-01

An inventory of energy models developed by or for state governments is presented, and certain models are discussed in depth. These models address a variety of purposes such as: supply or demand of energy or of certain types of energy; emergency management of energy; and energy economics. Ten models are described. The purpose, use, and history of the model is discussed, and information is given on the outputs, inputs, and mathematical structure of the model. The models include five models dealing with energy demand, one of which is econometric and four of which are econometric-engineering end-use models.

Advances in Geoscience Modeling: Smart Modeling Frameworks, Self-Describing Models and the Role of Standardized Metadata

NASA Astrophysics Data System (ADS)

Peckham, Scott

2016-04-01

Over the last decade, model coupling frameworks like CSDMS (Community Surface Dynamics Modeling System) and ESMF (Earth System Modeling Framework) have developed mechanisms that make it much easier for modelers to connect heterogeneous sets of process models in a plug-and-play manner to create composite "system models". These mechanisms greatly simplify code reuse, but must simultaneously satisfy many different design criteria. They must be able to mediate or compensate for differences between the process models, such as their different programming languages, computational grids, time-stepping schemes, variable names and variable units. However, they must achieve this interoperability in a way that: (1) is noninvasive, requiring only relatively small and isolated changes to the original source code, (2) does not significantly reduce performance, (3) is not time-consuming or confusing for a model developer to implement, (4) can very easily be updated to accommodate new versions of a given process model and (5) does not shift the burden of providing model interoperability to the model developers. In tackling these design challenges, model framework developers have learned that the best solution is to provide each model with a simple, standardized interface, i.e. a set of standardized functions that make the model: (1) fully-controllable by a caller (e.g. a model framework) and (2) self-describing with standardized metadata. Model control functions are separate functions that allow a caller to initialize the model, advance the model's state variables in time and finalize the model. Model description functions allow a caller to retrieve detailed information on the model's input and output variables, its computational grid and its timestepping scheme. If the caller is a modeling framework, it can use the self description functions to learn about each process model in a collection to be coupled and then automatically call framework service components (e.g. regridders, time interpolators and unit converters) as necessary to mediate the differences between them so they can work together. This talk will first review two key products of the CSDMS project, namely a standardized model interface called the Basic Model Interface (BMI) and the CSDMS Standard Names. The standard names are used in conjunction with BMI to provide a semantic matching mechanism that allows output variables from one process model or data set to be reliably used as input variables to other process models in a collection. They include not just a standardized naming scheme for model variables, but also a standardized set of terms for describing the attributes and assumptions of a given model. Recent efforts to bring powerful uncertainty analysis and inverse modeling toolkits such as DAKOTA into modeling frameworks will also be described. This talk will conclude with an overview of several related modeling projects that have been funded by NSF's EarthCube initiative, namely the Earth System Bridge, OntoSoft and GeoSemantics projects.

[A review on research of land surface water and heat fluxes].

PubMed

Sun, Rui; Liu, Changming

2003-03-01

Many field experiments were done, and soil-vegetation-atmosphere transfer(SVAT) models were stablished to estimate land surface heat fluxes. In this paper, the processes of experimental research on land surface water and heat fluxes are reviewed, and three kinds of SVAT model(single layer model, two layer model and multi-layer model) are analyzed. Remote sensing data are widely used to estimate land surface heat fluxes. Based on remote sensing and energy balance equation, different models such as simplified model, single layer model, extra resistance model, crop water stress index model and two source resistance model are developed to estimate land surface heat fluxes and evapotranspiration. These models are also analyzed in this paper.

Examination of simplified travel demand model. [Internal volume forecasting model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, R.L. Jr.; McFarlane, W.J.

1978-01-01

A simplified travel demand model, the Internal Volume Forecasting (IVF) model, proposed by Low in 1972 is evaluated as an alternative to the conventional urban travel demand modeling process. The calibration of the IVF model for a county-level study area in Central Wisconsin results in what appears to be a reasonable model; however, analysis of the structure of the model reveals two primary mis-specifications. Correction of the mis-specifications leads to a simplified gravity model version of the conventional urban travel demand models. Application of the original IVF model to ''forecast'' 1960 traffic volumes based on the model calibrated for 1970more » produces accurate estimates. Shortcut and ad hoc models may appear to provide reasonable results in both the base and horizon years; however, as shown by the IVF mode, such models will not always provide a reliable basis for transportation planning and investment decisions.« less

MPTinR: analysis of multinomial processing tree models in R.

PubMed

Singmann, Henrik; Kellen, David

2013-06-01

We introduce MPTinR, a software package developed for the analysis of multinomial processing tree (MPT) models. MPT models represent a prominent class of cognitive measurement models for categorical data with applications in a wide variety of fields. MPTinR is the first software for the analysis of MPT models in the statistical programming language R, providing a modeling framework that is more flexible than standalone software packages. MPTinR also introduces important features such as (1) the ability to calculate the Fisher information approximation measure of model complexity for MPT models, (2) the ability to fit models for categorical data outside the MPT model class, such as signal detection models, (3) a function for model selection across a set of nested and nonnested candidate models (using several model selection indices), and (4) multicore fitting. MPTinR is available from the Comprehensive R Archive Network at http://cran.r-project.org/web/packages/MPTinR/ .

Latent log-linear models for handwritten digit classification.

PubMed

Deselaers, Thomas; Gass, Tobias; Heigold, Georg; Ney, Hermann

2012-06-01

We present latent log-linear models, an extension of log-linear models incorporating latent variables, and we propose two applications thereof: log-linear mixture models and image deformation-aware log-linear models. The resulting models are fully discriminative, can be trained efficiently, and the model complexity can be controlled. Log-linear mixture models offer additional flexibility within the log-linear modeling framework. Unlike previous approaches, the image deformation-aware model directly considers image deformations and allows for a discriminative training of the deformation parameters. Both are trained using alternating optimization. For certain variants, convergence to a stationary point is guaranteed and, in practice, even variants without this guarantee converge and find models that perform well. We tune the methods on the USPS data set and evaluate on the MNIST data set, demonstrating the generalization capabilities of our proposed models. Our models, although using significantly fewer parameters, are able to obtain competitive results with models proposed in the literature.

Understanding and Predicting Urban Propagation Losses

DTIC Science & Technology

2009-09-01

6. Extended Hata Model ..........................22 7. Modified Hata Model ..........................22 8. Walfisch – Ikegami Model...39 4. COST (Extended) Hata Model ...................40 5. Modified Hata Model ..........................41 6. Walfisch- Ikegami Model...47 1. Scenario One – Walfisch- Ikegami Model ........51 2. Scenario Two – Modified Hata Model ...........52 3. Scenario Three – Urban Hata

A Framework for Sharing and Integrating Remote Sensing and GIS Models Based on Web Service

PubMed Central

Chen, Zeqiang; Lin, Hui; Chen, Min; Liu, Deer; Bao, Ying; Ding, Yulin

2014-01-01

Sharing and integrating Remote Sensing (RS) and Geographic Information System/Science (GIS) models are critical for developing practical application systems. Facilitating model sharing and model integration is a problem for model publishers and model users, respectively. To address this problem, a framework based on a Web service for sharing and integrating RS and GIS models is proposed in this paper. The fundamental idea of the framework is to publish heterogeneous RS and GIS models into standard Web services for sharing and interoperation and then to integrate the RS and GIS models using Web services. For the former, a “black box” and a visual method are employed to facilitate the publishing of the models as Web services. For the latter, model integration based on the geospatial workflow and semantic supported marching method is introduced. Under this framework, model sharing and integration is applied for developing the Pearl River Delta water environment monitoring system. The results show that the framework can facilitate model sharing and model integration for model publishers and model users. PMID:24901016

A framework for sharing and integrating remote sensing and GIS models based on Web service.

PubMed

Chen, Zeqiang; Lin, Hui; Chen, Min; Liu, Deer; Bao, Ying; Ding, Yulin

2014-01-01

Sharing and integrating Remote Sensing (RS) and Geographic Information System/Science (GIS) models are critical for developing practical application systems. Facilitating model sharing and model integration is a problem for model publishers and model users, respectively. To address this problem, a framework based on a Web service for sharing and integrating RS and GIS models is proposed in this paper. The fundamental idea of the framework is to publish heterogeneous RS and GIS models into standard Web services for sharing and interoperation and then to integrate the RS and GIS models using Web services. For the former, a "black box" and a visual method are employed to facilitate the publishing of the models as Web services. For the latter, model integration based on the geospatial workflow and semantic supported marching method is introduced. Under this framework, model sharing and integration is applied for developing the Pearl River Delta water environment monitoring system. The results show that the framework can facilitate model sharing and model integration for model publishers and model users.

Modeling pedestrian shopping behavior using principles of bounded rationality: model comparison and validation

NASA Astrophysics Data System (ADS)

Zhu, Wei; Timmermans, Harry

2011-06-01

Models of geographical choice behavior have been dominantly based on rational choice models, which assume that decision makers are utility-maximizers. Rational choice models may be less appropriate as behavioral models when modeling decisions in complex environments in which decision makers may simplify the decision problem using heuristics. Pedestrian behavior in shopping streets is an example. We therefore propose a modeling framework for pedestrian shopping behavior incorporating principles of bounded rationality. We extend three classical heuristic rules (conjunctive, disjunctive and lexicographic rule) by introducing threshold heterogeneity. The proposed models are implemented using data on pedestrian behavior in Wang Fujing Street, the city center of Beijing, China. The models are estimated and compared with multinomial logit models and mixed logit models. Results show that the heuristic models are the best for all the decisions that are modeled. Validation tests are carried out through multi-agent simulation by comparing simulated spatio-temporal agent behavior with the observed pedestrian behavior. The predictions of heuristic models are slightly better than those of the multinomial logit models.

The Sim-SEQ Project: Comparison of Selected Flow Models for the S-3 Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukhopadhyay, Sumit; Doughty, Christine A.; Bacon, Diana H.

Sim-SEQ is an international initiative on model comparison for geologic carbon sequestration, with an objective to understand and, if possible, quantify model uncertainties. Model comparison efforts in Sim-SEQ are at present focusing on one specific field test site, hereafter referred to as the Sim-SEQ Study site (or S-3 site). Within Sim-SEQ, different modeling teams are developing conceptual models of CO2 injection at the S-3 site. In this paper, we select five flow models of the S-3 site and provide a qualitative comparison of their attributes and predictions. These models are based on five different simulators or modeling approaches: TOUGH2/EOS7C, STOMP-CO2e,more » MoReS, TOUGH2-MP/ECO2N, and VESA. In addition to model-to-model comparison, we perform a limited model-to-data comparison, and illustrate how model choices impact model predictions. We conclude the paper by making recommendations for model refinement that are likely to result in less uncertainty in model predictions.« less

Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models.

PubMed

Jardine, Bartholomew; Raymond, Gary M; Bassingthwaighte, James B

2015-01-01

The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) ( http://www.physiome.org/jsim/) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle in writing complex models for physiological processes is the large amount of time it takes to model the myriad processes taking place simultaneously in cells, tissues, and organs. MPC replaces this task with code-generating algorithms that take model code from several different existing models and produce model code for a new JSim model. This is particularly useful during multi-scale model development where many variants are to be configured and tested against data. MPC encodes and preserves information about how a model is built from its simpler model modules, allowing the researcher to quickly substitute or update modules for hypothesis testing. MPC is implemented in Java and requires JSim to use its output. MPC source code and documentation are available at http://www.physiome.org/software/MPC/.

Comparison of dark energy models after Planck 2015

NASA Astrophysics Data System (ADS)

Xu, Yue-Yao; Zhang, Xin

2016-11-01

We make a comparison for ten typical, popular dark energy models according to their capabilities of fitting the current observational data. The observational data we use in this work include the JLA sample of type Ia supernovae observation, the Planck 2015 distance priors of cosmic microwave background observation, the baryon acoustic oscillations measurements, and the direct measurement of the Hubble constant. Since the models have different numbers of parameters, in order to make a fair comparison, we employ the Akaike and Bayesian information criteria to assess the worth of the models. The analysis results show that, according to the capability of explaining observations, the cosmological constant model is still the best one among all the dark energy models. The generalized Chaplygin gas model, the constant w model, and the α dark energy model are worse than the cosmological constant model, but still are good models compared to others. The holographic dark energy model, the new generalized Chaplygin gas model, and the Chevalliear-Polarski-Linder model can still fit the current observations well, but from an economically feasible perspective, they are not so good. The new agegraphic dark energy model, the Dvali-Gabadadze-Porrati model, and the Ricci dark energy model are excluded by the current observations.

Parametric regression model for survival data: Weibull regression model as an example

PubMed Central

2016-01-01

Weibull regression model is one of the most popular forms of parametric regression model that it provides estimate of baseline hazard function, as well as coefficients for covariates. Because of technical difficulties, Weibull regression model is seldom used in medical literature as compared to the semi-parametric proportional hazard model. To make clinical investigators familiar with Weibull regression model, this article introduces some basic knowledge on Weibull regression model and then illustrates how to fit the model with R software. The SurvRegCensCov package is useful in converting estimated coefficients to clinical relevant statistics such as hazard ratio (HR) and event time ratio (ETR). Model adequacy can be assessed by inspecting Kaplan-Meier curves stratified by categorical variable. The eha package provides an alternative method to model Weibull regression model. The check.dist() function helps to assess goodness-of-fit of the model. Variable selection is based on the importance of a covariate, which can be tested using anova() function. Alternatively, backward elimination starting from a full model is an efficient way for model development. Visualization of Weibull regression model after model development is interesting that it provides another way to report your findings. PMID:28149846

Inner Magnetosphere Modeling at the CCMC: Ring Current, Radiation Belt and Magnetic Field Mapping

NASA Astrophysics Data System (ADS)

Rastaetter, L.; Mendoza, A. M.; Chulaki, A.; Kuznetsova, M. M.; Zheng, Y.

2013-12-01

Modeling of the inner magnetosphere has entered center stage with the launch of the Van Allen Probes (RBSP) in 2012. The Community Coordinated Modeling Center (CCMC) has drastically improved its offerings of inner magnetosphere models that cover energetic particles in the Earth's ring current and radiation belts. Models added to the CCMC include the stand-alone Comprehensive Inner Magnetosphere-Ionosphere (CIMI) model by M.C. Fok, the Rice Convection Model (RCM) by R. Wolf and S. Sazykin and numerous versions of the Tsyganenko magnetic field model (T89, T96, T01quiet, TS05). These models join the LANL* model by Y. Yu hat was offered for instant run earlier in the year. In addition to these stand-alone models, the Comprehensive Ring Current Model (CRCM) by M.C. Fok and N. Buzulukova joined as a component of the Space Weather Modeling Framework (SWMF) in the magnetosphere model run-on-request category. We present modeling results of the ring current and radiation belt models and demonstrate tracking of satellites such as RBSP. Calculations using the magnetic field models include mappings to the magnetic equator or to minimum-B positions and the determination of foot points in the ionosphere.

A diversity index for model space selection in the estimation of benchmark and infectious doses via model averaging.

PubMed

Kim, Steven B; Kodell, Ralph L; Moon, Hojin

2014-03-01

In chemical and microbial risk assessments, risk assessors fit dose-response models to high-dose data and extrapolate downward to risk levels in the range of 1-10%. Although multiple dose-response models may be able to fit the data adequately in the experimental range, the estimated effective dose (ED) corresponding to an extremely small risk can be substantially different from model to model. In this respect, model averaging (MA) provides more robustness than a single dose-response model in the point and interval estimation of an ED. In MA, accounting for both data uncertainty and model uncertainty is crucial, but addressing model uncertainty is not achieved simply by increasing the number of models in a model space. A plausible set of models for MA can be characterized by goodness of fit and diversity surrounding the truth. We propose a diversity index (DI) to balance between these two characteristics in model space selection. It addresses a collective property of a model space rather than individual performance of each model. Tuning parameters in the DI control the size of the model space for MA. © 2013 Society for Risk Analysis.

Standard fire behavior fuel models: a comprehensive set for use with Rothermel's surface fire spread model

Treesearch

Joe H. Scott; Robert E. Burgan

2005-01-01

This report describes a new set of standard fire behavior fuel models for use with Rothermel's surface fire spread model and the relationship of the new set to the original set of 13 fire behavior fuel models. To assist with transition to using the new fuel models, a fuel model selection guide, fuel model crosswalk, and set of fuel model photos are provided.

[Parameters modification and evaluation of two evapotranspiration models based on Penman-Monteith model for summer maize].

PubMed

Wang, Juan; Wang, Jian Lin; Liu, Jia Bin; Jiang, Wen; Zhao, Chang Xing

2017-06-18

The dynamic variations of evapotranspiration (ET) and weather data during summer maize growing season in 2013-2015 were monitored with eddy covariance system, and the applicability of two operational models (FAO-PM model and KP-PM model) based on the Penman-Monteith model were analyzed. Firstly, the key parameters in the two models were calibrated with the measured data in 2013 and 2014; secondly, the daily ET in 2015 calculated by the FAO-PM model and KP-PM model was compared to the observed ET, respectively. Finally, the coefficients in the KP-PM model were further revised with the coefficients calculated according to the different growth stages, and the performance of the revised KP-PM model was also evaluated. These statistical parameters indicated that the calculated daily ET for 2015 by the FAO-PM model was closer to the observed ET than that by the KP-PM model. The daily ET calculated from the revised KP-PM model for daily ET was more accurate than that from the FAO-PM model. It was also found that the key parameters in the two models were correlated with weather conditions, so the calibration was necessary before using the models to predict the ET. The above results could provide some guidelines on predicting ET with the two models.

Implementation of Dryden Continuous Turbulence Model into Simulink for LSA-02 Flight Test Simulation

NASA Astrophysics Data System (ADS)

Ichwanul Hakim, Teuku Mohd; Arifianto, Ony

2018-04-01

Turbulence is a movement of air on small scale in the atmosphere that caused by instabilities of pressure and temperature distribution. Turbulence model is integrated into flight mechanical model as an atmospheric disturbance. Common turbulence model used in flight mechanical model are Dryden and Von Karman model. In this minor research, only Dryden continuous turbulence model were made. Dryden continuous turbulence model has been implemented, it refers to the military specification MIL-HDBK-1797. The model was implemented into Matlab Simulink. The model will be integrated with flight mechanical model to observe response of the aircraft when it is flight through turbulence field. The turbulence model is characterized by multiplying the filter which are generated from power spectral density with band-limited Gaussian white noise input. In order to ensure that the model provide a good result, model verification has been done by comparing the implemented model with the similar model that is provided in aerospace blockset. The result shows that there are some difference for 2 linear velocities (vg and wg), and 3 angular rate (pg, qg and rg). The difference is instantly caused by different determination of turbulence scale length which is used in aerospace blockset. With the adjustment of turbulence length in the implemented model, both model result the similar output.

THE EARTH SYSTEM PREDICTION SUITE: Toward a Coordinated U.S. Modeling Capability

PubMed Central

Theurich, Gerhard; DeLuca, C.; Campbell, T.; Liu, F.; Saint, K.; Vertenstein, M.; Chen, J.; Oehmke, R.; Doyle, J.; Whitcomb, T.; Wallcraft, A.; Iredell, M.; Black, T.; da Silva, AM; Clune, T.; Ferraro, R.; Li, P.; Kelley, M.; Aleinov, I.; Balaji, V.; Zadeh, N.; Jacob, R.; Kirtman, B.; Giraldo, F.; McCarren, D.; Sandgathe, S.; Peckham, S.; Dunlap, R.

2017-01-01

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users. The ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the U.S. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. This shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multi-agency development of coupled modeling systems, controlled experimentation and testing, and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NavGEM), HYbrid Coordinate Ocean Model (HYCOM), and Coupled Ocean Atmosphere Mesoscale Prediction System (COAMPS®); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and GEOS-5 atmospheric general circulation model. PMID:29568125

THE EARTH SYSTEM PREDICTION SUITE: Toward a Coordinated U.S. Modeling Capability.

PubMed

Theurich, Gerhard; DeLuca, C; Campbell, T; Liu, F; Saint, K; Vertenstein, M; Chen, J; Oehmke, R; Doyle, J; Whitcomb, T; Wallcraft, A; Iredell, M; Black, T; da Silva, A M; Clune, T; Ferraro, R; Li, P; Kelley, M; Aleinov, I; Balaji, V; Zadeh, N; Jacob, R; Kirtman, B; Giraldo, F; McCarren, D; Sandgathe, S; Peckham, S; Dunlap, R

2016-07-01

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users. The ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the U.S. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. This shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multi-agency development of coupled modeling systems, controlled experimentation and testing, and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NavGEM), HYbrid Coordinate Ocean Model (HYCOM), and Coupled Ocean Atmosphere Mesoscale Prediction System (COAMPS ® ); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and GEOS-5 atmospheric general circulation model.

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

NASA Technical Reports Server (NTRS)

Theurich, Gerhard; DeLuca, C.; Campbell, T.; Liu, F.; Saint, K.; Vertenstein, M.; Chen, J.; Oehmke, R.; Doyle, J.; Whitcomb, T.;

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

DOE PAGES

Theurich, Gerhard; DeLuca, C.; Campbell, T.; ...

2016-08-22

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open-source terms or to credentialed users. Furthermore, the ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the United States. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC)more » Layer, a set of ESMF-based component templates and interoperability conventions. Our shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multiagency development of coupled modeling systems; controlled experimentation and testing; and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NAVGEM), the Hybrid Coordinate Ocean Model (HYCOM), and the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and the Goddard Earth Observing System Model, version 5 (GEOS-5), atmospheric general circulation model.« less

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theurich, Gerhard; DeLuca, C.; Campbell, T.

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open-source terms or to credentialed users. Furthermore, the ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the United States. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC)more » Layer, a set of ESMF-based component templates and interoperability conventions. Our shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multiagency development of coupled modeling systems; controlled experimentation and testing; and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NAVGEM), the Hybrid Coordinate Ocean Model (HYCOM), and the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and the Goddard Earth Observing System Model, version 5 (GEOS-5), atmospheric general circulation model.« less

An ontology for component-based models of water resource systems

NASA Astrophysics Data System (ADS)

Elag, Mostafa; Goodall, Jonathan L.

2013-08-01

Component-based modeling is an approach for simulating water resource systems where a model is composed of a set of components, each with a defined modeling objective, interlinked through data exchanges. Component-based modeling frameworks are used within the hydrologic, atmospheric, and earth surface dynamics modeling communities. While these efforts have been advancing, it has become clear that the water resources modeling community in particular, and arguably the larger earth science modeling community as well, faces a challenge of fully and precisely defining the metadata for model components. The lack of a unified framework for model component metadata limits interoperability between modeling communities and the reuse of models across modeling frameworks due to ambiguity about the model and its capabilities. To address this need, we propose an ontology for water resources model components that describes core concepts and relationships using the Web Ontology Language (OWL). The ontology that we present, which is termed the Water Resources Component (WRC) ontology, is meant to serve as a starting point that can be refined over time through engagement by the larger community until a robust knowledge framework for water resource model components is achieved. This paper presents the methodology used to arrive at the WRC ontology, the WRC ontology itself, and examples of how the ontology can aid in component-based water resources modeling by (i) assisting in identifying relevant models, (ii) encouraging proper model coupling, and (iii) facilitating interoperability across earth science modeling frameworks.

Novel forecasting approaches using combination of machine learning and statistical models for flood susceptibility mapping.

PubMed

Shafizadeh-Moghadam, Hossein; Valavi, Roozbeh; Shahabi, Himan; Chapi, Kamran; Shirzadi, Ataollah

2018-07-01

In this research, eight individual machine learning and statistical models are implemented and compared, and based on their results, seven ensemble models for flood susceptibility assessment are introduced. The individual models included artificial neural networks, classification and regression trees, flexible discriminant analysis, generalized linear model, generalized additive model, boosted regression trees, multivariate adaptive regression splines, and maximum entropy, and the ensemble models were Ensemble Model committee averaging (EMca), Ensemble Model confidence interval Inferior (EMciInf), Ensemble Model confidence interval Superior (EMciSup), Ensemble Model to estimate the coefficient of variation (EMcv), Ensemble Model to estimate the mean (EMmean), Ensemble Model to estimate the median (EMmedian), and Ensemble Model based on weighted mean (EMwmean). The data set covered 201 flood events in the Haraz watershed (Mazandaran province in Iran) and 10,000 randomly selected non-occurrence points. Among the individual models, the Area Under the Receiver Operating Characteristic (AUROC), which showed the highest value, belonged to boosted regression trees (0.975) and the lowest value was recorded for generalized linear model (0.642). On the other hand, the proposed EMmedian resulted in the highest accuracy (0.976) among all models. In spite of the outstanding performance of some models, nevertheless, variability among the prediction of individual models was considerable. Therefore, to reduce uncertainty, creating more generalizable, more stable, and less sensitive models, ensemble forecasting approaches and in particular the EMmedian is recommended for flood susceptibility assessment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Exploring Several Methods of Groundwater Model Selection

NASA Astrophysics Data System (ADS)

Samani, Saeideh; Ye, Ming; Asghari Moghaddam, Asghar

2017-04-01

Selecting reliable models for simulating groundwater flow and solute transport is essential to groundwater resources management and protection. This work is to explore several model selection methods for avoiding over-complex and/or over-parameterized groundwater models. We consider six groundwater flow models with different numbers (6, 10, 10, 13, 13 and 15) of model parameters. These models represent alternative geological interpretations, recharge estimates, and boundary conditions at a study site in Iran. The models were developed with Model Muse, and calibrated against observations of hydraulic head using UCODE. Model selection was conducted by using the following four approaches: (1) Rank the models using their root mean square error (RMSE) obtained after UCODE-based model calibration, (2) Calculate model probability using GLUE method, (3) Evaluate model probability using model selection criteria (AIC, AICc, BIC, and KIC), and (4) Evaluate model weights using the Fuzzy Multi-Criteria-Decision-Making (MCDM) approach. MCDM is based on the fuzzy analytical hierarchy process (AHP) and fuzzy technique for order performance, which is to identify the ideal solution by a gradual expansion from the local to the global scale of model parameters. The KIC and MCDM methods are superior to other methods, as they consider not only the fit between observed and simulated data and the number of parameter, but also uncertainty in model parameters. Considering these factors can prevent from occurring over-complexity and over-parameterization, when selecting the appropriate groundwater flow models. These methods selected, as the best model, one with average complexity (10 parameters) and the best parameter estimation (model 3).

A comparative research of different ensemble surrogate models based on set pair analysis for the DNAPL-contaminated aquifer remediation strategy optimization.

PubMed

Hou, Zeyu; Lu, Wenxi; Xue, Haibo; Lin, Jin

2017-08-01

Surrogate-based simulation-optimization technique is an effective approach for optimizing the surfactant enhanced aquifer remediation (SEAR) strategy for clearing DNAPLs. The performance of the surrogate model, which is used to replace the simulation model for the aim of reducing computation burden, is the key of corresponding researches. However, previous researches are generally based on a stand-alone surrogate model, and rarely make efforts to improve the approximation accuracy of the surrogate model to the simulation model sufficiently by combining various methods. In this regard, we present set pair analysis (SPA) as a new method to build ensemble surrogate (ES) model, and conducted a comparative research to select a better ES modeling pattern for the SEAR strategy optimization problems. Surrogate models were developed using radial basis function artificial neural network (RBFANN), support vector regression (SVR), and Kriging. One ES model is assembling RBFANN model, SVR model, and Kriging model using set pair weights according their performance, and the other is assembling several Kriging (the best surrogate modeling method of three) models built with different training sample datasets. Finally, an optimization model, in which the ES model was embedded, was established to obtain the optimal remediation strategy. The results showed the residuals of the outputs between the best ES model and simulation model for 100 testing samples were lower than 1.5%. Using an ES model instead of the simulation model was critical for considerably reducing the computation time of simulation-optimization process and maintaining high computation accuracy simultaneously. Copyright © 2017 Elsevier B.V. All rights reserved.

Models Archive and ModelWeb at NSSDC

NASA Astrophysics Data System (ADS)

Bilitza, D.; Papitashvili, N.; King, J. H.

2002-05-01

In addition to its large data holdings, NASA's National Space Science Data Center (NSSDC) also maintains an archive of space physics models for public use (ftp://nssdcftp.gsfc.nasa.gov/models/). The more than 60 model entries cover a wide range of parameters from the atmosphere, to the ionosphere, to the magnetosphere, to the heliosphere. The models are primarily empirical models developed by the respective model authors based on long data records from ground and space experiments. An online model catalog (http://nssdc.gsfc.nasa.gov/space/model/) provides information about these and other models and links to the model software if available. We will briefly review the existing model holdings and highlight some of its usages and users. In response to a growing need by the user community, NSSDC began to develop web-interfaces for the most frequently requested models. These interfaces enable users to compute and plot model parameters online for the specific conditions that they are interested in. Currently included in the Modelweb system (http://nssdc.gsfc.nasa.gov/space/model/) are the following models: the International Reference Ionosphere (IRI) model, the Mass Spectrometer Incoherent Scatter (MSIS) E90 model, the International Geomagnetic Reference Field (IGRF) and the AP/AE-8 models for the radiation belt electrons and protons. User accesses to both systems have been steadily increasing over the last years with occasional spikes prior to large scientific meetings. The current monthly rate is between 5,000 to 10,000 accesses for either system; in February 2002 13,872 accesses were recorded to the Modelsweb and 7092 accesses to the models archive.

Towards methodical modelling: Differences between the structure and output dynamics of multiple conceptual models

NASA Astrophysics Data System (ADS)

Knoben, Wouter; Woods, Ross; Freer, Jim

2016-04-01

Conceptual hydrologic models consist of a certain arrangement of spatial and temporal dynamics consisting of stores, fluxes and transformation functions, depending on the modeller's choices and intended use. They have the advantages of being computationally efficient, being relatively easy model structures to reconfigure and having relatively low input data demands. This makes them well-suited for large-scale and large-sample hydrology, where appropriately representing the dominant hydrologic functions of a catchment is a main concern. Given these requirements, the number of parameters in the model cannot be too high, to avoid equifinality and identifiability issues. This limits the number and level of complexity of dominant hydrologic processes the model can represent. Specific purposes and places thus require a specific model and this has led to an abundance of conceptual hydrologic models. No structured overview of these models exists and there is no clear method to select appropriate model structures for different catchments. This study is a first step towards creating an overview of the elements that make up conceptual models, which may later assist a modeller in finding an appropriate model structure for a given catchment. To this end, this study brings together over 30 past and present conceptual models. The reviewed model structures are simply different configurations of three basic model elements (stores, fluxes and transformation functions), depending on the hydrologic processes the models are intended to represent. Differences also exist in the inner workings of the stores, fluxes and transformations, i.e. the mathematical formulations that describe each model element's intended behaviour. We investigate the hypothesis that different model structures can produce similar behavioural simulations. This can clarify the overview of model elements by grouping elements which are similar, which can improve model structure selection.

Synthesizing models useful for ecohydrology and ecohydraulic approaches: An emphasis on integrating models to address complex research questions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brewer, Shannon K.; Worthington, Thomas A.; Mollenhauer, Robert

Ecohydrology combines empiricism, data analytics, and the integration of models to characterize linkages between ecological and hydrological processes. A challenge for practitioners is determining which models best generalizes heterogeneity in hydrological behaviour, including water fluxes across spatial and temporal scales, integrating environmental and socio–economic activities to determine best watershed management practices and data requirements. We conducted a literature review and synthesis of hydrologic, hydraulic, water quality, and ecological models designed for solving interdisciplinary questions. We reviewed 1,275 papers and identified 178 models that have the capacity to answer an array of research questions about ecohydrology or ecohydraulics. Of these models,more » 43 were commonly applied due to their versatility, accessibility, user–friendliness, and excellent user–support. Forty–one of 43 reviewed models were linked to at least 1 other model especially: Water Quality Analysis Simulation Program (linked to 21 other models), Soil and Water Assessment Tool (19), and Hydrologic Engineering Center's River Analysis System (15). However, model integration was still relatively infrequent. There was substantial variation in model applications, possibly an artefact of the regional focus of research questions, simplicity of use, quality of user–support efforts, or a limited understanding of model applicability. Simply increasing the interoperability of model platforms, transformation of models to user–friendly forms, increasing user–support, defining the reliability and risk associated with model results, and increasing awareness of model applicability may promote increased use of models across subdisciplines. Furthermore, the current availability of models allows an array of interdisciplinary questions to be addressed, and model choice relates to several factors including research objective, model complexity, ability to link to other models, and interface choice.« less

Synthesizing models useful for ecohydrology and ecohydraulic approaches: An emphasis on integrating models to address complex research questions

USGS Publications Warehouse

Brewer, Shannon K.; Worthington, Thomas; Mollenhauer, Robert; Stewart, David; McManamay, Ryan; Guertault, Lucie; Moore, Desiree

2018-01-01

Ecohydrology combines empiricism, data analytics, and the integration of models to characterize linkages between ecological and hydrological processes. A challenge for practitioners is determining which models best generalizes heterogeneity in hydrological behaviour, including water fluxes across spatial and temporal scales, integrating environmental and socio‐economic activities to determine best watershed management practices and data requirements. We conducted a literature review and synthesis of hydrologic, hydraulic, water quality, and ecological models designed for solving interdisciplinary questions. We reviewed 1,275 papers and identified 178 models that have the capacity to answer an array of research questions about ecohydrology or ecohydraulics. Of these models, 43 were commonly applied due to their versatility, accessibility, user‐friendliness, and excellent user‐support. Forty‐one of 43 reviewed models were linked to at least 1 other model especially: Water Quality Analysis Simulation Program (linked to 21 other models), Soil and Water Assessment Tool (19), and Hydrologic Engineering Center's River Analysis System (15). However, model integration was still relatively infrequent. There was substantial variation in model applications, possibly an artefact of the regional focus of research questions, simplicity of use, quality of user‐support efforts, or a limited understanding of model applicability. Simply increasing the interoperability of model platforms, transformation of models to user‐friendly forms, increasing user‐support, defining the reliability and risk associated with model results, and increasing awareness of model applicability may promote increased use of models across subdisciplines. Nonetheless, the current availability of models allows an array of interdisciplinary questions to be addressed, and model choice relates to several factors including research objective, model complexity, ability to link to other models, and interface choice.

How does a three-dimensional continuum muscle model affect the kinematics and muscle strains of a finite element neck model compared to a discrete muscle model in rear-end, frontal, and lateral impacts.

PubMed

Hedenstierna, Sofia; Halldin, Peter

2008-04-15

A finite element (FE) model of the human neck with incorporated continuum or discrete muscles was used to simulate experimental impacts in rear, frontal, and lateral directions. The aim of this study was to determine how a continuum muscle model influences the impact behavior of a FE human neck model compared with a discrete muscle model. Most FE neck models used for impact analysis today include a spring element musculature and are limited to discrete geometries and nodal output results. A solid-element muscle model was thought to improve the behavior of the model by adding properties such as tissue inertia and compressive stiffness and by improving the geometry. It would also predict the strain distribution within the continuum elements. A passive continuum muscle model with nonlinear viscoelastic materials was incorporated into the KTH neck model together with active spring muscles and used in impact simulations. The resulting head and vertebral kinematics was compared with the results from a discrete muscle model as well as volunteer corridors. The muscle strain prediction was compared between the 2 muscle models. The head and vertebral kinematics were within the volunteer corridors for both models when activated. The continuum model behaved more stiffly than the discrete model and needed less active force to fit the experimental results. The largest difference was seen in the rear impact. The strain predicted by the continuum model was lower than for the discrete model. The continuum muscle model stiffened the response of the KTH neck model compared with a discrete model, and the strain prediction in the muscles was improved.

Synthesizing models useful for ecohydrology and ecohydraulic approaches: An emphasis on integrating models to address complex research questions

DOE PAGES

Brewer, Shannon K.; Worthington, Thomas A.; Mollenhauer, Robert; ...

2018-04-06

Ecohydrology combines empiricism, data analytics, and the integration of models to characterize linkages between ecological and hydrological processes. A challenge for practitioners is determining which models best generalizes heterogeneity in hydrological behaviour, including water fluxes across spatial and temporal scales, integrating environmental and socio–economic activities to determine best watershed management practices and data requirements. We conducted a literature review and synthesis of hydrologic, hydraulic, water quality, and ecological models designed for solving interdisciplinary questions. We reviewed 1,275 papers and identified 178 models that have the capacity to answer an array of research questions about ecohydrology or ecohydraulics. Of these models,more » 43 were commonly applied due to their versatility, accessibility, user–friendliness, and excellent user–support. Forty–one of 43 reviewed models were linked to at least 1 other model especially: Water Quality Analysis Simulation Program (linked to 21 other models), Soil and Water Assessment Tool (19), and Hydrologic Engineering Center's River Analysis System (15). However, model integration was still relatively infrequent. There was substantial variation in model applications, possibly an artefact of the regional focus of research questions, simplicity of use, quality of user–support efforts, or a limited understanding of model applicability. Simply increasing the interoperability of model platforms, transformation of models to user–friendly forms, increasing user–support, defining the reliability and risk associated with model results, and increasing awareness of model applicability may promote increased use of models across subdisciplines. Furthermore, the current availability of models allows an array of interdisciplinary questions to be addressed, and model choice relates to several factors including research objective, model complexity, ability to link to other models, and interface choice.« less

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment

PubMed Central

2014-01-01

Background Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. Results MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Conclusions Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy. PMID:24731387

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.

PubMed

Cao, Renzhi; Wang, Zheng; Cheng, Jianlin

2014-04-15

Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy.

Replicating Health Economic Models: Firm Foundations or a House of Cards?

PubMed

Bermejo, Inigo; Tappenden, Paul; Youn, Ji-Hee

2017-11-01

Health economic evaluation is a framework for the comparative analysis of the incremental health gains and costs associated with competing decision alternatives. The process of developing health economic models is usually complex, financially expensive and time-consuming. For these reasons, model development is sometimes based on previous model-based analyses; this endeavour is usually referred to as model replication. Such model replication activity may involve the comprehensive reproduction of an existing model or 'borrowing' all or part of a previously developed model structure. Generally speaking, the replication of an existing model may require substantially less effort than developing a new de novo model by bypassing, or undertaking in only a perfunctory manner, certain aspects of model development such as the development of a complete conceptual model and/or comprehensive literature searching for model parameters. A further motivation for model replication may be to draw on the credibility or prestige of previous analyses that have been published and/or used to inform decision making. The acceptability and appropriateness of replicating models depends on the decision-making context: there exists a trade-off between the 'savings' afforded by model replication and the potential 'costs' associated with reduced model credibility due to the omission of certain stages of model development. This paper provides an overview of the different levels of, and motivations for, replicating health economic models, and discusses the advantages, disadvantages and caveats associated with this type of modelling activity. Irrespective of whether replicated models should be considered appropriate or not, complete replicability is generally accepted as a desirable property of health economic models, as reflected in critical appraisal checklists and good practice guidelines. To this end, the feasibility of comprehensive model replication is explored empirically across a small number of recent case studies. Recommendations are put forward for improving reporting standards to enhance comprehensive model replicability.

Reducing hydrologic model uncertainty in monthly streamflow predictions using multimodel combination

NASA Astrophysics Data System (ADS)

Li, Weihua; Sankarasubramanian, A.

2012-12-01

Model errors are inevitable in any prediction exercise. One approach that is currently gaining attention in reducing model errors is by combining multiple models to develop improved predictions. The rationale behind this approach primarily lies on the premise that optimal weights could be derived for each model so that the developed multimodel predictions will result in improved predictions. A new dynamic approach (MM-1) to combine multiple hydrological models by evaluating their performance/skill contingent on the predictor state is proposed. We combine two hydrological models, "abcd" model and variable infiltration capacity (VIC) model, to develop multimodel streamflow predictions. To quantify precisely under what conditions the multimodel combination results in improved predictions, we compare multimodel scheme MM-1 with optimal model combination scheme (MM-O) by employing them in predicting the streamflow generated from a known hydrologic model (abcd model orVICmodel) with heteroscedastic error variance as well as from a hydrologic model that exhibits different structure than that of the candidate models (i.e., "abcd" model or VIC model). Results from the study show that streamflow estimated from single models performed better than multimodels under almost no measurement error. However, under increased measurement errors and model structural misspecification, both multimodel schemes (MM-1 and MM-O) consistently performed better than the single model prediction. Overall, MM-1 performs better than MM-O in predicting the monthly flow values as well as in predicting extreme monthly flows. Comparison of the weights obtained from each candidate model reveals that as measurement errors increase, MM-1 assigns weights equally for all the models, whereas MM-O assigns higher weights for always the best-performing candidate model under the calibration period. Applying the multimodel algorithms for predicting streamflows over four different sites revealed that MM-1 performs better than all single models and optimal model combination scheme, MM-O, in predicting the monthly flows as well as the flows during wetter months.

Comparing the cognitive differences resulting from modeling instruction: Using computer microworld and physical object instruction to model real world problems

NASA Astrophysics Data System (ADS)

Oursland, Mark David

This study compared the modeling achievement of students receiving mathematical modeling instruction using the computer microworld, Interactive Physics, and students receiving instruction using physical objects. Modeling instruction included activities where students applied the (a) linear model to a variety of situations, (b) linear model to two-rate situations with a constant rate, (c) quadratic model to familiar geometric figures. Both quantitative and qualitative methods were used to analyze achievement differences between students (a) receiving different methods of modeling instruction, (b) with different levels of beginning modeling ability, or (c) with different levels of computer literacy. Student achievement was analyzed quantitatively through a three-factor analysis of variance where modeling instruction, beginning modeling ability, and computer literacy were used as the three independent factors. The SOLO (Structure of the Observed Learning Outcome) assessment framework was used to design written modeling assessment instruments to measure the students' modeling achievement. The same three independent factors were used to collect and analyze the interviews and observations of student behaviors. Both methods of modeling instruction used the data analysis approach to mathematical modeling. The instructional lessons presented problem situations where students were asked to collect data, analyze the data, write a symbolic mathematical equation, and use equation to solve the problem. The researcher recommends the following practice for modeling instruction based on the conclusions of this study. A variety of activities with a common structure are needed to make explicit the modeling process of applying a standard mathematical model. The modeling process is influenced strongly by prior knowledge of the problem context and previous modeling experiences. The conclusions of this study imply that knowledge of the properties about squares improved the students' ability to model a geometric problem more than instruction in data analysis modeling. The uses of computer microworlds such as Interactive Physics in conjunction with cooperative groups are a viable method of modeling instruction.

A physical data model for fields and agents

NASA Astrophysics Data System (ADS)

de Jong, Kor; de Bakker, Merijn; Karssenberg, Derek

2016-04-01

Two approaches exist in simulation modeling: agent-based and field-based modeling. In agent-based (or individual-based) simulation modeling, the entities representing the system's state are represented by objects, which are bounded in space and time. Individual objects, like an animal, a house, or a more abstract entity like a country's economy, have properties representing their state. In an agent-based model this state is manipulated. In field-based modeling, the entities representing the system's state are represented by fields. Fields capture the state of a continuous property within a spatial extent, examples of which are elevation, atmospheric pressure, and water flow velocity. With respect to the technology used to create these models, the domains of agent-based and field-based modeling have often been separate worlds. In environmental modeling, widely used logical data models include feature data models for point, line and polygon objects, and the raster data model for fields. Simulation models are often either agent-based or field-based, even though the modeled system might contain both entities that are better represented by individuals and entities that are better represented by fields. We think that the reason for this dichotomy in kinds of models might be that the traditional object and field data models underlying those models are relatively low level. We have developed a higher level conceptual data model for representing both non-spatial and spatial objects, and spatial fields (De Bakker et al. 2016). Based on this conceptual data model we designed a logical and physical data model for representing many kinds of data, including the kinds used in earth system modeling (e.g. hydrological and ecological models). The goal of this work is to be able to create high level code and tools for the creation of models in which entities are representable by both objects and fields. Our conceptual data model is capable of representing the traditional feature data models and the raster data model, among many other data models. Our physical data model is capable of storing a first set of kinds of data, like omnipresent scalars, mobile spatio-temporal points and property values, and spatio-temporal rasters. With our poster we will provide an overview of the physical data model expressed in HDF5 and show examples of how it can be used to capture both object- and field-based information. References De Bakker, M, K. de Jong, D. Karssenberg. 2016. A conceptual data model and language for fields and agents. European Geosciences Union, EGU General Assembly, 2016, Vienna.

Students' Models of Curve Fitting: A Models and Modeling Perspective

ERIC Educational Resources Information Center

Gupta, Shweta

2010-01-01

The Models and Modeling Perspectives (MMP) has evolved out of research that began 26 years ago. MMP researchers use Model Eliciting Activities (MEAs) to elicit students' mental models. In this study MMP was used as the conceptual framework to investigate the nature of students' models of curve fitting in a problem-solving environment consisting of…

Modeling Information Accumulation in Psychological Tests Using Item Response Times

ERIC Educational Resources Information Center

Ranger, Jochen; Kuhn, Jörg-Tobias

2015-01-01

In this article, a latent trait model is proposed for the response times in psychological tests. The latent trait model is based on the linear transformation model and subsumes popular models from survival analysis, like the proportional hazards model and the proportional odds model. Core of the model is the assumption that an unspecified monotone…

Climate and atmospheric modeling studies

NASA Technical Reports Server (NTRS)

1992-01-01

The climate and atmosphere modeling research programs have concentrated on the development of appropriate atmospheric and upper ocean models, and preliminary applications of these models. Principal models are a one-dimensional radiative-convective model, a three-dimensional global model, and an upper ocean model. Principal applications were the study of the impact of CO2, aerosols, and the solar 'constant' on climate.

Models in Science Education: Applications of Models in Learning and Teaching Science

ERIC Educational Resources Information Center

Ornek, Funda

2008-01-01

In this paper, I discuss different types of models in science education and applications of them in learning and teaching science, in particular physics. Based on the literature, I categorize models as conceptual and mental models according to their characteristics. In addition to these models, there is another model called "physics model" by the…

Computer-Aided Modeling and Analysis of Power Processing Systems (CAMAPPS). Phase 1: Users handbook

NASA Technical Reports Server (NTRS)

Kim, S.; Lee, J.; Cho, B. H.; Lee, F. C.

1986-01-01

The EASY5 macro component models developed for the spacecraft power system simulation are described. A brief explanation about how to use the macro components with the EASY5 Standard Components to build a specific system is given through an example. The macro components are ordered according to the following functional group: converter power stage models, compensator models, current-feedback models, constant frequency control models, load models, solar array models, and shunt regulator models. Major equations, a circuit model, and a program listing are provided for each macro component.

Vector models and generalized SYK models

DOE PAGES

Peng, Cheng

2017-05-23

Here, we consider the relation between SYK-like models and vector models by studying a toy model where a tensor field is coupled with a vector field. By integrating out the tensor field, the toy model reduces to the Gross-Neveu model in 1 dimension. On the other hand, a certain perturbation can be turned on and the toy model flows to an SYK-like model at low energy. Furthermore, a chaotic-nonchaotic phase transition occurs as the sign of the perturbation is altered. We further study similar models that possess chaos and enhanced reparameterization symmetries.

Validation of the PVSyst Performance Model for the Concentrix CPV Technology

NASA Astrophysics Data System (ADS)

Gerstmaier, Tobias; Gomez, María; Gombert, Andreas; Mermoud, André; Lejeune, Thibault

2011-12-01

The accuracy of the two-stage PVSyst model for the Concentrix CPV Technology is determined by comparing modeled to measured values. For both stages, i) the module model and ii) the power plant model, the underlying approaches are explained and methods for obtaining the model parameters are presented. The performance of both models is quantified using 19 months of outdoor measurements for the module model and 9 months of measurements at four different sites for the power plant model. Results are presented by giving statistical quantities for the model accuracy.

Comparative Protein Structure Modeling Using MODELLER

PubMed Central

Webb, Benjamin; Sali, Andrej

2016-01-01

Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:27322406

A comparative study of turbulence models in predicting hypersonic inlet flows

NASA Technical Reports Server (NTRS)

Kapoor, Kamlesh

1993-01-01

A computational study has been conducted to evaluate the performance of various turbulence models. The NASA P8 inlet, which represents cruise condition of a typical hypersonic air-breathing vehicle, was selected as a test case for the study; the PARC2D code, which solves the full two dimensional Reynolds-averaged Navier-Stokes equations, was used. Results are presented for a total of six versions of zero- and two-equation turbulence models. Zero-equation models tested are the Baldwin-Lomax model, the Thomas model, and a combination of the two. Two-equation models tested are low-Reynolds number models (the Chien model and the Speziale model) and a high-Reynolds number model (the Launder and Spalding model).

The evolution of process-based hydrologic models: historical challenges and the collective quest for physical realism

NASA Astrophysics Data System (ADS)

Clark, Martyn P.; Bierkens, Marc F. P.; Samaniego, Luis; Woods, Ross A.; Uijlenhoet, Remko; Bennett, Katrina E.; Pauwels, Valentijn R. N.; Cai, Xitian; Wood, Andrew W.; Peters-Lidard, Christa D.

2017-07-01

The diversity in hydrologic models has historically led to great controversy on the correct approach to process-based hydrologic modeling, with debates centered on the adequacy of process parameterizations, data limitations and uncertainty, and computational constraints on model analysis. In this paper, we revisit key modeling challenges on requirements to (1) define suitable model equations, (2) define adequate model parameters, and (3) cope with limitations in computing power. We outline the historical modeling challenges, provide examples of modeling advances that address these challenges, and define outstanding research needs. We illustrate how modeling advances have been made by groups using models of different type and complexity, and we argue for the need to more effectively use our diversity of modeling approaches in order to advance our collective quest for physically realistic hydrologic models.

The evolution of process-based hydrologic models: historical challenges and the collective quest for physical realism

NASA Astrophysics Data System (ADS)

Clark, M. P.; Nijssen, B.; Wood, A.; Mizukami, N.; Newman, A. J.

2017-12-01

The diversity in hydrologic models has historically led to great controversy on the "correct" approach to process-based hydrologic modeling, with debates centered on the adequacy of process parameterizations, data limitations and uncertainty, and computational constraints on model analysis. In this paper, we revisit key modeling challenges on requirements to (1) define suitable model equations, (2) define adequate model parameters, and (3) cope with limitations in computing power. We outline the historical modeling challenges, provide examples of modeling advances that address these challenges, and define outstanding research needs. We illustrate how modeling advances have been made by groups using models of different type and complexity, and we argue for the need to more effectively use our diversity of modeling approaches in order to advance our collective quest for physically realistic hydrologic models.

Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons

NASA Technical Reports Server (NTRS)

Armstrong, T. W.; Colborn, B. L.

2000-01-01

The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP, LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir Space Station. This report gives the details of the model-data comparisons-summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a combination report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian-trapped radiation models.

Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons

NASA Technical Reports Server (NTRS)

Armstrong, T. W.; Colborn, B. L.

2000-01-01

The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP. LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir space station. This report gives the details of the model-data comparisons -- summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a companion report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian trapped radiation models.

Analysis of terahertz dielectric properties of pork tissue

NASA Astrophysics Data System (ADS)

Huang, Yuqing; Xie, Qiaoling; Sun, Ping

2017-10-01

Seeing that about 70% component of fresh biological tissues is water, many scientists try to use water models to describe the dielectric properties of biological tissues. The classical water dielectric models are Debye model, Double Debye model and Cole-Cole model. This work aims to determine a suitable model by comparing three models above with experimental data. These models are applied to fresh pork tissue. By means of least square method, the parameters of different models are fitted with the experimental data. Comparing different models on both dielectric function, the Cole-Cole model is verified the best to describe the experiments of pork tissue. The correction factor α of the Cole-Cole model is an important modification for biological tissues. So Cole-Cole model is supposed to be a priority selection to describe the dielectric properties for biological tissues in the terahertz range.

Dealing with dissatisfaction in mathematical modelling to integrate QFD and Kano’s model

NASA Astrophysics Data System (ADS)

Retno Sari Dewi, Dian; Debora, Joana; Edy Sianto, Martinus

2017-12-01

The purpose of the study is to implement the integration of Quality Function Deployment (QFD) and Kano’s Model into mathematical model. Voice of customer data in QFD was collected using questionnaire and the questionnaire was developed based on Kano’s model. Then the operational research methodology was applied to build the objective function and constraints in the mathematical model. The relationship between voice of customer and engineering characteristics was modelled using linier regression model. Output of the mathematical model would be detail of engineering characteristics. The objective function of this model is to maximize satisfaction and minimize dissatisfaction as well. Result of this model is 62% .The major contribution of this research is to implement the existing mathematical model to integrate QFD and Kano’s Model in the case study of shoe cabinet.

The Real and the Mathematical in Quantum Modeling: From Principles to Models and from Models to Principles

NASA Astrophysics Data System (ADS)

Plotnitsky, Arkady

2017-06-01

The history of mathematical modeling outside physics has been dominated by the use of classical mathematical models, C-models, primarily those of a probabilistic or statistical nature. More recently, however, quantum mathematical models, Q-models, based in the mathematical formalism of quantum theory have become more prominent in psychology, economics, and decision science. The use of Q-models in these fields remains controversial, in part because it is not entirely clear whether Q-models are necessary for dealing with the phenomena in question or whether C-models would still suffice. My aim, however, is not to assess the necessity of Q-models in these fields, but instead to reflect on what the possible applicability of Q-models may tell us about the corresponding phenomena there, vis-à-vis quantum phenomena in physics. In order to do so, I shall first discuss the key reasons for the use of Q-models in physics. In particular, I shall examine the fundamental principles that led to the development of quantum mechanics. Then I shall consider a possible role of similar principles in using Q-models outside physics. Psychology, economics, and decision science borrow already available Q-models from quantum theory, rather than derive them from their own internal principles, while quantum mechanics was derived from such principles, because there was no readily available mathematical model to handle quantum phenomena, although the mathematics ultimately used in quantum did in fact exist then. I shall argue, however, that the principle perspective on mathematical modeling outside physics might help us to understand better the role of Q-models in these fields and possibly to envision new models, conceptually analogous to but mathematically different from those of quantum theory, helpful or even necessary there or in physics itself. I shall suggest one possible type of such models, singularized probabilistic, SP, models, some of which are time-dependent, TDSP-models. The necessity of using such models may change the nature of mathematical modeling in science and, thus, the nature of science, as it happened in the case of Q-models, which not only led to a revolutionary transformation of physics but also opened new possibilities for scientific thinking and mathematical modeling beyond physics.

Vertically-Integrated Dual-Continuum Models for CO2 Injection in Fractured Aquifers

NASA Astrophysics Data System (ADS)

Tao, Y.; Guo, B.; Bandilla, K.; Celia, M. A.

2017-12-01

Injection of CO2 into a saline aquifer leads to a two-phase flow system, with supercritical CO2 and brine being the two fluid phases. Various modeling approaches, including fully three-dimensional (3D) models and vertical-equilibrium (VE) models, have been used to study the system. Almost all of that work has focused on unfractured formations. 3D models solve the governing equations in three dimensions and are applicable to generic geological formations. VE models assume rapid and complete buoyant segregation of the two fluid phases, resulting in vertical pressure equilibrium and allowing integration of the governing equations in the vertical dimension. This reduction in dimensionality makes VE models computationally more efficient, but the associated assumptions restrict the applicability of VE model to formations with moderate to high permeability. In this presentation, we extend the VE and 3D models for CO2 injection in fractured aquifers. This is done in the context of dual-continuum modeling, where the fractured formation is modeled as an overlap of two continuous domains, one representing the fractures and the other representing the rock matrix. Both domains are treated as porous media continua and can be modeled by either a VE or a 3D formulation. The transfer of fluid mass between rock matrix and fractures is represented by a mass transfer function connecting the two domains. We have developed a computational model that combines the VE and 3D models, where we use the VE model in the fractures, which typically have high permeability, and the 3D model in the less permeable rock matrix. A new mass transfer function is derived, which couples the VE and 3D models. The coupled VE-3D model can simulate CO2 injection and migration in fractured aquifers. Results from this model compare well with a full-3D model in which both the fractures and rock matrix are modeled with 3D models, with the hybrid VE-3D model having significantly reduced computational cost. In addition to the VE-3D model, we explore simplifications of the rock matrix domain by using sugar-cube and matchstick conceptualizations and develop VE-dual porosity and VE-matchstick models. These vertically-integrated dual-permeability and dual-porosity models provide a range of computationally efficient tools to model CO2 storage in fractured saline aquifers.

ATMOSPHERIC DISPERSAL AND DEPOSITION OF TEPHRA FROM A POTENTIAL VOLCANIC ERUPTION AT YUCCA MOUNTAIN, NEVADA

DOE Office of Scientific and Technical Information (OSTI.GOV)

C. Harrington

2004-10-25

The purpose of this model report is to provide documentation of the conceptual and mathematical model (Ashplume) for atmospheric dispersal and subsequent deposition of ash on the land surface from a potential volcanic eruption at Yucca Mountain, Nevada. This report also documents the ash (tephra) redistribution conceptual model. These aspects of volcanism-related dose calculation are described in the context of the entire igneous disruptive events conceptual model in ''Characterize Framework for Igneous Activity'' (BSC 2004 [DIRS 169989], Section 6.1.1). The Ashplume conceptual model accounts for incorporation and entrainment of waste fuel particles associated with a hypothetical volcanic eruption through themore » Yucca Mountain repository and downwind transport of contaminated tephra. The Ashplume mathematical model describes the conceptual model in mathematical terms to allow for prediction of radioactive waste/ash deposition on the ground surface given that the hypothetical eruptive event occurs. This model report also describes the conceptual model for tephra redistribution from a basaltic cinder cone. Sensitivity analyses and model validation activities for the ash dispersal and redistribution models are also presented. Analyses documented in this model report update the previous documentation of the Ashplume mathematical model and its application to the Total System Performance Assessment (TSPA) for the License Application (TSPA-LA) igneous scenarios. This model report also documents the redistribution model product outputs based on analyses to support the conceptual model. In this report, ''Ashplume'' is used when referring to the atmospheric dispersal model and ''ASHPLUME'' is used when referencing the code of that model. Two analysis and model reports provide direct inputs to this model report, namely ''Characterize Eruptive Processes at Yucca Mountain, Nevada and Number of Waste Packages Hit by Igneous Intrusion''. This model report provides direct inputs to the TSPA, which uses the ASHPLUME software described and used in this model report. Thus, ASHPLUME software inputs are inputs to this model report for ASHPLUME runs in this model report. However, ASHPLUME software inputs are outputs of this model report for ASHPLUME runs by TSPA.« less

Predicting motor vehicle collisions using Bayesian neural network models: an empirical analysis.

PubMed

Xie, Yuanchang; Lord, Dominique; Zhang, Yunlong

2007-09-01

Statistical models have frequently been used in highway safety studies. They can be utilized for various purposes, including establishing relationships between variables, screening covariates and predicting values. Generalized linear models (GLM) and hierarchical Bayes models (HBM) have been the most common types of model favored by transportation safety analysts. Over the last few years, researchers have proposed the back-propagation neural network (BPNN) model for modeling the phenomenon under study. Compared to GLMs and HBMs, BPNNs have received much less attention in highway safety modeling. The reasons are attributed to the complexity for estimating this kind of model as well as the problem related to "over-fitting" the data. To circumvent the latter problem, some statisticians have proposed the use of Bayesian neural network (BNN) models. These models have been shown to perform better than BPNN models while at the same time reducing the difficulty associated with over-fitting the data. The objective of this study is to evaluate the application of BNN models for predicting motor vehicle crashes. To accomplish this objective, a series of models was estimated using data collected on rural frontage roads in Texas. Three types of models were compared: BPNN, BNN and the negative binomial (NB) regression models. The results of this study show that in general both types of neural network models perform better than the NB regression model in terms of data prediction. Although the BPNN model can occasionally provide better or approximately equivalent prediction performance compared to the BNN model, in most cases its prediction performance is worse than the BNN model. In addition, the data fitting performance of the BPNN model is consistently worse than the BNN model, which suggests that the BNN model has better generalization abilities than the BPNN model and can effectively alleviate the over-fitting problem without significantly compromising the nonlinear approximation ability. The results also show that BNNs could be used for other useful analyses in highway safety, including the development of accident modification factors and for improving the prediction capabilities for evaluating different highway design alternatives.

Understanding seasonal variability of uncertainty in hydrological prediction

NASA Astrophysics Data System (ADS)

Li, M.; Wang, Q. J.

2012-04-01

Understanding uncertainty in hydrological prediction can be highly valuable for improving the reliability of streamflow prediction. In this study, a monthly water balance model, WAPABA, in a Bayesian joint probability with error models are presented to investigate the seasonal dependency of prediction error structure. A seasonal invariant error model, analogous to traditional time series analysis, uses constant parameters for model error and account for no seasonal variations. In contrast, a seasonal variant error model uses a different set of parameters for bias, variance and autocorrelation for each individual calendar month. Potential connection amongst model parameters from similar months is not considered within the seasonal variant model and could result in over-fitting and over-parameterization. A hierarchical error model further applies some distributional restrictions on model parameters within a Bayesian hierarchical framework. An iterative algorithm is implemented to expedite the maximum a posterior (MAP) estimation of a hierarchical error model. Three error models are applied to forecasting streamflow at a catchment in southeast Australia in a cross-validation analysis. This study also presents a number of statistical measures and graphical tools to compare the predictive skills of different error models. From probability integral transform histograms and other diagnostic graphs, the hierarchical error model conforms better to reliability when compared to the seasonal invariant error model. The hierarchical error model also generally provides the most accurate mean prediction in terms of the Nash-Sutcliffe model efficiency coefficient and the best probabilistic prediction in terms of the continuous ranked probability score (CRPS). The model parameters of the seasonal variant error model are very sensitive to each cross validation, while the hierarchical error model produces much more robust and reliable model parameters. Furthermore, the result of the hierarchical error model shows that most of model parameters are not seasonal variant except for error bias. The seasonal variant error model is likely to use more parameters than necessary to maximize the posterior likelihood. The model flexibility and robustness indicates that the hierarchical error model has great potential for future streamflow predictions.

[Suitability of four stomatal conductance models in agro-pastoral ecotone in North China: A case study for potato and oil sunflower.

PubMed

Huang, Ming Xia; Wang, Jing; Tang, Jian Zhao; Yu, Qiang; Zhang, Jun; Xue, Qing Yu; Chang, Qing; Tan, Mei Xiu

2016-11-18

The suitability of four popular empirical and semi-empirical stomatal conductance models (Jarvis model, Ball-Berry model, Leuning model and Medlyn model) was evaluated based on para-llel observation data of leaf stomatal conductance, leaf net photosynthetic rate and meteorological factors during the vigorous growing period of potato and oil sunflower at Wuchuan experimental station in agro-pastoral ecotone in North China. It was found that there was a significant linear relationship between leaf stomatal conductance and leaf net photosynthetic rate for potato, whereas the linear relationship appeared weaker for oil sunflower. The results of model evaluation showed that Ball-Berry model performed best in simulating leaf stomatal conductance of potato, followed by Leuning model and Medlyn model, while Jarvis model was the last in the performance rating. The root-mean-square error (RMSE) was 0.0331, 0.0371, 0.0456 and 0.0794 mol·m -2 ·s -1 , the normalized root-mean-square error (NRMSE) was 26.8%, 30.0%, 36.9% and 64.3%, and R-squared (R 2 ) was 0.96, 0.61, 0.91 and 0.88 between simulated and observed leaf stomatal conductance of potato for Ball-Berry model, Leuning model, Medlyn model and Jarvis model, respectively. For leaf stomatal conductance of oil sunflower, Jarvis model performed slightly better than Leuning model, Ball-Berry model and Medlyn model. RMSE was 0.2221, 0.2534, 0.2547 and 0.2758 mol·m -2 ·s -1 , NRMSE was 40.3%, 46.0%, 46.2% and 50.1%, and R 2 was 0.38, 0.22, 0.23 and 0.20 between simulated and observed leaf stomatal conductance of oil sunflower for Jarvis model, Leuning model, Ball-Berry model and Medlyn model, respectively. The path analysis was conducted to identify effects of specific meteorological factors on leaf stomatal conductance. The diurnal variation of leaf stomatal conductance was principally affected by vapour pressure saturation deficit for both potato and oil sunflower. The model evaluation suggested that the stomatal conductance models for oil sunflower are to be improved in further research.

Evaluation of chiller modeling approaches and their usability for fault detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sreedharan, Priya

Selecting the model is an important and essential step in model based fault detection and diagnosis (FDD). Several factors must be considered in model evaluation, including accuracy, training data requirements, calibration effort, generality, and computational requirements. All modeling approaches fall somewhere between pure first-principles models, and empirical models. The objective of this study was to evaluate different modeling approaches for their applicability to model based FDD of vapor compression air conditioning units, which are commonly known as chillers. Three different models were studied: two are based on first-principles and the third is empirical in nature. The first-principles models are themore » Gordon and Ng Universal Chiller model (2nd generation), and a modified version of the ASHRAE Primary Toolkit model, which are both based on first principles. The DOE-2 chiller model as implemented in CoolTools{trademark} was selected for the empirical category. The models were compared in terms of their ability to reproduce the observed performance of an older chiller operating in a commercial building, and a newer chiller in a laboratory. The DOE-2 and Gordon-Ng models were calibrated by linear regression, while a direct-search method was used to calibrate the Toolkit model. The ''CoolTools'' package contains a library of calibrated DOE-2 curves for a variety of different chillers, and was used to calibrate the building chiller to the DOE-2 model. All three models displayed similar levels of accuracy. Of the first principles models, the Gordon-Ng model has the advantage of being linear in the parameters, which allows more robust parameter estimation methods to be used and facilitates estimation of the uncertainty in the parameter values. The ASHRAE Toolkit Model may have advantages when refrigerant temperature measurements are also available. The DOE-2 model can be expected to have advantages when very limited data are available to calibrate the model, as long as one of the previously identified models in the CoolTools library matches the performance of the chiller in question.« less

PyMT: A Python package for model-coupling in the Earth sciences

NASA Astrophysics Data System (ADS)

Hutton, E.

2016-12-01

The current landscape of Earth-system models is not only broad in scientific scope, but also broad in type. On the one hand, the large variety of models is exciting, as it provides fertile ground for extending or linking models together in novel ways to answer new scientific questions. However, the heterogeneity in model type acts to inhibit model coupling, model development, or even model use. Existing models are written in a variety of programming languages, operate on different grids, use their own file formats (both for input and output), have different user interfaces, have their own time steps, etc. Each of these factors become obstructions to scientists wanting to couple, extend - or simply run - existing models. For scientists whose main focus may not be computer science these barriers become even larger and become significant logistical hurdles. And this is all before the scientific difficulties of coupling or running models are addressed. The CSDMS Python Modeling Toolkit (PyMT) was developed to help non-computer scientists deal with these sorts of modeling logistics. PyMT is the fundamental package the Community Surface Dynamics Modeling System uses for the coupling of models that expose the Basic Modeling Interface (BMI). It contains: Tools necessary for coupling models of disparate time and space scales (including grid mappers) Time-steppers that coordinate the sequencing of coupled models Exchange of data between BMI-enabled models Wrappers that automatically load BMI-enabled models into the PyMT framework Utilities that support open-source interfaces (UGRID, SGRID,CSDMS Standard Names, etc.) A collection of community-submitted models, written in a variety of programminglanguages, from a variety of process domains - but all usable from within the Python programming language A plug-in framework for adding additional BMI-enabled models to the framework In this presentation we intoduce the basics of the PyMT as well as provide an example of coupling models of different domains and grid types.

Can the super model (SUMO) method improve hydrological simulations? Exploratory tests with the GR hydrological models

NASA Astrophysics Data System (ADS)

Santos, Léonard; Thirel, Guillaume; Perrin, Charles

2017-04-01

Errors made by hydrological models may come from a problem in parameter estimation, uncertainty on observed measurements, numerical problems and from the model conceptualization that simplifies the reality. Here we focus on this last issue of hydrological modeling. One of the solutions to reduce structural uncertainty is to use a multimodel method, taking advantage of the great number and the variability of existing hydrological models. In particular, because different models are not similarly good in all situations, using multimodel approaches can improve the robustness of modeled outputs. Traditionally, in hydrology, multimodel methods are based on the output of the model (the simulated flow series). The aim of this poster is to introduce a different approach based on the internal variables of the models. The method is inspired by the SUper MOdel (SUMO, van den Berge et al., 2011) developed for climatology. The idea of the SUMO method is to correct the internal variables of a model taking into account the values of the internal variables of (an)other model(s). This correction is made bilaterally between the different models. The ensemble of the different models constitutes a super model in which all the models exchange information on their internal variables with each other at each time step. Due to this continuity in the exchanges, this multimodel algorithm is more dynamic than traditional multimodel methods. The method will be first tested using two GR4J models (in a state-space representation) with different parameterizations. The results will be presented and compared to traditional multimodel methods that will serve as benchmarks. In the future, other rainfall-runoff models will be used in the super model. References van den Berge, L. A., Selten, F. M., Wiegerinck, W., and Duane, G. S. (2011). A multi-model ensemble method that combines imperfect models through learning. Earth System Dynamics, 2(1) :161-177.

Downscaling GISS ModelE Boreal Summer Climate over Africa

NASA Technical Reports Server (NTRS)

Druyan, Leonard M.; Fulakeza, Matthew

2015-01-01

The study examines the perceived added value of downscaling atmosphere-ocean global climate model simulations over Africa and adjacent oceans by a nested regional climate model. NASA/Goddard Institute for Space Studies (GISS) coupled ModelE simulations for June- September 1998-2002 are used to form lateral boundary conditions for synchronous simulations by the GISS RM3 regional climate model. The ModelE computational grid spacing is 2deg latitude by 2.5deg longitude and the RM3 grid spacing is 0.44deg. ModelE precipitation climatology for June-September 1998-2002 is shown to be a good proxy for 30-year means so results based on the 5-year sample are presumed to be generally representative. Comparison with observational evidence shows several discrepancies in ModelE configuration of the boreal summer inter-tropical convergence zone (ITCZ). One glaring shortcoming is that ModelE simulations do not advance the West African rain band northward during the summer to represent monsoon precipitation onset over the Sahel. Results for 1998-2002 show that onset simulation is an important added value produced by downscaling with RM3. ModelE Eastern South Atlantic Ocean computed sea-surface temperatures (SST) are some 4 K warmer than reanalysis, contributing to large positive biases in overlying surface air temperatures (Tsfc). ModelE Tsfc are also too warm over most of Africa. RM3 downscaling somewhat mitigates the magnitude of Tsfc biases over the African continent, it eliminates the ModelE double ITCZ over the Atlantic and it produces more realistic orographic precipitation maxima. Parallel ModelE and RM3 simulations with observed SST forcing (in place of the predicted ocean) lower Tsfc errors but have mixed impacts on circulation and precipitation biases. Downscaling improvements of the meridional movement of the rain band over West Africa and the configuration of orographic precipitation maxima are realized irrespective of the SST biases.

A tool for multi-scale modelling of the renal nephron

PubMed Central

Nickerson, David P.; Terkildsen, Jonna R.; Hamilton, Kirk L.; Hunter, Peter J.

2011-01-01

We present the development of a tool, which provides users with the ability to visualize and interact with a comprehensive description of a multi-scale model of the renal nephron. A one-dimensional anatomical model of the nephron has been created and is used for visualization and modelling of tubule transport in various nephron anatomical segments. Mathematical models of nephron segments are embedded in the one-dimensional model. At the cellular level, these segment models use models encoded in CellML to describe cellular and subcellular transport kinetics. A web-based presentation environment has been developed that allows the user to visualize and navigate through the multi-scale nephron model, including simulation results, at the different spatial scales encompassed by the model description. The Zinc extension to Firefox is used to provide an interactive three-dimensional view of the tubule model and the native Firefox rendering of scalable vector graphics is used to present schematic diagrams for cellular and subcellular scale models. The model viewer is embedded in a web page that dynamically presents content based on user input. For example, when viewing the whole nephron model, the user might be presented with information on the various embedded segment models as they select them in the three-dimensional model view. Alternatively, the user chooses to focus the model viewer on a cellular model located in a particular nephron segment in order to view the various membrane transport proteins. Selecting a specific protein may then present the user with a description of the mathematical model governing the behaviour of that protein—including the mathematical model itself and various simulation experiments used to validate the model against the literature. PMID:22670210

An online model composition tool for system biology models

PubMed Central

2013-01-01

Background There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. Results We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Conclusions Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well. PMID:24006914

A parsimonious dynamic model for river water quality assessment.

PubMed

Mannina, Giorgio; Viviani, Gaspare

2010-01-01

Water quality modelling is of crucial importance for the assessment of physical, chemical, and biological changes in water bodies. Mathematical approaches to water modelling have become more prevalent over recent years. Different model types ranging from detailed physical models to simplified conceptual models are available. Actually, a possible middle ground between detailed and simplified models may be parsimonious models that represent the simplest approach that fits the application. The appropriate modelling approach depends on the research goal as well as on data available for correct model application. When there is inadequate data, it is mandatory to focus on a simple river water quality model rather than detailed ones. The study presents a parsimonious river water quality model to evaluate the propagation of pollutants in natural rivers. The model is made up of two sub-models: a quantity one and a quality one. The model employs a river schematisation that considers different stretches according to the geometric characteristics and to the gradient of the river bed. Each stretch is represented with a conceptual model of a series of linear channels and reservoirs. The channels determine the delay in the pollution wave and the reservoirs cause its dispersion. To assess the river water quality, the model employs four state variables: DO, BOD, NH(4), and NO. The model was applied to the Savena River (Italy), which is the focus of a European-financed project in which quantity and quality data were gathered. A sensitivity analysis of the model output to the model input or parameters was done based on the Generalised Likelihood Uncertainty Estimation methodology. The results demonstrate the suitability of such a model as a tool for river water quality management.

The cost of simplifying air travel when modeling disease spread.

PubMed

Lessler, Justin; Kaufman, James H; Ford, Daniel A; Douglas, Judith V

2009-01-01

Air travel plays a key role in the spread of many pathogens. Modeling the long distance spread of infectious disease in these cases requires an air travel model. Highly detailed air transportation models can be over determined and computationally problematic. We compared the predictions of a simplified air transport model with those of a model of all routes and assessed the impact of differences on models of infectious disease. Using U.S. ticket data from 2007, we compared a simplified "pipe" model, in which individuals flow in and out of the air transport system based on the number of arrivals and departures from a given airport, to a fully saturated model where all routes are modeled individually. We also compared the pipe model to a "gravity" model where the probability of travel is scaled by physical distance; the gravity model did not differ significantly from the pipe model. The pipe model roughly approximated actual air travel, but tended to overestimate the number of trips between small airports and underestimate travel between major east and west coast airports. For most routes, the maximum number of false (or missed) introductions of disease is small (<1 per day) but for a few routes this rate is greatly underestimated by the pipe model. If our interest is in large scale regional and national effects of disease, the simplified pipe model may be adequate. If we are interested in specific effects of interventions on particular air routes or the time for the disease to reach a particular location, a more complex point-to-point model will be more accurate. For many problems a hybrid model that independently models some frequently traveled routes may be the best choice. Regardless of the model used, the effect of simplifications and sensitivity to errors in parameter estimation should be analyzed.

Risk prediction models of breast cancer: a systematic review of model performances.

PubMed

Anothaisintawee, Thunyarat; Teerawattananon, Yot; Wiratkapun, Chollathip; Kasamesup, Vijj; Thakkinstian, Ammarin

2012-05-01

The number of risk prediction models has been increasingly developed, for estimating about breast cancer in individual women. However, those model performances are questionable. We therefore have conducted a study with the aim to systematically review previous risk prediction models. The results from this review help to identify the most reliable model and indicate the strengths and weaknesses of each model for guiding future model development. We searched MEDLINE (PubMed) from 1949 and EMBASE (Ovid) from 1974 until October 2010. Observational studies which constructed models using regression methods were selected. Information about model development and performance were extracted. Twenty-five out of 453 studies were eligible. Of these, 18 developed prediction models and 7 validated existing prediction models. Up to 13 variables were included in the models and sample sizes for each study ranged from 550 to 2,404,636. Internal validation was performed in four models, while five models had external validation. Gail and Rosner and Colditz models were the significant models which were subsequently modified by other scholars. Calibration performance of most models was fair to good (expected/observe ratio: 0.87-1.12), but discriminatory accuracy was poor to fair both in internal validation (concordance statistics: 0.53-0.66) and in external validation (concordance statistics: 0.56-0.63). Most models yielded relatively poor discrimination in both internal and external validation. This poor discriminatory accuracy of existing models might be because of a lack of knowledge about risk factors, heterogeneous subtypes of breast cancer, and different distributions of risk factors across populations. In addition the concordance statistic itself is insensitive to measure the improvement of discrimination. Therefore, the new method such as net reclassification index should be considered to evaluate the improvement of the performance of a new develop model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

M. A. Wasiolek

The purpose of this report is to document the biosphere model, the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN), which describes radionuclide transport processes in the biosphere and associated human exposure that may arise as the result of radionuclide release from the geologic repository at Yucca Mountain. The biosphere model is one of the process models that support the Yucca Mountain Project (YMP) Total System Performance Assessment (TSPA) for the license application (LA), the TSPA-LA. The ERMYN model provides the capability of performing human radiation dose assessments. This report documents the biosphere model, which includes: (1) Describing the referencemore » biosphere, human receptor, exposure scenarios, and primary radionuclides for each exposure scenario (Section 6.1); (2) Developing a biosphere conceptual model using site-specific features, events, and processes (FEPs), the reference biosphere, the human receptor, and assumptions (Section 6.2 and Section 6.3); (3) Building a mathematical model using the biosphere conceptual model and published biosphere models (Sections 6.4 and 6.5); (4) Summarizing input parameters for the mathematical model, including the uncertainty associated with input values (Section 6.6); (5) Identifying improvements in the ERMYN model compared with the model used in previous biosphere modeling (Section 6.7); (6) Constructing an ERMYN implementation tool (model) based on the biosphere mathematical model using GoldSim stochastic simulation software (Sections 6.8 and 6.9); (7) Verifying the ERMYN model by comparing output from the software with hand calculations to ensure that the GoldSim implementation is correct (Section 6.10); and (8) Validating the ERMYN model by corroborating it with published biosphere models; comparing conceptual models, mathematical models, and numerical results (Section 7).« less

Microphysics in the Multi-Scale Modeling Systems with Unified Physics

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.

2011-01-01

In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, the microphysics developments of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the heavy precipitation processes will be presented.

Intelligent Decisions Need Intelligent Choice of Models and Data - a Bayesian Justifiability Analysis for Models with Vastly Different Complexity

NASA Astrophysics Data System (ADS)

Nowak, W.; Schöniger, A.; Wöhling, T.; Illman, W. A.

2016-12-01

Model-based decision support requires justifiable models with good predictive capabilities. This, in turn, calls for a fine adjustment between predictive accuracy (small systematic model bias that can be achieved with rather complex models), and predictive precision (small predictive uncertainties that can be achieved with simpler models with fewer parameters). The implied complexity/simplicity trade-off depends on the availability of informative data for calibration. If not available, additional data collection can be planned through optimal experimental design. We present a model justifiability analysis that can compare models of vastly different complexity. It rests on Bayesian model averaging (BMA) to investigate the complexity/performance trade-off dependent on data availability. Then, we disentangle the complexity component from the performance component. We achieve this by replacing actually observed data by realizations of synthetic data predicted by the models. This results in a "model confusion matrix". Based on this matrix, the modeler can identify the maximum model complexity that can be justified by the available (or planned) amount and type of data. As a side product, the matrix quantifies model (dis-)similarity. We apply this analysis to aquifer characterization via hydraulic tomography, comparing four models with a vastly different number of parameters (from a homogeneous model to geostatistical random fields). As a testing scenario, we consider hydraulic tomography data. Using subsets of these data, we determine model justifiability as a function of data set size. The test case shows that geostatistical parameterization requires a substantial amount of hydraulic tomography data to be justified, while a zonation-based model can be justified with more limited data set sizes. The actual model performance (as opposed to model justifiability), however, depends strongly on the quality of prior geological information.

Model-based economic evaluation in Alzheimer's disease: a review of the methods available to model Alzheimer's disease progression.

PubMed

Green, Colin; Shearer, James; Ritchie, Craig W; Zajicek, John P

2011-01-01

To consider the methods available to model Alzheimer's disease (AD) progression over time to inform on the structure and development of model-based evaluations, and the future direction of modelling methods in AD. A systematic search of the health care literature was undertaken to identify methods to model disease progression in AD. Modelling methods are presented in a descriptive review. The literature search identified 42 studies presenting methods or applications of methods to model AD progression over time. The review identified 10 general modelling frameworks available to empirically model the progression of AD as part of a model-based evaluation. Seven of these general models are statistical models predicting progression of AD using a measure of cognitive function. The main concerns with models are on model structure, around the limited characterization of disease progression, and on the use of a limited number of health states to capture events related to disease progression over time. None of the available models have been able to present a comprehensive model of the natural history of AD. Although helpful, there are serious limitations in the methods available to model progression of AD over time. Advances are needed to better model the progression of AD and the effects of the disease on peoples' lives. Recent evidence supports the need for a multivariable approach to the modelling of AD progression, and indicates that a latent variable analytic approach to characterising AD progression is a promising avenue for advances in the statistical development of modelling methods. Copyright © 2011 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Nursing resources and responsibilities according to hospital organizational model for management of inflammatory bowel disease in Spain.

PubMed

Marín, Laura; Torrejón, Antonio; Oltra, Lorena; Seoane, Montserrat; Hernández-Sampelayo, Paloma; Vera, María Isabel; Casellas, Francesc; Alfaro, Noelia; Lázaro, Pablo; García-Sánchez, Valle

2011-06-01

Nurses play an important role in the multidisciplinary management of inflammatory bowel disease (IBD), but little is known about this role and the associated resources. To improve knowledge of resource availability for health care activities and the different organizational models in managing IBD in Spain. Cross-sectional study with data obtained by questionnaire directed at Spanish Gastroenterology Services (GS). Five GS models were identified according to whether they have: no specific service for IBD management (Model A); IBD outpatient office for physician consultations (Model B); general outpatient office for nurse consultations (Model C); both, Model B and Model C (Model D); and IBD Unit (Model E) when the hospital has a Comprehensive Care Unit for IBD with telephone helpline, computer, including a Model B. Available resources and activities performed were compared according to GS model (chi-square test and test for linear trend). Responses were received from 107 GS: 33 Model A (31%), 38 Model B (36%), 4 Model C (4%), 16 Model D (15%) and 16 Model E (15%). The model in which nurses have the most resources and responsibilities is the Model E. The more complete the organizational model, the more frequent the availability of nursing resources (educational material, databases, office, and specialized software) and responsibilities (management of walk-in appointments, provision of emotional support, health education, follow-up of drug treatment and treatment adherence) (p<0.05). Nurses have more resources and responsibilities the more complete is the organizational model for IBD management. Development of these areas may improve patient outcomes. Copyright © 2011 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

Template-free modeling by LEE and LEER in CASP11.

PubMed

Joung, InSuk; Lee, Sun Young; Cheng, Qianyi; Kim, Jong Yun; Joo, Keehyoung; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Plausible combinations: An improved method to evaluate the covariate structure of Cormack-Jolly-Seber mark-recapture models

USGS Publications Warehouse

Bromaghin, Jeffrey F.; McDonald, Trent L.; Amstrup, Steven C.

2013-01-01

Mark-recapture models are extensively used in quantitative population ecology, providing estimates of population vital rates, such as survival, that are difficult to obtain using other methods. Vital rates are commonly modeled as functions of explanatory covariates, adding considerable flexibility to mark-recapture models, but also increasing the subjectivity and complexity of the modeling process. Consequently, model selection and the evaluation of covariate structure remain critical aspects of mark-recapture modeling. The difficulties involved in model selection are compounded in Cormack-Jolly- Seber models because they are composed of separate sub-models for survival and recapture probabilities, which are conceptualized independently even though their parameters are not statistically independent. The construction of models as combinations of sub-models, together with multiple potential covariates, can lead to a large model set. Although desirable, estimation of the parameters of all models may not be feasible. Strategies to search a model space and base inference on a subset of all models exist and enjoy widespread use. However, even though the methods used to search a model space can be expected to influence parameter estimation, the assessment of covariate importance, and therefore the ecological interpretation of the modeling results, the performance of these strategies has received limited investigation. We present a new strategy for searching the space of a candidate set of Cormack-Jolly-Seber models and explore its performance relative to existing strategies using computer simulation. The new strategy provides an improved assessment of the importance of covariates and covariate combinations used to model survival and recapture probabilities, while requiring only a modest increase in the number of models on which inference is based in comparison to existing techniques.

Framework for Understanding Structural Errors (FUSE): A modular framework to diagnose differences between hydrological models

USGS Publications Warehouse

Clark, Martyn P.; Slater, Andrew G.; Rupp, David E.; Woods, Ross A.; Vrugt, Jasper A.; Gupta, Hoshin V.; Wagener, Thorsten; Hay, Lauren E.

2008-01-01

The problems of identifying the most appropriate model structure for a given problem and quantifying the uncertainty in model structure remain outstanding research challenges for the discipline of hydrology. Progress on these problems requires understanding of the nature of differences between models. This paper presents a methodology to diagnose differences in hydrological model structures: the Framework for Understanding Structural Errors (FUSE). FUSE was used to construct 79 unique model structures by combining components of 4 existing hydrological models. These new models were used to simulate streamflow in two of the basins used in the Model Parameter Estimation Experiment (MOPEX): the Guadalupe River (Texas) and the French Broad River (North Carolina). Results show that the new models produced simulations of streamflow that were at least as good as the simulations produced by the models that participated in the MOPEX experiment. Our initial application of the FUSE method for the Guadalupe River exposed relationships between model structure and model performance, suggesting that the choice of model structure is just as important as the choice of model parameters. However, further work is needed to evaluate model simulations using multiple criteria to diagnose the relative importance of model structural differences in various climate regimes and to assess the amount of independent information in each of the models. This work will be crucial to both identifying the most appropriate model structure for a given problem and quantifying the uncertainty in model structure. To facilitate research on these problems, the FORTRAN‐90 source code for FUSE is available upon request from the lead author.

Moving alcohol prevention research forward-Part II: new directions grounded in community-based system dynamics modeling.

PubMed

Apostolopoulos, Yorghos; Lemke, Michael K; Barry, Adam E; Lich, Kristen Hassmiller

2018-02-01

Given the complexity of factors contributing to alcohol misuse, appropriate epistemologies and methodologies are needed to understand and intervene meaningfully. We aimed to (1) provide an overview of computational modeling methodologies, with an emphasis on system dynamics modeling; (2) explain how community-based system dynamics modeling can forge new directions in alcohol prevention research; and (3) present a primer on how to build alcohol misuse simulation models using system dynamics modeling, with an emphasis on stakeholder involvement, data sources and model validation. Throughout, we use alcohol misuse among college students in the United States as a heuristic example for demonstrating these methodologies. System dynamics modeling employs a top-down aggregate approach to understanding dynamically complex problems. Its three foundational properties-stocks, flows and feedbacks-capture non-linearity, time-delayed effects and other system characteristics. As a methodological choice, system dynamics modeling is amenable to participatory approaches; in particular, community-based system dynamics modeling has been used to build impactful models for addressing dynamically complex problems. The process of community-based system dynamics modeling consists of numerous stages: (1) creating model boundary charts, behavior-over-time-graphs and preliminary system dynamics models using group model-building techniques; (2) model formulation; (3) model calibration; (4) model testing and validation; and (5) model simulation using learning-laboratory techniques. Community-based system dynamics modeling can provide powerful tools for policy and intervention decisions that can result ultimately in sustainable changes in research and action in alcohol misuse prevention. © 2017 Society for the Study of Addiction.

A Comparison of Two Mathematical Modeling Frameworks for Evaluating Sexually Transmitted Infection Epidemiology.

PubMed

Johnson, Leigh F; Geffen, Nathan

2016-03-01

Different models of sexually transmitted infections (STIs) can yield substantially different conclusions about STI epidemiology, and it is important to understand how and why models differ. Frequency-dependent models make the simplifying assumption that STI incidence is proportional to STI prevalence in the population, whereas network models calculate STI incidence more realistically by classifying individuals according to their partners' STI status. We assessed a deterministic frequency-dependent model approximation to a microsimulation network model of STIs in South Africa. Sexual behavior and demographic parameters were identical in the 2 models. Six STIs were simulated using each model: HIV, herpes, syphilis, gonorrhea, chlamydia, and trichomoniasis. For all 6 STIs, the frequency-dependent model estimated a higher STI prevalence than the network model, with the difference between the 2 models being relatively large for the curable STIs. When the 2 models were fitted to the same STI prevalence data, the best-fitting parameters differed substantially between models, with the frequency-dependent model suggesting more immunity and lower transmission probabilities. The fitted frequency-dependent model estimated that the effects of a hypothetical elimination of concurrent partnerships and a reduction in commercial sex were both smaller than estimated by the fitted network model, whereas the latter model estimated a smaller impact of a reduction in unprotected sex in spousal relationships. The frequency-dependent assumption is problematic when modeling short-term STIs. Frequency-dependent models tend to underestimate the importance of high-risk groups in sustaining STI epidemics, while overestimating the importance of long-term partnerships and low-risk groups.

Using Multivariate Adaptive Regression Spline and Artificial Neural Network to Simulate Urbanization in Mumbai, India

NASA Astrophysics Data System (ADS)

Ahmadlou, M.; Delavar, M. R.; Tayyebi, A.; Shafizadeh-Moghadam, H.

2015-12-01

Land use change (LUC) models used for modelling urban growth are different in structure and performance. Local models divide the data into separate subsets and fit distinct models on each of the subsets. Non-parametric models are data driven and usually do not have a fixed model structure or model structure is unknown before the modelling process. On the other hand, global models perform modelling using all the available data. In addition, parametric models have a fixed structure before the modelling process and they are model driven. Since few studies have compared local non-parametric models with global parametric models, this study compares a local non-parametric model called multivariate adaptive regression spline (MARS), and a global parametric model called artificial neural network (ANN) to simulate urbanization in Mumbai, India. Both models determine the relationship between a dependent variable and multiple independent variables. We used receiver operating characteristic (ROC) to compare the power of the both models for simulating urbanization. Landsat images of 1991 (TM) and 2010 (ETM+) were used for modelling the urbanization process. The drivers considered for urbanization in this area were distance to urban areas, urban density, distance to roads, distance to water, distance to forest, distance to railway, distance to central business district, number of agricultural cells in a 7 by 7 neighbourhoods, and slope in 1991. The results showed that the area under the ROC curve for MARS and ANN was 94.77% and 95.36%, respectively. Thus, ANN performed slightly better than MARS to simulate urban areas in Mumbai, India.

ModelMuse - A Graphical User Interface for MODFLOW-2005 and PHAST

USGS Publications Warehouse

Winston, Richard B.

2009-01-01

ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW-2005 and PHAST. This software package provides a GUI for creating the flow and transport input file for PHAST and the input files for MODFLOW-2005. In ModelMuse, the spatial data for the model is independent of the grid, and the temporal data is independent of the stress periods. Being able to input these data independently allows the user to redefine the spatial and temporal discretization at will. This report describes the basic concepts required to work with ModelMuse. These basic concepts include the model grid, data sets, formulas, objects, the method used to assign values to data sets, and model features. The ModelMuse main window has a top, front, and side view of the model that can be used for editing the model, and a 3-D view of the model that can be used to display properties of the model. ModelMuse has tools to generate and edit the model grid. It also has a variety of interpolation methods and geographic functions that can be used to help define the spatial variability of the model. ModelMuse can be used to execute both MODFLOW-2005 and PHAST and can also display the results of MODFLOW-2005 models. An example of using ModelMuse with MODFLOW-2005 is included in this report. Several additional examples are described in the help system for ModelMuse, which can be accessed from the Help menu.

Transient PVT measurements and model predictions for vessel heat transfer. Part II.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Felver, Todd G.; Paradiso, Nicholas Joseph; Winters, William S., Jr.

2010-07-01

Part I of this report focused on the acquisition and presentation of transient PVT data sets that can be used to validate gas transfer models. Here in Part II we focus primarily on describing models and validating these models using the data sets. Our models are intended to describe the high speed transport of compressible gases in arbitrary arrangements of vessels, tubing, valving and flow branches. Our models fall into three categories: (1) network flow models in which flow paths are modeled as one-dimensional flow and vessels are modeled as single control volumes, (2) CFD (Computational Fluid Dynamics) models inmore » which flow in and between vessels is modeled in three dimensions and (3) coupled network/CFD models in which vessels are modeled using CFD and flows between vessels are modeled using a network flow code. In our work we utilized NETFLOW as our network flow code and FUEGO for our CFD code. Since network flow models lack three-dimensional resolution, correlations for heat transfer and tube frictional pressure drop are required to resolve important physics not being captured by the model. Here we describe how vessel heat transfer correlations were improved using the data and present direct model-data comparisons for all tests documented in Part I. Our results show that our network flow models have been substantially improved. The CFD modeling presented here describes the complex nature of vessel heat transfer and for the first time demonstrates that flow and heat transfer in vessels can be modeled directly without the need for correlations.« less

Comparison of chiller models for use in model-based fault detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sreedharan, Priya; Haves, Philip

Selecting the model is an important and essential step in model based fault detection and diagnosis (FDD). Factors that are considered in evaluating a model include accuracy, training data requirements, calibration effort, generality, and computational requirements. The objective of this study was to evaluate different modeling approaches for their applicability to model based FDD of vapor compression chillers. Three different models were studied: the Gordon and Ng Universal Chiller model (2nd generation) and a modified version of the ASHRAE Primary Toolkit model, which are both based on first principles, and the DOE-2 chiller model, as implemented in CoolTools{trademark}, which ismore » empirical. The models were compared in terms of their ability to reproduce the observed performance of an older, centrifugal chiller operating in a commercial office building and a newer centrifugal chiller in a laboratory. All three models displayed similar levels of accuracy. Of the first principles models, the Gordon-Ng model has the advantage of being linear in the parameters, which allows more robust parameter estimation methods to be used and facilitates estimation of the uncertainty in the parameter values. The ASHRAE Toolkit Model may have advantages when refrigerant temperature measurements are also available. The DOE-2 model can be expected to have advantages when very limited data are available to calibrate the model, as long as one of the previously identified models in the CoolTools library matches the performance of the chiller in question.« less

Are Model Transferability And Complexity Antithetical? Insights From Validation of a Variable-Complexity Empirical Snow Model in Space and Time

NASA Astrophysics Data System (ADS)

Lute, A. C.; Luce, Charles H.

2017-11-01

The related challenges of predictions in ungauged basins and predictions in ungauged climates point to the need to develop environmental models that are transferable across both space and time. Hydrologic modeling has historically focused on modelling one or only a few basins using highly parameterized conceptual or physically based models. However, model parameters and structures have been shown to change significantly when calibrated to new basins or time periods, suggesting that model complexity and model transferability may be antithetical. Empirical space-for-time models provide a framework within which to assess model transferability and any tradeoff with model complexity. Using 497 SNOTEL sites in the western U.S., we develop space-for-time models of April 1 SWE and Snow Residence Time based on mean winter temperature and cumulative winter precipitation. The transferability of the models to new conditions (in both space and time) is assessed using non-random cross-validation tests with consideration of the influence of model complexity on transferability. As others have noted, the algorithmic empirical models transfer best when minimal extrapolation in input variables is required. Temporal split-sample validations use pseudoreplicated samples, resulting in the selection of overly complex models, which has implications for the design of hydrologic model validation tests. Finally, we show that low to moderate complexity models transfer most successfully to new conditions in space and time, providing empirical confirmation of the parsimony principal.

Geospace environment modeling 2008--2009 challenge: Dst index

USGS Publications Warehouse

Rastätter, L.; Kuznetsova, M.M.; Glocer, A.; Welling, D.; Meng, X.; Raeder, J.; Wittberger, M.; Jordanova, V.K.; Yu, Y.; Zaharia, S.; Weigel, R.S.; Sazykin, S.; Boynton, R.; Wei, H.; Eccles, V.; Horton, W.; Mays, M.L.; Gannon, J.

2013-01-01

This paper reports the metrics-based results of the Dst index part of the 2008–2009 GEM Metrics Challenge. The 2008–2009 GEM Metrics Challenge asked modelers to submit results for four geomagnetic storm events and five different types of observations that can be modeled by statistical, climatological or physics-based models of the magnetosphere-ionosphere system. We present the results of 30 model settings that were run at the Community Coordinated Modeling Center and at the institutions of various modelers for these events. To measure the performance of each of the models against the observations, we use comparisons of 1 hour averaged model data with the Dst index issued by the World Data Center for Geomagnetism, Kyoto, Japan, and direct comparison of 1 minute model data with the 1 minute Dst index calculated by the United States Geological Survey. The latter index can be used to calculate spectral variability of model outputs in comparison to the index. We find that model rankings vary widely by skill score used. None of the models consistently perform best for all events. We find that empirical models perform well in general. Magnetohydrodynamics-based models of the global magnetosphere with inner magnetosphere physics (ring current model) included and stand-alone ring current models with properly defined boundary conditions perform well and are able to match or surpass results from empirical models. Unlike in similar studies, the statistical models used in this study found their challenge in the weakest events rather than the strongest events.

Hybrid Forecasting of Daily River Discharges Considering Autoregressive Heteroscedasticity

NASA Astrophysics Data System (ADS)

Szolgayová, Elena Peksová; Danačová, Michaela; Komorniková, Magda; Szolgay, Ján

2017-06-01

It is widely acknowledged that in the hydrological and meteorological communities, there is a continuing need to improve the quality of quantitative rainfall and river flow forecasts. A hybrid (combined deterministic-stochastic) modelling approach is proposed here that combines the advantages offered by modelling the system dynamics with a deterministic model and a deterministic forecasting error series with a data-driven model in parallel. Since the processes to be modelled are generally nonlinear and the model error series may exhibit nonstationarity and heteroscedasticity, GARCH-type nonlinear time series models are considered here. The fitting, forecasting and simulation performance of such models have to be explored on a case-by-case basis. The goal of this paper is to test and develop an appropriate methodology for model fitting and forecasting applicable for daily river discharge forecast error data from the GARCH family of time series models. We concentrated on verifying whether the use of a GARCH-type model is suitable for modelling and forecasting a hydrological model error time series on the Hron and Morava Rivers in Slovakia. For this purpose we verified the presence of heteroscedasticity in the simulation error series of the KLN multilinear flow routing model; then we fitted the GARCH-type models to the data and compared their fit with that of an ARMA - type model. We produced one-stepahead forecasts from the fitted models and again provided comparisons of the model's performance.

RECURSIVE PROTEIN MODELING: A DIVIDE AND CONQUER STRATEGY FOR PROTEIN STRUCTURE PREDICTION AND ITS CASE STUDY IN CASP9

PubMed Central

CHENG, JIANLIN; EICKHOLT, JESSE; WANG, ZHENG; DENG, XIN

2013-01-01

After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of structural modeling, two types of modeling techniques — template-based modeling and template-free modeling — have been developed. Template-based modeling can often generate a moderate- to high-resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling, such as fragment-based assembly, may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e. certain) and template-free (i.e. uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can signicantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction. PMID:22809379

A new process sensitivity index to identify important system processes under process model and parametric uncertainty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Heng; Ye, Ming; Walker, Anthony P.

Hydrological models are always composed of multiple components that represent processes key to intended model applications. When a process can be simulated by multiple conceptual-mathematical models (process models), model uncertainty in representing the process arises. While global sensitivity analysis methods have been widely used for identifying important processes in hydrologic modeling, the existing methods consider only parametric uncertainty but ignore the model uncertainty for process representation. To address this problem, this study develops a new method to probe multimodel process sensitivity by integrating the model averaging methods into the framework of variance-based global sensitivity analysis, given that the model averagingmore » methods quantify both parametric and model uncertainty. A new process sensitivity index is derived as a metric of relative process importance, and the index includes variance in model outputs caused by uncertainty in both process models and model parameters. For demonstration, the new index is used to evaluate the processes of recharge and geology in a synthetic study of groundwater reactive transport modeling. The recharge process is simulated by two models that converting precipitation to recharge, and the geology process is also simulated by two models of different parameterizations of hydraulic conductivity; each process model has its own random parameters. The new process sensitivity index is mathematically general, and can be applied to a wide range of problems in hydrology and beyond.« less

Comparison of childbirth care models in public hospitals, Brazil.

PubMed

Vogt, Sibylle Emilie; Silva, Kátia Silveira da; Dias, Marcos Augusto Bastos

2014-04-01

To compare collaborative and traditional childbirth care models. Cross-sectional study with 655 primiparous women in four public health system hospitals in Belo Horizonte, MG, Southeastern Brazil, in 2011 (333 women for the collaborative model and 322 for the traditional model, including those with induced or premature labor). Data were collected using interviews and medical records. The Chi-square test was used to compare the outcomes and multivariate logistic regression to determine the association between the model and the interventions used. Paid work and schooling showed significant differences in distribution between the models. Oxytocin (50.2% collaborative model and 65.5% traditional model; p < 0.001), amniotomy (54.3% collaborative model and 65.9% traditional model; p = 0.012) and episiotomy (collaborative model 16.1% and traditional model 85.2%; p < 0.001) were less used in the collaborative model with increased application of non-pharmacological pain relief (85.0% collaborative model and 78.9% traditional model; p = 0.042). The association between the collaborative model and the reduction in the use of oxytocin, artificial rupture of membranes and episiotomy remained after adjustment for confounding. The care model was not associated with complications in newborns or mothers neither with the use of spinal or epidural analgesia. The results suggest that collaborative model may reduce interventions performed in labor care with similar perinatal outcomes.

Developing and upgrading of solar system thermal energy storage simulation models. Technical progress report, March 1, 1979-February 29, 1980

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhn, J K; von Fuchs, G F; Zob, A P

1980-05-01

Two water tank component simulation models have been selected and upgraded. These models are called the CSU Model and the Extended SOLSYS Model. The models have been standardized and links have been provided for operation in the TRNSYS simulation program. The models are described in analytical terms as well as in computer code. Specific water tank tests were performed for the purpose of model validation. Agreement between model data and test data is excellent. A description of the limitations has also been included. Streamlining results and criteria for the reduction of computer time have also been shown for both watermore » tank computer models. Computer codes for the models and instructions for operating these models in TRNSYS have also been included, making the models readily available for DOE and industry use. Rock bed component simulation models have been reviewed and a model selected and upgraded. This model is a logical extension of the Mumma-Marvin model. Specific rock bed tests have been performed for the purpose of validation. Data have been reviewed for consistency. Details of the test results concerned with rock characteristics and pressure drop through the bed have been explored and are reported.« less

Modeling approaches in avian conservation and the role of field biologists

USGS Publications Warehouse

Beissinger, Steven R.; Walters, J.R.; Catanzaro, D.G.; Smith, Kimberly G.; Dunning, J.B.; Haig, Susan M.; Noon, Barry; Stith, Bradley M.

2006-01-01

This review grew out of our realization that models play an increasingly important role in conservation but are rarely used in the research of most avian biologists. Modelers are creating models that are more complex and mechanistic and that can incorporate more of the knowledge acquired by field biologists. Such models require field biologists to provide more specific information, larger sample sizes, and sometimes new kinds of data, such as habitat-specific demography and dispersal information. Field biologists need to support model development by testing key model assumptions and validating models. The best conservation decisions will occur where cooperative interaction enables field biologists, modelers, statisticians, and managers to contribute effectively. We begin by discussing the general form of ecological models—heuristic or mechanistic, "scientific" or statistical—and then highlight the structure, strengths, weaknesses, and applications of six types of models commonly used in avian conservation: (1) deterministic single-population matrix models, (2) stochastic population viability analysis (PVA) models for single populations, (3) metapopulation models, (4) spatially explicit models, (5) genetic models, and (6) species distribution models. We end by considering their unique attributes, determining whether the assumptions that underlie the structure are valid, and testing the ability of the model to predict the future correctly.

Review: Regional groundwater flow modeling in heavily irrigated basins of selected states in the western United States

NASA Astrophysics Data System (ADS)

Rossman, Nathan R.; Zlotnik, Vitaly A.

2013-09-01

Water resources in agriculture-dominated basins of the arid western United States are stressed due to long-term impacts from pumping. A review of 88 regional groundwater-flow modeling applications from seven intensively irrigated western states (Arizona, California, Colorado, Idaho, Kansas, Nebraska and Texas) was conducted to provide hydrogeologists, modelers, water managers, and decision makers insight about past modeling studies that will aid future model development. Groundwater models were classified into three types: resource evaluation models (39 %), which quantify water budgets and act as preliminary models intended to be updated later, or constitute re-calibrations of older models; management/planning models (55 %), used to explore and identify management plans based on the response of the groundwater system to water-development or climate scenarios, sometimes under water-use constraints; and water rights models (7 %), used to make water administration decisions based on model output and to quantify water shortages incurred by water users or climate changes. Results for 27 model characteristics are summarized by state and model type, and important comparisons and contrasts are highlighted. Consideration of modeling uncertainty and the management focus toward sustainability, adaptive management and resilience are discussed, and future modeling recommendations, in light of the reviewed models and other published works, are presented.

Interpreting Musculoskeletal Models and Dynamic Simulations: Causes and Effects of Differences Between Models.

PubMed

Roelker, Sarah A; Caruthers, Elena J; Baker, Rachel K; Pelz, Nicholas C; Chaudhari, Ajit M W; Siston, Robert A

2017-11-01

With more than 29,000 OpenSim users, several musculoskeletal models with varying levels of complexity are available to study human gait. However, how different model parameters affect estimated joint and muscle function between models is not fully understood. The purpose of this study is to determine the effects of four OpenSim models (Gait2392, Lower Limb Model 2010, Full-Body OpenSim Model, and Full Body Model 2016) on gait mechanics and estimates of muscle forces and activations. Using OpenSim 3.1 and the same experimental data for all models, six young adults were scaled in each model, gait kinematics were reproduced, and static optimization estimated muscle function. Simulated measures differed between models by up to 6.5° knee range of motion, 0.012 Nm/Nm peak knee flexion moment, 0.49 peak rectus femoris activation, and 462 N peak rectus femoris force. Differences in coordinate system definitions between models altered joint kinematics, influencing joint moments. Muscle parameter and joint moment discrepancies altered muscle activations and forces. Additional model complexity yielded greater error between experimental and simulated measures; therefore, this study suggests Gait2392 is a sufficient model for studying walking in healthy young adults. Future research is needed to determine which model(s) is best for tasks with more complex motion.

Inter-sectoral comparison of model uncertainty of climate change impacts in Africa

NASA Astrophysics Data System (ADS)

van Griensven, Ann; Vetter, Tobias; Piontek, Franzisca; Gosling, Simon N.; Kamali, Bahareh; Reinhardt, Julia; Dinkneh, Aklilu; Yang, Hong; Alemayehu, Tadesse

2016-04-01

We present the model results and their uncertainties of an inter-sectoral impact model inter-comparison initiative (ISI-MIP) for climate change impacts in Africa. The study includes results on hydrological, crop and health aspects. The impact models used ensemble inputs consisting of 20 time series of daily rainfall and temperature data obtained from 5 Global Circulation Models (GCMs) and 4 Representative concentration pathway (RCP). In this study, we analysed model uncertainty for the Regional Hydrological Models, Global Hydrological Models, Malaria models and Crop models. For the regional hydrological models, we used 2 African test cases: the Blue Nile in Eastern Africa and the Niger in Western Africa. For both basins, the main sources of uncertainty are originating from the GCM and RCPs, while the uncertainty of the regional hydrological models is relatively low. The hydrological model uncertainty becomes more important when predicting changes on low flows compared to mean or high flows. For the other sectors, the impact models have the largest share of uncertainty compared to GCM and RCP, especially for Malaria and crop modelling. The overall conclusion of the ISI-MIP is that it is strongly advised to use ensemble modeling approach for climate change impact studies throughout the whole modelling chain.

Extended behavioural modelling of FET and lattice-mismatched HEMT devices

NASA Astrophysics Data System (ADS)

Khawam, Yahya; Albasha, Lutfi

2017-07-01

This study presents an improved large signal model that can be used for high electron mobility transistors (HEMTs) and field effect transistors using measurement-based behavioural modelling techniques. The steps for accurate large and small signal modelling for transistor are also discussed. The proposed DC model is based on the Fager model since it compensates between the number of model's parameters and accuracy. The objective is to increase the accuracy of the drain-source current model with respect to any change in gate or drain voltages. Also, the objective is to extend the improved DC model to account for soft breakdown and kink effect found in some variants of HEMT devices. A hybrid Newton's-Genetic algorithm is used in order to determine the unknown parameters in the developed model. In addition to accurate modelling of a transistor's DC characteristics, the complete large signal model is modelled using multi-bias s-parameter measurements. The way that the complete model is performed is by using a hybrid multi-objective optimisation technique (Non-dominated Sorting Genetic Algorithm II) and local minimum search (multivariable Newton's method) for parasitic elements extraction. Finally, the results of DC modelling and multi-bias s-parameters modelling are presented, and three-device modelling recommendations are discussed.

The regionalization of national-scale SPARROW models for stream nutrients

USGS Publications Warehouse

Schwarz, Gregory E.; Alexander, Richard B.; Smith, Richard A.; Preston, Stephen D.

2011-01-01

This analysis modifies the parsimonious specification of recently published total nitrogen (TN) and total phosphorus (TP) national-scale SPAtially Referenced Regressions On Watershed attributes models to allow each model coefficient to vary geographically among three major river basins of the conterminous United States. Regionalization of the national models reduces the standard errors in the prediction of TN and TP loads, expressed as a percentage of the predicted load, by about 6 and 7%. We develop and apply a method for combining national-scale and regional-scale information to estimate a hybrid model that imposes cross-region constraints that limit regional variation in model coefficients, effectively reducing the number of free model parameters as compared to a collection of independent regional models. The hybrid TN and TP regional models have improved model fit relative to the respective national models, reducing the standard error in the prediction of loads, expressed as a percentage of load, by about 5 and 4%. Only 19% of the TN hybrid model coefficients and just 2% of the TP hybrid model coefficients show evidence of substantial regional specificity (more than ±100% deviation from the national model estimate). The hybrid models have much greater precision in the estimated coefficients than do the unconstrained regional models, demonstrating the efficacy of pooling information across regions to improve regional models.

Modeling of Stiffness and Strength of Bone at Nanoscale.

PubMed

Abueidda, Diab W; Sabet, Fereshteh A; Jasiuk, Iwona M

2017-05-01

Two distinct geometrical models of bone at the nanoscale (collagen fibril and mineral platelets) are analyzed computationally. In the first model (model I), minerals are periodically distributed in a staggered manner in a collagen matrix while in the second model (model II), minerals form continuous layers outside the collagen fibril. Elastic modulus and strength of bone at the nanoscale, represented by these two models under longitudinal tensile loading, are studied using a finite element (FE) software abaqus. The analysis employs a traction-separation law (cohesive surface modeling) at various interfaces in the models to account for interfacial delaminations. Plane stress, plane strain, and axisymmetric versions of the two models are considered. Model II is found to have a higher stiffness than model I for all cases. For strength, the two models alternate the superiority of performance depending on the inputs and assumptions used. For model II, the axisymmetric case gives higher results than the plane stress and plane strain cases while an opposite trend is observed for model I. For axisymmetric case, model II shows greater strength and stiffness compared to model I. The collagen-mineral arrangement of bone at nanoscale forms a basic building block of bone. Thus, knowledge of its mechanical properties is of high scientific and clinical interests.

The Use of Behavior Models for Predicting Complex Operations

NASA Technical Reports Server (NTRS)

Gore, Brian F.

2010-01-01

Modeling and simulation (M&S) plays an important role when complex human-system notions are being proposed, developed and tested within the system design process. National Aeronautics and Space Administration (NASA) as an agency uses many different types of M&S approaches for predicting human-system interactions, especially when it is early in the development phase of a conceptual design. NASA Ames Research Center possesses a number of M&S capabilities ranging from airflow, flight path models, aircraft models, scheduling models, human performance models (HPMs), and bioinformatics models among a host of other kinds of M&S capabilities that are used for predicting whether the proposed designs will benefit the specific mission criteria. The Man-Machine Integration Design and Analysis System (MIDAS) is a NASA ARC HPM software tool that integrates many models of human behavior with environment models, equipment models, and procedural / task models. The challenge to model comprehensibility is heightened as the number of models that are integrated and the requisite fidelity of the procedural sets are increased. Model transparency is needed for some of the more complex HPMs to maintain comprehensibility of the integrated model performance. This will be exemplified in a recent MIDAS v5 application model and plans for future model refinements will be presented.

Processing Speed in Children: Examination of the Structure in Middle Childhood and Its Impact on Reading

ERIC Educational Resources Information Center

Gerst, Elyssa H.

2017-01-01

The primary aim of this study was to examine the structure of processing speed (PS) in middle childhood by comparing five theoretically driven models of PS. The models consisted of two conceptual models (a unitary model, a complexity model) and three methodological models (a stimulus material model, an output modality model, and a timing modality…

The Application of Various Nonlinear Models to Describe Academic Growth Trajectories: An Empirical Analysis Using Four-Wave Longitudinal Achievement Data from a Large Urban School District

ERIC Educational Resources Information Center

Shin, Tacksoo

2012-01-01

This study introduced various nonlinear growth models, including the quadratic conventional polynomial model, the fractional polynomial model, the Sigmoid model, the growth model with negative exponential functions, the multidimensional scaling technique, and the unstructured growth curve model. It investigated which growth models effectively…

Competency Modeling in Extension Education: Integrating an Academic Extension Education Model with an Extension Human Resource Management Model

ERIC Educational Resources Information Center

Scheer, Scott D.; Cochran, Graham R.; Harder, Amy; Place, Nick T.

2011-01-01

The purpose of this study was to compare and contrast an academic extension education model with an Extension human resource management model. The academic model of 19 competencies was similar across the 22 competencies of the Extension human resource management model. There were seven unique competencies for the human resource management model.…

Defining a Family of Cognitive Diagnosis Models Using Log-Linear Models with Latent Variables

ERIC Educational Resources Information Center

Henson, Robert A.; Templin, Jonathan L.; Willse, John T.

2009-01-01

This paper uses log-linear models with latent variables (Hagenaars, in "Loglinear Models with Latent Variables," 1993) to define a family of cognitive diagnosis models. In doing so, the relationship between many common models is explicitly defined and discussed. In addition, because the log-linear model with latent variables is a general model for…

A toolbox and a record for scientific model development

NASA Technical Reports Server (NTRS)

Ellman, Thomas

1994-01-01

Scientific computation can benefit from software tools that facilitate construction of computational models, control the application of models, and aid in revising models to handle new situations. Existing environments for scientific programming provide only limited means of handling these tasks. This paper describes a two pronged approach for handling these tasks: (1) designing a 'Model Development Toolbox' that includes a basic set of model constructing operations; and (2) designing a 'Model Development Record' that is automatically generated during model construction. The record is subsequently exploited by tools that control the application of scientific models and revise models to handle new situations. Our two pronged approach is motivated by our belief that the model development toolbox and record should be highly interdependent. In particular, a suitable model development record can be constructed only when models are developed using a well defined set of operations. We expect this research to facilitate rapid development of new scientific computational models, to help ensure appropriate use of such models and to facilitate sharing of such models among working computational scientists. We are testing this approach by extending SIGMA, and existing knowledge-based scientific software design tool.

A decision support model for investment on P2P lending platform.

PubMed

Zeng, Xiangxiang; Liu, Li; Leung, Stephen; Du, Jiangze; Wang, Xun; Li, Tao

2017-01-01

Peer-to-peer (P2P) lending, as a novel economic lending model, has triggered new challenges on making effective investment decisions. In a P2P lending platform, one lender can invest N loans and a loan may be accepted by M investors, thus forming a bipartite graph. Basing on the bipartite graph model, we built an iteration computation model to evaluate the unknown loans. To validate the proposed model, we perform extensive experiments on real-world data from the largest American P2P lending marketplace-Prosper. By comparing our experimental results with those obtained by Bayes and Logistic Regression, we show that our computation model can help borrowers select good loans and help lenders make good investment decisions. Experimental results also show that the Logistic classification model is a good complement to our iterative computation model, which motivates us to integrate the two classification models. The experimental results of the hybrid classification model demonstrate that the logistic classification model and our iteration computation model are complementary to each other. We conclude that the hybrid model (i.e., the integration of iterative computation model and Logistic classification model) is more efficient and stable than the individual model alone.

A decision support model for investment on P2P lending platform

PubMed Central

Liu, Li; Leung, Stephen; Du, Jiangze; Wang, Xun; Li, Tao

2017-01-01

Peer-to-peer (P2P) lending, as a novel economic lending model, has triggered new challenges on making effective investment decisions. In a P2P lending platform, one lender can invest N loans and a loan may be accepted by M investors, thus forming a bipartite graph. Basing on the bipartite graph model, we built an iteration computation model to evaluate the unknown loans. To validate the proposed model, we perform extensive experiments on real-world data from the largest American P2P lending marketplace—Prosper. By comparing our experimental results with those obtained by Bayes and Logistic Regression, we show that our computation model can help borrowers select good loans and help lenders make good investment decisions. Experimental results also show that the Logistic classification model is a good complement to our iterative computation model, which motivates us to integrate the two classification models. The experimental results of the hybrid classification model demonstrate that the logistic classification model and our iteration computation model are complementary to each other. We conclude that the hybrid model (i.e., the integration of iterative computation model and Logistic classification model) is more efficient and stable than the individual model alone. PMID:28877234

First-Order Model Management With Variable-Fidelity Physics Applied to Multi-Element Airfoil Optimization

NASA Technical Reports Server (NTRS)

Alexandrov, N. M.; Nielsen, E. J.; Lewis, R. M.; Anderson, W. K.

2000-01-01

First-order approximation and model management is a methodology for a systematic use of variable-fidelity models or approximations in optimization. The intent of model management is to attain convergence to high-fidelity solutions with minimal expense in high-fidelity computations. The savings in terms of computationally intensive evaluations depends on the ability of the available lower-fidelity model or a suite of models to predict the improvement trends for the high-fidelity problem, Variable-fidelity models can be represented by data-fitting approximations, variable-resolution models. variable-convergence models. or variable physical fidelity models. The present work considers the use of variable-fidelity physics models. We demonstrate the performance of model management on an aerodynamic optimization of a multi-element airfoil designed to operate in the transonic regime. Reynolds-averaged Navier-Stokes equations represent the high-fidelity model, while the Euler equations represent the low-fidelity model. An unstructured mesh-based analysis code FUN2D evaluates functions and sensitivity derivatives for both models. Model management for the present demonstration problem yields fivefold savings in terms of high-fidelity evaluations compared to optimization done with high-fidelity computations alone.

Macro-level pedestrian and bicycle crash analysis: Incorporating spatial spillover effects in dual state count models.

PubMed

Cai, Qing; Lee, Jaeyoung; Eluru, Naveen; Abdel-Aty, Mohamed

2016-08-01

This study attempts to explore the viability of dual-state models (i.e., zero-inflated and hurdle models) for traffic analysis zones (TAZs) based pedestrian and bicycle crash frequency analysis. Additionally, spatial spillover effects are explored in the models by employing exogenous variables from neighboring zones. The dual-state models such as zero-inflated negative binomial and hurdle negative binomial models (with and without spatial effects) are compared with the conventional single-state model (i.e., negative binomial). The model comparison for pedestrian and bicycle crashes revealed that the models that considered observed spatial effects perform better than the models that did not consider the observed spatial effects. Across the models with spatial spillover effects, the dual-state models especially zero-inflated negative binomial model offered better performance compared to single-state models. Moreover, the model results clearly highlighted the importance of various traffic, roadway, and sociodemographic characteristics of the TAZ as well as neighboring TAZs on pedestrian and bicycle crash frequency. Copyright © 2016 Elsevier Ltd. All rights reserved.

BioModels Database: a repository of mathematical models of biological processes.

PubMed

Chelliah, Vijayalakshmi; Laibe, Camille; Le Novère, Nicolas

2013-01-01

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

Documenting Models for Interoperability and Reusability ...

EPA Pesticide Factsheets

Many modeling frameworks compartmentalize science via individual models that link sets of small components to create larger modeling workflows. Developing integrated watershed models increasingly requires coupling multidisciplinary, independent models, as well as collaboration between scientific communities, since component-based modeling can integrate models from different disciplines. Integrated Environmental Modeling (IEM) systems focus on transferring information between components by capturing a conceptual site model; establishing local metadata standards for input/output of models and databases; managing data flow between models and throughout the system; facilitating quality control of data exchanges (e.g., checking units, unit conversions, transfers between software languages); warning and error handling; and coordinating sensitivity/uncertainty analyses. Although many computational software systems facilitate communication between, and execution of, components, there are no common approaches, protocols, or standards for turn-key linkages between software systems and models, especially if modifying components is not the intent. Using a standard ontology, this paper reviews how models can be described for discovery, understanding, evaluation, access, and implementation to facilitate interoperability and reusability. In the proceedings of the International Environmental Modelling and Software Society (iEMSs), 8th International Congress on Environmental Mod

CSR Model Implementation from School Stakeholder Perspectives

ERIC Educational Resources Information Center

Herrmann, Suzannah

2006-01-01

Despite comprehensive school reform (CSR) model developers' best intentions to make school stakeholders adhere strictly to the implementation of model components, school stakeholders implementing CSR models inevitably make adaptations to the CSR model. Adaptations are made to CSR models because school stakeholders internalize CSR model practices…

A comparison of simple global kinetic models for coal devolatilization with the CPD model

DOE PAGES

Richards, Andrew P.; Fletcher, Thomas H.

2016-08-01

Simulations of coal combustors and gasifiers generally cannot incorporate the complexities of advanced pyrolysis models, and hence there is interest in evaluating simpler models over ranges of temperature and heating rate that are applicable to the furnace of interest. In this paper, six different simple model forms are compared to predictions made by the Chemical Percolation Devolatilization (CPD) model. The model forms included three modified one-step models, a simple two-step model, and two new modified two-step models. These simple model forms were compared over a wide range of heating rates (5 × 10 3 to 10 6 K/s) at finalmore » temperatures up to 1600 K. Comparisons were made of total volatiles yield as a function of temperature, as well as the ultimate volatiles yield. Advantages and disadvantages for each simple model form are discussed. In conclusion, a modified two-step model with distributed activation energies seems to give the best agreement with CPD model predictions (with the fewest tunable parameters).« less

[Bone remodeling and modeling/mini-modeling.

PubMed

Hasegawa, Tomoka; Amizuka, Norio

Modeling, adapting structures to loading by changing bone size and shapes, often takes place in bone of the fetal and developmental stages, while bone remodeling-replacement of old bone into new bone-is predominant in the adult stage. Modeling can be divided into macro-modeling(macroscopic modeling)and mini-modeling(microscopic modeling). In the cellular process of mini-modeling, unlike bone remodeling, bone lining cells, i.e., resting flattened osteoblasts covering bone surfaces will become active form of osteoblasts, and then, deposit new bone onto the old bone without mediating osteoclastic bone resorption. Among the drugs for osteoporotic treatment, eldecalcitol(a vitamin D3 analog)and teriparatide(human PTH[1-34])could show mini-modeling based bone formation. Histologically, mature, active form of osteoblasts are localized on the new bone induced by mini-modeling, however, only a few cell layer of preosteoblasts are formed over the newly-formed bone, and accordingly, few osteoclasts are present in the region of mini-modeling. In this review, histological characteristics of bone remodeling and modeling including mini-modeling will be introduced.

An Introduction to Markov Modeling: Concepts and Uses

NASA Technical Reports Server (NTRS)

Boyd, Mark A.; Lau, Sonie (Technical Monitor)

1998-01-01

Kharkov modeling is a modeling technique that is widely useful for dependability analysis of complex fault tolerant systems. It is very flexible in the type of systems and system behavior it can model. It is not, however, the most appropriate modeling technique for every modeling situation. The first task in obtaining a reliability or availability estimate for a system is selecting which modeling technique is most appropriate to the situation at hand. A person performing a dependability analysis must confront the question: is Kharkov modeling most appropriate to the system under consideration, or should another technique be used instead? The need to answer this gives rise to other more basic questions regarding Kharkov modeling: what are the capabilities and limitations of Kharkov modeling as a modeling technique? How does it relate to other modeling techniques? What kind of system behavior can it model? What kinds of software tools are available for performing dependability analyses with Kharkov modeling techniques? These questions and others will be addressed in this tutorial.

The cerebro-cerebellum: Could it be loci of forward models?

PubMed

Ishikawa, Takahiro; Tomatsu, Saeka; Izawa, Jun; Kakei, Shinji

2016-03-01

It is widely accepted that the cerebellum acquires and maintain internal models for motor control. An internal model simulates mapping between a set of causes and effects. There are two candidates of cerebellar internal models, forward models and inverse models. A forward model transforms a motor command into a prediction of the sensory consequences of a movement. In contrast, an inverse model inverts the information flow of the forward model. Despite the clearly different formulations of the two internal models, it is still controversial whether the cerebro-cerebellum, the phylogenetically newer part of the cerebellum, provides inverse models or forward models for voluntary limb movements or other higher brain functions. In this article, we review physiological and morphological evidence that suggests the existence in the cerebro-cerebellum of a forward model for limb movement. We will also discuss how the characteristic input-output organization of the cerebro-cerebellum may contribute to forward models for non-motor higher brain functions. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Second Generation Crop Yield Models Review

NASA Technical Reports Server (NTRS)

Hodges, T. (Principal Investigator)

1982-01-01

Second generation yield models, including crop growth simulation models and plant process models, may be suitable for large area crop yield forecasting in the yield model development project. Subjective and objective criteria for model selection are defined and models which might be selected are reviewed. Models may be selected to provide submodels as input to other models; for further development and testing; or for immediate testing as forecasting tools. A plant process model may range in complexity from several dozen submodels simulating (1) energy, carbohydrates, and minerals; (2) change in biomass of various organs; and (3) initiation and development of plant organs, to a few submodels simulating key physiological processes. The most complex models cannot be used directly in large area forecasting but may provide submodels which can be simplified for inclusion into simpler plant process models. Both published and unpublished models which may be used for development or testing are reviewed. Several other models, currently under development, may become available at a later date.

Microphysics in Multi-scale Modeling System with Unified Physics

NASA Technical Reports Server (NTRS)

Tao, Wei-Kuo

2012-01-01

Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (1) a cloud-resolving model (Goddard Cumulus Ensemble model, GCE model), (2) a regional scale model (a NASA unified weather research and forecast, WRF), (3) a coupled CRM and global model (Goddard Multi-scale Modeling Framework, MMF), and (4) a land modeling system. The same microphysical processes, long and short wave radiative transfer and land processes and the explicit cloud-radiation, and cloud-land surface interactive processes are applied in this multi-scale modeling system. This modeling system has been coupled with a multi-satellite simulator to use NASA high-resolution satellite data to identify the strengths and weaknesses of cloud and precipitation processes simulated by the model. In this talk, a review of developments and applications of the multi-scale modeling system will be presented. In particular, the microphysics development and its performance for the multi-scale modeling system will be presented.

Mechanical model development of rolling bearing-rotor systems: A review

NASA Astrophysics Data System (ADS)

Cao, Hongrui; Niu, Linkai; Xi, Songtao; Chen, Xuefeng

2018-03-01

The rolling bearing rotor (RBR) system is the kernel of many rotating machines, which affects the performance of the whole machine. Over the past decades, extensive research work has been carried out to investigate the dynamic behavior of RBR systems. However, to the best of the authors' knowledge, no comprehensive review on RBR modelling has been reported yet. To address this gap in the literature, this paper reviews and critically discusses the current progress of mechanical model development of RBR systems, and identifies future trends for research. Firstly, five kinds of rolling bearing models, i.e., the lumped-parameter model, the quasi-static model, the quasi-dynamic model, the dynamic model, and the finite element (FE) model are summarized. Then, the coupled modelling between bearing models and various rotor models including De Laval/Jeffcott rotor, rigid rotor, transfer matrix method (TMM) models and FE models are presented. Finally, the paper discusses the key challenges of previous works and provides new insights into understanding of RBR systems for their advanced future engineering applications.

`Models of' versus `Models for'. Toward an Agent-Based Conception of Modeling in the Science Classroom

NASA Astrophysics Data System (ADS)

Gouvea, Julia; Passmore, Cynthia

2017-03-01

The inclusion of the practice of "developing and using models" in the Framework for K-12 Science Education and in the Next Generation Science Standards provides an opportunity for educators to examine the role this practice plays in science and how it can be leveraged in a science classroom. Drawing on conceptions of models in the philosophy of science, we bring forward an agent-based account of models and discuss the implications of this view for enacting modeling in science classrooms. Models, according to this account, can only be understood with respect to the aims and intentions of a cognitive agent (models for), not solely in terms of how they represent phenomena in the world (models of). We present this contrast as a heuristic— models of versus models for—that can be used to help educators notice and interpret how models are positioned in standards, curriculum, and classrooms.

Model Hierarchies in Edge-Based Compartmental Modeling for Infectious Disease Spread

PubMed Central

Miller, Joel C.; Volz, Erik M.

2012-01-01

We consider the family of edge-based compartmental models for epidemic spread developed in [11]. These models allow for a range of complex behaviors, and in particular allow us to explicitly incorporate duration of a contact into our mathematical models. Our focus here is to identify conditions under which simpler models may be substituted for more detailed models, and in so doing we define a hierarchy of epidemic models. In particular we provide conditions under which it is appropriate to use the standard mass action SIR model, and we show what happens when these conditions fail. Using our hierarchy, we provide a procedure leading to the choice of the appropriate model for a given population. Our result about the convergence of models to the Mass Action model gives clear, rigorous conditions under which the Mass Action model is accurate. PMID:22911242

The evolution of process-based hydrologic models: historical challenges and the collective quest for physical realism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, Martyn P.; Bierkens, Marc F. P.; Samaniego, Luis

The diversity in hydrologic models has historically led to great controversy on the correct approach to process-based hydrologic modeling, with debates centered on the adequacy of process parameterizations, data limitations and uncertainty, and computational constraints on model analysis. Here, we revisit key modeling challenges on requirements to (1) define suitable model equations, (2) define adequate model parameters, and (3) cope with limitations in computing power. We outline the historical modeling challenges, provide examples of modeling advances that address these challenges, and define outstanding research needs. We also illustrate how modeling advances have been made by groups using models of different type and complexity,more » and we argue for the need to more effectively use our diversity of modeling approaches in order to advance our collective quest for physically realistic hydrologic models.« less

The evolution of process-based hydrologic models: historical challenges and the collective quest for physical realism

DOE PAGES

Clark, Martyn P.; Bierkens, Marc F. P.; Samaniego, Luis; ...

2017-07-11

The diversity in hydrologic models has historically led to great controversy on the correct approach to process-based hydrologic modeling, with debates centered on the adequacy of process parameterizations, data limitations and uncertainty, and computational constraints on model analysis. Here, we revisit key modeling challenges on requirements to (1) define suitable model equations, (2) define adequate model parameters, and (3) cope with limitations in computing power. We outline the historical modeling challenges, provide examples of modeling advances that address these challenges, and define outstanding research needs. We also illustrate how modeling advances have been made by groups using models of different type and complexity,more » and we argue for the need to more effectively use our diversity of modeling approaches in order to advance our collective quest for physically realistic hydrologic models.« less

Modeling of near-wall turbulence

NASA Technical Reports Server (NTRS)

Shih, T. H.; Mansour, N. N.

1990-01-01

An improved k-epsilon model and a second order closure model is presented for low Reynolds number turbulence near a wall. For the k-epsilon model, a modified form of the eddy viscosity having correct asymptotic near wall behavior is suggested, and a model for the pressure diffusion term in the turbulent kinetic energy equation is proposed. For the second order closure model, the existing models are modified for the Reynolds stress equations to have proper near wall behavior. A dissipation rate equation for the turbulent kinetic energy is also reformulated. The proposed models satisfy realizability and will not produce unphysical behavior. Fully developed channel flows are used for model testing. The calculations are compared with direct numerical simulations. It is shown that the present models, both the k-epsilon model and the second order closure model, perform well in predicting the behavior of the near wall turbulence. Significant improvements over previous models are obtained.

[Modeling in value-based medicine].

PubMed

Neubauer, A S; Hirneiss, C; Kampik, A

2010-03-01

Modeling plays an important role in value-based medicine (VBM). It allows decision support by predicting potential clinical and economic consequences, frequently combining different sources of evidence. Based on relevant publications and examples focusing on ophthalmology the key economic modeling methods are explained and definitions are given. The most frequently applied model types are decision trees, Markov models, and discrete event simulation (DES) models. Model validation includes besides verifying internal validity comparison with other models (external validity) and ideally validation of its predictive properties. The existing uncertainty with any modeling should be clearly stated. This is true for economic modeling in VBM as well as when using disease risk models to support clinical decisions. In economic modeling uni- and multivariate sensitivity analyses are usually applied; the key concepts here are tornado plots and cost-effectiveness acceptability curves. Given the existing uncertainty, modeling helps to make better informed decisions than without this additional information.

Sequential Modelling of Building Rooftops by Integrating Airborne LIDAR Data and Optical Imagery: Preliminary Results

NASA Astrophysics Data System (ADS)

Sohn, G.; Jung, J.; Jwa, Y.; Armenakis, C.

2013-05-01

This paper presents a sequential rooftop modelling method to refine initial rooftop models derived from airborne LiDAR data by integrating it with linear cues retrieved from single imagery. A cue integration between two datasets is facilitated by creating new topological features connecting between the initial model and image lines, with which new model hypotheses (variances to the initial model) are produced. We adopt Minimum Description Length (MDL) principle for competing the model candidates and selecting the optimal model by considering the balanced trade-off between the model closeness and the model complexity. Our preliminary results, combined with the Vaihingen data provided by ISPRS WGIII/4 demonstrate the image-driven modelling cues can compensate the limitations posed by LiDAR data in rooftop modelling.

ModelMate - A graphical user interface for model analysis

USGS Publications Warehouse

Banta, Edward R.

2011-01-01

ModelMate is a graphical user interface designed to facilitate use of model-analysis programs with models. This initial version of ModelMate supports one model-analysis program, UCODE_2005, and one model software program, MODFLOW-2005. ModelMate can be used to prepare input files for UCODE_2005, run UCODE_2005, and display analysis results. A link to the GW_Chart graphing program facilitates visual interpretation of results. ModelMate includes capabilities for organizing directories used with the parallel-processing capabilities of UCODE_2005 and for maintaining files in those directories to be identical to a set of files in a master directory. ModelMate can be used on its own or in conjunction with ModelMuse, a graphical user interface for MODFLOW-2005 and PHAST.

[Model-based biofuels system analysis: a review].

PubMed

Chang, Shiyan; Zhang, Xiliang; Zhao, Lili; Ou, Xunmin

2011-03-01

Model-based system analysis is an important tool for evaluating the potential and impacts of biofuels, and for drafting biofuels technology roadmaps and targets. The broad reach of the biofuels supply chain requires that biofuels system analyses span a range of disciplines, including agriculture/forestry, energy, economics, and the environment. Here we reviewed various models developed for or applied to modeling biofuels, and presented a critical analysis of Agriculture/Forestry System Models, Energy System Models, Integrated Assessment Models, Micro-level Cost, Energy and Emission Calculation Models, and Specific Macro-level Biofuel Models. We focused on the models' strengths, weaknesses, and applicability, facilitating the selection of a suitable type of model for specific issues. Such an analysis was a prerequisite for future biofuels system modeling, and represented a valuable resource for researchers and policy makers.

An Immuno-epidemiological Model of Paratuberculosis

NASA Astrophysics Data System (ADS)

Martcheva, M.

2011-11-01

The primary objective of this article is to introduce an immuno-epidemiological model of paratuberculosis (Johne's disease). To develop the immuno-epidemiological model, we first develop an immunological model and an epidemiological model. Then, we link the two models through time-since-infection structure and parameters of the epidemiological model. We use the nested approach to compose the immuno-epidemiological model. Our immunological model captures the switch between the T-cell immune response and the antibody response in Johne's disease. The epidemiological model is a time-since-infection model and captures the variability of transmission rate and the vertical transmission of the disease. We compute the immune-response-dependent epidemiological reproduction number. Our immuno-epidemiological model can be used for investigation of the impact of the immune response on the epidemiology of Johne's disease.

Correlation of ground tests and analyses of a dynamically scaled Space Station model configuration

NASA Technical Reports Server (NTRS)

Javeed, Mehzad; Edighoffer, Harold H.; Mcgowan, Paul E.

1993-01-01

Verification of analytical models through correlation with ground test results of a complex space truss structure is demonstrated. A multi-component, dynamically scaled space station model configuration is the focus structure for this work. Previously established test/analysis correlation procedures are used to develop improved component analytical models. Integrated system analytical models, consisting of updated component analytical models, are compared with modal test results to establish the accuracy of system-level dynamic predictions. Design sensitivity model updating methods are shown to be effective for providing improved component analytical models. Also, the effects of component model accuracy and interface modeling fidelity on the accuracy of integrated model predictions is examined.

FacetModeller: Software for manual creation, manipulation and analysis of 3D surface-based models

NASA Astrophysics Data System (ADS)

Lelièvre, Peter G.; Carter-McAuslan, Angela E.; Dunham, Michael W.; Jones, Drew J.; Nalepa, Mariella; Squires, Chelsea L.; Tycholiz, Cassandra J.; Vallée, Marc A.; Farquharson, Colin G.

2018-01-01

The creation of 3D models is commonplace in many disciplines. Models are often built from a collection of tessellated surfaces. To apply numerical methods to such models it is often necessary to generate a mesh of space-filling elements that conforms to the model surfaces. While there are meshing algorithms that can do so, they place restrictive requirements on the surface-based models that are rarely met by existing 3D model building software. Hence, we have developed a Java application named FacetModeller, designed for efficient manual creation, modification and analysis of 3D surface-based models destined for use in numerical modelling.

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online

PubMed Central

Posada, David

2006-01-01

ModelTest server is a web-based application for the selection of models of nucleotide substitution using the program ModelTest. The server takes as input a text file with likelihood scores for the set of candidate models. Models can be selected with hierarchical likelihood ratio tests, or with the Akaike or Bayesian information criteria. The output includes several statistics for the assessment of model selection uncertainty, for model averaging or to estimate the relative importance of model parameters. The server can be accessed at . PMID:16845102

Application of surface complexation models to anion adsorption by natural materials

USDA-ARS?s Scientific Manuscript database

Various chemical models of ion adsorption will be presented and discussed. Chemical models, such as surface complexation models, provide a molecular description of anion adsorption reactions using an equilibrium approach. Two such models, the constant capacitance model and the triple layer model w...

Space Environments and Effects: Trapped Proton Model

NASA Technical Reports Server (NTRS)

Huston, S. L.; Kauffman, W. (Technical Monitor)

2002-01-01

An improved model of the Earth's trapped proton environment has been developed. This model, designated Trapped Proton Model version 1 (TPM-1), determines the omnidirectional flux of protons with energy between 1 and 100 MeV throughout near-Earth space. The model also incorporates a true solar cycle dependence. The model consists of several data files and computer software to read them. There are three versions of the mo'del: a FORTRAN-Callable library, a stand-alone model, and a Web-based model.

The NASA Marshall engineering thermosphere model

NASA Technical Reports Server (NTRS)

Hickey, Michael Philip

1988-01-01

Described is the NASA Marshall Engineering Thermosphere (MET) Model, which is a modified version of the MFSC/J70 Orbital Atmospheric Density Model as currently used in the J70MM program at MSFC. The modifications to the MFSC/J70 model required for the MET model are described, graphical and numerical examples of the models are included, as is a listing of the MET model computer program. Major differences between the numerical output from the MET model and the MFSC/J70 model are discussed.

Wind turbine model and loop shaping controller design

NASA Astrophysics Data System (ADS)

Gilev, Bogdan

2017-12-01

A model of a wind turbine is evaluated, consisting of: wind speed model, mechanical and electrical model of generator and tower oscillation model. Model of the whole system is linearized around of a nominal point. By using the linear model with uncertainties is synthesized a uncertain model. By using the uncertain model is developed a H∞ controller, which provide mode of stabilizing the rotor frequency and damping the tower oscillations. Finally is simulated work of nonlinear system and H∞ controller.

Simulated Students and Classroom Use of Model-Based Intelligent Tutoring

NASA Technical Reports Server (NTRS)

Koedinger, Kenneth R.

2008-01-01

Two educational uses of models and simulations: 1) Students create models and use simulations ; and 2) Researchers create models of learners to guide development of reliably effective materials. Cognitive tutors simulate and support tutoring - data is crucial to create effective model. Pittsburgh Science of Learning Center: Resources for modeling, authoring, experimentation. Repository of data and theory. Examples of advanced modeling efforts: SimStudent learns rule-based model. Help-seeking model: Tutors metacognition. Scooter uses machine learning detectors of student engagement.

Modeling for Battery Prognostics

NASA Technical Reports Server (NTRS)

Kulkarni, Chetan S.; Goebel, Kai; Khasin, Michael; Hogge, Edward; Quach, Patrick

2017-01-01

For any battery-powered vehicles (be it unmanned aerial vehicles, small passenger aircraft, or assets in exoplanetary operations) to operate at maximum efficiency and reliability, it is critical to monitor battery health as well performance and to predict end of discharge (EOD) and end of useful life (EOL). To fulfil these needs, it is important to capture the battery's inherent characteristics as well as operational knowledge in the form of models that can be used by monitoring, diagnostic, and prognostic algorithms. Several battery modeling methodologies have been developed in last few years as the understanding of underlying electrochemical mechanics has been advancing. The models can generally be classified as empirical models, electrochemical engineering models, multi-physics models, and molecular/atomist. Empirical models are based on fitting certain functions to past experimental data, without making use of any physicochemical principles. Electrical circuit equivalent models are an example of such empirical models. Electrochemical engineering models are typically continuum models that include electrochemical kinetics and transport phenomena. Each model has its advantages and disadvantages. The former type of model has the advantage of being computationally efficient, but has limited accuracy and robustness, due to the approximations used in developed model, and as a result of such approximations, cannot represent aging well. The latter type of model has the advantage of being very accurate, but is often computationally inefficient, having to solve complex sets of partial differential equations, and thus not suited well for online prognostic applications. In addition both multi-physics and atomist models are computationally expensive hence are even less suited to online application An electrochemistry-based model of Li-ion batteries has been developed, that captures crucial electrochemical processes, captures effects of aging, is computationally efficient, and is of suitable accuracy for reliable EOD prediction in a variety of operational profiles. The model can be considered an electrochemical engineering model, but unlike most such models found in the literature, certain approximations are done that allow to retain computational efficiency for online implementation of the model. Although the focus here is on Li-ion batteries, the model is quite general and can be applied to different chemistries through a change of model parameter values. Progress on model development, providing model validation results and EOD prediction results is being presented.

Comparison of modeling methods to predict the spatial distribution of deep-sea coral and sponge in the Gulf of Alaska

NASA Astrophysics Data System (ADS)

Rooper, Christopher N.; Zimmermann, Mark; Prescott, Megan M.

2017-08-01

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska's marine waters, and are associated with many different species of fishes and invertebrates. These ecosystems are vulnerable to the effects of commercial fishing activities and climate change. We compared four commonly used species distribution models (general linear models, generalized additive models, boosted regression trees and random forest models) and an ensemble model to predict the presence or absence and abundance of six groups of benthic invertebrate taxa in the Gulf of Alaska. All four model types performed adequately on training data for predicting presence and absence, with regression forest models having the best overall performance measured by the area under the receiver-operating-curve (AUC). The models also performed well on the test data for presence and absence with average AUCs ranging from 0.66 to 0.82. For the test data, ensemble models performed the best. For abundance data, there was an obvious demarcation in performance between the two regression-based methods (general linear models and generalized additive models), and the tree-based models. The boosted regression tree and random forest models out-performed the other models by a wide margin on both the training and testing data. However, there was a significant drop-off in performance for all models of invertebrate abundance ( 50%) when moving from the training data to the testing data. Ensemble model performance was between the tree-based and regression-based methods. The maps of predictions from the models for both presence and abundance agreed very well across model types, with an increase in variability in predictions for the abundance data. We conclude that where data conforms well to the modeled distribution (such as the presence-absence data and binomial distribution in this study), the four types of models will provide similar results, although the regression-type models may be more consistent with biological theory. For data with highly zero-inflated distributions and non-normal distributions such as the abundance data from this study, the tree-based methods performed better. Ensemble models that averaged predictions across the four model types, performed better than the GLM or GAM models but slightly poorer than the tree-based methods, suggesting ensemble models might be more robust to overfitting than tree methods, while mitigating some of the disadvantages in predictive performance of regression methods.

A toy terrestrial carbon flow model

NASA Technical Reports Server (NTRS)

Parton, William J.; Running, Steven W.; Walker, Brian

1992-01-01

A generalized carbon flow model for the major terrestrial ecosystems of the world is reported. The model is a simplification of the Century model and the Forest-Biogeochemical model. Topics covered include plant production, decomposition and nutrient cycling, biomes, the utility of the carbon flow model for predicting carbon dynamics under global change, and possible applications to state-and-transition models and environmentally driven global vegetation models.

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

PubMed Central

2010-01-01

Background Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License. PMID:20587024

Drift-Scale Coupled Processes (DST and THC Seepage) Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

P. Dixon

The purpose of this Model Report (REV02) is to document the unsaturated zone (UZ) models used to evaluate the potential effects of coupled thermal-hydrological-chemical (THC) processes on UZ flow and transport. This Model Report has been developed in accordance with the ''Technical Work Plan for: Performance Assessment Unsaturated Zone'' (Bechtel SAIC Company, LLC (BSC) 2002 [160819]). The technical work plan (TWP) describes planning information pertaining to the technical scope, content, and management of this Model Report in Section 1.12, Work Package AUZM08, ''Coupled Effects on Flow and Seepage''. The plan for validation of the models documented in this Model Reportmore » is given in Attachment I, Model Validation Plans, Section I-3-4, of the TWP. Except for variations in acceptance criteria (Section 4.2), there were no deviations from this TWP. This report was developed in accordance with AP-SIII.10Q, ''Models''. This Model Report documents the THC Seepage Model and the Drift Scale Test (DST) THC Model. The THC Seepage Model is a drift-scale process model for predicting the composition of gas and water that could enter waste emplacement drifts and the effects of mineral alteration on flow in rocks surrounding drifts. The DST THC model is a drift-scale process model relying on the same conceptual model and much of the same input data (i.e., physical, hydrological, thermodynamic, and kinetic) as the THC Seepage Model. The DST THC Model is the primary method for validating the THC Seepage Model. The DST THC Model compares predicted water and gas compositions, as well as mineral alteration patterns, with observed data from the DST. These models provide the framework to evaluate THC coupled processes at the drift scale, predict flow and transport behavior for specified thermal-loading conditions, and predict the evolution of mineral alteration and fluid chemistry around potential waste emplacement drifts. The DST THC Model is used solely for the validation of the THC Seepage Model and is not used for calibration to measured data.« less

Review: To be or not to be an identifiable model. Is this a relevant question in animal science modelling?

PubMed

Muñoz-Tamayo, R; Puillet, L; Daniel, J B; Sauvant, D; Martin, O; Taghipoor, M; Blavy, P

2018-04-01

What is a good (useful) mathematical model in animal science? For models constructed for prediction purposes, the question of model adequacy (usefulness) has been traditionally tackled by statistical analysis applied to observed experimental data relative to model-predicted variables. However, little attention has been paid to analytic tools that exploit the mathematical properties of the model equations. For example, in the context of model calibration, before attempting a numerical estimation of the model parameters, we might want to know if we have any chance of success in estimating a unique best value of the model parameters from available measurements. This question of uniqueness is referred to as structural identifiability; a mathematical property that is defined on the sole basis of the model structure within a hypothetical ideal experiment determined by a setting of model inputs (stimuli) and observable variables (measurements). Structural identifiability analysis applied to dynamic models described by ordinary differential equations (ODEs) is a common practice in control engineering and system identification. This analysis demands mathematical technicalities that are beyond the academic background of animal science, which might explain the lack of pervasiveness of identifiability analysis in animal science modelling. To fill this gap, in this paper we address the analysis of structural identifiability from a practitioner perspective by capitalizing on the use of dedicated software tools. Our objectives are (i) to provide a comprehensive explanation of the structural identifiability notion for the community of animal science modelling, (ii) to assess the relevance of identifiability analysis in animal science modelling and (iii) to motivate the community to use identifiability analysis in the modelling practice (when the identifiability question is relevant). We focus our study on ODE models. By using illustrative examples that include published mathematical models describing lactation in cattle, we show how structural identifiability analysis can contribute to advancing mathematical modelling in animal science towards the production of useful models and, moreover, highly informative experiments via optimal experiment design. Rather than attempting to impose a systematic identifiability analysis to the modelling community during model developments, we wish to open a window towards the discovery of a powerful tool for model construction and experiment design.

Ecosystem Model Skill Assessment. Yes We Can!

PubMed Central

Olsen, Erik; Fay, Gavin; Gaichas, Sarah; Gamble, Robert; Lucey, Sean; Link, Jason S.

2016-01-01

Need to Assess the Skill of Ecosystem Models Accelerated changes to global ecosystems call for holistic and integrated analyses of past, present and future states under various pressures to adequately understand current and projected future system states. Ecosystem models can inform management of human activities in a complex and changing environment, but are these models reliable? Ensuring that models are reliable for addressing management questions requires evaluating their skill in representing real-world processes and dynamics. Skill has been evaluated for just a limited set of some biophysical models. A range of skill assessment methods have been reviewed but skill assessment of full marine ecosystem models has not yet been attempted. Northeast US Atlantis Marine Ecosystem Model We assessed the skill of the Northeast U.S. (NEUS) Atlantis marine ecosystem model by comparing 10-year model forecasts with observed data. Model forecast performance was compared to that obtained from a 40-year hindcast. Multiple metrics (average absolute error, root mean squared error, modeling efficiency, and Spearman rank correlation), and a suite of time-series (species biomass, fisheries landings, and ecosystem indicators) were used to adequately measure model skill. Overall, the NEUS model performed above average and thus better than expected for the key species that had been the focus of the model tuning. Model forecast skill was comparable to the hindcast skill, showing that model performance does not degenerate in a 10-year forecast mode, an important characteristic for an end-to-end ecosystem model to be useful for strategic management purposes. Skill Assessment Is Both Possible and Advisable We identify best-practice approaches for end-to-end ecosystem model skill assessment that would improve both operational use of other ecosystem models and future model development. We show that it is possible to not only assess the skill of a complicated marine ecosystem model, but that it is necessary do so to instill confidence in model results and encourage their use for strategic management. Our methods are applicable to any type of predictive model, and should be considered for use in fields outside ecology (e.g. economics, climate change, and risk assessment). PMID:26731540

Challenges and opportunities for integrating lake ecosystem modelling approaches

USGS Publications Warehouse

Mooij, Wolf M.; Trolle, Dennis; Jeppesen, Erik; Arhonditsis, George; Belolipetsky, Pavel V.; Chitamwebwa, Deonatus B.R.; Degermendzhy, Andrey G.; DeAngelis, Donald L.; Domis, Lisette N. De Senerpont; Downing, Andrea S.; Elliott, J. Alex; Ruberto, Carlos Ruberto; Gaedke, Ursula; Genova, Svetlana N.; Gulati, Ramesh D.; Hakanson, Lars; Hamilton, David P.; Hipsey, Matthew R.; Hoen, Jochem 't; Hulsmann, Stephan; Los, F. Hans; Makler-Pick, Vardit; Petzoldt, Thomas; Prokopkin, Igor G.; Rinke, Karsten; Schep, Sebastiaan A.; Tominaga, Koji; Van Dam, Anne A.; Van Nes, Egbert H.; Wells, Scott A.; Janse, Jan H.

2010-01-01

A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and trait-based models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.

Combination of Alternative Models by Mutual Data Assimilation: Supermodeling With A Suite of Primitive Equation Models

NASA Astrophysics Data System (ADS)

Duane, G. S.; Selten, F.

2016-12-01

Different models of climate and weather commonly give projections/predictions that differ widely in their details. While averaging of model outputs almost always improves results, nonlinearity implies that further improvement can be obtained from model interaction in run time, as has already been demonstrated with toy systems of ODEs and idealized quasigeostrophic models. In the supermodeling scheme, models effectively assimilate data from one another and partially synchronize with one another. Spread among models is manifest as a spread in possible inter-model connection coefficients, so that the models effectively "agree to disagree". Here, we construct a supermodel formed from variants of the SPEEDO model, a primitive-equation atmospheric model (SPEEDY) coupled to ocean and land. A suite of atmospheric models, coupled to the same ocean and land, is chosen to represent typical differences among climate models by varying model parameters. Connections are introduced between all pairs of corresponding independent variables at synoptic-scale intervals. Strengths of the inter-atmospheric connections can be considered to represent inverse inter-model observation error. Connection strengths are adapted based on an established procedure that extends the dynamical equations of a pair of synchronizing systems to synchronize parameters as well. The procedure is applied to synchronize the suite of SPEEDO models with another SPEEDO model regarded as "truth", adapting the inter-model connections along the way. The supermodel with trained connections gives marginally lower error in all fields than any weighted combination of the separate model outputs when used in "weather-prediction mode", i.e. with constant nudging to truth. Stronger results are obtained if a supermodel is used to predict the formation of coherent structures or the frequency of such. Partially synchronized SPEEDO models give a better representation of the blocked-zonal index cycle than does a weighted average of the constituent model outputs. We have thus shown that supermodeling and the synchronization-based procedure to adapt inter-model connections give results superior to output averaging not only with highly nonlinear toy systems, but with smaller nonlinearities as occur in climate models.

[Analyzing and modeling methods of near infrared spectroscopy for in-situ prediction of oil yield from oil shale].

PubMed

Liu, Jie; Zhang, Fu-Dong; Teng, Fei; Li, Jun; Wang, Zhi-Hong

2014-10-01

In order to in-situ detect the oil yield of oil shale, based on portable near infrared spectroscopy analytical technology, with 66 rock core samples from No. 2 well drilling of Fuyu oil shale base in Jilin, the modeling and analyzing methods for in-situ detection were researched. By the developed portable spectrometer, 3 data formats (reflectance, absorbance and K-M function) spectra were acquired. With 4 different modeling data optimization methods: principal component-mahalanobis distance (PCA-MD) for eliminating abnormal samples, uninformative variables elimination (UVE) for wavelength selection and their combina- tions: PCA-MD + UVE and UVE + PCA-MD, 2 modeling methods: partial least square (PLS) and back propagation artificial neural network (BPANN), and the same data pre-processing, the modeling and analyzing experiment were performed to determine the optimum analysis model and method. The results show that the data format, modeling data optimization method and modeling method all affect the analysis precision of model. Results show that whether or not using the optimization method, reflectance or K-M function is the proper spectrum format of the modeling database for two modeling methods. Using two different modeling methods and four different data optimization methods, the model precisions of the same modeling database are different. For PLS modeling method, the PCA-MD and UVE + PCA-MD data optimization methods can improve the modeling precision of database using K-M function spectrum data format. For BPANN modeling method, UVE, UVE + PCA-MD and PCA- MD + UVE data optimization methods can improve the modeling precision of database using any of the 3 spectrum data formats. In addition to using the reflectance spectra and PCA-MD data optimization method, modeling precision by BPANN method is better than that by PLS method. And modeling with reflectance spectra, UVE optimization method and BPANN modeling method, the model gets the highest analysis precision, its correlation coefficient (Rp) is 0.92, and its standard error of prediction (SEP) is 0.69%.

Bayesian multimodel inference of soil microbial respiration models: Theory, application and future prospective

NASA Astrophysics Data System (ADS)

Elshall, A. S.; Ye, M.; Niu, G. Y.; Barron-Gafford, G.

2015-12-01

Models in biogeoscience involve uncertainties in observation data, model inputs, model structure, model processes and modeling scenarios. To accommodate for different sources of uncertainty, multimodal analysis such as model combination, model selection, model elimination or model discrimination are becoming more popular. To illustrate theoretical and practical challenges of multimodal analysis, we use an example about microbial soil respiration modeling. Global soil respiration releases more than ten times more carbon dioxide to the atmosphere than all anthropogenic emissions. Thus, improving our understanding of microbial soil respiration is essential for improving climate change models. This study focuses on a poorly understood phenomena, which is the soil microbial respiration pulses in response to episodic rainfall pulses (the "Birch effect"). We hypothesize that the "Birch effect" is generated by the following three mechanisms. To test our hypothesis, we developed and assessed five evolving microbial-enzyme models against field measurements from a semiarid Savannah that is characterized by pulsed precipitation. These five model evolve step-wise such that the first model includes none of these three mechanism, while the fifth model includes the three mechanisms. The basic component of Bayesian multimodal analysis is the estimation of marginal likelihood to rank the candidate models based on their overall likelihood with respect to observation data. The first part of the study focuses on using this Bayesian scheme to discriminate between these five candidate models. The second part discusses some theoretical and practical challenges, which are mainly the effect of likelihood function selection and the marginal likelihood estimation methods on both model ranking and Bayesian model averaging. The study shows that making valid inference from scientific data is not a trivial task, since we are not only uncertain about the candidate scientific models, but also about the statistical methods that are used to discriminate between these models.

Ecosystem Model Skill Assessment. Yes We Can!

PubMed

Olsen, Erik; Fay, Gavin; Gaichas, Sarah; Gamble, Robert; Lucey, Sean; Link, Jason S

2016-01-01

Accelerated changes to global ecosystems call for holistic and integrated analyses of past, present and future states under various pressures to adequately understand current and projected future system states. Ecosystem models can inform management of human activities in a complex and changing environment, but are these models reliable? Ensuring that models are reliable for addressing management questions requires evaluating their skill in representing real-world processes and dynamics. Skill has been evaluated for just a limited set of some biophysical models. A range of skill assessment methods have been reviewed but skill assessment of full marine ecosystem models has not yet been attempted. We assessed the skill of the Northeast U.S. (NEUS) Atlantis marine ecosystem model by comparing 10-year model forecasts with observed data. Model forecast performance was compared to that obtained from a 40-year hindcast. Multiple metrics (average absolute error, root mean squared error, modeling efficiency, and Spearman rank correlation), and a suite of time-series (species biomass, fisheries landings, and ecosystem indicators) were used to adequately measure model skill. Overall, the NEUS model performed above average and thus better than expected for the key species that had been the focus of the model tuning. Model forecast skill was comparable to the hindcast skill, showing that model performance does not degenerate in a 10-year forecast mode, an important characteristic for an end-to-end ecosystem model to be useful for strategic management purposes. We identify best-practice approaches for end-to-end ecosystem model skill assessment that would improve both operational use of other ecosystem models and future model development. We show that it is possible to not only assess the skill of a complicated marine ecosystem model, but that it is necessary do so to instill confidence in model results and encourage their use for strategic management. Our methods are applicable to any type of predictive model, and should be considered for use in fields outside ecology (e.g. economics, climate change, and risk assessment).

iMarNet: an ocean biogeochemistry model inter-comparison project within a common physical ocean modelling framework

NASA Astrophysics Data System (ADS)

Kwiatkowski, L.; Yool, A.; Allen, J. I.; Anderson, T. R.; Barciela, R.; Buitenhuis, E. T.; Butenschön, M.; Enright, C.; Halloran, P. R.; Le Quéré, C.; de Mora, L.; Racault, M.-F.; Sinha, B.; Totterdell, I. J.; Cox, P. M.

2014-07-01

Ocean biogeochemistry (OBGC) models span a wide range of complexities from highly simplified, nutrient-restoring schemes, through nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, through to models that represent a broader trophic structure by grouping organisms as plankton functional types (PFT) based on their biogeochemical role (Dynamic Green Ocean Models; DGOM) and ecosystem models which group organisms by ecological function and trait. OBGC models are now integral components of Earth System Models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here, we present an inter-comparison of six OBGC models that were candidates for implementation within the next UK Earth System Model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the Nucleus for the European Modelling of the Ocean (NEMO) ocean general circulation model (GCM), and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform or underperform all other models across all metrics. Nonetheless, the simpler models that are easier to tune are broadly closer to observations across a number of fields, and thus offer a high-efficiency option for ESMs that prioritise high resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low resolution climate dynamics and high complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry-climate interactions.

iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework

NASA Astrophysics Data System (ADS)

Kwiatkowski, L.; Yool, A.; Allen, J. I.; Anderson, T. R.; Barciela, R.; Buitenhuis, E. T.; Butenschön, M.; Enright, C.; Halloran, P. R.; Le Quéré, C.; de Mora, L.; Racault, M.-F.; Sinha, B.; Totterdell, I. J.; Cox, P. M.

2014-12-01

Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry-climate interactions.

Design of Soil Salinity Policies with Tinamit, a Flexible and Rapid Tool to Couple Stakeholder-Built System Dynamics Models with Physically-Based Models

NASA Astrophysics Data System (ADS)

Malard, J. J.; Baig, A. I.; Hassanzadeh, E.; Adamowski, J. F.; Tuy, H.; Melgar-Quiñonez, H.

2016-12-01

Model coupling is a crucial step to constructing many environmental models, as it allows for the integration of independently-built models representing different system sub-components to simulate the entire system. Model coupling has been of particular interest in combining socioeconomic System Dynamics (SD) models, whose visual interface facilitates their direct use by stakeholders, with more complex physically-based models of the environmental system. However, model coupling processes are often cumbersome and inflexible and require extensive programming knowledge, limiting their potential for continued use by stakeholders in policy design and analysis after the end of the project. Here, we present Tinamit, a flexible Python-based model-coupling software tool whose easy-to-use API and graphical user interface make the coupling of stakeholder-built SD models with physically-based models rapid, flexible and simple for users with limited to no coding knowledge. The flexibility of the system allows end users to modify the SD model as well as the linking variables between the two models themselves with no need for recoding. We use Tinamit to couple a stakeholder-built socioeconomic model of soil salinization in Pakistan with the physically-based soil salinity model SAHYSMOD. As climate extremes increase in the region, policies to slow or reverse soil salinity buildup are increasing in urgency and must take both socioeconomic and biophysical spheres into account. We use the Tinamit-coupled model to test the impact of integrated policy options (economic and regulatory incentives to farmers) on soil salinity in the region in the face of future climate change scenarios. Use of the Tinamit model allowed for rapid and flexible coupling of the two models, allowing the end user to continue making model structure and policy changes. In addition, the clear interface (in contrast to most model coupling code) makes the final coupled model easily accessible to stakeholders with limited technical background.

Bayesian Model Selection under Time Constraints

NASA Astrophysics Data System (ADS)

Hoege, M.; Nowak, W.; Illman, W. A.

2017-12-01

Bayesian model selection (BMS) provides a consistent framework for rating and comparing models in multi-model inference. In cases where models of vastly different complexity compete with each other, we also face vastly different computational runtimes of such models. For instance, time series of a quantity of interest can be simulated by an autoregressive process model that takes even less than a second for one run, or by a partial differential equations-based model with runtimes up to several hours or even days. The classical BMS is based on a quantity called Bayesian model evidence (BME). It determines the model weights in the selection process and resembles a trade-off between bias of a model and its complexity. However, in practice, the runtime of models is another weight relevant factor for model selection. Hence, we believe that it should be included, leading to an overall trade-off problem between bias, variance and computing effort. We approach this triple trade-off from the viewpoint of our ability to generate realizations of the models under a given computational budget. One way to obtain BME values is through sampling-based integration techniques. We argue with the fact that more expensive models can be sampled much less under time constraints than faster models (in straight proportion to their runtime). The computed evidence in favor of a more expensive model is statistically less significant than the evidence computed in favor of a faster model, since sampling-based strategies are always subject to statistical sampling error. We present a straightforward way to include this misbalance into the model weights that are the basis for model selection. Our approach follows directly from the idea of insufficient significance. It is based on a computationally cheap bootstrapping error estimate of model evidence and is easy to implement. The approach is illustrated in a small synthetic modeling study.

Prediction-error variance in Bayesian model updating: a comparative study

NASA Astrophysics Data System (ADS)

Asadollahi, Parisa; Li, Jian; Huang, Yong

2017-04-01

In Bayesian model updating, the likelihood function is commonly formulated by stochastic embedding in which the maximum information entropy probability model of prediction error variances plays an important role and it is Gaussian distribution subject to the first two moments as constraints. The selection of prediction error variances can be formulated as a model class selection problem, which automatically involves a trade-off between the average data-fit of the model class and the information it extracts from the data. Therefore, it is critical for the robustness in the updating of the structural model especially in the presence of modeling errors. To date, three ways of considering prediction error variances have been seem in the literature: 1) setting constant values empirically, 2) estimating them based on the goodness-of-fit of the measured data, and 3) updating them as uncertain parameters by applying Bayes' Theorem at the model class level. In this paper, the effect of different strategies to deal with the prediction error variances on the model updating performance is investigated explicitly. A six-story shear building model with six uncertain stiffness parameters is employed as an illustrative example. Transitional Markov Chain Monte Carlo is used to draw samples of the posterior probability density function of the structure model parameters as well as the uncertain prediction variances. The different levels of modeling uncertainty and complexity are modeled through three FE models, including a true model, a model with more complexity, and a model with modeling error. Bayesian updating is performed for the three FE models considering the three aforementioned treatments of the prediction error variances. The effect of number of measurements on the model updating performance is also examined in the study. The results are compared based on model class assessment and indicate that updating the prediction error variances as uncertain parameters at the model class level produces more robust results especially when the number of measurement is small.

Comparison and Analysis of Geometric Correction Models of Spaceborne SAR

PubMed Central

Jiang, Weihao; Yu, Anxi; Dong, Zhen; Wang, Qingsong

2016-01-01

Following the development of synthetic aperture radar (SAR), SAR images have become increasingly common. Many researchers have conducted large studies on geolocation models, but little work has been conducted on the available models for the geometric correction of SAR images of different terrain. To address the terrain issue, four different models were compared and are described in this paper: a rigorous range-doppler (RD) model, a rational polynomial coefficients (RPC) model, a revised polynomial (PM) model and an elevation derivation (EDM) model. The results of comparisons of the geolocation capabilities of the models show that a proper model for a SAR image of a specific terrain can be determined. A solution table was obtained to recommend a suitable model for users. Three TerraSAR-X images, two ALOS-PALSAR images and one Envisat-ASAR image were used for the experiment, including flat terrain and mountain terrain SAR images as well as two large area images. Geolocation accuracies of the models for different terrain SAR images were computed and analyzed. The comparisons of the models show that the RD model was accurate but was the least efficient; therefore, it is not the ideal model for real-time implementations. The RPC model is sufficiently accurate and efficient for the geometric correction of SAR images of flat terrain, whose precision is below 0.001 pixels. The EDM model is suitable for the geolocation of SAR images of mountainous terrain, and its precision can reach 0.007 pixels. Although the PM model does not produce results as precise as the other models, its efficiency is excellent and its potential should not be underestimated. With respect to the geometric correction of SAR images over large areas, the EDM model has higher accuracy under one pixel, whereas the RPC model consumes one third of the time of the EDM model. PMID:27347973

Towards policy relevant environmental modeling: contextual validity and pragmatic models

USGS Publications Warehouse

Miles, Scott B.

2000-01-01

"What makes for a good model?" In various forms, this question is a question that, undoubtedly, many people, businesses, and institutions ponder with regards to their particular domain of modeling. One particular domain that is wrestling with this question is the multidisciplinary field of environmental modeling. Examples of environmental models range from models of contaminated ground water flow to the economic impact of natural disasters, such as earthquakes. One of the distinguishing claims of the field is the relevancy of environmental modeling to policy and environment-related decision-making in general. A pervasive view by both scientists and decision-makers is that a "good" model is one that is an accurate predictor. Thus, determining whether a model is "accurate" or "correct" is done by comparing model output to empirical observations. The expected outcome of this process, usually referred to as "validation" or "ground truthing," is a stamp on the model in question of "valid" or "not valid" that serves to indicate whether or not the model will be reliable before it is put into service in a decision-making context. In this paper, I begin by elaborating on the prevailing view of model validation and why this view must change. Drawing from concepts coming out of the studies of science and technology, I go on to propose a contextual view of validity that can overcome the problems associated with "ground truthing" models as an indicator of model goodness. The problem of how we talk about and determine model validity has much to do about how we perceive the utility of environmental models. In the remainder of the paper, I argue that we should adopt ideas of pragmatism in judging what makes for a good model and, in turn, developing good models. From such a perspective of model goodness, good environmental models should facilitate communication, convey—not bury or "eliminate"—uncertainties, and, thus, afford the active building of consensus decisions, instead of promoting passive or self-righteous decisions.

On Using Meta-Modeling and Multi-Modeling to Address Complex Problems

ERIC Educational Resources Information Center

Abu Jbara, Ahmed

2013-01-01

Models, created using different modeling techniques, usually serve different purposes and provide unique insights. While each modeling technique might be capable of answering specific questions, complex problems require multiple models interoperating to complement/supplement each other; we call this Multi-Modeling. To address the syntactic and…

Preparing the Model for Prediction Across Scales (MPAS) for global retrospective air quality modeling

EPA Science Inventory

The US EPA has a plan to leverage recent advances in meteorological modeling to develop a "Next-Generation" air quality modeling system that will allow consistent modeling of problems from global to local scale. The meteorological model of choice is the Model for Predic...

Model Comparison of Bayesian Semiparametric and Parametric Structural Equation Models

ERIC Educational Resources Information Center

Song, Xin-Yuan; Xia, Ye-Mao; Pan, Jun-Hao; Lee, Sik-Yum

2011-01-01

Structural equation models have wide applications. One of the most important issues in analyzing structural equation models is model comparison. This article proposes a Bayesian model comparison statistic, namely the "L[subscript nu]"-measure for both semiparametric and parametric structural equation models. For illustration purposes, we consider…

National Centers for Environmental Prediction

Science.gov Websites

Modeling Mesoscale Modeling Marine Modeling and Analysis Teams Climate Data Assimilation Ensembles and Post / VISION | About EMC EMC > Mesoscale Modeling > MODELS Home Mission Models R & D Collaborators Cyclone Tracks & Verification Implementation Info FAQ Disclaimer More Info MESOSCALE MODELING SREF

Computer Models of Personality: Implications for Measurement

ERIC Educational Resources Information Center

Cranton, P. A.

1976-01-01

Current research on computer models of personality is reviewed and categorized under five headings: (1) models of belief systems; (2) models of interpersonal behavior; (3) models of decision-making processes; (4) prediction models; and (5) theory-based simulations of specific processes. The use of computer models in personality measurement is…

Uses of Computer Simulation Models in Ag-Research and Everyday Life

USDA-ARS?s Scientific Manuscript database

When the news media talks about models they could be talking about role models, fashion models, conceptual models like the auto industry uses, or computer simulation models. A computer simulation model is a computer code that attempts to imitate the processes and functions of certain systems. There ...

A Framework of Operating Models for Interdisciplinary Research Programs in Clinical Service Organizations

ERIC Educational Resources Information Center

King, Gillian; Currie, Melissa; Smith, Linda; Servais, Michelle; McDougall, Janette

2008-01-01

A framework of operating models for interdisciplinary research programs in clinical service organizations is presented, consisting of a "clinician-researcher" skill development model, a program evaluation model, a researcher-led knowledge generation model, and a knowledge conduit model. Together, these models comprise a tailored, collaborative…

Modelling Students' Visualisation of Chemical Reaction

ERIC Educational Resources Information Center

Cheng, Maurice M. W.; Gilbert, John K.

2017-01-01

This paper proposes a model-based notion of "submicro representations of chemical reactions". Based on three structural models of matter (the simple particle model, the atomic model and the free electron model of metals), we suggest there are two major models of reaction in school chemistry curricula: (a) reactions that are simple…

Multilevel and Latent Variable Modeling with Composite Links and Exploded Likelihoods

ERIC Educational Resources Information Center

Rabe-Hesketh, Sophia; Skrondal, Anders

2007-01-01

Composite links and exploded likelihoods are powerful yet simple tools for specifying a wide range of latent variable models. Applications considered include survival or duration models, models for rankings, small area estimation with census information, models for ordinal responses, item response models with guessing, randomized response models,…

Planning Major Curricular Change.

ERIC Educational Resources Information Center

Kirkland, Travis P.

Decision-making and change models can take many forms. One researcher (Nordvall, 1982) has suggested five conceptual models for introducing change: a political model; a rational decision-making model; a social interaction decision model; the problem-solving method; and an adaptive/linkage model which is an amalgam of each of the other models.…

UNITED STATES METEOROLOGICAL DATA - DAILY AND HOURLY FILES TO SUPPORT PREDICTIVE EXPOSURE MODELING

EPA Science Inventory

ORD numerical models for pesticide exposure include a model of spray drift (AgDisp), a cropland pesticide persistence model (PRZM), a surface water exposure model (EXAMS), and a model of fish bioaccumulation (BASS). A unified climatological database for these models has been asse...

Enhancement of the Acquisition Process for a Combat System-A Case Study to Model the Workflow Processes for an Air Defense System Acquisition

DTIC Science & Technology

2009-12-01

Business Process Modeling BPMN Business Process Modeling Notation SoA Service-oriented Architecture UML Unified Modeling Language CSP...system developers. Supporting technologies include Business Process Modeling Notation ( BPMN ), Unified Modeling Language (UML), model-driven architecture

Improving a complex finite-difference ground water flow model through the use of an analytic element screening model

USGS Publications Warehouse

Hunt, R.J.; Anderson, M.P.; Kelson, V.A.

1998-01-01

This paper demonstrates that analytic element models have potential as powerful screening tools that can facilitate or improve calibration of more complicated finite-difference and finite-element models. We demonstrate how a two-dimensional analytic element model was used to identify errors in a complex three-dimensional finite-difference model caused by incorrect specification of boundary conditions. An improved finite-difference model was developed using boundary conditions developed from a far-field analytic element model. Calibration of a revised finite-difference model was achieved using fewer zones of hydraulic conductivity and lake bed conductance than the original finite-difference model. Calibration statistics were also improved in that simulated base-flows were much closer to measured values. The improved calibration is due mainly to improved specification of the boundary conditions made possible by first solving the far-field problem with an analytic element model.This paper demonstrates that analytic element models have potential as powerful screening tools that can facilitate or improve calibration of more complicated finite-difference and finite-element models. We demonstrate how a two-dimensional analytic element model was used to identify errors in a complex three-dimensional finite-difference model caused by incorrect specification of boundary conditions. An improved finite-difference model was developed using boundary conditions developed from a far-field analytic element model. Calibration of a revised finite-difference model was achieved using fewer zones of hydraulic conductivity and lake bed conductance than the original finite-difference model. Calibration statistics were also improved in that simulated base-flows were much closer to measured values. The improved calibration is due mainly to improved specification of the boundary conditions made possible by first solving the far-field problem with an analytic element model.

A stochastic model for tumor geometry evolution during radiation therapy in cervical cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yifang; Lee, Chi-Guhn; Chan, Timothy C. Y., E-mail: tcychan@mie.utoronto.ca

2014-02-15

Purpose: To develop mathematical models to predict the evolution of tumor geometry in cervical cancer undergoing radiation therapy. Methods: The authors develop two mathematical models to estimate tumor geometry change: a Markov model and an isomorphic shrinkage model. The Markov model describes tumor evolution by investigating the change in state (either tumor or nontumor) of voxels on the tumor surface. It assumes that the evolution follows a Markov process. Transition probabilities are obtained using maximum likelihood estimation and depend on the states of neighboring voxels. The isomorphic shrinkage model describes tumor shrinkage or growth in terms of layers of voxelsmore » on the tumor surface, instead of modeling individual voxels. The two proposed models were applied to data from 29 cervical cancer patients treated at Princess Margaret Cancer Centre and then compared to a constant volume approach. Model performance was measured using sensitivity and specificity. Results: The Markov model outperformed both the isomorphic shrinkage and constant volume models in terms of the trade-off between sensitivity (target coverage) and specificity (normal tissue sparing). Generally, the Markov model achieved a few percentage points in improvement in either sensitivity or specificity compared to the other models. The isomorphic shrinkage model was comparable to the Markov approach under certain parameter settings. Convex tumor shapes were easier to predict. Conclusions: By modeling tumor geometry change at the voxel level using a probabilistic model, improvements in target coverage and normal tissue sparing are possible. Our Markov model is flexible and has tunable parameters to adjust model performance to meet a range of criteria. Such a model may support the development of an adaptive paradigm for radiation therapy of cervical cancer.« less

The Radiative Forcing Model Intercomparison Project (RFMIP): Assessment and characterization of forcing to enable feedback studies

NASA Astrophysics Data System (ADS)

Pincus, R.; Stevens, B. B.; Forster, P.; Collins, W.; Ramaswamy, V.

2014-12-01

The Radiative Forcing Model Intercomparison Project (RFMIP): Assessment and characterization of forcing to enable feedback studies An enormous amount of attention has been paid to the diversity of responses in the CMIP and other multi-model ensembles. This diversity is normally interpreted as a distribution in climate sensitivity driven by some distribution of feedback mechanisms. Identification of these feedbacks relies on precise identification of the forcing to which each model is subject, including distinguishing true error from model diversity. The Radiative Forcing Model Intercomparison Project (RFMIP) aims to disentangle the role of forcing from model sensitivity as determinants of varying climate model response by carefully characterizing the radiative forcing to which such models are subject and by coordinating experiments in which it is specified. RFMIP consists of four activities: 1) An assessment of accuracy in flux and forcing calculations for greenhouse gases under past, present, and future climates, using off-line radiative transfer calculations in specified atmospheres with climate model parameterizations and reference models 2) Characterization and assessment of model-specific historical forcing by anthropogenic aerosols, based on coordinated diagnostic output from climate models and off-line radiative transfer calculations with reference models 3) Characterization of model-specific effective radiative forcing, including contributions of model climatology and rapid adjustments, using coordinated climate model integrations and off-line radiative transfer calculations with a single fast model 4) Assessment of climate model response to precisely-characterized radiative forcing over the historical record, including efforts to infer true historical forcing from patterns of response, by direct specification of non-greenhouse-gas forcing in a series of coordinated climate model integrations This talk discusses the rationale for RFMIP, provides an overview of the four activities, and presents preliminary motivating results.

Greedy Sampling and Incremental Surrogate Model-Based Tailoring of Aeroservoelastic Model Database for Flexible Aircraft

NASA Technical Reports Server (NTRS)

Wang, Yi; Pant, Kapil; Brenner, Martin J.; Ouellette, Jeffrey A.

2018-01-01

This paper presents a data analysis and modeling framework to tailor and develop linear parameter-varying (LPV) aeroservoelastic (ASE) model database for flexible aircrafts in broad 2D flight parameter space. The Kriging surrogate model is constructed using ASE models at a fraction of grid points within the original model database, and then the ASE model at any flight condition can be obtained simply through surrogate model interpolation. The greedy sampling algorithm is developed to select the next sample point that carries the worst relative error between the surrogate model prediction and the benchmark model in the frequency domain among all input-output channels. The process is iterated to incrementally improve surrogate model accuracy till a pre-determined tolerance or iteration budget is met. The methodology is applied to the ASE model database of a flexible aircraft currently being tested at NASA/AFRC for flutter suppression and gust load alleviation. Our studies indicate that the proposed method can reduce the number of models in the original database by 67%. Even so the ASE models obtained through Kriging interpolation match the model in the original database constructed directly from the physics-based tool with the worst relative error far below 1%. The interpolated ASE model exhibits continuously-varying gains along a set of prescribed flight conditions. More importantly, the selected grid points are distributed non-uniformly in the parameter space, a) capturing the distinctly different dynamic behavior and its dependence on flight parameters, and b) reiterating the need and utility for adaptive space sampling techniques for ASE model database compaction. The present framework is directly extendible to high-dimensional flight parameter space, and can be used to guide the ASE model development, model order reduction, robust control synthesis and novel vehicle design of flexible aircraft.

Mind the Noise When Identifying Computational Models of Cognition from Brain Activity.

PubMed

Kolossa, Antonio; Kopp, Bruno

2016-01-01

The aim of this study was to analyze how measurement error affects the validity of modeling studies in computational neuroscience. A synthetic validity test was created using simulated P300 event-related potentials as an example. The model space comprised four computational models of single-trial P300 amplitude fluctuations which differed in terms of complexity and dependency. The single-trial fluctuation of simulated P300 amplitudes was computed on the basis of one of the models, at various levels of measurement error and at various numbers of data points. Bayesian model selection was performed based on exceedance probabilities. At very low numbers of data points, the least complex model generally outperformed the data-generating model. Invalid model identification also occurred at low levels of data quality and under low numbers of data points if the winning model's predictors were closely correlated with the predictors from the data-generating model. Given sufficient data quality and numbers of data points, the data-generating model could be correctly identified, even against models which were very similar to the data-generating model. Thus, a number of variables affects the validity of computational modeling studies, and data quality and numbers of data points are among the main factors relevant to the issue. Further, the nature of the model space (i.e., model complexity, model dependency) should not be neglected. This study provided quantitative results which show the importance of ensuring the validity of computational modeling via adequately prepared studies. The accomplishment of synthetic validity tests is recommended for future applications. Beyond that, we propose to render the demonstration of sufficient validity via adequate simulations mandatory to computational modeling studies.

Chasing Perfection: Should We Reduce Model Uncertainty in Carbon Cycle-Climate Feedbacks

NASA Astrophysics Data System (ADS)

Bonan, G. B.; Lombardozzi, D.; Wieder, W. R.; Lindsay, K. T.; Thomas, R. Q.

2015-12-01

Earth system model simulations of the terrestrial carbon (C) cycle show large multi-model spread in the carbon-concentration and carbon-climate feedback parameters. Large differences among models are also seen in their simulation of global vegetation and soil C stocks and other aspects of the C cycle, prompting concern about model uncertainty and our ability to faithfully represent fundamental aspects of the terrestrial C cycle in Earth system models. Benchmarking analyses that compare model simulations with common datasets have been proposed as a means to assess model fidelity with observations, and various model-data fusion techniques have been used to reduce model biases. While such efforts will reduce multi-model spread, they may not help reduce uncertainty (and increase confidence) in projections of the C cycle over the twenty-first century. Many ecological and biogeochemical processes represented in Earth system models are poorly understood at both the site scale and across large regions, where biotic and edaphic heterogeneity are important. Our experience with the Community Land Model (CLM) suggests that large uncertainty in the terrestrial C cycle and its feedback with climate change is an inherent property of biological systems. The challenge of representing life in Earth system models, with the rich diversity of lifeforms and complexity of biological systems, may necessitate a multitude of modeling approaches to capture the range of possible outcomes. Such models should encompass a range of plausible model structures. We distinguish between model parameter uncertainty and model structural uncertainty. Focusing on improved parameter estimates may, in fact, limit progress in assessing model structural uncertainty associated with realistically representing biological processes. Moreover, higher confidence may be achieved through better process representation, but this does not necessarily reduce uncertainty.

Clarity versus complexity: land-use modeling as a practical tool for decision-makers

USGS Publications Warehouse

Sohl, Terry L.; Claggett, Peter

2013-01-01

The last decade has seen a remarkable increase in the number of modeling tools available to examine future land-use and land-cover (LULC) change. Integrated modeling frameworks, agent-based models, cellular automata approaches, and other modeling techniques have substantially improved the representation of complex LULC systems, with each method using a different strategy to address complexity. However, despite the development of new and better modeling tools, the use of these tools is limited for actual planning, decision-making, or policy-making purposes. LULC modelers have become very adept at creating tools for modeling LULC change, but complicated models and lack of transparency limit their utility for decision-makers. The complicated nature of many LULC models also makes it impractical or even impossible to perform a rigorous analysis of modeling uncertainty. This paper provides a review of land-cover modeling approaches and the issues causes by the complicated nature of models, and provides suggestions to facilitate the increased use of LULC models by decision-makers and other stakeholders. The utility of LULC models themselves can be improved by 1) providing model code and documentation, 2) through the use of scenario frameworks to frame overall uncertainties, 3) improving methods for generalizing key LULC processes most important to stakeholders, and 4) adopting more rigorous standards for validating models and quantifying uncertainty. Communication with decision-makers and other stakeholders can be improved by increasing stakeholder participation in all stages of the modeling process, increasing the transparency of model structure and uncertainties, and developing user-friendly decision-support systems to bridge the link between LULC science and policy. By considering these options, LULC science will be better positioned to support decision-makers and increase real-world application of LULC modeling results.

Modeling Methods

USGS Publications Warehouse

Healy, Richard W.; Scanlon, Bridget R.

2010-01-01

Simulation models are widely used in all types of hydrologic studies, and many of these models can be used to estimate recharge. Models can provide important insight into the functioning of hydrologic systems by identifying factors that influence recharge. The predictive capability of models can be used to evaluate how changes in climate, water use, land use, and other factors may affect recharge rates. Most hydrological simulation models, including watershed models and groundwater-flow models, are based on some form of water-budget equation, so the material in this chapter is closely linked to that in Chapter 2. Empirical models that are not based on a water-budget equation have also been used for estimating recharge; these models generally take the form of simple estimation equations that define annual recharge as a function of precipitation and possibly other climatic data or watershed characteristics.Model complexity varies greatly. Some models are simple accounting models; others attempt to accurately represent the physics of water movement through each compartment of the hydrologic system. Some models provide estimates of recharge explicitly; for example, a model based on the Richards equation can simulate water movement from the soil surface through the unsaturated zone to the water table. Recharge estimates can be obtained indirectly from other models. For example, recharge is a parameter in groundwater-flow models that solve for hydraulic head (i.e. groundwater level). Recharge estimates can be obtained through a model calibration process in which recharge and other model parameter values are adjusted so that simulated water levels agree with measured water levels. The simulation that provides the closest agreement is called the best fit, and the recharge value used in that simulation is the model-generated estimate of recharge.

Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

DOE PAGES

Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

2015-10-30

An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

Forecasting plant phenology: evaluating the phenological models for Betula pendula and Padus racemosa spring phases, Latvia.

PubMed

Kalvāns, Andis; Bitāne, Māra; Kalvāne, Gunta

2015-02-01

A historical phenological record and meteorological data of the period 1960-2009 are used to analyse the ability of seven phenological models to predict leaf unfolding and beginning of flowering for two tree species-silver birch Betula pendula and bird cherry Padus racemosa-in Latvia. Model stability is estimated performing multiple model fitting runs using half of the data for model training and the other half for evaluation. Correlation coefficient, mean absolute error and mean squared error are used to evaluate model performance. UniChill (a model using sigmoidal development rate and temperature relationship and taking into account the necessity for dormancy release) and DDcos (a simple degree-day model considering the diurnal temperature fluctuations) are found to be the best models for describing the considered spring phases. A strong collinearity between base temperature and required heat sum is found for several model fitting runs of the simple degree-day based models. Large variation of the model parameters between different model fitting runs in case of more complex models indicates similar collinearity and over-parameterization of these models. It is suggested that model performance can be improved by incorporating the resolved daily temperature fluctuations of the DDcos model into the framework of the more complex models (e.g. UniChill). The average base temperature, as found by DDcos model, for B. pendula leaf unfolding is 5.6 °C and for the start of the flowering 6.7 °C; for P. racemosa, the respective base temperatures are 3.2 °C and 3.4 °C.

A toolbox and record for scientific models

NASA Technical Reports Server (NTRS)

Ellman, Thomas

1994-01-01

Computational science presents a host of challenges for the field of knowledge-based software design. Scientific computation models are difficult to construct. Models constructed by one scientist are easily misapplied by other scientists to problems for which they are not well-suited. Finally, models constructed by one scientist are difficult for others to modify or extend to handle new types of problems. Construction of scientific models actually involves much more than the mechanics of building a single computational model. In the course of developing a model, a scientist will often test a candidate model against experimental data or against a priori expectations. Test results often lead to revisions of the model and a consequent need for additional testing. During a single model development session, a scientist typically examines a whole series of alternative models, each using different simplifying assumptions or modeling techniques. A useful scientific software design tool must support these aspects of the model development process as well. In particular, it should propose and carry out tests of candidate models. It should analyze test results and identify models and parts of models that must be changed. It should determine what types of changes can potentially cure a given negative test result. It should organize candidate models, test data, and test results into a coherent record of the development process. Finally, it should exploit the development record for two purposes: (1) automatically determining the applicability of a scientific model to a given problem; (2) supporting revision of a scientific model to handle a new type of problem. Existing knowledge-based software design tools must be extended in order to provide these facilities.

More than a name: Heterogeneity in characteristics of models of maternity care reported from the Australian Maternity Care Classification System validation study.

PubMed

Donnolley, Natasha R; Chambers, Georgina M; Butler-Henderson, Kerryn A; Chapman, Michael G; Sullivan, Elizabeth A

2017-08-01

Without a standard terminology to classify models of maternity care, it is problematic to compare and evaluate clinical outcomes across different models. The Maternity Care Classification System is a novel system developed in Australia to classify models of maternity care based on their characteristics and an overarching broad model descriptor (Major Model Category). This study aimed to assess the extent of variability in the defining characteristics of models of care grouped to the same Major Model Category, using the Maternity Care Classification System. All public hospital maternity services in New South Wales, Australia, were invited to complete a web-based survey classifying two local models of care using the Maternity Care Classification System. A descriptive analysis of the variation in 15 attributes of models of care was conducted to evaluate the level of heterogeneity within and across Major Model Categories. Sixty-nine out of seventy hospitals responded, classifying 129 models of care. There was wide variation in a number of important attributes of models classified to the same Major Model Category. The category of 'Public hospital maternity care' contained the most variation across all characteristics. This study demonstrated that although models of care can be grouped into a distinct set of Major Model Categories, there are significant variations in models of the same type. This could result in seemingly 'like' models of care being incorrectly compared if grouped only by the Major Model Category. Copyright © 2017 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

The Diffusion Model Is Not a Deterministic Growth Model: Comment on Jones and Dzhafarov (2014)

PubMed Central

Smith, Philip L.; Ratcliff, Roger; McKoon, Gail

2015-01-01

Jones and Dzhafarov (2014) claim that several current models of speeded decision making in cognitive tasks, including the diffusion model, can be viewed as special cases of other general models or model classes. The general models can be made to match any set of response time (RT) distribution and accuracy data exactly by a suitable choice of parameters and so are unfalsifiable. The implication of their claim is that models like the diffusion model are empirically testable only by artificially restricting them to exclude unfalsifiable instances of the general model. We show that Jones and Dzhafarov’s argument depends on enlarging the class of “diffusion” models to include models in which there is little or no diffusion. The unfalsifiable models are deterministic or near-deterministic growth models, from which the effects of within-trial variability have been removed or in which they are constrained to be negligible. These models attribute most or all of the variability in RT and accuracy to across-trial variability in the rate of evidence growth, which is permitted to be distributed arbitrarily and to vary freely across experimental conditions. In contrast, in the standard diffusion model, within-trial variability in evidence is the primary determinant of variability in RT. Across-trial variability, which determines the relative speed of correct responses and errors, is theoretically and empirically constrained. Jones and Dzhafarov’s attempt to include the diffusion model in a class of models that also includes deterministic growth models misrepresents and trivializes it and conveys a misleading picture of cognitive decision-making research. PMID:25347314

Evaluating model structure adequacy: The case of the Maggia Valley groundwater system, southern Switzerland

USGS Publications Warehouse

Hill, Mary C.; L. Foglia,; S. W. Mehl,; P. Burlando,

2013-01-01

Model adequacy is evaluated with alternative models rated using model selection criteria (AICc, BIC, and KIC) and three other statistics. Model selection criteria are tested with cross-validation experiments and insights for using alternative models to evaluate model structural adequacy are provided. The study is conducted using the computer codes UCODE_2005 and MMA (MultiModel Analysis). One recharge alternative is simulated using the TOPKAPI hydrological model. The predictions evaluated include eight heads and three flows located where ecological consequences and model precision are of concern. Cross-validation is used to obtain measures of prediction accuracy. Sixty-four models were designed deterministically and differ in representation of river, recharge, bedrock topography, and hydraulic conductivity. Results include: (1) What may seem like inconsequential choices in model construction may be important to predictions. Analysis of predictions from alternative models is advised. (2) None of the model selection criteria consistently identified models with more accurate predictions. This is a disturbing result that suggests to reconsider the utility of model selection criteria, and/or the cross-validation measures used in this work to measure model accuracy. (3) KIC displayed poor performance for the present regression problems; theoretical considerations suggest that difficulties are associated with wide variations in the sensitivity term of KIC resulting from the models being nonlinear and the problems being ill-posed due to parameter correlations and insensitivity. The other criteria performed somewhat better, and similarly to each other. (4) Quantities with high leverage are more difficult to predict. The results are expected to be generally applicable to models of environmental systems.

The Hyper-Envelope Modeling Interface (HEMI): A Novel Approach Illustrated Through Predicting Tamarisk (Tamarix spp.) Habitat in the Western USA

USGS Publications Warehouse

Graham, Jim; Young, Nick; Jarnevich, Catherine S.; Newman, Greg; Evangelista, Paul; Stohlgren, Thomas J.

2013-01-01

Habitat suitability maps are commonly created by modeling a species’ environmental niche from occurrences and environmental characteristics. Here, we introduce the hyper-envelope modeling interface (HEMI), providing a new method for creating habitat suitability models using Bezier surfaces to model a species niche in environmental space. HEMI allows modeled surfaces to be visualized and edited in environmental space based on expert knowledge and does not require absence points for model development. The modeled surfaces require relatively few parameters compared to similar modeling approaches and may produce models that better match ecological niche theory. As a case study, we modeled the invasive species tamarisk (Tamarix spp.) in the western USA. We compare results from HEMI with those from existing similar modeling approaches (including BioClim, BioMapper, and Maxent). We used synthetic surfaces to create visualizations of the various models in environmental space and used modified area under the curve (AUC) statistic and akaike information criterion (AIC) as measures of model performance. We show that HEMI produced slightly better AUC values, except for Maxent and better AIC values overall. HEMI created a model with only ten parameters while Maxent produced a model with over 100 and BioClim used only eight. Additionally, HEMI allowed visualization and editing of the model in environmental space to develop alternative potential habitat scenarios. The use of Bezier surfaces can provide simple models that match our expectations of biological niche models and, at least in some cases, out-perform more complex approaches.

Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

Probabilistic Graphical Model Representation in Phylogenetics

PubMed Central

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

Field Test of a Hybrid Finite-Difference and Analytic Element Regional Model.

PubMed

Abrams, D B; Haitjema, H M; Feinstein, D T; Hunt, R J

2016-01-01

Regional finite-difference models often have cell sizes that are too large to sufficiently model well-stream interactions. Here, a steady-state hybrid model is applied whereby the upper layer or layers of a coarse MODFLOW model are replaced by the analytic element model GFLOW, which represents surface waters and wells as line and point sinks. The two models are coupled by transferring cell-by-cell leakage obtained from the original MODFLOW model to the bottom of the GFLOW model. A real-world test of the hybrid model approach is applied on a subdomain of an existing model of the Lake Michigan Basin. The original (coarse) MODFLOW model consists of six layers, the top four of which are aggregated into GFLOW as a single layer, while the bottom two layers remain part of MODFLOW in the hybrid model. The hybrid model and a refined "benchmark" MODFLOW model simulate similar baseflows. The hybrid and benchmark models also simulate similar baseflow reductions due to nearby pumping when the well is located within the layers represented by GFLOW. However, the benchmark model requires refinement of the model grid in the local area of interest, while the hybrid approach uses a gridless top layer and is thus unaffected by grid discretization errors. The hybrid approach is well suited to facilitate cost-effective retrofitting of existing coarse grid MODFLOW models commonly used for regional studies because it leverages the strengths of both finite-difference and analytic element methods for predictions in mildly heterogeneous systems that can be simulated with steady-state conditions. © 2015, National Ground Water Association.

Documenting Models for Interoperability and Reusability (proceedings)

EPA Science Inventory

Many modeling frameworks compartmentalize science via individual models that link sets of small components to create larger modeling workflows. Developing integrated watershed models increasingly requires coupling multidisciplinary, independent models, as well as collaboration be...

Documenting Models for Interoperability and Reusability

EPA Science Inventory

Many modeling frameworks compartmentalize science via individual models that link sets of small components to create larger modeling workflows. Developing integrated watershed models increasingly requires coupling multidisciplinary, independent models, as well as collaboration be...

Integration of Tuyere, Raceway and Shaft Models for Predicting Blast Furnace Process

NASA Astrophysics Data System (ADS)

Fu, Dong; Tang, Guangwu; Zhao, Yongfu; D'Alessio, John; Zhou, Chenn Q.

2018-06-01

A novel modeling strategy is presented for simulating the blast furnace iron making process. Such physical and chemical phenomena are taking place across a wide range of length and time scales, and three models are developed to simulate different regions of the blast furnace, i.e., the tuyere model, the raceway model and the shaft model. This paper focuses on the integration of the three models to predict the entire blast furnace process. Mapping output and input between models and an iterative scheme are developed to establish communications between models. The effects of tuyere operation and burden distribution on blast furnace fuel efficiency are investigated numerically. The integration of different models provides a way to realistically simulate the blast furnace by improving the modeling resolution on local phenomena and minimizing the model assumptions.

Accounting for uncertainty in health economic decision models by using model averaging.

PubMed

Jackson, Christopher H; Thompson, Simon G; Sharples, Linda D

2009-04-01

Health economic decision models are subject to considerable uncertainty, much of which arises from choices between several plausible model structures, e.g. choices of covariates in a regression model. Such structural uncertainty is rarely accounted for formally in decision models but can be addressed by model averaging. We discuss the most common methods of averaging models and the principles underlying them. We apply them to a comparison of two surgical techniques for repairing abdominal aortic aneurysms. In model averaging, competing models are usually either weighted by using an asymptotically consistent model assessment criterion, such as the Bayesian information criterion, or a measure of predictive ability, such as Akaike's information criterion. We argue that the predictive approach is more suitable when modelling the complex underlying processes of interest in health economics, such as individual disease progression and response to treatment.

Palm: Easing the Burden of Analytical Performance Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tallent, Nathan R.; Hoisie, Adolfy

2014-06-01

Analytical (predictive) application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult because they must be both accurate and concise. To ease the burden of performance modeling, we developed Palm, a modeling tool that combines top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. To express insight, Palm defines a source code modeling annotation language. By coordinating models and source code, Palm's models are `first-class' and reproducible. Unlike prior work, Palm formally links models, functions, and measurements. As a result, Palm (a) uses functions to either abstract or express complexitymore » (b) generates hierarchical models (representing an application's static and dynamic structure); and (c) automatically incorporates measurements to focus attention, represent constant behavior, and validate models. We discuss generating models for three different applications.« less

A Hybrid 3D Indoor Space Model

NASA Astrophysics Data System (ADS)

Jamali, Ali; Rahman, Alias Abdul; Boguslawski, Pawel

2016-10-01

GIS integrates spatial information and spatial analysis. An important example of such integration is for emergency response which requires route planning inside and outside of a building. Route planning requires detailed information related to indoor and outdoor environment. Indoor navigation network models including Geometric Network Model (GNM), Navigable Space Model, sub-division model and regular-grid model lack indoor data sources and abstraction methods. In this paper, a hybrid indoor space model is proposed. In the proposed method, 3D modeling of indoor navigation network is based on surveying control points and it is less dependent on the 3D geometrical building model. This research proposes a method of indoor space modeling for the buildings which do not have proper 2D/3D geometrical models or they lack semantic or topological information. The proposed hybrid model consists of topological, geometrical and semantical space.

Modified hyperbolic sine model for titanium dioxide-based memristive thin films

NASA Astrophysics Data System (ADS)

Abu Bakar, Raudah; Syahirah Kamarozaman, Nur; Fazlida Hanim Abdullah, Wan; Herman, Sukreen Hana

2018-03-01

Since the emergence of memristor as the newest fundamental circuit elements, studies on memristor modeling have been evolved. To date, the developed models were based on the linear model, linear ionic drift model using different window functions, tunnelling barrier model and hyperbolic-sine function based model. Although using hyperbolic-sine function model could predict the memristor electrical properties, the model was not well fitted to the experimental data. In order to improve the performance of the hyperbolic-sine function model, the state variable equation was modified. On the one hand, the addition of window function cannot provide an improved fitting. By multiplying the Yakopcic’s state variable model to Chang’s model on the other hand resulted in the closer agreement with the TiO2 thin film experimental data. The percentage error was approximately 2.15%.

Resident Role Modeling: "It Just Happens".

PubMed

Sternszus, Robert; Macdonald, Mary Ellen; Steinert, Yvonne

2016-03-01

Role modeling by staff physicians is a significant component of the clinical teaching of students and residents. However, the importance of resident role modeling has only recently emerged, and residents' understanding of themselves as role models has yet to be explored. This study sought to understand residents' perceptions of themselves as role models, describe how residents learn about role modeling, and identify ways to improve resident role modeling. Fourteen semistructured interviews were conducted with residents in internal medicine, general surgery, and pediatrics at the McGill University Faculty of Medicine between April and September 2013. Interviews were audio-recorded and subsequently transcribed for analysis; iterative analysis followed principles of qualitative description. Four primary themes were identified through data analysis: residents perceived role modeling as the demonstration of "good" behaviors in the clinical context; residents believed that learning from their role modeling "just happens" as long as learners are "watching"; residents did not equate role modeling with being a role model; and residents learned about role modeling from watching their positive and negative role models. While residents were aware that students and junior colleagues learned from their modeling, they were often not aware of role modeling as it was occurring; they also believed that learning from role modeling "just happens" and did not always see themselves as role models. Helping residents view effective role modeling as a deliberate process rather than something that "just happens" may improve clinical teaching across the continuum of medical education.

Why Bother to Calibrate? Model Consistency and the Value of Prior Information

NASA Astrophysics Data System (ADS)

Hrachowitz, Markus; Fovet, Ophelie; Ruiz, Laurent; Euser, Tanja; Gharari, Shervan; Nijzink, Remko; Savenije, Hubert; Gascuel-Odoux, Chantal

2015-04-01

Hydrological models frequently suffer from limited predictive power despite adequate calibration performances. This can indicate insufficient representations of the underlying processes. Thus ways are sought to increase model consistency while satisfying the contrasting priorities of increased model complexity and limited equifinality. In this study the value of a systematic use of hydrological signatures and expert knowledge for increasing model consistency was tested. It was found that a simple conceptual model, constrained by 4 calibration objective functions, was able to adequately reproduce the hydrograph in the calibration period. The model, however, could not reproduce 20 hydrological signatures, indicating a lack of model consistency. Subsequently, testing 11 models, model complexity was increased in a stepwise way and counter-balanced by using prior information about the system to impose "prior constraints", inferred from expert knowledge and to ensure a model which behaves well with respect to the modeller's perception of the system. We showed that, in spite of unchanged calibration performance, the most complex model set-up exhibited increased performance in the independent test period and skill to reproduce all 20 signatures, indicating a better system representation. The results suggest that a model may be inadequate despite good performance with respect to multiple calibration objectives and that increasing model complexity, if efficiently counter-balanced by available prior constraints, can increase predictive performance of a model and its skill to reproduce hydrological signatures. The results strongly illustrate the need to balance automated model calibration with a more expert-knowledge driven strategy of constraining models.

Why Bother and Calibrate? Model Consistency and the Value of Prior Information.

NASA Astrophysics Data System (ADS)

Hrachowitz, M.; Fovet, O.; Ruiz, L.; Euser, T.; Gharari, S.; Nijzink, R.; Freer, J. E.; Savenije, H.; Gascuel-Odoux, C.

2014-12-01

Hydrological models frequently suffer from limited predictive power despite adequate calibration performances. This can indicate insufficient representations of the underlying processes. Thus ways are sought to increase model consistency while satisfying the contrasting priorities of increased model complexity and limited equifinality. In this study the value of a systematic use of hydrological signatures and expert knowledge for increasing model consistency was tested. It was found that a simple conceptual model, constrained by 4 calibration objective functions, was able to adequately reproduce the hydrograph in the calibration period. The model, however, could not reproduce 20 hydrological signatures, indicating a lack of model consistency. Subsequently, testing 11 models, model complexity was increased in a stepwise way and counter-balanced by using prior information about the system to impose "prior constraints", inferred from expert knowledge and to ensure a model which behaves well with respect to the modeller's perception of the system. We showed that, in spite of unchanged calibration performance, the most complex model set-up exhibited increased performance in the independent test period and skill to reproduce all 20 signatures, indicating a better system representation. The results suggest that a model may be inadequate despite good performance with respect to multiple calibration objectives and that increasing model complexity, if efficiently counter-balanced by available prior constraints, can increase predictive performance of a model and its skill to reproduce hydrological signatures. The results strongly illustrate the need to balance automated model calibration with a more expert-knowledge driven strategy of constraining models.

Process consistency in models: The importance of system signatures, expert knowledge, and process complexity

NASA Astrophysics Data System (ADS)

Hrachowitz, M.; Fovet, O.; Ruiz, L.; Euser, T.; Gharari, S.; Nijzink, R.; Freer, J.; Savenije, H. H. G.; Gascuel-Odoux, C.

2014-09-01

Hydrological models frequently suffer from limited predictive power despite adequate calibration performances. This can indicate insufficient representations of the underlying processes. Thus, ways are sought to increase model consistency while satisfying the contrasting priorities of increased model complexity and limited equifinality. In this study, the value of a systematic use of hydrological signatures and expert knowledge for increasing model consistency was tested. It was found that a simple conceptual model, constrained by four calibration objective functions, was able to adequately reproduce the hydrograph in the calibration period. The model, however, could not reproduce a suite of hydrological signatures, indicating a lack of model consistency. Subsequently, testing 11 models, model complexity was increased in a stepwise way and counter-balanced by "prior constraints," inferred from expert knowledge to ensure a model which behaves well with respect to the modeler's perception of the system. We showed that, in spite of unchanged calibration performance, the most complex model setup exhibited increased performance in the independent test period and skill to better reproduce all tested signatures, indicating a better system representation. The results suggest that a model may be inadequate despite good performance with respect to multiple calibration objectives and that increasing model complexity, if counter-balanced by prior constraints, can significantly increase predictive performance of a model and its skill to reproduce hydrological signatures. The results strongly illustrate the need to balance automated model calibration with a more expert-knowledge-driven strategy of constraining models.

Nonlinear time series modeling and forecasting the seismic data of the Hindu Kush region

NASA Astrophysics Data System (ADS)

Khan, Muhammad Yousaf; Mittnik, Stefan

2018-01-01

In this study, we extended the application of linear and nonlinear time models in the field of earthquake seismology and examined the out-of-sample forecast accuracy of linear Autoregressive (AR), Autoregressive Conditional Duration (ACD), Self-Exciting Threshold Autoregressive (SETAR), Threshold Autoregressive (TAR), Logistic Smooth Transition Autoregressive (LSTAR), Additive Autoregressive (AAR), and Artificial Neural Network (ANN) models for seismic data of the Hindu Kush region. We also extended the previous studies by using Vector Autoregressive (VAR) and Threshold Vector Autoregressive (TVAR) models and compared their forecasting accuracy with linear AR model. Unlike previous studies that typically consider the threshold model specifications by using internal threshold variable, we specified these models with external transition variables and compared their out-of-sample forecasting performance with the linear benchmark AR model. The modeling results show that time series models used in the present study are capable of capturing the dynamic structure present in the seismic data. The point forecast results indicate that the AR model generally outperforms the nonlinear models. However, in some cases, threshold models with external threshold variables specification produce more accurate forecasts, indicating that specification of threshold time series models is of crucial importance. For raw seismic data, the ACD model does not show an improved out-of-sample forecasting performance over the linear AR model. The results indicate that the AR model is the best forecasting device to model and forecast the raw seismic data of the Hindu Kush region.

Modeling habitat for Marbled Murrelets on the Siuslaw National Forest, Oregon, using lidar data

USGS Publications Warehouse

Hagar, Joan C.; Aragon, Ramiro; Haggerty, Patricia; Hollenbeck, Jeff P.

2018-03-28

Habitat models using lidar-derived variables that quantify fine-scale variation in vegetation structure can improve the accuracy of occupancy estimates for canopy-dwelling species over models that use variables derived from other remote sensing techniques. However, the ability of models developed at such a fine spatial scale to maintain accuracy at regional or larger spatial scales has not been tested. We tested the transferability of a lidar-based habitat model for the threatened Marbled Murrelet (Brachyramphus marmoratus) between two management districts within a larger regional conservation zone in coastal western Oregon. We compared the performance of the transferred model against models developed with data from the application location. The transferred model had good discrimination (AUC = 0.73) at the application location, and model performance was further improved by fitting the original model with coefficients from the application location dataset (AUC = 0.79). However, the model selection procedure indicated that neither of these transferred models were considered competitive with a model trained on local data. The new model trained on data from the application location resulted in the selection of a slightly different set of lidar metrics from the original model, but both transferred and locally trained models consistently indicated positive relationships between the probability of occupancy and lidar measures of canopy structural complexity. We conclude that while the locally trained model had superior performance for local application, the transferred model could reasonably be applied to the entire conservation zone.

How Qualitative Methods Can be Used to Inform Model Development.

PubMed

Husbands, Samantha; Jowett, Susan; Barton, Pelham; Coast, Joanna

2017-06-01

Decision-analytic models play a key role in informing healthcare resource allocation decisions. However, there are ongoing concerns with the credibility of models. Modelling methods guidance can encourage good practice within model development, but its value is dependent on its ability to address the areas that modellers find most challenging. Further, it is important that modelling methods and related guidance are continually updated in light of any new approaches that could potentially enhance model credibility. The objective of this article was to highlight the ways in which qualitative methods have been used and recommended to inform decision-analytic model development and enhance modelling practices. With reference to the literature, the article discusses two key ways in which qualitative methods can be, and have been, applied. The first approach involves using qualitative methods to understand and inform general and future processes of model development, and the second, using qualitative techniques to directly inform the development of individual models. The literature suggests that qualitative methods can improve the validity and credibility of modelling processes by providing a means to understand existing modelling approaches that identifies where problems are occurring and further guidance is needed. It can also be applied within model development to facilitate the input of experts to structural development. We recommend that current and future model development would benefit from the greater integration of qualitative methods, specifically by studying 'real' modelling processes, and by developing recommendations around how qualitative methods can be adopted within everyday modelling practice.

Large-scale model quality assessment for improving protein tertiary structure prediction.

PubMed

Cao, Renzhi; Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2015-06-15

Sampling structural models and ranking them are the two major challenges of protein structure prediction. Traditional protein structure prediction methods generally use one or a few quality assessment (QA) methods to select the best-predicted models, which cannot consistently select relatively better models and rank a large number of models well. Here, we develop a novel large-scale model QA method in conjunction with model clustering to rank and select protein structural models. It unprecedentedly applied 14 model QA methods to generate consensus model rankings, followed by model refinement based on model combination (i.e. averaging). Our experiment demonstrates that the large-scale model QA approach is more consistent and robust in selecting models of better quality than any individual QA method. Our method was blindly tested during the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11) as MULTICOM group. It was officially ranked third out of all 143 human and server predictors according to the total scores of the first models predicted for 78 CASP11 protein domains and second according to the total scores of the best of the five models predicted for these domains. MULTICOM's outstanding performance in the extremely competitive 2014 CASP11 experiment proves that our large-scale QA approach together with model clustering is a promising solution to one of the two major problems in protein structure modeling. The web server is available at: http://sysbio.rnet.missouri.edu/multicom_cluster/human/. © The Author 2015. Published by Oxford University Press.

An algorithm to detect and communicate the differences in computational models describing biological systems.

PubMed

Scharm, Martin; Wolkenhauer, Olaf; Waltemath, Dagmar

2016-02-15

Repositories support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available in repositories, such as the BioModels database or the Physiome Model Repository, a framework to track the differences between models and their versions is essential to compare and combine models. Difference detection not only allows users to study the history of models but also helps in the detection of errors and inconsistencies. Existing repositories lack algorithms to track a model's development over time. Focusing on SBML and CellML, we present an algorithm to accurately detect and describe differences between coexisting versions of a model with respect to (i) the models' encoding, (ii) the structure of biological networks and (iii) mathematical expressions. This algorithm is implemented in a comprehensive and open source library called BiVeS. BiVeS helps to identify and characterize changes in computational models and thereby contributes to the documentation of a model's history. Our work facilitates the reuse and extension of existing models and supports collaborative modelling. Finally, it contributes to better reproducibility of modelling results and to the challenge of model provenance. The workflow described in this article is implemented in BiVeS. BiVeS is freely available as source code and binary from sems.uni-rostock.de. The web interface BudHat demonstrates the capabilities of BiVeS at budhat.sems.uni-rostock.de. © The Author 2015. Published by Oxford University Press.

Experiments in concept modeling for radiographic image reports.

PubMed Central

Bell, D S; Pattison-Gordon, E; Greenes, R A

1994-01-01

OBJECTIVE: Development of methods for building concept models to support structured data entry and image retrieval in chest radiography. DESIGN: An organizing model for chest-radiographic reporting was built by analyzing manually a set of natural-language chest-radiograph reports. During model building, clinician-informaticians judged alternative conceptual structures according to four criteria: content of clinically relevant detail, provision for semantic constraints, provision for canonical forms, and simplicity. The organizing model was applied in representing three sample reports in their entirety. To explore the potential for automatic model discovery, the representation of one sample report was compared with the noun phrases derived from the same report by the CLARIT natural-language processing system. RESULTS: The organizing model for chest-radiographic reporting consists of 62 concept types and 17 relations, arranged in an inheritance network. The broadest types in the model include finding, anatomic locus, procedure, attribute, and status. Diagnoses are modeled as a subtype of finding. Representing three sample reports in their entirety added 79 narrower concept types. Some CLARIT noun phrases suggested valid associations among subtypes of finding, status, and anatomic locus. CONCLUSIONS: A manual modeling process utilizing explicitly stated criteria for making modeling decisions produced an organizing model that showed consistency in early testing. A combination of top-down and bottom-up modeling was required. Natural-language processing may inform model building, but algorithms that would replace manual modeling were not discovered. Further progress in modeling will require methods for objective model evaluation and tools for formalizing the model-building process. PMID:7719807

A strategy to establish Food Safety Model Repositories.

PubMed

Plaza-Rodríguez, C; Thoens, C; Falenski, A; Weiser, A A; Appel, B; Kaesbohrer, A; Filter, M

2015-07-02

Transferring the knowledge of predictive microbiology into real world food manufacturing applications is still a major challenge for the whole food safety modelling community. To facilitate this process, a strategy for creating open, community driven and web-based predictive microbial model repositories is proposed. These collaborative model resources could significantly improve the transfer of knowledge from research into commercial and governmental applications and also increase efficiency, transparency and usability of predictive models. To demonstrate the feasibility, predictive models of Salmonella in beef previously published in the scientific literature were re-implemented using an open source software tool called PMM-Lab. The models were made publicly available in a Food Safety Model Repository within the OpenML for Predictive Modelling in Food community project. Three different approaches were used to create new models in the model repositories: (1) all information relevant for model re-implementation is available in a scientific publication, (2) model parameters can be imported from tabular parameter collections and (3) models have to be generated from experimental data or primary model parameters. All three approaches were demonstrated in the paper. The sample Food Safety Model Repository is available via: http://sourceforge.net/projects/microbialmodelingexchange/files/models and the PMM-Lab software can be downloaded from http://sourceforge.net/projects/pmmlab/. This work also illustrates that a standardized information exchange format for predictive microbial models, as the key component of this strategy, could be established by adoption of resources from the Systems Biology domain. Copyright © 2015. Published by Elsevier B.V.

The LUE data model for representation of agents and fields

NASA Astrophysics Data System (ADS)

de Jong, Kor; Schmitz, Oliver; Karssenberg, Derek

2017-04-01

Traditionally, agents-based and field-based modelling environments use different data models to represent the state of information they manipulate. In agent-based modelling, involving the representation of phenomena as objects bounded in space and time, agents are often represented by classes, each of which represents a particular kind of agent and all its properties. Such classes can be used to represent entities like people, birds, cars and countries. In field-based modelling, involving the representation of the environment as continuous fields, fields are often represented by a discretization of space, using multidimensional arrays, each storing mostly a single attribute. Such arrays can be used to represent the elevation of the land-surface, the pH of the soil, or the population density in an area, for example. Representing a population of agents by class instances grouped in collections is an intuitive way of organizing information. A drawback, though, is that models in which class instances grouping properties are stored in collections are less efficient (execute slower) than models in which collections of properties are grouped. The field representation, on the other hand, is convenient for the efficient execution of models. Another drawback is that, because the data models used are so different, integrating agent-based and field-based models becomes difficult, since the model builder has to deal with multiple concepts, and often multiple modelling environments. With the development of the LUE data model [1] we aim at representing agents and fields within a single paradigm, by combining the advantages of the data models used in agent-based and field-based data modelling. This removes the barrier for writing integrated agent-based and field-based models. The resulting data model is intuitive to use and allows for efficient execution of models. LUE is both a high-level conceptual data model and a low-level physical data model. The LUE conceptual data model is a generalization of the data models used in agent-based and field-based modelling. The LUE physical data model [2] is an implementation of the LUE conceptual data model in HDF5. In our presentation we will provide details of our approach to organizing information about agents and fields. We will show examples of agent and field data represented by the conceptual and physical data model. References: [1] de Bakker, M.P., de Jong, K., Schmitz, O., Karssenberg, D., 2016. Design and demonstration of a data model to integrate agent-based and field-based modelling. Environmental Modelling and Software. http://dx.doi.org/10.1016/j.envsoft.2016.11.016 [2] de Jong, K., 2017. LUE source code. https://github.com/pcraster/lue

A New Simplified Source Model to Explain Strong Ground Motions from a Mega-Thrust Earthquake - Application to the 2011 Tohoku Earthquake (Mw9.0) -

NASA Astrophysics Data System (ADS)

Nozu, A.

2013-12-01

A new simplified source model is proposed to explain strong ground motions from a mega-thrust earthquake. The proposed model is simpler, and involves less model parameters, than the conventional characterized source model, which itself is a simplified expression of actual earthquake source. In the proposed model, the spacio-temporal distribution of slip within a subevent is not modeled. Instead, the source spectrum associated with the rupture of a subevent is modeled and it is assumed to follow the omega-square model. By multiplying the source spectrum with the path effect and the site amplification factor, the Fourier amplitude at a target site can be obtained. Then, combining it with Fourier phase characteristics of a smaller event, the time history of strong ground motions from the subevent can be calculated. Finally, by summing up contributions from the subevents, strong ground motions from the entire rupture can be obtained. The source model consists of six parameters for each subevent, namely, longitude, latitude, depth, rupture time, seismic moment and corner frequency of the subevent. Finite size of the subevent can be taken into account in the model, because the corner frequency of the subevent is included in the model, which is inversely proportional to the length of the subevent. Thus, the proposed model is referred to as the 'pseudo point-source model'. To examine the applicability of the model, a pseudo point-source model was developed for the 2011 Tohoku earthquake. The model comprises nine subevents, located off Miyagi Prefecture through Ibaraki Prefecture. The velocity waveforms (0.2-1 Hz), the velocity envelopes (0.2-10 Hz) and the Fourier spectra (0.2-10 Hz) at 15 sites calculated with the pseudo point-source model agree well with the observed ones, indicating the applicability of the model. Then the results were compared with the results of a super-asperity (SPGA) model of the same earthquake (Nozu, 2012, AGU), which can be considered as an example of characterized source models. Although the pseudo point-source model involves much less model parameters than the super-asperity model, the errors associated with the former model were comparable to those for the latter model for velocity waveforms and envelopes. Furthermore, the errors associated with the former model were much smaller than those for the latter model for Fourier spectra. These evidences indicate the usefulness of the pseudo point-source model. Comparison of the observed (black) and synthetic (red) Fourier spectra. The spectra are the composition of two horizontal components and smoothed with a Parzen window with a band width of 0.05 Hz.

Model and Interoperability using Meta Data Annotations

NASA Astrophysics Data System (ADS)

David, O.

2011-12-01

Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside. While providing all those capabilities, a significant reduction in the size of the model source code was achieved. To support the benefit of annotations for a modeler, studies were conducted to evaluate the effectiveness of an annotation based framework approach with other modeling frameworks and libraries, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A typical hydrological model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks.

A BRDF statistical model applying to space target materials modeling

NASA Astrophysics Data System (ADS)

Liu, Chenghao; Li, Zhi; Xu, Can; Tian, Qichen

2017-10-01

In order to solve the problem of poor effect in modeling the large density BRDF measured data with five-parameter semi-empirical model, a refined statistical model of BRDF which is suitable for multi-class space target material modeling were proposed. The refined model improved the Torrance-Sparrow model while having the modeling advantages of five-parameter model. Compared with the existing empirical model, the model contains six simple parameters, which can approximate the roughness distribution of the material surface, can approximate the intensity of the Fresnel reflectance phenomenon and the attenuation of the reflected light's brightness with the azimuth angle changes. The model is able to achieve parameter inversion quickly with no extra loss of accuracy. The genetic algorithm was used to invert the parameters of 11 different samples in the space target commonly used materials, and the fitting errors of all materials were below 6%, which were much lower than those of five-parameter model. The effect of the refined model is verified by comparing the fitting results of the three samples at different incident zenith angles in 0° azimuth angle. Finally, the three-dimensional modeling visualizations of these samples in the upper hemisphere space was given, in which the strength of the optical scattering of different materials could be clearly shown. It proved the good describing ability of the refined model at the material characterization as well.

Relative efficiency of joint-model and full-conditional-specification multiple imputation when conditional models are compatible: The general location model.

PubMed

Seaman, Shaun R; Hughes, Rachael A

2018-06-01

Estimating the parameters of a regression model of interest is complicated by missing data on the variables in that model. Multiple imputation is commonly used to handle these missing data. Joint model multiple imputation and full-conditional specification multiple imputation are known to yield imputed data with the same asymptotic distribution when the conditional models of full-conditional specification are compatible with that joint model. We show that this asymptotic equivalence of imputation distributions does not imply that joint model multiple imputation and full-conditional specification multiple imputation will also yield asymptotically equally efficient inference about the parameters of the model of interest, nor that they will be equally robust to misspecification of the joint model. When the conditional models used by full-conditional specification multiple imputation are linear, logistic and multinomial regressions, these are compatible with a restricted general location joint model. We show that multiple imputation using the restricted general location joint model can be substantially more asymptotically efficient than full-conditional specification multiple imputation, but this typically requires very strong associations between variables. When associations are weaker, the efficiency gain is small. Moreover, full-conditional specification multiple imputation is shown to be potentially much more robust than joint model multiple imputation using the restricted general location model to mispecification of that model when there is substantial missingness in the outcome variable.

Lessons from Climate Modeling on the Design and Use of Ensembles for Crop Modeling

NASA Technical Reports Server (NTRS)

Wallach, Daniel; Mearns, Linda O.; Ruane, Alexander C.; Roetter, Reimund P.; Asseng, Senthold

2016-01-01

Working with ensembles of crop models is a recent but important development in crop modeling which promises to lead to better uncertainty estimates for model projections and predictions, better predictions using the ensemble mean or median, and closer collaboration within the modeling community. There are numerous open questions about the best way to create and analyze such ensembles. Much can be learned from the field of climate modeling, given its much longer experience with ensembles. We draw on that experience to identify questions and make propositions that should help make ensemble modeling with crop models more rigorous and informative. The propositions include defining criteria for acceptance of models in a crop MME, exploring criteria for evaluating the degree of relatedness of models in a MME, studying the effect of number of models in the ensemble, development of a statistical model of model sampling, creation of a repository for MME results, studies of possible differential weighting of models in an ensemble, creation of single model ensembles based on sampling from the uncertainty distribution of parameter values or inputs specifically oriented toward uncertainty estimation, the creation of super ensembles that sample more than one source of uncertainty, the analysis of super ensemble results to obtain information on total uncertainty and the separate contributions of different sources of uncertainty and finally further investigation of the use of the multi-model mean or median as a predictor.

Assessing Ecosystem Model Performance in Semiarid Systems

NASA Astrophysics Data System (ADS)

Thomas, A.; Dietze, M.; Scott, R. L.; Biederman, J. A.

2017-12-01

In ecosystem process modelling, comparing outputs to benchmark datasets observed in the field is an important way to validate models, allowing the modelling community to track model performance over time and compare models at specific sites. Multi-model comparison projects as well as models themselves have largely been focused on temperate forests and similar biomes. Semiarid regions, on the other hand, are underrepresented in land surface and ecosystem modelling efforts, and yet will be disproportionately impacted by disturbances such as climate change due to their sensitivity to changes in the water balance. Benchmarking models at semiarid sites is an important step in assessing and improving models' suitability for predicting the impact of disturbance on semiarid ecosystems. In this study, several ecosystem models were compared at a semiarid grassland in southwestern Arizona using PEcAn, or the Predictive Ecosystem Analyzer, an open-source eco-informatics toolbox ideal for creating the repeatable model workflows necessary for benchmarking. Models included SIPNET, DALEC, JULES, ED2, GDAY, LPJ-GUESS, MAESPA, CLM, CABLE, and FATES. Comparison between model output and benchmarks such as net ecosystem exchange (NEE) tended to produce high root mean square error and low correlation coefficients, reflecting poor simulation of seasonality and the tendency for models to create much higher carbon sources than observed. These results indicate that ecosystem models do not currently adequately represent semiarid ecosystem processes.

The relationship between digital model accuracy and time-dependent deformation of alginate impressions.

PubMed

Alcan, Toros; Ceylanoğlu, Cenk; Baysal, Bekir

2009-01-01

To investigate the effects of different storage periods of alginate impressions on digital model accuracy. A total of 105 impressions were taken from a master model with three different brands of alginates and were poured into stone models in five different storage periods. In all, 21 stone models were poured and immediately were scanned, and 21 digital models were prepared. The remaining 84 impressions were poured after 1, 2, 3, and 4 days, respectively. Five linear measurements were made by three researchers on the master model, the stone models, and the digital models. Time-dependent deformation of alginate impressions at different storage periods and the accuracy of traditional stone models and digital models were evaluated separately. Both the stone models and the digital models were highly correlated with the master model. Significant deformities in the alginate impressions were noted at different storage periods of 1 to 4 days. Alginate impressions of different brands also showed significant differences between each other on the first, third, and fourth days. Digital orthodontic models are as reliable as traditional stone models and probably will become the standard for orthodontic clinical use. Storing alginate impressions in sealed plastic bags for up to 4 days caused statistically significant deformation of alginate impressions, but the magnitude of these deformations did not appear to be clinically relevant and had no adverse effect on digital modeling.

Chemometrics-assisted spectrophotometry method for the determination of chemical oxygen demand in pulping effluent.

PubMed

Chen, Honglei; Chen, Yuancai; Zhan, Huaiyu; Fu, Shiyu

2011-04-01

A new method has been developed for the determination of chemical oxygen demand (COD) in pulping effluent using chemometrics-assisted spectrophotometry. Two calibration models were established by inducing UV-visible spectroscopy (model 1) and derivative spectroscopy (model 2), combined with the chemometrics software Smica-P. Correlation coefficients of the two models are 0.9954 (model 1) and 0.9963 (model 2) when COD of samples is in the range of 0 to 405 mg/L. Sensitivities of the two models are 0.0061 (model 1) and 0.0056 (model 2) and method detection limits are 2.02-2.45 mg/L (model 1) and 2.13-2.51 mg/L (model 2). Validation experiment showed that the average standard deviation of model 2 was 1.11 and that of model 1 was 1.54. Similarly, average relative error of model 2 (4.25%) was lower than model 1 (5.00%), which indicated that the predictability of model 2 was better than that of model 1. Chemometrics-assisted spectrophotometry method did not need chemical reagents and digestion which were required in the conventional methods, and the testing time of the new method was significantly shorter than the conventional ones. The proposed method can be used to measure COD in pulping effluent as an environmentally friendly approach with satisfactory results.

Improved two-equation k-omega turbulence models for aerodynamic flows

NASA Technical Reports Server (NTRS)

Menter, Florian R.

1992-01-01

Two new versions of the k-omega two-equation turbulence model will be presented. The new Baseline (BSL) model is designed to give results similar to those of the original k-omega model of Wilcox, but without its strong dependency on arbitrary freestream values. The BSL model is identical to the Wilcox model in the inner 50 percent of the boundary-layer but changes gradually to the high Reynolds number Jones-Launder k-epsilon model (in a k-omega formulation) towards the boundary-layer edge. The new model is also virtually identical to the Jones-Lauder model for free shear layers. The second version of the model is called Shear-Stress Transport (SST) model. It is based on the BSL model, but has the additional ability to account for the transport of the principal shear stress in adverse pressure gradient boundary-layers. The model is based on Bradshaw's assumption that the principal shear stress is proportional to the turbulent kinetic energy, which is introduced into the definition of the eddy-viscosity. Both models are tested for a large number of different flowfields. The results of the BSL model are similar to those of the original k-omega model, but without the undesirable freestream dependency. The predictions of the SST model are also independent of the freestream values and show excellent agreement with experimental data for adverse pressure gradient boundary-layer flows.

Efficient polarimetric BRDF model.

PubMed

Renhorn, Ingmar G E; Hallberg, Tomas; Boreman, Glenn D

2015-11-30

The purpose of the present manuscript is to present a polarimetric bidirectional reflectance distribution function (BRDF) model suitable for hyperspectral and polarimetric signature modelling. The model is based on a further development of a previously published four-parameter model that has been generalized in order to account for different types of surface structures (generalized Gaussian distribution). A generalization of the Lambertian diffuse model is presented. The pBRDF-functions are normalized using numerical integration. Using directional-hemispherical reflectance (DHR) measurements, three of the four basic parameters can be determined for any wavelength. This simplifies considerably the development of multispectral polarimetric BRDF applications. The scattering parameter has to be determined from at least one BRDF measurement. The model deals with linear polarized radiation; and in similarity with e.g. the facet model depolarization is not included. The model is very general and can inherently model extreme surfaces such as mirrors and Lambertian surfaces. The complex mixture of sources is described by the sum of two basic models, a generalized Gaussian/Fresnel model and a generalized Lambertian model. Although the physics inspired model has some ad hoc features, the predictive power of the model is impressive over a wide range of angles and scattering magnitudes. The model has been applied successfully to painted surfaces, both dull and glossy and also on metallic bead blasted surfaces. The simple and efficient model should be attractive for polarimetric simulations and polarimetric remote sensing.

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3

PubMed Central

Smith, Lucian P.; Hucka, Michael; Hoops, Stefan; Finney, Andrew; Ginkel, Martin; Myers, Chris J.; Moraru, Ion; Liebermeister, Wolfram

2017-01-01

Summary Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional “port” construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be “flattened” to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models. PMID:26528566