Understanding the impacts of care farms on health and well-being of disadvantaged populations: a protocol of the Evaluating Community Orders (ECO) pilot study

INTRODUCTION

Care farms, where all or part of the farm is used for therapeutic purposes, show much potential for improving the health and well-being of a range of disadvantaged groups. Studies to date have been qualitative or observational, with limited empirical evidence of the effectiveness of care farms in improving health and well-being. Understanding the underlying mechanisms that lead to improvements for different disadvantaged groups is a further gap in the evidence. Participants in this study are offenders serving community orders. Their low socioeconomic status and poor health outcomes relative to the general population exemplifies disadvantage.

METHODS AND ANALYSIS

This paper describes the protocol of a study to understand the impacts of care farms and to pilot the design and tools for a study to assess cost-effectiveness of care farms in improving the quality of life of offenders. As a pilot study, no power calculation has been conducted. However, 150 offenders serving community sentences on care farms and 150 on other probation locations (eg, litter picking, painting) will be recruited over a 1-year period. Changes in quality of life, measured by Clinical Outcome in Routine Evaluation-Outcome Measure, health and reconvictions of offenders at care farms compared to other probation locations will be analysed to inform the sample size calculation for the follow on study. The feasibility of recruitment, retention, collecting cost data and modelling cost-effectiveness will also be assessed. The study will use qualitative methods to explore the experiences of offenders attending care farms and perceptions of probation and care farm staff on the processes and impacts of the intervention.

ETHICS AND DISSEMINATION

Findings will be published and inform development of a natural experiment and will be disseminated to probation services, care farms and academics. University of Leeds Ethical Review Board approved: SoMREC/13/014. National Offender Management Service (NOMS) approved: 2013-257.

Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs

The utility of genotype imputation in genome-wide association studies is increasing as progressively larger reference panels are improved and expanded through whole-genome sequencing. Developing general guidelines for optimally cost-effective imputation, however, requires evaluation of performance issues that include the relative utility of study-specific compared with general/multipopulation reference panels; genotyping with various array scaffolds; effects of different ethnic backgrounds; and assessment of ranges of allele frequencies. Here we compared the effectiveness of study-specific reference panels to the commonly used 1000 Genomes Project (1000G) reference panels in the isolated Sardinian population and in cohorts of European ancestry including samples from Minnesota (USA). We also examined different combinations of genome-wide and custom arrays for baseline genotypes. In Sardinians, the study-specific reference panel provided better coverage and genotype imputation accuracy than the 1000G panels and other large European panels. In fact, even gene-centered custom arrays (interrogating ~200 000 variants) provided highly informative content across the entire genome. Gain in accuracy was also observed for Minnesotans using the study-specific reference panel, although the increase was smaller than in Sardinians, especially for rare variants. Notably, a combined panel including both study-specific and 1000G reference panels improved imputation accuracy only in the Minnesota sample, and only at rare sites. Finally, we found that when imputation is performed with a study-specific reference panel, cutoffs different from the standard thresholds of MACH-Rsq and IMPUTE-INFO metrics should be used to efficiently filter badly imputed rare variants. This study thus provides general guidelines for researchers planning large-scale genetic studies.

Genetic variants regulating immune cell levels in health and disease

The complex network of specialized cells and molecules in the immune system has evolved to defend against pathogens, but inadvertent immune system attacks on "self" result in autoimmune disease. Both genetic regulation of immune cell levels and their relationships with autoimmunity are largely undetermined. Here, we report genetic contributions to quantitative levels of 95 cell types encompassing 272 immune traits, in a cohort of 1,629 individuals from four clustered Sardinian villages. We first estimated trait heritability, showing that it can be substantial, accounting for up to 87% of the variance (mean 41%). Next, by assessing ∼8.2 million variants that we identified and confirmed in an extended set of 2,870 individuals, 23 independent variants at 13 loci associated with at least one trait. Notably, variants at three loci (HLA, IL2RA, and SH2B3/ATXN2) overlap with known autoimmune disease associations. These results connect specific cellular phenotypes to specific genetic variants, helping to explicate their involvement in disease.

TRIM3, a tumor suppressor linked to regulation of p21(Waf1/Cip1.)

The TRIM family of genes is largely studied because of their roles in development, differentiation and host cell antiviral defenses; however, roles in cancer biology are emerging. Loss of heterozygosity of the TRIM3 locus in ∼20% of human glioblastomas raised the possibility that this NHL-domain containing member of the TRIM gene family might be a mammalian tumor suppressor. Consistent with this, reducing TRIM3 expression increased the incidence of and accelerated the development of platelet-derived growth factor -induced glioma in mice. Furthermore, TRIM3 can bind to the cdk inhibitor p21(WAF1/CIP1). Thus, we conclude that TRIM3 is a tumor suppressor mapping to chromosome 11p15.5 and that it might block tumor growth by sequestering p21 and preventing it from facilitating the accumulation of cyclin D1-cdk4.

Cortisol response to synacthen stimulation is attenuated following abusive head trauma

BACKGROUND

Child abuse and other early-life environmental stressors are known to affect the hypothalamic-pituitary-adrenal axis. We sought to compare synacthen-stimulated cortisol responses in children who suffered inflicted or accidental traumatic brain injury (TBI).

METHODS

Children with a history of early-childhood TBI were recruited from the Starship Children's Hospital database (Auckland, New Zealand, 1992-2010). All underwent a low-dose ACTH(1-24) (synacthen 1 μg IV) test, and serum cortisol response was compared between inflicted (TBI(I) ) and accidental (TBI(A) ) groups.

RESULTS

We assessed 64 children with TBI(I) and 134 with TBI(A) . Boys were more likely than girls to suffer accidental (P < 0·001), but not inflicted TBI. TBI(I) children displayed a 14% reduction in peak stimulated cortisol in comparison with the TBI(A) group (P < 0·001), as well as reduced cortisol responses at + 30 (P < 0·01) and + 60 min (P < 0·001). Importantly, these differences were not associated with severity of injury. The odds ratio of TBI(I) children having a mother who suffered domestic violence during pregnancy was 6·2 times that of the TBI(A) group (P < 0·001). However, reported domestic violence during pregnancy or placement of child in foster care did not appear to affect cortisol responses.

CONCLUSION

Synacthen-stimulated cortisol response is attenuated following inflicted TBI in early childhood. This may reflect chronic exposure to environmental stress as opposed to pituitary injury or early-life programming.

Reading acquisition reorganizes the phonological awareness network only in alphabetic writing systems

It is unknown how experience with different types of orthographies influences the neural basis of oral language processing. In order to determine the effects of alphabetic and nonalphabetic writing systems, the current study examined the influence of learning to read on oral language in English and Chinese speakers. Children (8-12 years olds) and adults made rhyming judgments to pairs of spoken words during functional magnetic resonance imaging (fMRI). Developmental increases were seen only for English speakers in the left hemisphere phonological network (superior temporal gyrus (STG), inferior parietal lobule, and inferior frontal gyrus). The increase in the STG was more pronounced for words with conflicting orthography (e.g. pint-mint; jazz-has) even though access to orthography was irrelevant to the task. Moreover, higher reading skill was correlated with greater activation in the STG only for English speaking children. The effects suggest that learning to read reorganizes the phonological awareness network only for alphabetic and not logographic writing systems because of differences in the principles for mapping between orthographic and phonological representations. The reorganization of the auditory cortex may result in better phonological awareness skills in alphabetic readers.

Permanent hypopituitarism is rare after structural traumatic brain injury in early childhood

BACKGROUND

We sought to determine the incidence of permanent hypopituitarism in a potentially high-risk group: young children after structural traumatic brain injury (TBI).

METHODS

We conducted a cross-sectional study with longitudinal follow-up. Dynamic tests of pituitary function (GH and ACTH) were performed in all subjects and potential abnormalities critically evaluated. Puberty was clinically staged; baseline thyroid function, prolactin, IGF-I, serum sodium, and osmolality were compared with age-matched data. Diagnosis of GH deficiency was based on an integrated assessment of stimulated GH peak (<5 μg/liter suggestive of deficiency), IGF-I, and growth pattern. ACTH deficiency was diagnosed based on a subnormal response to two serial Synacthen tests (peak cortisol <500 nmol/liter) and a metyrapone test.

RESULTS

We studied 198 survivors of structural TBI sustained in early childhood (112 male, age at injury 1.7 ± 1.5 yr) 6.5 ± 3.2 yr after injury. Sixty-four of the injuries (33%) were inflicted and 134 (68%) accidental. Two participants had developed precocious puberty, which is within the expected background population rate. Peak stimulated GH was subnormal in 16 participants (8%), in the context of normal IGF-I and normal growth. Stimulated peak cortisol was low in 17 (8%), but all had normal ACTH function on follow-up. One participant had a transient low serum T(4). Therefore, no cases of hypopituitarism were recorded.

CONCLUSION

Permanent hypopituitarism is rare after both inflicted and accidental structural TBI in early childhood. Precocious puberty was the only pituitary hormone abnormality found, but the prevalence did not exceed that of the normal population.