Integrating sample similarities into latent class analysis: a tree-structured shrinkage approach

This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicate a priori higher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models with tree-structured shrinkage. The proposed approach enables (1) borrowing of information across leaves, (2) estimating data-driven leaf groups with distinct vectors of class probabilities, and (3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.     

Metacercarial dispersion and intracellular parasitism in a strigeid trematode

Combes C. and Nassi H. 1977. Metacercarial dispersion and intracellular parasitism in a strigeid trematode. International Journal for Parasitology7: 501–503. The life cycle of Apatemon graciliformis Szidat, 1928 (Trematoda, Strigeidae), a parasite of Biorrphalaria glabrata in Guadeloupe, involves a novel mode of transmission, experimentally demonstrated, between the second intermediate host and the definitive host. The furcocercariae penetrate gravid females of the ovoviviparous fish, Poecilia reticulata, and develop into metacercariae in vitelline vesicles of the embryos where they encyst a short time before parturition. The young guppies are born infected with 1–3 metacercariae. It is considered that young infected fish are more prone to predation by the definitive host, thereby increasing the probability of the cycle being completed. Domestic ducks have been experimentally infected with these metacercariae. If cercariae penetrate non-gravid P. reticulata, they enter the oocytes; this represents a phase of intracellular parasitism.     

Studies on the lipid metabolism of the metacercariae of Clinostomum complanatum (Trematoda: Digenea)

Metacercariae of Clinostomum complanatum possess considerable amounts of lipids. Fractionation of the lipids shows triglycerides and phospholipids as the major components whereas cholesterol and free fatty acids are minor components. Furthermore phospholipid fractions by thin layer chromatography reveal lecithin and cephalin as the major polar lipids whereas lysolecithin and lysocephalin are present in small fractions. The specific activity of lipase (E.C. 3.1.1.3) is 150.8 μg free fatty acids liberated/mg protein/h. Epinephrine, testosterone, insulin, sodium fluoride and iodoacetate stimulated, but 2-propanol inhibited, the lipase activity.     

Effects of host endocrine gland removal on the permissive status of laboratory rodents to infection by Schistosoma mansoni

Knopf P. M. and Soliman M. 1980. Effects of host endocrine gland removal on the permissive status of laboratory rodents to infection by Schistosoma mansoni. International Journal for Parasitology, 10: 197–204. The capacity of Schistosoma mansoni to complete its life cycle was compared in CD-1 mice (permissive hosts) and Sprague-Dawley rats (nonpermissive hosts) from which the pituitary gland had been removed prior to infection with cercariae. Except for a modest decrease in egg burden, none of the parameters of worm life cycle assessed were affected in hypophysectomized mice. In contrast, all these parameters were affected in hypophysectomized rats, e.g. onset of adult worm elimination was delayed, worm development improved, oviposition increased and miracidia developed. Effects of removal from rats of the thyroid/parathyroid glands on the parasite life cycle were similar to hypophysectomy; adrenalectomy or gonadectomy were without affect. Differences between thyroidectomized and thymectomized rats are discussed. It is concluded that host hormones contribute to the nonpermissive status of rats to Schistosoma mansoni infections.     

Boophilus microplus: characterization of larval proteases.

Cercariae of Schistosoma mansoni were treated with undecenyl-pseudothiourea. After centrifugation, they agglutinated into a mass. Resuspended in water, they remained immobilized. When injected sub-cutaneously into mice, they produced bisexual infections. The immobilizing drug effect, together with a reduced worm recovery rate, are time and concentration dependent. The cercariae become avirulent (99.8%) only when the flame cell is affected. Immobilizing and “cercaricidal” effects are not necessarily related properties; the latter can be determined only by in vivo tests of infectivity. No protection against reinfection was noticed in mice injected with immobilized cercariae of reduced virulence. The immobilized cercariae produced infections with a 0.7% worm recovery rate by percutaneous exposure, compared to 2.2% by subcutaneous injection. Normal cercariae produced infections with average recovery rates of 11.1% subcutaneously and 45% percutaneously.     

The ecology of chronic wasting disease in wildlife

Prions are misfolded infectious proteins responsible for a group of fatal neurodegenerative diseases termed transmissible spongiform encephalopathy or prion diseases. Chronic Wasting Disease (CWD) is the prion disease with the highest spillover potential, affecting at least seven Cervidae (deer) species. The zoonotic potential of CWD is inconclusive and cannot be ruled out. A risk of infection for other domestic and wildlife species is also plausible. Here, we review the current status of the knowledge with respect to CWD ecology in wildlife. Our current understanding of the geographic distribution of CWD lacks spatial and temporal detail, does not consider the biogeography of infectious diseases, and is largely biased by sampling based on hunters' cooperation and funding available for each region. Limitations of the methods used for data collection suggest that the extent and prevalence of CWD in wildlife is underestimated. If the zoonotic potential of CWD is confirmed in the short term, as suggested by recent results obtained in experimental animal models, there will be limited accurate epidemiological data to inform public health. Research gaps in CWD prion ecology include the need to identify specific biological characteristics of potential CWD reservoir species that better explain susceptibility to spillover, landscape and climate configurations that are suitable for CWD transmission, and the magnitude of sampling bias in our current understanding of CWD distribution and risk. Addressing these research gaps will help anticipate novel areas and species where CWD spillover is expected, which will inform control strategies. From an ecological perspective, control strategies could include assessing restoration of natural predators of CWD reservoirs, ultrasensitive CWD detection in biotic and abiotic reservoirs, and deer density and landscape modification to reduce CWD spread and prevalence.     

Evidence for Zoonotic Potential of Enterocytozoon bieneusi in Its First Molecular Characterization in Captive Mammals at Bangladesh National Zoo

To determine the occurrence and genotypes of Enterocytozoon bieneusi in captive mammals at Bangladesh National Zoo and to assess their zoonotic significance, 200 fecal samples from 32 mammalian species were examined using a nested PCR and sequencing of internal transcribed spacer (ITS) gene. Enterocytozoon bieneusi was detected in 16.5% (33/200) of the samples. Seven different ITS genotypes were identified, including two known genotypes (D and J) and five new ones (BAN4 to BAN8). Genotype D was the most common genotype being observed in 19 isolates. In phylogenetic analysis, four genotypes (D, BAN4, BAN5, and BAN6), detected in 30 isolates (90.9%), belonged to Group 1 having zoonotic potential. The sequence of genotype J found in a Malayan pangolin was clustered in so‐called ruminant‐specific Group 2. The other two genotypes BAN7 and BAN8 were clustered in primate‐specific Group 5. To our knowledge, this is the first report of molecular characterization of E. bieneusi in Bangladesh, particularly in captive‐bred wildlife in this country. The potentially zoonotic genotypes of E. bieneusi are maintained in zoo mammals that may transmit among these animals and to the humans through environmental contamination or contact.     

The phylogenetic range of bacterial and viral pathogens of vertebrates

Many major human pathogens are multihost pathogens, able to infect other vertebrate species. Describing the general patterns of host–pathogen associations across pathogen taxa is therefore important to understand risk factors for human disease emergence. However, there is a lack of comprehensive curated databases for this purpose, with most previous efforts focusing on viruses. Here, we report the largest manually compiled host–pathogen association database, covering 2,595 bacteria and viruses infecting 2,656 vertebrate hosts. We also build a tree for host species using nine mitochondrial genes, giving a quantitative measure of the phylogenetic similarity of hosts. We find that the majority of bacteria and viruses are specialists infecting only a single host species, with bacteria having a significantly higher proportion of specialists compared to viruses. Conversely, multihost viruses have a more restricted host range than multihost bacteria. We perform multiple analyses of factors associated with pathogen richness per host species and the pathogen traits associated with greater host range and zoonotic potential. We show that factors previously identified as important for zoonotic potential in viruses—such as phylogenetic range, research effort, and being vector‐borne—are also predictive in bacteria. We find that the fraction of pathogens shared between two hosts decreases with the phylogenetic distance between them. Our results suggest that host phylogenetic similarity is the primary factor for host‐switching in pathogens.