Experience on postmortem minimally invasive tissue sampling to ascertain the cause of death determination in South African children: A case for implementing as standard of care

Determining the death burden for prioritising public health interventions necessitates detailed data on the causal pathways to death. Postmortem minimally invasive tissue sampling (MITS), incorporating histology, molecular and microbial culture diagnostics, enhances cause-of-death attribution, particularly for infectious deaths. MITS proves a valid alternative to full diagnostic autopsies, especially in low- and middle-income countries. In Soweto, South Africa (SA), the Child Health and Mortality Prevention Surveillance (CHAMPS) programme has delineated over 1 000 child and stillbirth deaths since 2017. This SA CHAMPS site supports advocating for the use of postmortem MITS as routine practice, for more granular insights into under-5 mortality causes. This knowledge is crucial for SA's pursuit of Sustainable Development Goal 3.2, targeting reduced neonatal and under-5 mortality rates. This commentary explores the public health advantages and ethicolegal considerations surrounding implementing MITS as standard of care for stillbirths, neonatal and paediatric deaths in SA. Furthermore, based on the data from CHAMPS, we present three pragmatic algorithmic approaches to the wide array of testing options for cost-effectiveness and scalability of postmortem MITS in South African state facilities.

Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care

OBJECTIVE

The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis.

METHODS

We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded.

RESULTS

We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers.

CONCLUSION

In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.

COVID-19 infection and maternal morbidity in critical care units in Scotland: a national cohort study

BACKGROUND

Previous research has shown that, in comparison with non-pregnant women of reproductive age, pregnant women with COVID-19 are more likely to be admitted to critical care, receive invasive ventilation, and die. At present there are limited data in relation to outcomes and healthcare utilisation following hospital discharge of pregnant and recently pregnant women admitted to critical care.

METHODS

A national cohort study of pregnant and recently pregnant women who were admitted to critical care in Scotland with confirmed or suspected COVID-19. We examined hospital outcomes as well as hospital re-admission rates.

RESULTS

Between March 2020 and March 2022, 75 pregnant or recently pregnant women with laboratory-confirmed COVID-19 were admitted to 24 Intensive Care Units across Scotland. Almost two thirds (n=49, 65%) were from the most deprived socio-economic areas. Complete 90-day acute hospital re-admission data were available for 74 (99%) patients. Nine (12%) women required an emergency non-obstetric hospital re-admission within 90 days. Less than 5% of the cohort had received any form of vaccination.

CONCLUSIONS

This national cohort study has demonstrated that pregnant or recently pregnant women admitted to critical care with COVID-19 were more likely to reside in areas of socio-economic deprivation, and fewer than 5% of the cohort had received any form of vaccination. More targeted public health campaigning across the socio-economic gradient is urgently required.

Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry

BACKGROUND

Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months.

METHODS

We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed.

RESULTS

We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05).

CONCLUSION

While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.

Severe maternal morbidity in Scotland

Using a cohort study design, we analysed 17 diagnoses and 9 interventions (including critical care admission) as a composite measure of severe maternal morbidity for pregnancies recorded over 14 years in Scotland. There were 762,918 pregnancies, of which 7947 (10 in 1000 pregnancies) recorded 9345 severe maternal morbidity events, 2802 episodes of puerperal sepsis being the most common (30%). Severe maternal morbidity incidence increased from 9 in 1000 pregnancies in 2012 to 17 in 1000 pregnancies in 2018, due in part to puerperal sepsis recording. The odds ratio (95%CI) for severe maternal morbidity was higher for: older women, for instance 1.22 (1.13-1.33) for women aged 35-39 years and 1.44 (1.27-1.63) for women aged > 40 years compared with those aged 25-29 years; obese women, for instance 1.13 (1.06-1.21) for BMI 30-40 kg.m-2 and 1.32 (1.15-1.51) for BMI > 40 kg.m-2 compared with BMI 18.5-24.9 kg.m-2 ; multiple pregnancy, 2.39 (2.09-2.74); and previous caesarean delivery, 1.52 (1.40-1.65). The median (IQR [range]) hospital stay was 3 (2-5 [1-8]) days with severe maternal morbidity and 2 (1-3 [1-5]) days without. Forty-one women died during pregnancy or up to 42 days after delivery, representing mortality rates per 100,000 pregnancies of about 365 with severe maternal morbidity and 1.6 without. There were 1449 women admitted to critical care, 807 (58%) for mechanical ventilation or support of at least two organs. We recorded an incidence of severe maternal morbidity higher than previously published, possibly because sepsis was coded inaccurately in our databases. Further research may determine the value of this composite measure of severe maternal morbidity.

Adrenergic signaling controls early transcriptional programs during CD8+ T cell responses to viral infection

Norepinephrine is a key sympathetic neurotransmitter, which acts to suppress CD8 ⁺ T cell cytokine secretion and lytic activity by signaling through the β2-adrenergic receptor (ADRB2). Although ADRB2 signaling is considered generally immunosuppressive, its role in regulating the differentiation of effector T cells in response to infection has not been investigated. Using an adoptive transfer approach, we compared the expansion and differentiation of wild type (WT) to Adrb2^-/- CD8 ⁺ T cells throughout the primary response to vesicular stomatitis virus (VSV) infection in vivo. We measured the dynamic changes in transcriptome profiles of antigen-specific CD8 ⁺ T cells as they responded to VSV. Within the first 7 days of infection, WT cells out-paced the expansion of Adrb2^-/- cells, which correlated with reduced expression of IL-2 and the IL-2Rα in the absence of ADRB2. RNASeq analysis identified over 300 differentially expressed genes that were both temporally regulated following infection and selectively regulated in WT vs Adrb2^-/- cells. These genes contributed to major transcriptional pathways including cytokine receptor activation, signaling in cancer, immune deficiency, and neurotransmitter pathways. By parsing genes within groups that were either induced or repressed over time in response to infection, we identified three main branches of genes that were differentially regulated by the ADRB2. These gene sets were predicted to be regulated by specific transcription factors involved in effector T cell development, such as Tbx21 and Eomes. Collectively, these data demonstrate a significant role for ADRB2 signaling in regulating key transcriptional pathways during CD8 ⁺ T cells responses to infection that may dramatically impact their functional capabilities and downstream memory cell development.

Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis

BACKGROUND

Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry.

METHODS

In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months.

RESULTS

One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability.

CONCLUSION

High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.

HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome

Colorectal cancer (CRC) is one of the most lethal malignancies. The extreme heterogeneity in survival rate is driving the need for new prognostic biomarkers. Human endogenous retroviruses (hERVs) have been suggested to influence tumor progression, oncogenesis and elicit an immune response. We examined multiple next-generation sequencing (NGS)-derived biomarkers in 114 CRC patients with paired whole-exome and whole-transcriptome sequencing (WES and WTS, respectively). First, we demonstrate that the median expression of hERVs can serve as a potential biomarker for prognosis, relapse, and resistance to chemotherapy in stage II and III CRC. We show that hERV expression and CD8+ tumor-infiltrating T-lymphocytes (TILs) synergistically stratify overall and relapse-free survival (OS and RFS): the median OS of the CD8-/hERV+ subgroup was 29.8 months compared with 37.5 months for other subgroups (HR = 4.4, log-rank P < 0.001). Combing NGS-based biomarkers (hERV/CD8 status) with clinicopathological factors provided a better prediction of patient survival compared to clinicopathological factors alone. Moreover, we explored the association between genomic and transcriptomic features of tumors with high hERV expression and establish this subtype as distinct from previously described consensus molecular subtypes of CRC. Overall, our results underscore a previously unknown role for hERVs in leading to a more aggressive subtype of CRC.

Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

Development and Analytical Validation of a DNA Dual-Strand Approach for the US Food and Drug Administration-Approved Next-Generation Sequencing-Based Praxis Extended RAS Panel for Metastatic Colorectal Cancer Samples

A next-generation sequencing method was developed that can distinguish single-stranded modifications from low-frequency somatic mutations present on both strands of DNA in formalin-fixed paraffin-embedded colorectal cancer samples. We applied this method for analytical validation of the Praxis Extended RAS Panel, a US Food and Drug Administration-approved companion diagnostic for panitumumab, on the Illumina MiSeqDx platform. With the use of the TruSeq amplicon workflow, both strands of DNA from the starting material were interrogated independently. Mutations were reported only if found on both strands; artifacts usually present on only one strand would not be reported. A total of 56 mutations were targeted within the KRAS and NRAS genes. A minimum read depth of 1800× per amplicon is required per sample but averaged >30,000× at maximum multiplexing levels. Analytical validation studies were performed to determine the simultaneous detection of mutations on both strands, reproducibility, assay detection level, precision of the assay across various factors, and the impact of interfering substances. In conclusion, this assay can clearly distinguish single-stranded artifacts from low-frequency mutations. Furthermore, the assay is accurate, precise, and reproducible, can achieve consistent detection of a mutation at 5% mutation frequency, exhibits minimal impact from tested interfering substances, and can simultaneously detect 56 mutations in a single run using 10 samples plus controls.

Memory CD8+ T Cell Development is Controlled by the Sympathetic Nervous System

Immune memory is critical for protection from repeated infections by pathogenic organisms and is the basis for the success of vaccines. Memory CD8+ T cell development is guided by important signals that alter their function and transcriptional program, enabling them to persist as pools of primed memory cells capable of rapid response. Lymphoid organs are highly innervated by sympathetic neurons that secrete norepinephrine as the primary neurotransmitter, which places the nervous and immune systems in direct communication. CD8+ T cells express the β2-adrenergic receptor (ADRB2), and we found that it was required for the development of long-lived memory cells in response to virus infection. The failure of Adrb2−/− T cells to form memory populations correlated with profound differences in gene expression and predicted upstream regulators during the early stages of T cell priming. Thus, the sympathetic nervous system controls memory CD8+ T cell development through ADRB2 signaling.

Human milk oligosaccharide categories define the microbiota composition in human colostrum

Human milk oligosaccharides (HMOs) are structurally diverse unconjugated glycans with a composition unique to each lactating mother. While HMOs have been shown to have an impact on the development of infant gut microbiota, it is not well known if HMOs also already affect milk microbial composition. To address this question, we analysed eleven colostrum samples for HMO content by high-pressure liquid chromatography and microbiota composition by quantitative PCR. Higher total HMO concentration was associated with higher counts of Bifidobacterium spp. (ρ=0.63, P=0.036). A distinctive effect was seen when comparing different HMO groups: positive correlations were observed between sialylated HMOs and Bifidobacterium breve (ρ=0.84, P=0.001), and non-fucosylated/non-sialylated HMOs and Bifidobacterium longum group (ρ=0.65, P=0.030). In addition to associations between HMOs and bifidobacteria, positive correlations were observed between fucosylated HMOs and Akkermansia muciniphila (ρ=0.70, P=0.017), and between fucosylated/sialylated HMOs and Staphylococcus aureus (ρ=0.75, P=0.007). Our results suggest that the characterised HMOs have an effect on specific microbial groups in human milk. Both oligosaccharides and microbes provide a concise inoculum for the compositional development of the infant gut microbiota.

Abstract 3585: Determination of gene amplifications with a next-generation sequencing cancer panel

TruSight® Tumor 15* (TST15) uses next-generation sequencing technology to detect somatic point mutations, insertions, and deletions in 15 genes that are commonly mutated in solid tumors. It accurately detects low-frequency mutations with low DNA input and is optimized for formalin-fixed, paraffin-embedded (FFPE) tumor tissue. The test is a multiplexed PCR panel that includes primers to support amplification detection in the EGFR, ERBB2, and MET genes.

Here we describe development of a bioinformatics analysis method to enable detection of these gene amplifications. DNA extracted from 31 FFPE samples with amplifications in EGFR, ERBB2, or MET—some with dual amplifications—were diluted with DNA extracted from 18 normal FFPE samples to create a total of 67 unique samples at low-level amplification. Undiluted and diluted samples were assessed for quality based on amplifiability (ΔCq or library yield) and tested with TST15. For comparison, the samples were also tested with droplet digital PCR (ddPCR) to determine the copy ratio of target to wild type. For amplifiable samples, the TST15 algorithm was able to detect amplifications in EGFR and ERBB2 at ddPCR ratios of 1.4 and 1.6, respectively. ddPCR was unable to accurately quantify low MET amplifications; therefore, expected ddPCR ratios were used for comparison. The TST15 algorithm was able to detect amplifications in MET samples at an expected ddPCR ratio of 1.3. Poor sample quality (i.e., high ΔCq or low library yield) impaired amplification detection. In some samples, the presence of multiple amplifications also impaired detection.

The addition of this algorithm to the TST15 workflow will allow researchers to more accurately characterize tumor samples by detecting somatic mutations and amplifications simultaneously.

*For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Ina L. Deras, Aaron Wise, Chen Zhao, Christine Glidewell-Kenney, Phillip Le, Elizabeth Upsall Aderhold, Karen Gutekunst. Determination of gene amplifications with a next-generation sequencing cancer panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3585. doi:10.1158/1538-7445.AM2017-3585

Abstract 427: A path towards determining tumor mutation burden and identifying neoantigens using next-generation sequencing (NGS)

Introduction: The recent clinical demonstrations that cancer immunotherapy is effective for some patients, but not others has led to widespread interest in identifying cancer genetic factors that can predict positive response. Importantly, it has been shown by various studies that tumor mutation burden (TMB) and predicted neoantigen load correlate with patient response to checkpoint inhibitors. This project aims to develop a clinical next-generation sequencing (NGS) assay that utilizes TMB and neoantigen information to guide cancer immunotherapy selection.

Experimental Procedures: Whole exome sequencing (WES) and whole transcriptome sequencing (WTS) libraries were generated using Illumina’s TruSeq® Exome and RNA Access library preparation kits, respectively. The samples were pair-end sequenced (2x75bp) using HiSeq® 2000 and 2500 instruments.

Data Summary: Here, we demonstrate a workflow using tumor/normal WES and tumor-only WTS to determine expressed TMB. Using the WES data, we were also able to accurately identify human leukocyte antigen (HLA) major histocompatibility complex (MHC) Class I genes at four-digit resolution. We then identified putative neoantigens, defined as peptides with mutated amino acids, that were expressed in the tumor samples and predicted to bind to the respective HLA sequences. In addition, as a path towards developing a clinical assay for TMB and neoantigen determination, we tested the ability of reagents developed for Illumina’s Trusight® Tumor 170 panel to be used for an exome panel. With workflow modifications, we achieved comparable quality of sequencing metrics as compared to the TruSeq® Exome kit.

Conclusion: Our data demonstrate a path towards developing a clinical assay that can be used to assess TMB and neoantigen candidates.

Citation Format: Alex So, Shannon Kaplan, Nai-yu Wang, Shile Zhang, Aaron Wise, Kristina Kruglyak, Karen Gutekunst. A path towards determining tumor mutation burden and identifying neoantigens using next-generation sequencing (NGS) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 427. doi:10.1158/1538-7445.AM2017-427

A transcription factor hierarchy defines an environmental stress response network

Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive transcription factor (TF) networks in multicellular organisms have been limited. The phytohormone abscisic acid (ABA) influences the expression of thousands of genes, allowing us to characterize complex stress-responsive regulatory networks. Using chromatin immunoprecipitation sequencing, we identified genome-wide targets of 21 ABA-related TFs to construct a comprehensive regulatory network in Arabidopsis thaliana Determinants of dynamic TF binding and a hierarchy among TFs were defined, illuminating the relationship between differential gene expression patterns and ABA pathway feedback regulation. By extrapolating regulatory characteristics of observed canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness and demonstrated their utility to modulate plant resilience to osmotic stress.

cDREM: inferring dynamic combinatorial gene regulation

Genes are often combinatorially regulated by multiple transcription factors (TFs). Such combinatorial regulation plays an important role in development and facilitates the ability of cells to respond to different stresses. While a number of approaches have utilized sequence and ChIP-based datasets to study combinational regulation, these have often ignored the combinational logic and the dynamics associated with such regulation. Here we present cDREM, a new method for reconstructing dynamic models of combinatorial regulation. cDREM integrates time series gene expression data with (static) protein interaction data. The method is based on a hidden Markov model and utilizes the sparse group Lasso to identify small subsets of combinatorially active TFs, their time of activation, and the logical function they implement. We tested cDREM on yeast and human data sets. Using yeast we show that the predicted combinatorial sets agree with other high throughput genomic datasets and improve upon prior methods developed to infer combinatorial regulation. Applying cDREM to study human response to flu, we were able to identify several combinatorial TF sets, some of which were known to regulate immune response while others represent novel combinations of important TFs.

In vitro susceptibility of Clostridium difficile to SMT19969 and comparators, as well as the killing kinetics and post-antibiotic effects of SMT19969 and comparators against C. difficile

OBJECTIVES

SMT19969 is a novel antimicrobial under clinical development for the treatment of Clostridium difficile infection (CDI). The objective was to determine the comparative susceptibility of 82 C. difficile clinical isolates (which included ribotype 027 isolates and isolates with reduced metronidazole susceptibility) to SMT19969, fidaxomicin, vancomycin and metronidazole and to determine the killing kinetics and post-antibiotic effects of SMT19969, fidaxomicin and vancomycin against C. difficile.

METHODS

MICs were determined by agar incorporation. Killing kinetics and post-antibiotic effects were determined against C. difficile BI1, 630 and 5325 (ribotypes 027, 012 and 078, respectively).

RESULTS

SMT19969 showed potent inhibition of C. difficile (MIC90=0.125 mg/L) and was markedly more active than either metronidazole (MIC90 = 8 mg/L) or vancomycin (MIC90 = 2 mg/L). There were no differences in susceptibility to SMT19969 between different ribotypes. Fidaxomicin was typically one doubling dilution more active than SMT19969 and both agents maintained activity against isolates with reduced susceptibility to metronidazole. In addition, SMT19969 was bactericidal against the C. difficile strains tested, with reductions in viable counts to below the limit of detection by 24 h post-inoculation. Vancomycin was bacteriostatic against all three strains. Fidaxomicin was bactericidal although reduced killing was observed at concentrations <20 × MIC against C. difficile BI1 (ribotype 027) compared with other strains tested.

CONCLUSIONS

These data demonstrate that SMT19969 is associated with potent and bactericidal activity against the strains tested and support further investigation of SMT19969 as potential therapy for CDI.

SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data

MOTIVATION

Current methods for reconstructing dynamic regulatory networks are focused on modeling a single response network using model organisms or cell lines. Unlike these models or cell lines, humans differ in their background expression profiles due to age, genetics and life factors. In addition, there are often differences in start and end times for time series human data and in the rate of progress based on the specific individual. Thus, new methods are required to integrate time series data from multiple individuals when modeling and constructing disease response networks.

RESULTS

We developed Scalable Models for the Analysis of Regulation from Time Series (SMARTS), a method integrating static and time series data from multiple individuals to reconstruct condition-specific response networks in an unsupervised way. Using probabilistic graphical models, SMARTS iterates between reconstructing different regulatory networks and assigning individuals to these networks, taking into account varying individual start times and response rates. These models can be used to group different sets of patients and to identify transcription factors that differentiate the observed responses between these groups. We applied SMARTS to analyze human response to influenza and mouse brain development. In both cases, it was able to greatly improve baseline groupings while identifying key relevant TFs that differ between the groups. Several of these groupings and TFs are known to regulate the relevant processes while others represent novel hypotheses regarding immune response and development.

AVAILABILITY AND IMPLEMENTATION

Software and Supplementary information are available at http://sb.cs.cmu.edu/smarts/.

CONTACT

zivbj@cs.cmu.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The Emotional Self-Efficacy Scale

Emotional self-efficacy (ESE) is an important aspect of emotional functioning, with current measures for children and adolescents focused on the measurement of self-beliefs in relation to the management of emotions. In the present study, we report the psychometric properties of the first adaptation of the Emotional Self-Efficacy Scale for youth (Youth-ESES) that measures additional aspects of ESE, such as perceiving and understanding emotions and helping others modulate their emotions. Participants were 192 young adolescents aged 11 to 13 years from a U.K. state school. They completed the Youth-ESES and measures of ability emotional intelligence (EI) and cognitive ability. Results support the same four-factor structure that has been previously documented using the adult version of the ESES, with the four subscales being largely independent from cognitive ability and only moderately related to ability EI. However, the four subscales were less differentiated in the present study compared with adult data previously published, suggesting that there is a strong general factor underlying young adolescents’ ESE scores. Overall, the results suggest that the adapted Youth-ESES can be reliably used with youth, and that confidence in how a young person feels about his or her emotional functioning remains distinct from emotional skill.

Breastfeeding trends in Cambodia, and the increased use of breast-milk substitute-why is it a danger?

A cross-sectional analysis of the Cambodia Demographic Health Surveys from 2000, 2005 and 2010 was conducted to observe the national trends in infant and young child feeding practices. The results showed that rates of exclusive breastfeeding among infants aged 0–5.9 months have increased substantially since 2000, concurrent with an increase in the rates of early initiation of breastfeeding and a reduction in the giving of pre-lacteal feeds. However, the proportion of infants being fed with breast-milk substitutes (BMS) during 0–5.9 months doubled in 5 years (3.4% to 7.0%) from 2000 to 2005, but then did not increase from 2005, likely due to extensive public health campaigns on exclusive breastfeeding. BMS use increased among children aged 6–23.9 months from 2000 to 2010 (4.8% to 9.3%). 26.1% of women delivering in a private clinic provided their child with breast-milk substitute at 0–5.9 months, which is five times more than women delivering in the public sector (5.1%), and the greatest increase in bottle use happened among the urban poor (5.8% to 21.7%). These findings are discussed with reference to the increased supply and marketing of BMS that is occurring in Cambodia.

DOC-MEK: a double-blind randomized phase II trial of docetaxel with or without selumetinib in wild-type BRAF advanced melanoma

BACKGROUND

Treatment options for wild-type BRAF melanoma patients remain limited. Selumetinib, a MEK 1/2 inhibitor, suppresses pERK levels independent of BRAF and NRAS mutation status, and combination with docetaxel has demonstrated synergy in xenograft models. The aim of this study was to assess the efficacy and safety of selumetinib plus docetaxel as first-line treatment in patients with wild-type BRAF advanced melanoma.

PATIENTS AND METHODS

In this double-blind multicentre phase II trial patients with wild-type BRAF melanoma were randomized (1:1) to docetaxel with selumetinib or placebo. Docetaxel 75 mg/m(2) was administered intravenously every 3 weeks up to six cycles. Selumetinib 75 mg or placebo was given orally twice daily until disease progression or unacceptable toxicity. The primary end point was progression-free survival (PFS). Tumour NRAS mutation status was analysed retrospectively and correlated with treatment outcomes.

RESULTS

Eighty-three patients were randomized to docetaxel plus selumetinib (n = 41) or docetaxel plus placebo (n = 42). The PFS hazard ratio (HR) (selumetinib:placebo) was 0.75 [90% confidence interval (CI) 0.50-1.14; P = 0.130], with a median PFS of 4.23 months (90% CI 3.63-6.90) for docetaxel plus selumetinib and 3.93 months (90% CI 2.07-4.16) for docetaxel alone. There was no significant difference in overall survival. The objective response rate was 32% with selumetinib versus 14% with placebo (P = 0.059). In a retrospective subset analysis, NRAS mutation status did not affect significantly upon clinical outcomes in either arm. The combination of docetaxel and selumetinib could be administered effectively to patients with metastatic melanoma, although the combination was less well tolerated than docetaxel alone.

CONCLUSIONS

The combination of docetaxel with selumetinib showed no significant improvement in PFS compared with docetaxel alone, although more patients showed a response to combination therapy. We found no evidence to support using tumour NRAS mutation as a basis for selecting patients for combined MEK inhibitor and chemotherapy.

CLINICAL TRIAL

DOC-MEK (EudraCT no: 2009-018153-23).

Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells

BACKGROUND

Carbon catabolite repression (CCR) is critical for optimal bacterial growth, and in bacterial (and yeast) cells it leads to their selective consumption of a single substrate from a complex environment. However, the root cause(s) for the development of this regulatory mechanism is unknown. Previously, a flux balance model (FBAwMC) of Escherichia coli metabolism that takes into account the crowded intracellular milieu of the bacterial cell correctly predicted selective glucose uptake in a medium containing five different carbon sources, suggesting that CCR may be an adaptive mechanism that ensures optimal bacterial metabolic network activity for growth.

RESULTS

Here, we show that slowly growing E. coli cells do not display CCR in a mixed substrate culture and gradual activation of CCR correlates with an increasing rate of E. coli cell growth and proliferation. In contrast, CCR mutant cells do not achieve fast growth in mixed substrate culture, and display differences in their cell volume and density compared to wild-type cells. Analyses of transcriptome data from wt E. coli cells indicate the expected regulation of substrate uptake and metabolic pathway utilization upon growth rate change. We also find that forced transient increase of intracellular crowding or transient perturbation of CCR delay cell growth, the latter leading to associated cell density-and volume alterations.

CONCLUSIONS

CCR is activated at an increased bacterial cell growth rate when it is required for optimal cell growth while intracellular macromolecular density is maintained within a narrow physiological range. In addition to CCR, there are likely to be other regulatory mechanisms of cell metabolism that have evolved to ensure optimal cell growth in the context of the fundamental biophysical constraint imposed by intracellular molecular crowding.

Matching experiments across species using expression values and textual information

Motivation: With the vast increase in the number of gene expression datasets deposited in public databases, novel techniques are required to analyze and mine this wealth of data. Similar to the way BLAST enables cross-species comparison of sequence data, tools that enable cross-species expression comparison will allow us to better utilize these datasets: cross-species expression comparison enables us to address questions in evolution and development, and further allows the identification of disease-related genes and pathways that play similar roles in humans and model organisms. Unlike sequence, which is static, expression data changes over time and under different conditions. Thus, a prerequisite for performing cross-species analysis is the ability to match experiments across species.

Results: To enable better cross-species comparisons, we developed methods for automatically identifying pairs of similar expression datasets across species. Our method uses a co-training algorithm to combine a model of expression similarity with a model of the text which accompanies the expression experiments. The co-training method outperforms previous methods based on expression similarity alone. Using expert analysis, we show that the new matches identified by our method indeed capture biological similarities across species. We then use the matched expression pairs between human and mouse to recover known and novel cycling genes as well as to identify genes with possible involvement in diabetes. By providing the ability to identify novel candidate genes in model organisms, our method opens the door to new models for studying diseases.

Availability: Source code and supplementary information is available at: www.andrew.cmu.edu/user/aaronwis/cotrain12.

Contact:zivbj@cs.cmu.edu

Supplementary information:Supplementary data are available at Bioinformatics online.

Sulfidation of silver nanoparticles decreases Escherichia coli growth inhibition

Sulfidation of metallic nanoparticles such as silver nanoparticles (AgNPs) released to the environment may be an important detoxification mechanism. Two types of AgNPs-an engineered polydisperse and aggregated AgNP powder, and a laboratory-synthesized, relatively monodisperse AgNP aqueous dispersion-were studied. The particles were sulfidized to varying degrees and characterized to determine the effect of initial AgNP polydispersity and aggregation state on AgNP sulfidation, and then exposed to Escherichia coli to determine if the degree of sulfidation of pristine AgNPs affects growth inhibition of bacteria. The extent of sulfidation was found to depend on the HS(-)/Ag ratio. However, for the same reaction times, the more monodisperse particles were fully transformed to Ag(2)S, and the polydisperse, aggregated particles were not fully sulfidized, thus preserving the toxic potential of Ag(0) in the aggregates. A higher Ag(2)S:Ag(0) ratio in the sulfidized nanoparticles resulted in less growth inhibition of E. coli over 6 h of exposure. These results suggest that the initial properties of AgNPs can affect sulfidation products, which in turn affect microbial growth inhibition, and that these properties should be considered in assessing the environmental impact of AgNPs.

Preferences for steaming of vegetables

BACKGROUND

Steaming retains vitamins and phytochemicals in vegetables better than boiling; thus, it is important to promote this cooking method. The present study aimed to determine what vegetable would be best to use in a campaign to promote steaming.

METHODS

Carrots, broccoli and green cabbage were boiled, steamed or microwave steamed. Untrained assessors (n = 50) evaluated the sensory properties of appearance, texture, taste and overall acceptability using a hedonic rating test on a scale from 1-9. Average scores for overall acceptability were calculated for each type of cooking according to the assessors' usual cooking method.

RESULTS

For all features, steaming and microwave steaming were rated significantly higher than boiling for broccoli (for acceptability 6.2 and 7.1 versus 5.1; P < 0.001), whereas carrots were similarly considered better for flavour and overall acceptability. Generally, cabbage was rated lower for all features, with no differences amongst the cooking methods (4.9-5.2 for acceptability). Only two of twenty-one subjects who usually boil vegetables preferred the boiled vegetables in the present study.

CONCLUSIONS

Generally, steaming and microwave steaming were preferred for certain vegetables, even by those who normally boil them. Barriers to change need to be considered when planning the promotion of steaming as a regular method of cooking vegetables, although it may be more convincing to use vegetables such as broccoli that are perceived as being most acceptable when steamed.

Dietary fat and cecal microbial activity in the rat

Weanling rats were fed low-fat (1% w/w safflower oil) or high-fat (1% w/w safflower oil plus 35% w/w beef fat or cocoa butter) diets for 30 days, and the activities of five cecal microbial enzymes were determined. When compared with the low-fat diet, beef fat significantly increased total cecal beta-glucuronidase activity, but cocoa butter, with a similar fatty acid composition, did not. Both high-fat diets significantly decreased total cecal azoreductase, beta-glucosidase, and nitrate reductase activities, but neither significantly affected urease activity. When expressed as specific activities (per 10(11) bacteria), cocoa butter decreased azoreductase, and beef fat caused increases of beta-glucuronidase and urease. Beef fat, but not cocoa butter, significantly reduced cecal bacterial numbers when compared to the low-fat diet. Both high-fat diets led to equivalent reductions in the proportion of aerobic bacteria.

Systematic review of randomized controlled trials of low-carbohydrate vs. low-fat/low-calorie diets in the management of obesity and its comorbidities

There are few studies comparing the effects of low-carbohydrate/high-protein diets with low-fat/high-carbohydrate diets for obesity and cardiovascular disease risk. This systematic review focuses on randomized controlled trials of low-carbohydrate diets compared with low-fat/low-calorie diets. Studies conducted in adult populations with mean or median body mass index of > or =28 kg m(-2) were included. Thirteen electronic databases were searched and randomized controlled trials from January 2000 to March 2007 were evaluated. Trials were included if they lasted at least 6 months and assessed the weight-loss effects of low-carbohydrate diets against low-fat/low-calorie diets. For each study, data were abstracted and checked by two researchers prior to electronic data entry. The computer program Review Manager 4.2.2 was used for the data analysis. Thirteen articles met the inclusion criteria. There were significant differences between the groups for weight, high-density lipoprotein cholesterol, triacylglycerols and systolic blood pressure, favouring the low-carbohydrate diet. There was a higher attrition rate in the low-fat compared with the low-carbohydrate groups suggesting a patient preference for a low-carbohydrate/high-protein approach as opposed to the Public Health preference of a low-fat/high-carbohydrate diet. Evidence from this systematic review demonstrates that low-carbohydrate/high-protein diets are more effective at 6 months and are as effective, if not more, as low-fat diets in reducing weight and cardiovascular disease risk up to 1 year. More evidence and longer-term studies are needed to assess the long-term cardiovascular benefits from the weight loss achieved using these diets.

Use of Cryopreserved Cells for Enabling Greater Flexibility in Compound Profiling

Measurement of intracellular calcium release following agonist challenge within cells expressing the relevant membrane protein is a commonly used format to derive structure-activity relationship (SAR) data within a compound profiling assay. The Fluorometric Imaging Plate Reader (FLIPR) has become the gold standard for this purpose. FLIPR traditionally uses cells that are maintained in continuous culture for compound profiling of iterative chemistry campaigns. This supply dictates that assays can only be run on 4 of 5 weekdays, or alternative cell culture machinery is required such that plating can occur remotely at the weekend. The data reported here demonstrate that high-quality compound profiling data can be generated from the use of cryopreserved cells and that these cells can also be plated at various densities to generate equivalent data between 24 and 72 h post-plating. Hence, the authors report a method that allows data generation throughout the week and without the requirement of highly automated cell culture or continuous culture. ( Journal of Biomolecular Screening 2008:354-362)

Equine multinodular pulmonary fibrosis: a newly recognized herpesvirus-associated fibrotic lung disease

Pulmonary fibrosis and interstitial lung disease are poorly understood in horses; the causes of such conditions are rarely identified. Equine herpesvirus 5 (EHV-5) is a gamma-herpesvirus of horses that has not been associated with disease in horses. Pathologic and virologic findings from 24 horses with progressive nodular fibrotic lung disease associated with EHV-5 infection are described and compared with 23 age-matched control animals. Gross lesions consisted of multiple nodules of fibrosis throughout the lungs. Histologically, there was marked interstitial fibrosis, often with preservation of an "alveolar-like" architecture, lined by cuboidal epithelial cells. The airways contained primarily neutrophils and macrophages. Rare macrophages contained large eosinophilic intranuclear viral inclusion bodies; similar inclusion bodies were also found cytologically. The inclusions were identified as herpesviral-like particles by transmission electron microscopy in a single horse. In situ hybridization was used to detect EHV-5 nucleic acids within occasional macrophage nuclei. With polymerase chain reaction (PCR), the herpesviral DNA polymerase gene was detected in 19/24 (79.2%) of affected horses and 2/23 (8.7%) of the control horses. Virus genera-specific PCR was used to detect EHV-5 in all of the affected horses and none of the control horses. EHV-2 was detected in 8/24 (33.3%) of affected horses and 1/9 (11.1%) of the control horses. This disease has not been reported before, and the authors propose that based upon the characteristic gross and histologic findings, the disease be known as equine multinodular pulmonary fibrosis. Further, we propose that this newly described disease develops in association with infection by the equine gamma-herpesvirus, EHV-5.

Orphan seven transmembrane receptor screening

Drug discovery has successfully exploited the superfamily of seven transmembrane receptors (7TMR), with over 35% of clinically marketed drugs targeting them. However, it is clear that there remains an undefined potential within this protein family for successful drugs of the future. The human genome sequencing project identified approximately 720 genes that belong to the 7TMR superfamily. Around half of these genes encode sensory receptors, while the other half are potential drug targets. Natural ligands have been identified for approximately 215 of these, leaving 155 receptors classified as orphan 7TMRs having no known ligand. Deorphanisation of these receptors by identification of natural ligands has been the traditional method enabling target validation by use of these ligands as tools to define biological relevance and disease association. Such ligands have been paired with their cognate receptor experimentally by screening of small molecule and peptide ligands, reverse pharmacology and the use of bioinformatics to predict candidate ligands. In this manuscript, we review the methodologies developed for the identification of ligands at orphan 7TMRs and exemplify these with case studies.

Peliod hepatocellular carcinoma in a domesticated ferret (Mustela putorius furo)

Peliod hepatocellular carcinoma was diagnosed in a domesticated ferret (Mustela putorius furo). The diagnosis was made using immunohistochemical analysis, histologic examination, and the accepted classification schemes based on histomorphologic features. Bilateral, adrenocortical hyperplasia also was evident. Speculation about a possible association between the variant of hepatocellular neoplasia diagnosed in this animal and its adrenal pathologic changes was done.

Meningoencephalomyelitis caused by Neospora caninum in a juvenile fallow deer (Dama dama)

Neosporosis, caused by the protozoan parasite Neospora caninum, is a serious cause of bovine abortion, stillbirth and perinatal death. This paper reports a clinical neosporosis in a 3-week-old fallow deer (Dama dama). The fawn was full term and appeared normal at birth. Histological lesions consisted of a multifocal necrotizing and granulomatous meningoencephalomyelitis, with intralesional protozoal cysts. Positive immunohistochemical staining and characteristic PCR products confirmed the diagnosis of N. caninum infection.

West Nile virus infection in Eastern fox squirrels (Sciurus niger)

Since the initial outbreak of West Nile virus (WNV) in the northeastern United States in 1999, the virus has rapidly spread westward and southward across the USA, causing high mortality in crows as well as sporadic mortality in horses, humans, and a wide variety of birds. In 2002 the epidemic widened as hundreds of equine and human cases and sporadic cases in other mammalian species were reported. This is the first report of WNV infection in three Eastern fox squirrels (Sciurus niger). Neurologic signs included head tilt, uncoordinated movement, paralysis, and tremors. Gross lesions were absent. Microscopic lesions consisted of lymphoplasmacytic inflammation involving the brain, heart, kidney, and liver. Formalin-fixed tissues from the three squirrels were tested for WNV antigen by immunohistochemical staining and for WNV-specific RNA by reverse transcriptase-polymerase chain reaction (RT-PCR). The kidneys of all three squirrels stained positive with immunohistochemistry for WNV, whereas the brain and heart were positive in only one animal. Two of the three squirrels were positive for WNV by RT-PCR.

The rabbit motilin receptor: molecular characterisation and pharmacology

Following identification of the human motilin receptor, we isolated the rabbit orthologue by PCR amplification and found this to be 85% identical to the open reading frame of the human receptor. The protein encoded was 84% identical to the human polypeptide. In HEK293T cells transfected with the rabbit receptor, motilin concentration-dependently increased intracellular calcium mobilisation (pEC50=9.25). After transfection with Go1alpha, motilin similarly stimulated [35S]GTPgammaS binding (pEC50=8.87). Using both systems, similar values were obtained with the human receptor, with rank-order potencies of motilin=[Nle13]-motilin>erythromycin; ghrelin was ineffective. In circular muscle preparations of rabbit gastric antrum, [Nle13]-motilin 0.1-30 nM concentration-dependently increased the amplitude of electrically-evoked, neuronally-mediated contractions (pEC50=8.3); higher concentrations increased the muscle tension (30-3000 nM). Both responses to [Nle13]-motilin faded rapidly during its continual presence. Rat or human ghrelin 0.01-10 microM were without activity. Erythromycin 30-3000 nM and 10 microM, respectively, increased neuronal activity and muscle tension in rabbit stomach. Unlike [Nle13]-motilin, the increase in neuronal activity did not fade during continual presence of submaximally-effective concentrations of erythromycin; some fade was observed at higher concentrations. We conclude that the pharmacology of the rabbit motilin receptor is similar to the human orthologue and, when expressed as a recombinant, comparable to the native receptor. However, in terms of their ability to increase neuronal activity in rabbit stomach, [Nle13]-motilin and erythromycin are distinguished by different response kinetics, reflecting different rates of ligand degradation and/or interaction with the receptor.

Relationship between knowledge and claimed compliance with genuine and false nutrition messages

Nutrition education messages about eight different foods, four of them genuine and four false, were set in a Latin square and eight questionnaires were produced and distributed to customers sitting in a cafe. For each message, subjects were asked to score the extent of their agreement and compliance. Scores were adjusted to remove effects of sex, age group and social class. Correlation coefficients between agreement and compliance scores were significant (P < 0.001) for each message. Subjects who had correct knowledge tended towards correct behaviour and those who agreed with misconceptions tended to have incorrect behaviour.

Design and analysis of food frequency questionnaires--review and novel method

A novel method is proposed for the design and analysis of a food frequency questionnaire facilitated by a computer program. The method relies on a weighed inventory undertaken by a sample of the population that is combined into a database along with the nutrient analyses of the foods consumed. The program provides an interface that enables the researcher to see the total amount of each food that was consumed, decide on what questions to ask and allocate the relevant foods to these questions. The approach means that all foods consumed can appear in the questionnaire. The nutrient analysis for each question is a weighted mean depending on the inventory. The portion weight employed for each question is derived from the weights of foods consumed in the inventory and any misperceptions in the frequency of consumption of all the subjects are corrected by calculating a factor to multiply by the frequency from the questionnaire. A viability study established the practicability of the method.

Gabapentin is not a GABAB receptor agonist

Recent experiments have demonstrated that formation of functional type B gamma-aminobutyric acid (GABA(B)) receptors requires co-expression of two receptor subunits, GABA(B1) and GABA(B2). Despite the identification of these subunits and a number of associated splice variants, there has been little convincing evidence of pharmacological diversity between GABA(B) receptors comprising different subunit combinations. However, Ng et al. [Mol. Pharmacol., 59 (2000) 144] have recently suggested a novel and important pharmacological difference between GABA(B) receptor heterodimers expressing the GABA(B1a) and GABA(B1b) receptor subunits. This study suggested that the antiepileptic GABA analogue gabapentin (Neurontin) is an agonist at GABA(B) receptors expressing the GABA(B1a) but not the GABA(B1b) receptor subunit. The importance of this finding with respect to identifying novel GABA(B) receptor subunit specific agonists prompted us to repeat these experiments in our own [35S]-GTPgammaS binding and second messenger assay systems. Here we report that gabapentin was completely inactive at recombinant GABA(B) heterodimers expressing either GABA(B1a) or GABA(B1b) receptor subunits in combination with GABA(B2) receptor subunits. In addition, in both CA1 and CA3 pyramidal neurones from rodent hippocampal slices we were unable to demonstrate any agonist-like effects of gabapentin at either pre- or post-synaptic GABA(B) receptors. In contrast, gabapentin activated a GABA(A) receptor mediated chloride conductance. Our data suggest that gabapentin is not a GABA(B)-receptor agonist let alone a GABA(B) receptor subunit selective agonist.