SimpactCyan 1.0 : an open-source simulator for individual-based models in HIV epidemiology with R and Python interfaces

SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework

Additional record of Janetogalathea californiensis (Anomura: Galatheidae) from the central Gulf of California, Mexico, with notes on its distribution

Specimens of galatheids Janetogalathea californiensis (Benedict, 1902) were collected in the northern portion of the Central Gulf of California and represent the third record for this species in the area. Illustrations of the material collected in the Gulf of California are provided and some differences are noted when compared to the description of the paralectotypes. Depth range of the species is discussed and set at 87-786 m. The presence of a wide and deep Oxygen Minimum Zone in the area is believed to limit the dispersion of J. californiensis to the south and to deeper water of the gulf

Characterization of shallow groundwater in Eocene sediments of Panama Canal Watershed using electrical techniques

This work is focused on the detection of seepages caused by the affluent located in a small area of the Panama Canal Basin during the dry season, and to define the subsurface stratigraphy (Eocene sediments) that characterize this area through a geophysical survey. Two electrical resistivity tomography were developed to identify the extent of infiltration and the nature of the clay layers vertically and laterally, these results were corroborated by a drilling operation in the vicinity of electrical tests and based on this information, established a model for a two-dimensional geoelectric profile in order to compare (i) the pseudo-sections of synthetic and measured apparent electrical resistivity, and (ii) the electrical resistivity tomography as a result of the inversions of such pseudo-sections. The results of electrical resistivity tomography obtained in the two profiles revealed the existence of (i) a surface layer moderately resistant (18-85 ohm.m) with a thickness not exceeding 1,8 m, (ii) an area of high electrical conductivity (3,8 to 10,7 ohm.m) with a thickness not exceeding 9.5 m and (iii) a resistant substratum with electrical resistivity values calculated in excess of 30,1 ohm.m and a range depth ranging from 2 to 11,5 m. The drilling operation in the vicinity of the geophysical tests revealed the presence of clay with varying moisture content and density, and thicknesses that corroborate the results of the geophysical evidence. The two-dimensional geoelectrical model of Profile 1 was established according to the results of electrical resistivity tomography as well as the profile and information of the drilling operation. Based on the results of this study, we conclude that the infiltrations generated by the affluent in this part of the Isthmus of Panama are very important, even in periods when precipitation levels are

A CT-based revised description and phylogenetic analysis of the skull of the basal maniraptoran Ornitholestes hermanni Osborn 1903

Ornitholestes hermanni was one of the first small-bodiedtheropods named in the 1900s. It is known from a singlespecimen discovered during the American MuseumExpedition of 1900, at the Jurassic Morrison Formationsite known as Bone Cabin Quarry, in Wyoming. It haslong been a critical taxon in understanding the evolutionof the Coelurosauria, the clade that includestyrannosauroids, living birds, and their commonancestors. The holotype specimen comprises a nearlycomplete skull and most of a postcranial skeleton. Despitethis abundant material, its precise phylogeneticrelationships have been difficult to determine. This is inpart due to the intense mediolateral crushing of the skulland the relatively generalized postcranial anatomy. Herewe present the results of a micro- computed tomographybasedinvestigation of the cranial anatomy and subsequentincorporation of these data into a phylogenetic data matrixdesigned to test coelurosaurian interrelationships. We findrobust evidence across different optimality criteria thatOrnitholestes is the earliest-branching oviraptorosaurianspecies. Using parsimony as an optimality criterion, thisphylogenetic position is supported by 14 unambiguoussynapomorphies, including: a short frontal process of thepostorbital; short, deep, and pendant paroccipitalprocesses; a large mandibular foramen; an anterodorsallyoriented dentary symphysis; a surangular that is longerthan the dentary; short maxillary and dentary tooth rows;and procumbent dentary and premaxillary teeth. UsingBayesian fossilized birth-death models, we find highposterior probabilities (>.99) that Ornitholestes is theearliest-branching oviraptorosaurian species. Weadditionally find strong support in both analyses that thesuperficially bat-like and possibly arborealscansoriopterygids are an early branching lineage withinOviraptorosauria. This new phylogenetic position fills in apersistent ghost lineage in Oviraptorosauria and confirmsthat scansoriopterygids are basally branchingoviraptorosaurians that represent an independent origin ofaerial habits, separate from those of dromaeosaurs andavialans.Fil: Chapelle, Kimberley E.. American Museum of Natural History; Estados UnidosFil: Norell, Mark. American Museum of Natural History; Estados UnidosFil: Ford, David P.. University of the Witwatersrand; SudáfricaFil: Hendrickx, Christophe. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Radermacher, Viktor J.. University of Minnesota; Estados UnidosFil: Balanoff, Amy. University Johns Hopkins; Estados UnidosFil: Zanno, Lindsay E.. North Carolina Museum of Natural Sciences; Estados UnidosFil: Choiniere, Jonah N.. University of the Witwatersrand; Sudáfrica81st Annual Meeting of the Society of Vertebrate PaleontologyMc LeanEstados UnidosSociety of Vertebrate Paleontolog

Identifying factors associated with sedentary time after stroke. Secondary analysis of pooled data from nine primary studies.

<p><b>Background</b>: High levels of sedentary time increases the risk of cardiovascular disease, including recurrent stroke.</p> <p><b>Objective</b>: This study aimed to identify factors associated with high sedentary time in community-dwelling people with stroke.</p> <p><b>Methods</b>: For this data pooling study, authors of published and ongoing trials that collected sedentary time data, using the activPAL monitor, in community-dwelling people with stroke were invited to contribute their raw data. The data was reprocessed, algorithms were created to identify sleep-wake time and determine the percentage of waking hours spent sedentary. We explored demographic and stroke-related factors associated with total sedentary time and time in uninterrupted sedentary bouts using unique, both univariable and multivariable, regression analyses.</p> <p><b>Results</b>: The 274 included participants were from Australia, Canada, and the United Kingdom, and spent, on average, 69% (SD 12.4) of their waking hours sedentary. Of the demographic and stroke-related factors, slower walking speeds were significantly and independently associated with a higher percentage of waking hours spent sedentary (p = 0.001) and uninterrupted sedentary bouts of <i>>30</i> and <i>>60 min</i> (p = 0.001 and p = 0.004, respectively). Regression models explained 11–19% of the variance in total sedentary time and time in prolonged sedentary bouts.</p> <p><b>Conclusion</b>: We found that variability in sedentary time of people with stroke was largely unaccounted for by demographic and stroke-related variables. Behavioral and environmental factors are likely to play an important role in sedentary behavior after stroke. Further work is required to develop and test effective interventions to address sedentary behavior after stroke.</p