Publications

predators, prey and habitat structure: can key conservation areas and early signs of population collapse be detected in neotropical forests?	tropical forests with a low human population and absence of large-scale deforestation provide unique opportunities to study successful conservation strategies, which should be based on adequate monitoring tools. this study explored the conservation status of a large predator, the jaguar, considered an indicator of the maintenance of how well ecological processes are maintained. we implemented an original integrative approach, exploring successive ecosystem status proxies, from habitats and respo ...	2016	27828993
genetic diversity and population structure of mesoamerican jaguars (panthera onca): implications for conservation and management.	mesoamerican jaguars (panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. this is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild a ...	2016	27783617
isolation of primary fibroblast culture from wildlife: the panthera onca case to preserve a south american endangered species.	cell line establishment of somatic cells is a valuable resource to preserve genetic material of rare, difficult-to-find, endangered and giant species like jaguar (panthera onca), the largest south american felid. this unit focuses on the isolation and culture of fibroblasts from jaguar skin and muscle biopsies, and ear cartilage dissection immediately after death to preserve one of the several endangered species in this biome. these culture techniques enabled us to contribute 570 samples from 45 ...	2016	27723084
assessing the umbrella value of a range-wide conservation network for jaguars (panthera onca).	umbrella species are employed as conservation short-cuts for the design of reserves or reserve networks. however, empirical data on the effectiveness of umbrellas is equivocal, which has prevented more widespread application of this conservation strategy. we perform a novel, large-scale evaluation of umbrella species by assessing the potential umbrella value of a jaguar (panthera onca) conservation network (consisting of viable populations and corridors) that extends from mexico to argentina. us ...	2016	27509752
space use and movement of a neotropical top predator: the endangered jaguar.	accurately estimating home range and understanding movement behavior can provide important information on ecological processes. advances in data collection and analysis have improved our ability to estimate home range and movement parameters, both of which have the potential to impact species conservation. fitting continuous-time movement model to data and incorporating the autocorrelated kernel density estimator (akde), we investigated range residency of forty-four jaguars fit with gps collars ...	2016	28030568
implications of fine-grained habitat fragmentation and road mortality for jaguar conservation in the atlantic forest, brazil.	jaguar (panthera onca) populations in the upper paraná river, in the brazilian atlantic forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. we developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the ...	2016	27973584
multiconformation, density functional theory-based pka prediction in application to large, flexible organic molecules with diverse functional groups.	we consider the conformational flexibility of molecules and its implications for micro- and macro-pka. the corresponding formulas are derived and discussed against the background of a comprehensive scientific and algorithmic description of the latest version of our computer program jaguar pka, a density functional theory-based pka predictor, which is now capable of acting on multiple conformations explicitly. jaguar pka is essentially a complex computational workflow incorporating research and t ...	2016	27951674
exploiting expression patterns across multiple tissues to map expression quantitative trait loci.	in order to better understand complex diseases, it is important to understand how genetic variation in the regulatory regions affects gene expression. genetic variants found in these regulatory regions have been shown to activate transcription in a tissue-specific manner. therefore, it is important to map the aforementioned expression quantitative trait loci (eqtl) using a statistically disciplined approach that jointly models all the tissues and makes use of all the information available to max ...	2016	27341818
brain acetylcholinesterase of jaguar cichlid (parachromis managuensis): from physicochemical and kinetic properties to its potential as biomarker of pesticides and metal ions.	this contribution aimed to characterize physicochemical and kinetic parameters of the brain cholinesterases (ches) from parachromis managuensis and investigate the in vitro effects of pesticides and metal ions on its activity intending to propose as biomarker. this species is suitable for this investigation because (1) it was recently introduced in brazil becoming invasive (no restrictions on capture) and (2) occupies the top of the food chain (being subject to bioaccumulation). the enzyme extra ...	2016	27288599
fine-scale habitat segregation between two ecologically similar top predators.	similar, coexisting species often segregate along the spatial ecological axis. here, we examine if two top predators (jaguars and pumas) present different fine-scale habitat use in areas of coexistence, and discuss if the observed pattern can be explained by the risk of interference competition between them. interference competition theory predicts that pumas should avoid habitats or areas used by jaguars (the dominant species), and as a consequence should present more variability of niche param ...	2016	27187596
megalictis, the bone-crushing giant mustelid (carnivora, mustelidae, oligobuninae) from the early miocene of north america.	we describe cranial and mandibular remains of three undescribed individuals of the giant mustelid megalictis ferox matthew, 1907 from the latest arikareean (ar4), early miocene mammal fauna of nebraska, and wyoming (usa) housed at the american museum of natural history (new york, usa). our phylogenetic hypothesis indicates that ar4 specimens assigned to m. ferox constitute a monophyletic group. we assign three additional species previously referred to paroligobunis to megalictis: m. simplicidens ...	2016	27054570
expanding dp4: application to drug compounds and automation.	the dp4 parameter, which provides a confidence level for nmr assignment, has been widely used to help assign the structures of many stereochemically-rich molecules. we present an improved version of the procedure, which can be downloaded as python script instead of running within a web-browser, and which analyses output from open-source molecular modelling programs (tinker and nwchem) in addition to being able to use output from commercial packages (schrodinger's macromodel and jaguar; gaussian) ...	2016	27045792
highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules.	we have developed and implemented pseudospectral time-dependent density-functional theory (tddft) in the quantum mechanics package jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (flr) or the tamm-dancoff approximation (tda) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to ...	2016	27013141
terrestrial mammal occupancy in the context of widespread forest loss and a proposed interoceanic canal in nicaragua's decreasingly remote south caribbean region.	central america is experiencing rapid forest loss and habitat degradation both inside and outside of protected areas. despite increasing deforestation, the caribbean region of nicaragua plays an important role in the survival or extinction of large mammal populations in central america given that it still retains core areas of habitat for large mammal species. the proposed interoceanic canal project that would bisect the southern half of this caribbean region represents a new threat that, combin ...	2016	27007122
genetic variability and structure of jaguar (panthera onca) in mexican zoos.	genealogical records of animals (studbook) are created to avoid reproduction between closely related individuals, which could cause inbreeding, particularly for such endangered species as the panthera onca (linnaeus, 1758). jaguar is the largest felid in the americas and is considered an important ecological key species. in mexico, wild jaguar populations have been significantly reduced in recent decades, and population decline typically accompany decreases in genetic variation. there is no curr ...	2016	26790662
assessing the umbrella value of a range-wide conservation network for jaguars (panthera onca).	umbrella species are employed as conservation short-cuts for the design of reserves or reserve networks. however, empirical data on the effectiveness of umbrellas is equivocal, which has prevented more widespread application of this conservation strategy. we perform a novel, large-scale evaluation of umbrella species by assessing the potential umbrella value of a jaguar (panthera onca) conservation network (consisting of viable populations and corridors) that extends from mexico to argentina. us ...	2016	28581663
a comparative analysis of genetic diversity and structure in jaguars (panthera onca), pumas (puma concolor), and ocelots (leopardus pardalis) in fragmented landscapes of a critical mesoamerican linkage zone.	with increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. this study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple neotropical felids coexisting across a fragmented landscape in belize, central america. we ...	2016	26974968
characterization and manipulation of reproductive cycles in the jaguar (panthera onca).	basic reproductive information in female jaguars (panthera onca) is lacking, thus longitudinal fecal samples from seven females were analyzed via enzyme immunoassay to measure estradiol and progestin metabolites throughout the year. mean estrus length of 194 estrus periods measured hormonally was 6.5±0.3d, mean peak fecal estradiol concentration was 138.7±5.7ng/g; and in one female, estrus resumption occurred approximately 15d post-partum. ovulation, as indicted by sustained elevated progestin c ...	2016	26399935
the complete mitochondrial genome structure of the jaguar (panthera onca).	the jaguar (panthera onca) is the largest felid in the western hemisphere, and the only member of the panthera genus in the new world. the jaguar inhabits most countries within central and south america, and is considered near threatened by the international union for the conservation of nature. this study represents the first sequence of the entire jaguar mitogenome, which was the only panthera mitogenome that had not been sequenced. the jaguar mitogenome is 17,049 bases and possesses the same ...	2016	25010076
[the jaguar panthera onca (carnivora: felidae) in “el cielo” biosphere reserve, tamaulipas, mexico].	information on the ecology of jaguars (panthera onca) in “el cielo” biosphere reserve in tamaulipas, mexico is scant and limited to anecdotic records in a handful of publications. the objectives of our study were to: a) determine population density and structure of jaguars, b) compare their activity patterns with that of pumas (puma concolor), c) ascertain potential prey relative abundance, and d) evaluate local resident’s perception on loss of domestic animals due to jaguar predation. between a ...	2016	29465909
non-invasive pregnancy diagnosis in big cats using the pgfm (13,14-dihydro-15-keto-pgf2α) assay.	non-invasive monitoring of hormones using feces has become a vital tool for reproductive management and reliable pregnancy diagnosis in big cats. previous studies described the pgf2α metabolite (pgfm) as an indicator of pregnancy in various feline species. the present study aimed to standardize pregnancy detection in big cats like the tiger (panthera tigris), jaguar (panthera onca) and lion (panthera leo) using fecal samples. high-performance liquid chromatography (hplc) and liquid chromatograph ...	2015	26633886
feeding interactions in an assemblage of terrestrial carnivores in central mexico.	we evaluated the strategies of resources partitioning among species, dietary overlap and niche breadth in an assemblage of carnivores integrated by top predators (puma concolor and panthera onca) and mesopredators(leoparduspardalis,leoparduswiedii,puma yagouaroundi,nasuanarica andurocyoncinereoargenteus). the aim of this study was to investigate the mechanisms explaining the coexistence among species at a temperate zone in central mexico.	2015	31966103
population genetics of jaguars (panthera onca) in the brazilian pantanal: molecular evidence for demographic connectivity on a regional scale.	habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. for these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. the pantanal is among the best examples of a region with a large jaguar population in a healthy environment. here, we analyz ...	2015	26245785
jaguar attack on a child: case report and literature review.	jaguar attacks on humans rarely occur in the wild. when they do, they are often fatal. we describe a jaguar attack on a three-year-old girl near her home deep in a remote area of the guyanese jungle. the patient had a complex but, relatively, rapid transport to a medical treatment facility for her life-threatening injuries. the child, who suffered typical jaguar-inflicted injury patterns and survived, is highlighted. we review jaguar anatomy, environmental status, hunting and killing behaviors, ...	2015	25834674
quality vs. quantity: assessing the visibility of the jaguars housed at chester zoo, uk.	to fulfill an educational or visitor-related role in the zoo's collection, a species needs to be visible to the visiting public. however, this may not always be achievable for animals housed in naturalistic enclosures, particularly species which are highly camouflaged and have an elusive nature, such as jaguars. four jaguars housed at chester zoo (uk) were studied to assess the quality of visibility from the public viewing area and to provide recommendations for assessing visibility to evaluate ...	2015	25652718
[population estimates and conservation of felids (carnivora: felidae) in northern quintana roo, mexico].	wildlife density estimates provide an idea of the current state of populations, and in some cases, reflect the conservation status of ecosystems, essential aspects for effective management actions. in mexico, several regions have been identified as high priority areas for the conservation of species that have some level of risk, like the yucatan peninsula (yp), where the country has the largest population of jaguars. however, little is known about the current status of threatened and endangered ...	2015	26666134
ocelot population status in protected brazilian atlantic forest.	forest fragmentation and habitat loss are detrimental to top carnivores, such as jaguars (panthera onca) and pumas (puma concolor), but effects on mesocarnivores, such as ocelots (leopardus pardalis), are less clear. ocelots need native forests, but also might benefit from the local extirpation of larger cats such as pumas and jaguars through mesopredator release. we used a standardized camera trap protocol to assess ocelot populations in six protected areas of the atlantic forest in southeaster ...	2015	26560347
pathology in practice. concurrent metastatic mammary adenocarcinoma and ovarian cystadenocarcinoma in a jaguar.		2015	26517614
serosurvey of smooth brucella, leptospira spp. and toxoplasma gondii in free-ranging jaguars (panthera onca) and domestic animals from brazil.	this study investigated the exposure of jaguar populations and domestic animals to smooth brucella, leptospira spp. and toxoplasma gondii in the cerrado, pantanal and amazon biomes of brazil. between february 2000 and january 2010, serum samples from 31 jaguars (panthera onca), 1,245 cattle (bos taurus), 168 domestic dogs (canis lupus familiaris) and 29 domestic cats (felis catus) were collected and analysed by rose bengal test for smooth brucella, microscopic agglutination test for leptospira s ...	2015	26605787
detection of leptospira spp. and brucella abortus antibodies in free-living jaguars (panthera onca) in two protected areas of northern pantanal, brazil.	this study aimed to assess the exposure of free-living jaguars (panthera onca) to leptospira spp. and brucella abortus in two conservation units in the pantanal of mato grosso, brazil. the presence of antibodies in blood samples of eleven jaguars was investigated using autochthonous antigens isolated in brazil added to reference antigen collection applied to diagnosis of leptospirosis by microscopic agglutination test (mat). the rose bengal test was applied for b. abortus antibodies. two (18.2%) ...	2015	25923900
partially resistant cucurbita pepo showed late onset of the zucchini yellow mosaic virus infection due to rapid activation of defense mechanisms as compared to susceptible cultivar.	zucchini yellow mosaic virus (zymv) is an emerging viral pathogen in cucurbit-growing areas wordwide. infection causes significant yield losses in several species of the family cucurbitaceae. to identify proteins potentially involved with resistance toward infection by the severe zymv-h isolate, two cucurbita pepo cultivars (zelena susceptible and jaguar partially resistant) were analyzed using a two-dimensional gel electrophoresis-based proteomic approach. initial symptoms on leaves (clearing v ...	2015	25972878
are private reserves effective for jaguar conservation?	we present the first study of density and apparent survival for a jaguar (panthera onca) population in northern mexico using 13 years of camera trap data from 2000 to 2012. we used the barker robust design model which combines data from closed sampling periods and resight data between these periods to estimate apparent survival and abundance. we identified 467 jaguar pictures that corresponded to 48 jaguar individuals. we included camera type and field technician as covariates for detection prob ...	2015	26398115
water use efficiency and productivity of habanero pepper (capsicum chinense jacq.) based on two transplanting dates.	habanero pepper production was assessed with drip irrigation and plastic mulch, based on two transplanting dates. the objectives of the study were: (i) to evaluate the effect of two transplanting dates and the use of plastic mulch on water productivity and habanero pepper fruit yield under drip irrigation conditions; and (ii) to determine the profitability and economic viability of the product in the regional market. the work was conducted in the municipality of huimanguillo, state of tabasco, m ...	2015	25812098
impact of jaguar panthera onca (carnivora: felidae) predation on marine turtle populations in tortuguero, caribbean coast of costa rica.	little is known about the effects of jaguars on the population of marine turtles nesting in tortuguero national park, costa rica. this study assessed jaguar predation impact on three species of marine turtles (chelonia mydas, dermochelys coriacea and eretmochelys imbricata) that nest in tortuguero beach. jaguar predation data was obtained by using two methodologies, literature review (historical records prior the year 2005) and weekly surveys along the 29 km stretch of beach during the period 20 ...	2015	26666135
ecological relationships of meso-scale distribution in 25 neotropical vertebrate species.	vertebrates are a vital ecological component of amazon forest biodiversity. although vertebrates are a functionally important part of various ecosystem services they continue to be threatened by anthropogenic impacts throughout the amazon. here we use a standardized, regularly spaced arrangement of camera traps within 25km2 to provide a baseline assessment of vertebrate species diversity in a sustainable use protected area in the eastern brazilian amazon. we examined seasonal differences in the ...	2015	25938582
cultural significance of wild mammals in mayan and mestizo communities of the lacandon rainforest, chiapas, mexico.	several ethnobiology studies evaluate the cultural significance (cs) of plants and mushrooms. however, this is not the case for mammals. it is important to make studies of cs allowing the comparison of cultural groups because the value given to groups of organisms may be based on different criteria. such information would be valuable for wildlife preservation plans. in this study, the most culturally significant species of mammals from the lacandon rainforest (chiapas, mexico) for people from tw ...	2015	25947968
jaguar (panthera onca linnaeus, 1758) roadkill in brazilian atlantic forest and implications for species conservation.	we report the roadkill of a jaguar in one of the longest highways in brazil (br-101), in the stretch where this road crosses one of the most important atlantic forest remnants in the country: the linhares-sooretama block. the jaguar population present in this area represents the very last in entire espírito santo state. there is an approved project to the lines duplication of the entire br-101 highway and the company responsible by the work has already started the first activities in the state. ...	2015	26421765
evaluating landscape connectivity for puma concolor and panthera onca among atlantic forest protected areas.	strictly protected areas and riparian forests in brazil are rarely large enough or connected enough to maintain viable populations of carnivores and animal movement over time, but these characteristics are fundamental for species conservation as they prevent the extinction of isolated animal populations. therefore, the need to maintain connectivity for these species in human-dominated atlantic landscapes is critical. in this study, we evaluated the landscape connectivity for large carnivores (co ...	2015	25860593
late pleistocene carnivores (carnivora: mammalia) from a cave sedimentary deposit in northern brazil.	the brazilian quaternary terrestrial carnivora are represented by the following families: canidae, felidae, ursidae, procyonidae mephitidae and mustelidae. their recent evolutionary history in south america is associated with the uplift of the panamanian isthmus, and which enabled the great american biotic interchange (gabi). here we present new fossil records of carnivora found in a cave in aurora do tocantins, tocantins, northern brazil. a stratigraphical controlled collection in the sedimenta ...	2014	25590705
late pleistocene carnivores (carnivora: mammalia) from a cave sedimentary deposit in northern brazil.	the brazilian quaternary terrestrial carnivora are represented by the following families: canidae, felidae, ursidae, procyonidae mephitidae and mustelidae. their recent evolutionary history in south america is associated with the uplift of the panamanian isthmus, and which enabled the great american biotic interchange (gabi). here we present new fossil records of carnivora found in a cave in aurora do tocantins, tocantins, northern brazil. a stratigraphical controlled collection in the sedimenta ...	2014	25424041
habitat features influencing jaguar panthera onca (carnivora: felidae) occupancy in tortuguero national park, costa rica.	habitat characteristics and human activities are known to play a major role in the occupancy of jaguars panthera onca across their range, however the key variables influencing jaguar distribution in tortuguero national park, costa rica, have yet to be identified. this study evaluated jaguar occupancy in tortuguero national park and the surrounding area. jaguar detection/non-detection data was collected using digital camera traps distributed within the boundaries of the protected area. local comm ...	2014	25720179
resistance to antibiotics of clinical relevance in the fecal microbiota of mexican wildlife.	there are a growing number of reports of antibiotic resistance (atbr) in bacteria living in wildlife. this is a cause for concern as atbr in wildlife represents a potential public health threat. however, little is known about the factors that might determine the presence, abundance and dispersion of atbr bacteria in wildlife. here, we used culture and molecular methods to assess atbr in bacteria in fecal samples from howler monkeys (alouatta palliata), spider monkeys (ateles geoffroyi), tapirs ( ...	2014	25233089
do attacks by jaguars panthera onca and pumas puma concolor (carnivora: felidae) on livestock correlate with species richness and relative abundance of wild prey?	abstract: attacks by big cats on livestock are one of the major causes of human-felid conflicts and, therefore, an important factor in the conservation of these species. it has been argued that a reduction in natural prey abundance promotes attacks on domestic species, but few studies have tested this statement, and some have delivered contradictory results. we investigated whether the occurrence of attacks to livestock by jaguar and puma relates to the abundance and richness of their natural pr ...	2014	25720180
similarities between salmonella enteritidis isolated from humans and captive wild animals in south africa.	salmonella is well recognized as an aetiological agent of gastrointestinal and diarrhoeal disease. salmonella enterica serotype enteritidis (salmonella enteritidis) is one of the commonest serotypes associated with foodborne illness. in south africa, we compared salmonella enteritidis strains isolated from humans with gastroenteritis and strains isolated from captive wild animals, between june 2011 and july 2012.	2014	25500660
using detection dogs and genetic analyses of scat to expand knowledge and assist felid conservation in misiones, argentina.	many carnivores require large ranges to meet their ecological and energetic needs; however, anthropogenic changes threaten species and their habitats. camera traps have been used to effectively collect data on carnivores in a variety of habitat types; however, a single survey effort is typically limited to species that have similar body size, habitat use and movement patterns, and individual identification of animals is not always possible. we evaluated whether scat detection dogs could effectiv ...	2014	25236691
noninvasive individual and species identification of jaguars (panthera onca), pumas (puma concolor) and ocelots (leopardus pardalis) in belize, central america using cross-species microsatellites and faecal dna.	there is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. this is especially important for molecular scatology studies occurring in challenging tropical environments where dna degrades quickly and the quality of faecal samples varies greatly. we optimized 14 polymorphic microsatellite loci for jaguars (panthera onca), pumas (puma concolor) and ocelots (leopardus pardalis) and assessed their utility for ...	2014	24751217
sperm preservation by freeze-drying for the conservation of wild animals.	sperm preservation is a useful technique for the maintenance of biological resources in experimental and domestic animals, and in wild animals. a new preservation method has been developed that enables sperm to be stored for a long time in a refrigerator at 4 °c. sperm are freeze-dried in a solution containing 10 mm tris and 1 mm edta. using this method, liquid nitrogen is not required for the storage and transportation of sperm. we demonstrate that chimpanzee, giraffe, jaguar, weasel and the lo ...	2014	25409172
evaluating the performance of parallel subsurface simulators: an illustrative example with pflotran.	[1] to better inform the subsurface scientist on the expected performance of parallel simulators, this work investigates performance of the reactive multiphase flow and multicomponent biogeochemical transport code pflotran as it is applied to several realistic modeling scenarios run on the jaguar supercomputer. after a brief introduction to the code's parallel layout and code design, pflotran's parallel performance (measured through strong and weak scalability analyses) is evaluated in the conte ...	2014	25506097
[choledocholithiasis and pregnancy. hybrid laparo-endoscopic treatment in one step].	complications associated with choledocholithiasis are uncommon during pregnancy. however, when it occurs, the morbidity and mortality related for the product and the mother increases, so a proper treatment is imperative in these patients.	2014	25312319
the potential connectivity of waterhole networks and the effectiveness of a protected area under various drought scenarios.	landscape connectivity is considered a priority for ecosystem conservation because it may mitigate the synergistic effects of climate change and habitat loss. climate change predictions suggest changes in precipitation regimes, which will affect the availability of water resources, with potential consequences for landscape connectivity. the greater calakmul region of the yucatan peninsula (mexico) has experienced a 16% decrease in precipitation over the last 50 years, which we hypothesise has af ...	2014	24830392
[environmental safety assessment on the new super absorbent polymers applied into a soil-chinese cabbage system].	super absorbent polymers (saps), a new water retention material, have a potential for application in water-saving agricultural production. in this study, we investigated the effects of saps, synthesized from natural plant extracts, on chinese cabbage fresh weight, soil water content, soil water stable aggregates, soil microbial biomass (carbon) and soil microbial respiration under three water conditions (excessive, normal and deficient) and two saps application strategies (bulk treatment and spr ...	2014	24812978
accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer.	in this paper we give the current state of high-throughput virtual screening. we describe a case study of using a task-parallel mpi (message passing interface) version of autodock4 [1], [2] to run a virtual high-throughput screen of one-million compounds on the jaguar cray xk6 supercomputer at oak ridge national laboratory. we include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. a detailed tutorial, scripts, and source ...	2014	24729746
first report of fluazuron resistance in rhipicephalus microplus: a field tick population resistant to six classes of acaricides.	the control of the cattle tick rhipicephalus microplus is based mainly on the use of chemical acaricides, which has contributed to the emerging problem of selection of resistant tick populations. currently, there are six main classes of acaricides commercially available in brazil to control cattle ticks, with fluazuron, a tick growth regulator with acaricidal properties, being the only active ingredient with no previous reports of resistance. ticks (designated the jaguar strain) were collected i ...	2014	24560364
cutaneous adenocarcinoma of sebaceous gland in a captive male jaguar (<i>panthera onca</i>): a case report.	high incidence of neoplasia in captive jaguar (panthera onca) has been recorded but there have been no reports of cutaneous adenocarcinoma of the sebaceous gland. a high incidence of neoplasia has been detected in captive jaguars, possibly associated with longevity and husbandry practices in captivity. neoplasm is a major cause of mortality in jaguar. tumours of sebaceous gland are common in older domestic felids. a case of cutaneous adenocarcinoma of the sebaceous gland was diagnosed in a male ...	2014	28235310
effects of natural environmental conditions on faecal glucocorticoid metabolite concentrations in jaguars (panthera onca) in belize.	in situ studies that rely on non-invasive faecal hormone monitoring are subject to problems due to potential changes in hormone concentrations in samples exposed to field conditions. in this study, we conducted an environmental validation for measurement of faecal glucocorticoid metabolites (fgms) in jaguars (panthera onca). we collected fresh faeces (e.g. no older than 8 h) from jaguars (six males and four females), housed at the belize zoo, and exposed them randomly to two environmental condit ...	2014	27293660
first report of cabbage head rot caused by fusarium avenaceum in poland.	cabbage (brassica oleracea l. var. capitata l.) is an important crop in poland. symptoms of a disease affecting cabbage were observed in 2012 and 2013 both in mid-august during the growing season and during storage in january and february. the disease affected about 30 to 40% of crops grown on ~9,000 ha over three locations: charsznica in south poland and bedlno and skierniewice in central poland. circular, watery lesions ranging from 10 to 60 mm in diameter on the surface of affected cabbage he ...	2014	30703911
localization and mobility of synaptic vesicles in myosin vi mutants of drosophila.	at the drosophila neuromuscular junction (nmj), synaptic vesicles are mobile; however, the mechanisms that regulate vesicle traffic at the nerve terminal are not fully understood. myosin vi has been shown to be important for proper synaptic physiology and morphology at the nmj, likely by functioning as a vesicle tether. here we investigate vesicle dynamics in myosin vi mutants of drosophila.	2014	25062032
jaguar: junction alignments to genome for rna-seq reads.	jaguar is an alignment protocol for rna-seq reads that uses an extended reference to increase alignment sensitivity. it uses bwa to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of a single read spanning multiple exons. reads aligned to the transcript models are then re-mapped on to genomic coordinates, transforming alignments that span multiple exons into large-gapped alignments on the genome. while ...	2014	25062255
yasuní--a hotspot for jaguars panthera onca (carnivora: felidae)? camera-traps and jaguar activity at tiputini biodiversity station, ecuador.	jaguars (panthera onca) are the largest predator in lowland forests of amazonia but there have been few studies on their occurrence and activity in such forests. here, we used camera traps to document the occurrence and activity of jaguars within a local area (-650ha) of lowland forest of eastern ecuador, over two sample periods (2005-2008, 7 222 trap days; 2010-2012, 6 199 trap days). we accumulated 151 independent photos of jaguars (189 total photographs) that represented 21 different individu ...	2014	25102650
the nature of fatty acid interaction with a polyelectrolyte-surfactant pair revealed by nmr spectroscopy.	the interaction mechanisms of an oppositely charged polyelectrolyte-surfactant pair and dodecanoic (lauric) acid (la) were experimentally investigated using a combination of nuclear magnetic resonance (nmr) techniques. it is observed that la significantly affects the interaction between the anionic surfactant sodium dodecylethersulfate (sdes) and the cationic polymer guar modified with grafted hydroxypropyl trimethylammonium chloride (jaguar c13 bf). typically, oppositely charged polymers and su ...	2014	25109504
identification of areas in brazil that optimize conservation of forest carbon, jaguars, and biodiversity.	a major question in global environmental policy is whether schemes to reduce carbon pollution through forest management, such as reducing emissions from deforestation and degradation (redd+), can also benefit biodiversity conservation in tropical countries. we identified municipalities in brazil that are priorities for reducing rates of deforestation and thus preserving carbon stocks that are also conservation targets for the endangered jaguar (panthera onca) and biodiversity in general. prelimi ...	2014	24372997
in vitro analysis suggests that difference in cell movement during direct interaction can generate various pigment patterns in vivo.	pigment patterns of organisms have invoked strong interest from not only biologists but also, scientists in many other fields. zebrafish is a useful model animal for studying the mechanism of pigment pattern formation. the zebrafish stripe pattern is primarily two types of pigment cells: melanophores and xanthophores. previous studies have reported that interactions among these pigment cells are important for pattern formation. in the recent report, we found that the direct contact by xanthophor ...	2014	24449859
potential improvements for dual directional view displays.	dual directional view (ddv) displays show different images to different viewers. for example, the driver of a car looking at a central ddv display could view navigation information, while the passenger, looking from a different angle, could be watching a movie. this technology, which has now established itself on the dashboards of high-end jaguar, mercedes, and range rover cars, is manufactured by sharp corporation using a well-known parallax barrier technique. unfortunately parallax barriers ar ...	2014	24514196
prediction of hydration free energies for the sampl4 diverse set of compounds using molecular dynamics simulations with the opls-aa force field.	all-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of small molecules as part of the sampl4 challenge. compounds were parametrized on the basis of the opls-aa force field using three different protocols for deriving partial charges: (1) using existing opls-aa atom types and charges with minor adjustments of partial charges on equivalent connecting atoms and derivation of new parameters for a number of distinct chemical groups (n-a ...	2014	24557853
'mystery big cats' in the peruvian amazon: morphometrics solve a cryptozoological mystery.	two big cat skulls procured from hunters of yanachaga national park, peru, were reported as those of cats informally dubbed the 'striped tiger' and 'anomalous jaguar'. observations suggested that both skulls were distinct from those of jaguars, associated descriptions of integument did not conform to this species, and it has been implied that both represent members of one or two novel species. we sought to resolve the identity of the skulls using morphometrics. dna could not be retrieved since b ...	2014	24688867
identification of priority conservation areas and potential corridors for jaguars in the caatinga biome, brazil.	the jaguar, panthera onca, is a top predator with the extant population found within the brazilian caatinga biome now known to be on the brink of extinction. designing new conservation units and potential corridors are therefore crucial for the long-term survival of the species within the caatinga biome. thus, our aims were: 1) to recognize suitable areas for jaguar occurrence, 2) to delineate areas for jaguar conservation (pjcus), 3) to design corridors among priority areas, and 4) to prioritiz ...	2014	24709817
cutaneous adenocarcinoma of sebaceous gland in a captive male jaguar panthera onca: a case report.	high incidence of neoplasia in captive jaguar (panthera onca) has been recorded but there have been no reports of cutaneous adenocarcinoma of the sebaceous gland. a high incidence of neoplasia has been detected in captive jaguars, possibly associated with longevity and husbandry practices in captivity. neoplasm is a major cause of mortality in jaguar. tumours of sebaceous gland are common in older domestic felids. a case of cutaneous adenocarcinoma of the sebaceous gland was diagnosed in a male ...	2014	24831350
evaluation of four raw meat diets using domestic cats, captive exotic felids, and cecectomized roosters.	our objective was to evaluate raw meat diets for captive exotic and domestic carnivores containing traditional and alternative raw meat sources, specifically, beef trimmings, bison trimmings, elk muscle meat, and horse trimmings. we aimed to examine diet composition and protein quality; apparent total tract energy and macronutrient digestibility in domestic cats, african wildcats, jaguars, and malayan tigers; and me and fecal fermentative end-products in domestic cats. because of variation in th ...	2013	23048161
peritoneal mesothelioma in a jaguar (panthera onca).	a 21-yr-old female jaguar (panthera onca) died in a zoo in teresina, piaui, brazil, following a history of abdominal distension, ascites, anorexia, and dyspnea. at necropsy, a dark red, watery, blood-tinged serous fluid was present in the abdominal cavity. the peritoneum was thick with firm, yellow, villous projections. histologically, the tumors were composed of a biphasic population of cells, which reacted to anti-cytokeratin and anti-vimentin antibodies, consistent with a biphasic benign meso ...	2013	24063103
morphology of the lingual papillae in the jaguar.	we examined the dorsal lingual surfaces of an adult jaguar (panthera onca) by scanning electron microscopy. the tongue of the jaguar was about 17 cm long, and the center of the lingual apex became hollow. there were 7 vallate papillae in total. the filiform papilla on the lingual apex consisted of a larger main papilla and some secondary papillae. the connective tissue core of the filiform papilla was mountain-like in shape. the connective tissue core of the fungiform papilla was mushroom-like i ...	2013	23614980
nanog is an essential factor for induction of pluripotency in somatic cells from endangered felids.	nanog has an important role in pluripotency induction in bovines and snow leopards. to examine whether it was required for wild felids globally, we examined the induction of pluripotency in felids from asia (bengal tiger, panthera tigris), africa (serval, leptailurus serval), and the americas (jaguar, panthera onca). dermal fibroblasts were transduced with genes encoding the human transcription factors oct4, sox2, klf4, and cmyc with or without nanog. both four- and five-factor induction resulte ...	2013	23514873
serosurvey for selected viral infections in free-ranging jaguars (panthera onca) and domestic carnivores in brazilian cerrado, pantanal, and amazon.	we investigated the exposure of jaguar (panthera onca) populations and domestic carnivores to selected viral infections in the cerrado, amazon, and pantanal biomes of brazil. between february 2000 and january 2010, we collected serum samples from 31 jaguars, 174 dogs (canis lupus familiaris), and 35 domestic cats (felis catus). serologic analyses for antibodies to rabies virus, canine distemper virus (cdv), feline immunodeficiency virus (fiv), and for feline leukemia virus (felv) antigen were co ...	2013	23778599
novel ehrlichia and hepatozoon agents infecting the crab-eating fox (cerdocyon thous) in southeastern brazil.	this study evaluated infection by vector-borne agents in 58 crab-eating fox (cerdocyon thous l.) that were road-killed in an atlantic rainforest reserve in the state of espírito santo, southeastern brazil. spleen, lung, or blood samples collected from the foxes were tested in the laboratory by a battery of polymerase chain reaction (pcr) assays targeting bacteria of the genera rickettsia, borrelia, coxiella, anaplasma, and ehrlichia; and protozoa of the genera babesia, hepatozoon, and leishmania ...	2013	23802461
cross transmission of gastrointestinal nematodes between captive neotropical felids and feral cats.	pathogen cross transmission between wildlife and domestic animals represents an extinction risk for wildlife; however, reliable verification is difficult to perform, and in some cases, it is even considered unlikely to be conducted. the aim of this work was to identify cross transmission of helminths between feral cats and captive wild felids at a zoological park in southeastern mexico. feces were collected from jaguars (panthera onca), cougars (puma concolor), ocelots (leopardus pardalis), marg ...	2013	24450052
influence of dietary fiber type and amount on energy and nutrient digestibility, fecal characteristics, and fecal fermentative end-product concentrations in captive exotic felids fed a raw beef-based diet.	little nutritional or metabolic information has been collected from captive exotic cats fed raw diets. in particular, fiber types and concentrations for use in raw meat-based diets for captive exotic felids have not been well studied. our objective was to evaluate the effects of fiber type and concentration on apparent total tract energy and macronutrient digestibility, fecal characteristics, and fecal fermentative end-products in captive exotic felids. four animals of each captive exotic specie ...	2013	23463568
seroprevalence of toxoplasma gondii infection in captive mammals in three zoos in mexico city, mexico.	antibodies to toxoplasma gondii were determined in 167 mammals in three zoos in mexico city, mexico, using the modified agglutination test (mat). overall, antibodies to t. gondii were found in 89 (53.3%) of the 167 animals tested. antibodies were found in 35 of 43 wild felidae: 2 of 2 bobcats (lynx rufus); 4 of 4 cougars (puma concolor); 10 of 13 jaguars (panthera onca); 5 of 5 leopards (panthera pardus); 7 of 7 lions (panthera leo); 2 of 3 tigers (panthera tigris); 2 of 3 ocelots (leopardus par ...	2013	24063119
anatomical study of the forearm and hand nerves of the domestic cat ( felis catus), puma ( puma concolor) and jaguar ( panthera onca).	the innervation of the forearm and hand regions of cats has not been well described despite its importance for any surgery or any neurological disorder. it is probably the main area where disorders of peripheral nerves in this species are observed. in felines, the forelimbs facilitate the jump and represent the most important way for capturing prey. the main muscles and nerves involved in this activity are located in the region of the forearm and hand. the aim of the present study was to provide ...	2013	22783947
picobirnavirus in captive animals from uruguay: identification of new hosts.	the picobirnaviruses (pbvs) have been detected in several species of animals from different countries worldwide, including in south america. the host range of these viruses has increased in recent years; thus, in order to contribute to the knowledge in this topic we analyzed samples from captivity animals from uruguay. we found the presence of pbvs in four species of animals, panthera leo, panthera onca, puma concolor and oncifelis geoffroyi, representing new pbv-susceptible hosts. all strains b ...	2013	22759924
atlantic rainforest's jaguars in decline.		2013	24264975
a new machairodont from the palmetto fauna (early pliocene) of florida, with comments on the origin of the smilodontini (mammalia, carnivora, felidae).	south-central florida's latest hemphillian palmetto fauna includes two machairodontine felids, the lion-sized machairodus coloradensis and a smaller, jaguar-sized species, initially referred to megantereon hesperus based on a single, relatively incomplete mandible. this made the latter the oldest record of megantereon, suggesting a new world origin of the genus. subsequent workers variously accepted or rejected this identification and biogeographic scenario. fortunately, new material, which pres ...	2013	23516394
high proportion of male faeces in jaguar populations.	faeces provide relevant biological information which includes, with the application of genetic techniques, the sex and identity of individuals that defecated, thus providing potentially useful data on the behaviour and ecology of individuals, as well as the dynamics and structure of populations. this paper presents estimates of the sex ratio of different felid species (jaguar, panthera onca; puma, puma concolor; and ocelot/margay, leopardus pardalis/leopardus wiedi) as observed in field collecte ...	2012	23285226
[mammals of zoque forest, mexico: richness, use and conservation].	zoque forest is one of the richest and threatened regions in southeastern mexico, and for which few studies on mammal biology and use are available. here we analyzed the conservation status of mammalian species according to mexican and international laws, with an updated checklist of mammals in this forest, and some information on their use by some rural communities. basic information was obtained from national and international collections and publications. a total of 42 fieldtrips, that follow ...	2012	23894946
the making of a monster: postnatal ontogenetic changes in craniomandibular shape in the great sabercat smilodon.	derived sabercats had craniomandibular morphologies that in many respects were highly different from those of extant felids, and this has often been interpreted functionally as adaptations for predation at extreme gape angles with hypertrophied upper canines. it is unknown how much of this was a result of intraspecific postnatal ontogeny, since juveniles of sabercats are rare and no quantitative study has been made of craniomandibular ontogeny. postnatal ontogenetic craniomandibular shape change ...	2012	22235326
investigation of super learner methodology on hiv-1 small sample: application on jaguar trial data.	background. many statistical models have been tested to predict phenotypic or virological response from genotypic data. a statistical framework called super learner has been introduced either to compare different methods/learners (discrete super learner) or to combine them in a super learner prediction method. methods. the jaguar trial is used to apply the super learner framework. the jaguar study is an "add-on" trial comparing the efficacy of adding didanosine to an on-going failing regimen. ou ...	2012	22550568
abc transporters as a multidrug detoxification mechanism in rhipicephalus (boophilus) microplus.	atp-binding cassette (abc) transporters are responsible for pumping drugs across membranes and are an important drug detoxification mechanism. since abc transporters act on a wide spectrum of chemical compounds, they have been associated with multidrug resistance phenotype in various parasites and cancer cells. here, we document the presence of a rhipicephalus (boophilus) microplus tick population (jaguar) resistant to four acaricide classes (organophosphates (op), synthetic pyrethroids (sp), am ...	2012	22926678
assessment of effectiveness of endovascular treatment of common and external iliac artery stenosis/occlusion using self-expanding jaguar sm stents.	the goal of this work was to assess the effectiveness of endovascular treatment of common and external iliac artery stenosis/occlusion classified according to tasc using a self-expanding stent jaguar sm. the study group included 95 patients (61 men and 34 women) who underwent treatment for stenosis or occlusion of lower limb arteries at the department of radiology of the university hospital in bialystok and the diagnostic radiology department of the central clinical hospital of the ministry of i ...	2012	23269933
hematology and serum chemistry of free-ranging jaguars (panthera onca).	we collected and analyzed blood samples from 12 free-ranging jaguars (panthera onca). clinical examinations, hematology, and serum chemistry indicate the jaguars were in good overall health. results may help as values for free-ranging jaguars under the same handling conditions.	2012	23060521
[potential distribution of jaguar, panthera onca (carnivora: felidae) in guerrero, mexico: persistence of areas for its conservation].	studies about the permanence of natural protected areas are important, because they contribute to the promotion of the conservation target and to optimize economical and human resources of specific areas. although there are no natural protected areas in guerrero, it has suitable habitat for the jaguar, a common species used for planning and management of conservation areas. since, there is actual evidence that environmental and anthropogenic variables may modify vertebrate species distribution w ...	2012	23025104
a home on the range: after years of legal wrangling, the u.s. government says it will designate critical habitat for the jaguar.		2012	22779259
bite force estimation and the fiber architecture of felid masticatory muscles.	increasingly, analyses of craniodental dietary adaptations take into account mechanical properties of foods. however, masticatory muscle fiber architecture has been described for relatively few lineages, even though an understanding of the scaling of this anatomy can yield important information about adaptations for stretch and strength in the masticatory system. data on the mandibular adductors of 28 specimens from nine species of felids representing nearly the entire body size range of the fam ...	2012	22707481
pigment pattern formation by contact-dependent depolarization.	although recent experimental studies have suggested that the interactions among the pigment cells play a key role in the skin pattern formation, details of the mechanism remain largely unknown. by using an in vitro cell culture system, we have detected interactions between the two pigment cell types, melanophores and xanthophores, in the zebrafish skin. during primary culture, the melanophore membrane transiently depolarizes when contacted with the dendrites of a xanthophore. this depolarization ...	2012	22323812
prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the opls-aa force field.	all-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the sampl3 challenge. all compounds were parameterized within the framework of the opls-aa force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermodynamic integration. three different approaches to deriving partial charge parameters were pursued: (1) u ...	2012	22187140
effect of cationic polymers on foam rheological properties.	we study the effect of two cationic polymers, with trade names jaguar c13s and merquat 100, on the rheological properties of foams stabilized with a mixture of anionic and zwitterionic surfactants (sodium lauryloxyethylene sulfate and cocoamidopropyl betaine). a series of five cosurfactants are used to compare the effect of these polymers on foaming systems with high and low surface dilatational moduli. the experiments revealed that the addition of jaguar to the foaming solutions leads to (1) a ...	2012	22168570
noninvasive monitoring of adrenocortical function in captive jaguars (panthera onca).	jaguars are threatened with extinction throughout their range. a sustainable captive population can serve as a hedge against extinction, but only if they are healthy and reproduce. understanding how jaguars respond to stressors may help improve the captive environment and enhance their wellbeing. thus, our objectives were to: (1) conduct an adrenocorticotrophic hormone (acth) challenge to validate a cortisol radioimmunoassay (ria) for noninvasive monitoring of adrenocortical function in jaguars; ...	2012	21953790
standard gibbs free energies of reactions of ozone with free radicals in aqueous solution: quantum-chemical calculations.	free radicals are common intermediates in the chemistry of ozone in aqueous solution. their reactions with ozone have been probed by calculating the standard gibbs free energies of such reactions using density functional theory (jaguar 7.6 program). o(2) reacts fast and irreversibly only with simple carbon-centered radicals. in contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-cente ...	2011	21910507
stochastic simulation of uranium migration at the hanford 300 area.	this work focuses on the quantification of groundwater flow and subsequent u(vi) transport uncertainty due to heterogeneity in the sediment permeability at the hanford 300 area. u(vi) migration at the site is simulated with multiple realizations of stochastically-generated high resolution permeability fields and comparisons are made of cumulative water and u(vi) flux to the columbia river. the massively parallel reactive flow and transport code pflotran is employed utilizing 40,960 processor cor ...	2011	20510479
reproduction of soybean cyst nematode on dry bean cultivars over multiple generations.	phaseolus vulgaris is a host of soybean cyst nematode (scn; heterodera glycines), a pathogen recently introduced into the major dry bean production area of north dakota and northern minnesota. the nematode reproduces less on most bean classes compared with soybean but can reduce plant growth and seed yield. an important question is the following: will scn adapt to dry bean and, over time, increase in ability to reproduce on roots? to answer this question, the following experiments were conducted ...	2011	30731694
deux chevaux, jaguar--or ford.		2011	3113564
attacks by jaguars (panthera onca) on humans in central brazil: report of three cases, with observation of a death.	conflicts between humans and big cats have been known for centuries throughout the world, but have intensified in recent decades. recently, attacks by panthera onca on humans in brazil have been brought to the forefront through exposure in the press and because of the severity of the attacks. we report 3 cases of patients attacked by jaguars in provoked and predatory situations. two patients survived the attacks and one died. attack mechanisms and lesions in victims are discussed. the attacks de ...	2011	21396857
identification of neotropical felid faeces using rcp-pcr.	faeces similarity among sympatric felid species has generally hampered their use in distributional, demographic and dietary studies. here, we present a new and simple approach based on a set of species-specific primers, for the unambiguous identification of faeces from sympatric neotropical felids (i.e. puma, jaguar, jaguarundi and ocelot/ margay). this method, referred to as rapid classificatory protocol-pcr (rcp-pcr), consists of a single-tube multiplex pcr yielding species-specific banding pa ...	2011	21429118