HAPMAP: a computer program for the linkage analysis of haploids.

The development of technology for the detection of variations in DNA sequence is permitting the rapid mapping of the genomes of many organisms

The association of criminal justice supervision setting with overdose mortality: a longitudinal cohort study.

Background and aimsDespite the high prevalence of substance use among people in the US criminal justice system, little is known about the incidence of overdose mortality by use patterns, drug convictions and supervision setting. We examined the associations between these characteristics and overdose mortality.DesignRetrospective cohort study.Setting and participantsIndividuals sentenced to prison, jail, probation or jail plus probation for a felony conviction in Michigan, USA from 2003 to 2006.MeasurementsUsing the National Death Index, we assessed overdose mortality to December 2012. We calculated overdose mortality rates by pre-sentence opioid use, drug convictions and supervision setting. Multivariable analyses were conducted using competing risks regression with time-varying covariates.FindingsAmong 140 266 individuals followed over a mean of 7.84 years [standard deviation (SD) = 1.52], 14.9% of the 1131 deaths were due to overdose (102.8 per 100 000 person-years). Over the follow-up, more than half of overdose deaths occurred in the community (57.7%), nearly a third (28.8%) on probation and 12.8% on parole. The adjusted risk of overdose death was lower on probation [hazard ratio (HR) = 0.71, 95% confidence interval (CI) = 0.60, 0.85] than in the community without probation or parole (HR = 1.00) but not significantly different on parole (HR = 1.13, 95% CI = 0.87, 1.47). Pre-sentence daily opioid use (HR = 3.54, 95% CI = 3.24, 3.87) was associated with an increased risk. Drug possession (HR = 1.11, 95% CI = 0.93, 1.31) and delivery convictions (HR = 0.92, 95% CI = 0.77, 1.09) were not significantly associated with overdose mortality.ConclusionsBased on the absolute or relative risk, parole, probation and community settings are appropriate settings for enhanced overdose prevention interventions. Ensuring that individuals with pre-sentence opioid use have access to harm reduction and drug treatment services may help to prevent overdose among people involved with the criminal justice system

Modifier loci condition autoimmunity provoked by Aire deficiency

Loss of function mutations in the autoimmune regulator (Aire) gene in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy patients and mutant mice lead to autoimmune manifestations that segregate as a monogenic trait, but with wide variation in the spectrum of organs targeted. To investigate the cause of this variability, the Aire knockout mutation was backcrossed to mice of diverse genetic backgrounds. The background loci strongly influenced the pattern of organs that were targeted (stomach, eye, pancreas, liver, ovary, thyroid, and salivary gland) and the severity of the targeting (particularly strong on the nonobese diabetic background, but very mild on the C57BL/6 background). Autoantibodies mimicked the disease pattern, with oligoclonal reactivity to a few antigens that varied between Aire-deficient strains. Congenic analysis and a whole genome scan showed that autoimmunity to each organ had a distinctive pattern of genetic control and identified several regions that controlled the pattern of targeting, including the major histocompatibility complex and regions of Chr1 and Chr3 previously identified in controlling type 1 diabetes

Brain networks for temporal adaptation, anticipation, and sensory-motor integration in rhythmic human behavior

Human interaction often requires the precise yet flexible interpersonal coordination of rhythmic behavior, as in group music making. The present fMRI study investigates the functional brain networks that may facilitate such behavior by enabling temporal adaptation (error correction), prediction, and the monitoring and integration of information about ‘self’ and the external environment. Participants were required to synchronize finger taps with computer-controlled auditory sequences that were presented either at a globally steady tempo with local adaptations to the participants' tap timing (Virtual Partner task) or with gradual tempo accelerations and decelerations but without adaptation (Tempo Change task). Connectome-based predictive modelling was used to examine patterns of brain functional connectivity related to individual differences in behavioral performance and parameter estimates from the adaptation and anticipation model (ADAM) of sensorimotor synchronization for these two tasks under conditions of varying cognitive load. Results revealed distinct but overlapping brain networks associated with ADAM-derived estimates of temporal adaptation, anticipation, and the integration of self-controlled and externally controlled processes across task conditions. The partial overlap between ADAM networks suggests common hub regions that modulate functional connectivity within and between the brain's resting-state networks and additional sensory-motor regions and subcortical structures in a manner reflecting coordination skill. Such network reconfiguration might facilitate sensorimotor synchronization by enabling shifts in focus on internal and external information, and, in social contexts requiring interpersonal coordination, variations in the degree of simultaneous integration and segregation of these information sources in internal models that support self, other, and joint action planning and prediction

Historic and contemporary use of catfish aquaculture by piscivorous birds in the Mississippi Delta

Piscivorous birds are the primary source of catfish (Ictalurus spp.) depredation at aquaculture facilities in northwestern Mississippi. Of particular concern is the Double-crested Cormorant (Phalacrocorax auritus), which can cost aquaculture producers millions of dollars annually through the depredation of cultured fish. Historical research conducted in the early 2000s estimated cormorant use of aquaculture ponds in the region, but aquaculture area has decreased by more than 70% since those estimates were made. With less aquaculture available, we predicted cormorant densities on aquaculture would be greater today than historically. Applying a similar methodology as in historical studies, we used aerial surveys to collect data on cormorants at night roosts and using catfish aquaculture ponds during 3 consecutive winter seasons, beginning in 2015. Although the mean annual number of cormorants at roosts in the Delta during our study was 64% less than historically, we found no significant change in densities on aquaculture, suggesting that aquaculture area is likely the factor influencing cormorant occurrence in northwestern Mississippi. During contemporary surveys we also measured the abundance of Great Blue Herons (Ardea herodias) and Great Egrets (A. alba) on the aquaculture clusters, and built predictive models of abundance relative to variables associated with forage at and surrounding the clusters. We found abundance of all 3 species was strongly related to the amount of aquaculture area both within and surrounding a cluster, although patterns varied by species. Cormorant abundance was also greater on clusters with proportionately more food fish (≥20 cm in length) than fingerlings (\u3c20 cm) and was positively related to the proximity and size of night roosts. The relationships described here can be used by producers and wildlife managers to predict the abundance of these piscivorous birds at aquaculture facilities and to design efficient management plans to mitigate potential impacts of depredation and disease

Piscivorous Bird Use of Aquaculture and Natural Water Bodies in Mississippi

Double crested cormorants (Phalacrocorax auritus) and great egrets (Ardea alba) have an extensive history of human wildlife conflict with the aquaculture industry of western Mississippi, USA, due to their depredation of cultured catfish (Ictalurus spp.). Although aquaculture is abundant, western Mississippi also contains naturally occurring water bodies that offer alternative forage opportunities to these species. How cormorants or egrets distribute themselves among these 2 foraging options is unknown, but it has been generally assumed each species uses aquaculture disproportionately more because of the high density of available prey. To test this assumption, we surveyed these species on aquaculture and naturally occurring water bodies using aerial surveys from October through April of 2015–2016, 2016–2017, and 2017–2018. We modeled the proportion of each species on aquaculture as a function of year, date, and weather-related variables using quasi binomial generalized linear models. Egrets used aquaculture consistently more than what was proportionally available to them and use was not influenced by any of the variables we measured. Proportional use of aquaculture by cormorants was lowest during October through January but steadily increased through April, indicating a distribution shift toward aquaculture in the months immediately prior to their migration. The highest proportional use of aquaculture by cormorants occurred in 2016, a year when lethal control measures were not allowed against cormorants. Conversely, the least proportion of cormorants on aquaculture was in 2015 when cormorants could be lethally controlled under authority of an Aquaculture Depredation Order. This trend highlights the potential influence of changes in mortality risk, caused by changes in policy regarding lethal take of cormorants, on cormorant distribution between foraging option

Long term changes in aquaculture influence migration, regional abundance, and distribution of an avian species

Agricultural development has been causing changes to the environment and the abundance and distribution of avian species. Agriculture is dynamic with changes in products occurring at large scales over relatively short time periods. The catfish aquaculture industry is one such agriculture industry that has undergone dramatic changes over the last 25 years. The double-crested cormorant (Nannopterum auritum) is a piscivorous bird that has an extensive history with the aquaculture industry of Mississippi due to its depredation of cultured catfish. A large-scale monitoring program began in 1989 to estimate the abundance and location of cormorants at every known roost in the primary catfish producing region of the state, regionally known as the Delta. We used this data set to address hypotheses pertaining to cormorant ecology within the Delta over time, particularly in relation to aquaculture. We found that, although the Midwest breeding population of cormorants has been increasing, the abundance of cormorants wintering in the Delta has been decreasing, closely following the decline of aquaculture, suggesting aquaculture area is the primary reason for cormorant inhabitation of the region. We also modeled cormorant presence and abundance at all roost sites to determine what factors most influenced cormorant distribution. Aquaculture area around roosts was a significant predictor of both cormorant presence and abundance. However, the influence of aquaculture area was seasonally dependent, with greater positive influences occurring prior to migration. Lastly, we found peak cormorant abundance in the Delta is occurring 2.14 days earlier each year, which may be indicative of changes to migration phenology. Information gained using this large dataset aids in cormorant damage mitigation and to further our understanding of cormorant ecology. Data indicate changes in agriculture, and potentially climate change, can influence phenology, distribution, and abundance of avian species at large geographic scales

Fine Scale Characteristics of Catfish Aquaculture Ponds Influencing Use by Double-Crested Cormorants (Phalacrocorax auritus) in Northwest Mississippi

Double-crested Cormorants (Phalacrocorax auritus) are the main source of depredation at catfish aquaculture facilities in Northwest Mississippi, resulting in significant economic loss. Understanding factors related to pond selection by cormorants could aid in mitigation practices to minimize further loss. We constructed occupancy models to estimate the probability of cormorant presence on catfish ponds against multiple variables associated with each ponds physical surroundings and internal conditions. We also explored cormorant use of aquaculture and natural habitat by using logistic regression to model the proportion of cormorants on aquaculture compared to natural habitat and influences of seasonal variation. Cormorant presence data was collected by aerial survey (n=35) from October to April, of 2015-2017, accounting for an average of 973 catfish ponds and 26 natural water bodies each year. Our results indicate ponds located farther away from trees and activity centers, such as farm workshops, have a higher probability of cormorant use. Larger ponds, and ponds nearer the edge of pond clusters also have an increased probability of use. Specific pond contents influenced cormorant use, including fish species cultured, pond systems, and fish types. From October through January cormorants were distributed more on natural habitat. However, cormorants’ proportional use of aquaculture steadily increased beginning in February. This temporal shift from natural habitat toward aquaculture coincides with cormorant spring migration, indicating an increase in foraging of catfish in preparation for the migration north