Lessons from Fraxinus, a crowd-sourced citizen science game in genomics

In 2013, in response to an epidemic of ash dieback disease in England the previous year, we launched a Facebook-based game called Fraxinus to enable non-scientists to contribute to genomics studies of the pathogen that causes the disease and the ash trees that are devastated by it. Over a period of 51 weeks players were able to match computational alignments of genetic sequences in 78% of cases, and to improve them in 15% of cases. We also found that most players were only transiently interested in the game, and that the majority of the work done was performed by a small group of dedicated players. Based on our experiences we have built a linear model for the length of time that contributors are likely to donate to a crowd-sourced citizen science project. This model could serve a guide for the design and implementation of future crowd-sourced citizen science initiatives.

'You are just left to get on with it': qualitative study of patient and carer experiences of the transition to secondary progressive multiple sclerosis

OBJECTIVES

Although the transition to secondary progressive multiple sclerosis (SPMS) is known to be a period of uncertainty for clinicians, who may find progressive disease challenging to objectively identify, little research has explored the experiences of patients and carers specifically during this transition period. Our objective was to explore what patients and their carers understand about their disease stage and describe their experiences and perspectives on the transition to SPMS.

DESIGN

Semistructured qualitative interviews and subsequent validation focus groups were analysed using inductive thematic analysis.

SETTING

South East Wales, UK.

PARTICIPANTS

20 patients with MS and 13 carers were interviewed. Eight patients and two carers participated in focus groups.

RESULTS

Four main themes around disease progression were identified. 'Realisation' describes how patients came to understand they had SPMS while 'reaction' describes their response to this realisation. The 'realities' of living with SPMS, including dealing with the healthcare system during this period, were described along with 'future challenges' envisaged by patients and carers.

CONCLUSIONS

Awareness that the transition to SPMS has occurred, and subsequent emotional reactions and coping strategies, varied widely between patients and their carers. The process of diagnosing the transition was often not transparent and some individuals wanted information to help them understand what the transition to SPMS meant for them.

A distinct pre-existing inflammatory tumour microenvironment is associated with chemotherapy resistance in high-grade serous epithelial ovarian cancer

Background:

Chemotherapy resistance is a major determinant of poor overall survival rates in high-grade serous ovarian cancer (HGSC). We have previously shown that gene expression alterations affecting the NF-κB pathway characterise chemotherapy resistance in HGSC, suggesting that the regulation of an immune response may be associated with this phenotype.

Methods:

Given that intrinsic drug resistance pre-exists and is governed by both tumour and host factors, the current study was performed to examine the cross-talk between tumour inflammatory microenvironment and cancer cells, and their roles in mediating differential chemotherapy response in HGSC patients. Expression profiling of a panel of 184 inflammation-related genes was performed in 15 chemoresistant and 19 chemosensitive HGSC tumours using the NanoString nCounter platform.

Results:

A total of 11 significantly differentially expressed genes were found to distinguish the two groups. As STAT1 was the most significantly differentially expressed gene (P=0.003), we validated the expression of STAT1 protein by immunohistochemistry using an independent cohort of 183 (52 resistant and 131 sensitive) HGSC cases on a primary tumour tissue microarray. Relative expression levels were subjected to Kaplan–Meier survival analysis and Cox proportional hazard regression models.

Conclusions:

This study confirms that higher STAT1 expression is significantly associated with increased progression-free survival and that this protein together with other mediators of tumour–host microenvironment can be applied as a novel response predictive biomarker in HGSC. Furthermore, an overall underactive immune microenvironment suggests that the pre-existing state of the tumour immune microenvironment could determine response to chemotherapy in HGSC.

Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere

BACKGROUND AND AIMS

To form nitrogen-fixing nodules on pea roots, Rhizobium leguminosarum biovar viciae must be competitive in the rhizosphere. Our aim was to identify genes important for rhizosphere fitness.

METHODS

Signature-tagged mutants were screened using microarrays to identify mutants reduced for growth in pea rhizospheres. Candidate mutants were assessed relative to controls for growth in minimal medium, growth in pea rhizospheres and for infection of peas in mixed inoculants. Mutated genes were identified by DNA sequencing and confirmed by transduction.

RESULTS

Of 5508 signature-tagged mutants, microarrays implicated 50 as having decreased rhizosphere fitness. Growth tests identified six mutants with rhizosphere-specific phenotypes. The mutation in one of the genes (araE) was in an arabinose catabolism operon and blocked growth on arabinose. The mutation in another gene (pcaM), encoding a predicted solute binding protein for protocatechuate and hydroxybenzoate uptake, decreased growth on protocatechuate. Both mutants were decreased for nodule infection competitiveness with mixed inoculants, but nodulated peas normally when inoculated alone. Other mutants with similar phenotypes had mutations predicted to affect secondary metabolism.

CONCLUSIONS

Catabolism of arabinose and protocatechuate in the pea rhizosphere is important for competitiveness of R.l. viciae. Other genes predicted to be involved in secondary metabolism are also important.

Association between electronic health records and health care utilization

BACKGROUND

The federal government is investing approximately $20 billion in electronic health records (EHRs), in part to address escalating health care costs. However, empirical evidence that provider use of EHRs decreases health care costs is limited.

OBJECTIVE

To determine any association between EHRs and health care utilization.

METHODS

We conducted a cohort study (2008-2009) in the Hudson Valley, a multi-payer, multiprovider community in New York State. We included 328 primary care physicians in predominantly small practices (median practice size four primary care physicians), who were caring for 223,772 patients. Data from an independent practice association was used to determine adoption of EHRs. Claims data aggregated across five commercial health plans was used to characterize seven types of health care utilization: primary care visits, specialist visits, radiology tests, laboratory tests, emergency department visits, hospital admissions, and readmissions. We used negative binomial regression to determine associations between EHR adoption and each utilization outcome, adjusting for ten physician characteristics.

RESULTS

Approximately half (48%) of the physicians were using paper records and half (52%) were using EHRs. For every 100 patients seen by physicians using EHRs, there were 14 fewer specialist visits (adjusted p < 0.01) and 9 fewer radiology tests (adjusted p = 0.01). There were no significant differences in rates of primary care visits, laboratory tests, emergency department visits, hospitalizations or readmissions.

CONCLUSIONS

Patients of primary care providers who used EHRs were less likely to have specialist visits and radiology tests than patients of primary care providers who did not use EHRs.

Health and reproductive experiences of women with an FMR1 premutation with and without fragile X premature ovarian insufficiency

Recently, research has indicated an increased risk for greater medical and emotional comorbidity and physical health symptoms among women with an FMR1 expansion. However, these studies have generally been limited in their ability to model multiple risk factors associated with these symptoms by small numbers (n = 112–146) of participants. This study used survey methodology to examine the health experiences of 458 adult women with the premutation with and without a history of a fragile X primary ovarian insufficiency (FXPOI) diagnosis. Results suggest similar findings to those reported in the literature with regard to the frequency of medical, emotional, and reproductive experiences of women with the premutation. In addition to expected reproductive differences, women with a diagnosis of FXPOI were also more likely to experience dizziness, nausea, and muscle weakness than women without a diagnosis of FXPOI. Women with and without FXPOI were more likely to have used reproductive assistance and were more likely to have experienced preeclampsia during at least one pregnancy than is reported in the general population. Having comorbid depression and anxiety was predictive of increased medical conditions and increased daily physical health symptoms.

Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins

In Rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by CinR, which induces the cinIS operon. CinI synthesizes an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots.

Influence of cold walls on PET image quantification and volume segmentation: a phantom study

PURPOSE

Commercially available fillable plastic inserts used in positron emission tomography phantoms usually have thick plastic walls, separating their content from the background activity. These "cold" walls can modify the intensity values of neighboring active regions due to the partial volume effect, resulting in errors in the estimation of standardized uptake values. Numerous papers suggest that this is an issue for phantom work simulating tumor tissue, quality control, and calibration work. This study aims to investigate the influence of the cold plastic wall thickness on the quantification of 18F-fluorodeoxyglucose on the image activity recovery and on the performance of advanced automatic segmentation algorithms for the delineation of active regions delimited by plastic walls.

METHODS

A commercial set of six spheres of different diameters was replicated using a manufacturing technique which achieves a reduction in plastic walls thickness of up to 90%, while keeping the same internal volume. Both sets of thin- and thick-wall inserts were imaged simultaneously in a custom phantom for six different tumor-to-background ratios. Intensity values were compared in terms of mean and maximum standardized uptake values (SUVs) in the spheres and mean SUV of the hottest 1 ml region (SUVmax, SUVmean, and SUVpeak). The recovery coefficient (RC) was also derived for each sphere. The results were compared against the values predicted by a theoretical model of the PET-intensity profiles for the same tumor-to-background ratios (TBRs), sphere sizes, and wall thicknesses. In addition, ten automatic segmentation methods, written in house, were applied to both thin- and thick-wall inserts. The contours obtained were compared to computed tomography derived gold standard ("ground truth"), using five different accuracy metrics.

RESULTS

The authors' results showed that thin-wall inserts achieved significantly higher SUVmean, SUVmax, and RC values (up to 25%, 16%, and 25% higher, respectively) compared to thick-wall inserts, which was in agreement with the theory. This effect decreased with increasing sphere size and TBR, and resulted in substantial (>5%) differences between thin- and thick-wall inserts for spheres up to 30 mm diameter and TBR up to 4. Thinner plastic walls were also shown to significantly improve the delineation accuracy for the majority of the segmentation methods tested, by increasing the proportion of lesion voxels detected, although the errors in image quantification remained non-negligible.

CONCLUSIONS

This study quantified the significant effect of a 90% reduction in the thickness of insert walls on SUV quantification and PET-based boundary detection. Mean SUVs inside the inserts and recovery coefficients were particularly affected by the presence of thick cold walls, as predicted by a theoretical approach. The accuracy of some delineation algorithms was also significantly improved by the introduction of thin wall inserts instead of thick wall inserts. This study demonstrates the risk of errors deriving from the use of cold wall inserts to assess and compare the performance of PET segmentation methods.

Differences in post-mortem findings after stillbirth in women with and without diabetes

AIMS

The reason for the fivefold increased risk of stillbirth in women with diabetes is not known. Further understanding of the underlying mechanisms may facilitate identification of pregnancies at increased risk. We have compared post-mortem reports in matched pairs of stillbirths in women with and without diabetes.

METHODS

Post-mortem reports were provided by the Centre for Maternal and Child Enquiries. Stillbirths as a result of lethal congenital and genetic abnormalities were excluded. Whole body, placenta and organ weights and histo-pathological findings in cases and controls were compared and also related to published reference values.

RESULTS

We analysed post-mortem reports on 23 matched pairs of stillbirths from 2009 to 2010. Mean placental weight in women with diabetes was 75 g less than in control subjects (95% CI -143 to -7 g; P = 0.032). In maternal diabetes, the thymus was often small and showed a 'starry sky' pattern on histology in 11 of 20 cases compared with four of 22 controls (P = 0.03). This histological finding was associated with a particularly low mean placental weight z-score -2.1 (1.1) standard deviations below a reference population corrected for gestational age.

CONCLUSIONS

In over half of the stillbirths occurring in women with diabetes, there was a 'starry sky' appearance in the fetal thymus on histology, this being associated with a small placenta. These findings are consistent with a critical subacute metabolic disturbance being a prominent cause of the increased risk of stillbirth in pregnancies complicated by maternal diabetes.

Validation of a power-law noise model for simulating small-scale breast tissue

We have validated a small-scale breast tissue model based on power-law noise. A set of 110 patient images served as truth. The statistical model parameters were determined by matching the radially averaged power-spectrum of the projected simulated tissue with that of the central tomosynthesis patient breast projections. Observer performance in a signal-known exactly detection task in simulated and actual breast backgrounds was compared. Observers included human readers, a pre-whitening observer model and a channelized Hotelling observer model. For all observers, good agreement between performance in the simulated and actual backgrounds was found, both in the tomosynthesis central projections and the reconstructed images. This tissue model can be used for breast x-ray imaging system optimization. The complete statistical description of the model is provided.

Nef-specific CD8+ T cell responses contribute to HIV-1 immune control

Recent studies in the SIV-macaque model of HIV infection suggest that Nef-specific CD8+ T-cell responses may mediate highly effective immune control of viraemia. In HIV infection Nef recognition dominates in acute infection, but in large cohort studies of chronically infected subjects, breadth of T cell responses to Nef has not been correlated with significant viraemic control. Improved disease outcomes have instead been associated with targeting Gag and, in some cases, Pol. However analyses of the breadth of Nef-specific T cell responses have been confounded by the extreme immunogenicity and multiple epitope overlap within the central regions of Nef, making discrimination of distinct responses impossible via IFN-gamma ELISPOT assays. Thus an alternative approach to assess Nef as an immune target is needed. Here, we show in a cohort of >700 individuals with chronic C-clade infection that >50% of HLA-B-selected polymorphisms within Nef are associated with a predicted fitness cost to the virus, and that HLA-B alleles that successfully drive selection within Nef are those linked with lower viral loads. Furthermore, the specific CD8+ T cell epitopes that are restricted by protective HLA Class I alleles correspond substantially to effective SIV-specific epitopes in Nef. Distinguishing such individual HIV-specific responses within Nef requires specific peptide-MHC I tetramers. Overall, these data suggest that CD8+ T cell targeting of certain specific Nef epitopes contributes to HIV suppression. These data suggest that a re-evaluation of the potential use of Nef in HIV T-cell vaccine candidates would be justified.

Nonsuicidal self-injury among adolescents: a training priority for primary care providers

Primary care providers were surveyed to determine how prepared they feel to address nonsuicidal self-injury (NSSI) among adolescents, their interest in training on NSSI, and factors associated with routinely asking about NSSI when providing health supervision. Participants included family medicine physicians (n = 260), pediatricians (n = 127), family nurse practitioners (n = 96), and pediatric nurse practitioners (n = 54). Almost 50% felt unprepared to address NSSI, and over 70% wanted training in this area. Overall, relative to other areas of mental health care, clinicians felt least prepared to address and wanted more training on NSSI. Just 27% reported they routinely inquired about NSSI during health supervision. Factors associated with routinely asking about NSSI were identifying as female (OR = 2.37; 95% CI = 1.25-4.49), feeling better prepared to address NSSI (OR = 1.51; 95% CI = 1.04-2.20), and more frequently using a psychosocial interview to identify adolescents in distress (OR = 1.23; 95% CI = 1.02-1.48). Teaching clinicians to assess NSSI within a psychosocial interview may increase screening for and identification of the behavior among adolescents in primary care.

Somatoform disorders among patients attending walk-in clinics in Trinidad: prevalence and association with depression and anxiety

Objectives Somatoform disorders are common in international primary care settings, but have been little studied in the developing world. The objective of this study was to determine the prevalence of severe undifferentiated somatoform disorder, and its relationship to depression and anxiety, among patients attending walk-in clinics in Trinidad. Methods The study participants, who were all aged 18 years or older and attending walk-in clinics at 16 randomly selected health centres, were surveyed between May and August 2007 using the PRIME-MD questionnaire. Results There were 594 participants (the response rate was 92%), of whom 72.7% were female. Their ages ranged from 18 to 93 years, and 54.5% were over 50 years of age. In total, 37.2% were married and 25.9% were single. Indo-Trinidadians represented 43.1% and Afro-Trinidadians represented 36% of the study sample; 56.5% of the participants reported that their income was less than US$ 400 per month, and 65.7% were unemployed. At walk-in clinics in Trinidad, the estimated prevalence of severe undifferentiated somatoform disorder was 10.3% (95% CI: 7.86-12.74), that of hypochondriasis was 28.5% (95% CI: 24.9-32.1), and that of body dysmorphic disorder was 15.8% (95% CI: 11.9-18.7). Severe undifferentiated somatoform disorder was statistically significantly associated with gender and ethnicity but not with age, level of education, employment status or income. Chi-square testing found significant associations between the presence of severe undifferentiated somatoform disorder and both depression and anxiety (P < 0.05), between hypochondriasis and both anxiety and depression (P < 0.05), and between body dysmorphic disorder and depression (P < 0.05) but not anxiety. Regression analysis suggested that the demographic features that predicted severe undifferentiated somatoform disorder were being female or Indo-Trinidadian. Conclusions Walk-in clinics in Trinidad that serve older patients on a lower income have a high proportion of patients with somatoform disorders as measured by the PRIME-MD scale. These patients exhibit many features of anxiety and depression. These findings have implications for medical training and service delivery.