Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

Chemical genetic screens are a powerful tool for exploring how cancer cells' response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or nuclear factor κB (NF-κB) inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

Chemical genetic screens are a powerful tool for exploring how cancer cells' response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or NF-kB inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.

Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

Single-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which frustrates efforts to compare the gene expression programs of different cell types. "Spike-in" RNA standards help control for technical variation in scRNA-seq, but using them with recently developed, ultra-scalable scRNA-seq methods based on combinatorial indexing is not feasible. Here, we describe a simple and cost-effective method for normalizing transcript counts and subtracting technical variability that improves differential expression analysis in scRNA-seq. The method affixes a ladder of synthetic single-stranded DNA oligos to each cell that appears in its RNA-seq library. With improved normalization we explore chemical perturbations with broad or highly specific effects on gene regulation, including RNA pol II elongation, histone deacetylation, and activation of the glucocorticoid receptor. Our methods reveal that inhibiting histone deacetylation prevents cells from executing their canonical program of changes following glucocorticoid stimulation.

Abstract 2281: Impact of DNA contaminants on next-generation sequencing data quality

Nucleic acid purification and clean-up are critical steps for genomics applications, including next-generation sequencing (NGS). Variability in the quality of sample extraction methods can result in differential removal of inhibitors, or reaction contaminants, that diminish NGS experimental data quality. To maximize sample recovery and create more consistent results, efficient removal of inhibitors or contaminants is critical during nucleic acid isolation and purification. In this study, we examine the effect of three common tissue-specific nucleic acid contaminants: (1) collagen, (2) myoglobin, and (3) melanin, on NGS library prep and sequencing metrics. These contaminants are present in skin and muscle tissue and are known to cause inhibition of PCR reactions. In addition, we will extract DNA from both of these samples types and evaluate the performance of two commonly used DNA extraction technologies: (1) magnetic bead-based clean-up; and (2) silica-based columns, for their ability to remove contaminants from DNA extractions and the differential effect of these extraction methods on downstream NGS metrics. These findings demonstrate the importance of the choice of extraction chemistry on NGS metrics and read quality. We also demonstrate that magnetic bead-based- protocols offer a superior reliable, rapid, automatable method to produce high quality DNA and remove contaminants.

Citation Format: Amy Dubinsky, Lauren Saunders. Impact of DNA contaminants on next-generation sequencing data quality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2281.

[Voiding dysfunction and access to toilets among elementary school children: A Toulouse school district study]

Not urinating regularly, voluntarily restraining oneself at school promotes the occurrence of voiding disorders.

AIM

To determine the prevalence of such disorders in elementary schools (students from 1st to 5th grade) and analyze the role of access to school toilets on voiding habits.

METHOD

Observational, descriptive epidemiological study during the 2017-2018 school year by electronic questionnaire with parents of pupils attending elementary school.

RESULTS

2119 questionnaires were analyzed. The graders sex ratio was 1.07 (1087 boys). 410 families (19%) were classified as "popular" class. First, second and third graders represented 60% of the enrollment (N = 1273). Overall use of school toilets was 87% and 69% of students had appropriate use for urine. The main obstacles to their use were lack of hygiene and comfort (51%), lack of security or privacy (33%), limited accessibility (28%). The overall prevalence of urinary elimination disorders was 9%. Girls had more inappropriate use of the toilet for urine (36% vs 27%, OR 1.5, P = 0.0004). The factors associated with urinary elimination disorders were: not using the toilet (13% vs 9 %, OR 1.5, P = 0.04), being a girl (14% vs 5%, OR 3.5, P < 0.0001), belonging to the working class (14% vs 8% OR 1.8, P = 0.0008).

CONCLUSION

This situation, which is a long-denounced major public health problem, mainly affects girls and also reveals social inequalities in the use of school toilets.

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of information transferred from a potential regulator to its downstream target. We apply Scribe and other leading approaches for causal network reconstruction to several types of single-cell measurements and show that there is a dramatic drop in performance for "pseudotime"-ordered single-cell data compared with true time-series data. We demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods such as "RNA velocity" restore some degree of coupling through an analysis of chromaffin cell fate commitment. These analyses highlight a shortcoming in experimental and computational methods for analyzing gene regulation at single-cell resolution and suggest ways of overcoming it.

Visual Immunoprecipitate Assay (VIP) for Listeria monocytogenes and Related Listeria Species Detection in Selected Foods: Collaborative Study

Six foods representing a variety of food products were analyzed by the Assurance Listeria polyclonal enzyme immunoassay (EIA) and by either the Bacteriological Analytical Manual or the U.S. Department of Agriculture culture method for detecting Listeria monocytogenes and related Listeria species. Samples of each food type, at each inoculation level, were analyzed simultaneously by both methods. A total of 19 laboratories representing federal government agencies and private industry in the United States and Canada participated. Food types were inoculated with Listeria species including L. monocytogenes, with the exception of 3 lots of green beans, which were naturally contaminated. During this study, 1764 samples and controls were analyzed and confirmed, of which 492 were positive and 947 were negative by both methods. There were 159 samples that were positive by culture method but negative by the EIA and 188 that were negative by culture method but positive by EIA. Twenty-two samples were negative by EIA and by culture method but confirmed positive when Assurance selective enrichment broths were subcultured to selective agar. The Assurance polyclonal EIA for detecting L. monocytogenes and related Listeria species in foods has been adopted first action by AOAC INTERNATIONAL.

Dry Rehydratable Film Method for Enumerating Confirmed Escherichia coli in Poultry, Meats, and Seafood: Collaborative Study

A rehydratable dry-film plating method for Escherichia coli, the Petrifilm E. coli/Coliform (EC) Count Plate in foods, has been compared with the AOAC INTERNATIONAL most probable number (MPN) method. Eleven laboratories participated in the collaborative study. Three E. coli levels in 8 samples each of frozen raw ground turkey, frozen raw ground beef, and frozen cooked fish were tested in duplicate. Mean log counts for the Petri film plate procedure were not significantly different from those for the MPN procedure for cooked fish samples inoculated with low or high inocula levels, for samples of raw turkey inoculated at medium level, and for beef inoculated at low, medium, and high levels. Repeatability and reproducibility vari ances of the Petrifilm EC Plate method recorded at 24 h were as good as or better than those of the MPN method. The dry rehydratable film method for enumerating confirmed E. coli in poultry, meats, and seafood has been adopted first action by AOAC INTERNATIONAL.

High-Sensitivity Dry Rehydratable Film Method for Enumeration of Coliforms in Dairy Products: Collaborative Study

A dry-film coliform count plate that is inoculated with 5 mL sample was compared with the Violet Red Bile Agar plate method in a collaborative study by 18 laboratories. Products analyzed were 2% milk, chocolate milk, cream, vanilla ice cream, cottage cheese, and cheese. Collaborators tested blind duplicate uninoculated samples and samples inoculated at low, medium, and high level. Significantly (P< 0.05) higher numbers of coliforms were recovered by the dry-film method from 2% milk samples at the 3 inoculum levels, the chocolate milk at the low- and high-inoculum levels, and the cream at the high-inoculum level. Significantly higher counts were obtained by the agar method for cottage cheese samples at the low-inoculum level. The repeatability standard deviation for the dry-film method was significantly higher for the high-inoculum level chocolate milk sample and the medium-inoculum level cottage cheese. The same statistic was significantly higher for the agar method at all 3 inoculum levels in the 2% milk and the medium-inoculum level cream. The high-sensitivity dry rehydratable film method for enumeration of coliforms in dairy products has been adopted first action by AOAC INTERNATIONAL.

Assurance Polyclonal Enzyme Immunoassay for Detection of Listeria monocytogenes and Related Listeria Species in Selected Foods: Collaborative Study

Six foods representing a variety of food products were analyzed by the Assurance Listeria polyclonal enzyme immunoassay (EIA) and by either the Bacteriological Analytical Manual or the U.S. Department of Agriculture culture method for detecting Listeria monocytogenes and related Listeria species. Samples of each food type, at each inoculation level, were analyzed simultaneously by both methods. A total of 19 laboratories representing federal government agencies and private industry in the United States and Canada participated. Food types were inoculated with Listeria species including L. monocytogenes, with the exception of 3 lots of green beans, which were naturally contaminated. During this study, 1764 samples and controls were analyzed and confirmed, of which 492 were positive and 947 were negative by both methods. There were 159 samples that were positive by culture method but negative by the EIA and 188 that were negative by culture method but positive by EIA. Twenty-two samples were negative by EIA and by culture method but confirmed positive when Assurance selective enrichment broths were subcultured to selective agar. The Assurance polyclonal EIA for detecting L. monocytogenes and related Listeria species in foods has been adopted first action by AOAC INTERNATIONAL.

Massively multiplex chemical transcriptomics at single-cell resolution

High-throughput chemical screens typically use coarse assays such as cell survival, limiting what can be learned about mechanisms of action, off-target effects, and heterogeneous responses. Here, we introduce "sci-Plex," which uses "nuclear hashing" to quantify global transcriptional responses to thousands of independent perturbations at single-cell resolution. As a proof of concept, we applied sci-Plex to screen three cancer cell lines exposed to 188 compounds. In total, we profiled ~650,000 single-cell transcriptomes across ~5000 independent samples in one experiment. Our results reveal substantial intercellular heterogeneity in response to specific compounds, commonalities in response to families of compounds, and insight into differential properties within families. In particular, our results with histone deacetylase inhibitors support the view that chromatin acts as an important reservoir of acetate in cancer cells.

3M™ Petrifilm™ Enterobacteriaceae Count Plate Method for Enumeration of Enterobacteriaceae in Selected Foods: Collaborative Study

The practice of detecting and enumerating all oxidase-negative, glucose-fermenting-Gram-negative rods (i.e., the family Enterobacteriaceae) isused to indicate unsanitary or inadequate food processing conditions. The objective of this interlaboratory collaborative study was to evaluate and compare the methods described in Standard Methods for the Examination of Dairy Products (SMEDP) and the Compendium of Methods for the Microbiological Examination of Foods (Compendium) with a commercial product, the 3M™ Petrifilm™ Enterobacteriaceae Count Plate, for the recovery of Enterobacteriaceae in foods. Six foods—cheddar cheese, milk, flour, frozen prepared meals, frozen broccoli, and nut pieces—were analyzed for Enterobacteriaceae by 12 collaborating laboratories. For each food tested, the collaborators received 8 blind test portions consisting of a control test portion and 3 levels of inoculated test portion, each in duplicate. Each test portion was tested by the Petrifilm Enterobacteriaceae Count Plate method as well as the SMEDP or Compendium methods. The precision estimates (repeat-ability or within-laboratory variation, and reproducibility or between-laboratory variation) were calculated with standard statistical techniques.

Dry Rehydratable Film Method for Rapid Enumeration of Coliforms in Foods (3M™ Petrifilm™ Rapid Coliform Count Plate): Collaborative Study

A rehydratable dry-film plating method for coliforms in foods, the 3M™ Petrifilm™ Rapid Coliform Count plate method, was compared with the U.S. Food and Drug Administration's Bacteriological Analytical Manual method for nondairy foods and the American Public Health Association's Standard Methods for the Examination of Dairy Products (SMEDP) method for dairy foods. Six food types, vanilla ice cream, cheddar cheese, fresh refrigerated uncooked pasta, wheat flour, prepared frozen macaroni and cheese, and frozen hash browns, were analyzed for coliforms by 11 collaborating laboratories. For each food product tested, the collaborators received 8 blind samples consisting of a control sample and 3 levels of inoculated sample, each in duplicate. The mean log counts for the methods were comparable. The repeatability and reproducibility variances of the Petrifilm Rapid Coliform Count method at 14 and 24 h were not significantly different from those of the standard methods.

VIDAS® Enzyme-Linked Immunofluorescent Assay for Detection of Listeria in Foods: Collaborative Study

The VIDAS LIS method and the traditional culture methods for detection of Listeria species in food were evaluated in a multilaboratory comparative study. The 6 foods tested were either naturally contaminated or inoculated with 3 different concentrations of Listeria. Results for each food and each contamination level with the VIDAS LIS method were as good as or better than those obtained with the traditional culture method. Of 1558 samples tested, 935 were positive: 839 by the VIDAS method and 809 by standard culture methods. Overall false negative rates were 10.3 and 13.5% for the VIDAS LIS and culture methods, respectively. The false positive rate for the VIDAS LIS assay was 1.4% based on 9 VIDAS LIS positive assays that did not confirm positive by isolation of Listeria. The agreement between the VIDAS LIS and culture methods for all samples tested was 86%.

Abstract 2233: Correlation between mutations found in FFPE tumor tissue and paired cfDNA samples

Cell free DNA (cfDNA) consists of small (150 - 500 bp) DNA fragments that circulate in the blood. cfDNA levels tend to be low in healthy, non-pregnant patients, and increase in patients with cancer, pregnancy, or extensive damage to tissue. cfDNA is believe to derive mostly from apoptotic cells, and biomarkers for a variety of diseases have been found in cfDNA. As cfDNA is extracted from blood, it is a non-invasive way to detect disease; however, there is some concern that cfDNA does not contain the same biomarkers as tumor tissue. This study measures the efficacy of cfDNA as a biomarker detection medium by comparing mutations found in both FFPE tumor samples and paired cfDNA samples. This study determines whether the same biomarkers are found in each sample type, and which of those can be used as biomarkers in both and which are preferred biomarkers for only a single sample type. Trends in mutation detection with the two different sample types are discussed.

Citation Format: Lauren Saunders, Antonia Hur, Brittany Niccum, Asmita Patel. Correlation between mutations found in FFPE tumor tissue and paired cfDNA samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2233.

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana

Single cell RNA sequencing can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach to Arabidopsis (Arabidopsis thaliana) root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat-shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana

Single cell RNA sequencing can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach to Arabidopsis (Arabidopsis thaliana) root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat-shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.

A multicentre, UK, retrospective, observational study to assess the effectiveness of insulin glargine 300 units/ml in treating people with Type 1 diabetes mellitus in routine clinical practice (SPARTA)

AIM

To conduct an open-label study to provide UK real-world evidence regarding the use of insulin glargine 300 units/ml (U300) in people with Type 1 diabetes mellitus.

METHODS

People with Type 1 diabetes who had been prescribed U300 ≥6 months before data collection and had HbA_1c levels recorded within 3 months prior to U300 (baseline) were included. The primary endpoint was change in HbA_1c from baseline to month 6 after U300 initiation. Other endpoints included number of documented hypoglycaemic and diabetic ketoacidosis episodes, and change in daily basal insulin dose.

RESULTS

A total of 298 people with Type 1 diabetes were included [mean age 42.1 years, mean HbA_1c 79 mmol/mol (9.4%)]. After U300 initiation, the mean reduction in HbA_1c from baseline to month 6 was -4 mmol/mol (-0.4%; P<0.001; n=188). The total daily basal insulin dose at 6 months was 1.3 units higher than at the time of U300 initiation (P<0.001; n=275) but was not significantly different from the prior basal insulin dose. There was no clinically significant difference in weight between baseline and month 6 [mean difference +0.7 kg, 95% CI -0.1, 1.5; P=0.084; n=115). During the 6 months before and after U300 initiation, severe hypoglycaemic episodes were documented for 6/298 and 4/298 participants. Diabetic ketoacidosis episodes requiring Accident and Emergency department visits or hospitalization were documented for 4/298 and 6/298 participants, before and after U300 initiation, respectively.

CONCLUSIONS

In people with Type 1 diabetes, a change in basal insulin to U300 was associated with clinically and statistically significant HbA_1c improvements, without significant changes in basal insulin dose and weight. Documented severe hypoglycaemia episodes and diabetic ketoacidosis requiring Accident and Emergency department visits or hospitalization were low and similar before and after U300 initiation.

Epidermal growth factor receptor activity is elevated in glioma cancer stem cells and is required to maintain chemotherapy and radiation resistance

Glioblastoma remains among the most aggressive of all human and canine malignancies, displaying high mortality rates and limited treatment options. We propose that given the similarities between canine and human gliomas, such as incidence of occurrence, histopathology, molecular characteristics, and response to therapy, that canine gliomas are a natural model of the human disease. A range of human and canine tumours have been shown to harbor specific subpopulations of cells with stem cell-like properties that initiate and maintain neoplasticity while resisting conventional therapies. Here, we show that both canine and human glioma cell lines contain a small population of cancer stem cells (CSCs), and by molecular profiling highlight the important role of the epidermal growth factor receptor (EGFR) pathway in canine CSCs. EGFR signaling is crucial in the regulation of cancer cell proliferation, migration and survival. To date EGFR-targeted interventions alone have been largely ineffective. Our findings confirm that specifically inhibiting EGFR signaling alone has no significant effect on the viability of CSCs. However inhibition of EGFR did enhance the chemo- and radio-sensitivity of both canine and human glioma CSCs, enabling this resistant, tumourigenic population of cells to be effectively targeted by conventional therapies.

Hypertensive disorders of pregnancy and gestational diabetes mellitus among French Caribbean women chronically exposed to chlordecone

Few studies have explored the consequences of environmental exposure to organochlorine pesticides for gestational hypertension (GH), preeclampsia (PE) and gestational diabetes mellitus (GDM). Chlordecone is a persistent organochlorine pesticide that was used intensively, and almost exclusively, in the French West Indies until 1993. We investigated the impact of prenatal exposure to chlordecone on the occurrence of GDM, GH and PE by studying 779 pregnant women enrolled in a prospective mother-child cohort (Timoun Study) in Guadeloupe between 2004 and 2007. Chlordecone exposure was determined by assaying maternal plasma and information about pregnancy complications was obtained from midwives, pediatricians and hospital medical records after delivery. The risks of GH (n=65), PE (n=31) and GDM (n=71) were estimated by multiple logistic regression including potential confounders. Levels of chlordecone plasma concentration in the third (OR=0.2; 95% confidence interval (CI): 0.1, 0.5) and fourth quartiles (OR=0.3; 95% CI: 0.2, 0.7) were associated with a statistically significant decrease in the risk of GH. A log10 increase in chlordecone concentration was significantly associated with lower risk of GH (OR=0.4; 95% CI: 0.2, 0.6). No significant associations were observed between the chlordecone exposure and the risk of PE or GDM. This study suggests an inverse association between chlordecone exposure during pregnancy and GH. Further studies are required to determine the underlying mechanism, or the potential unknown confounding factors, resulting in this association.

Improving prediction of surgical site infection risk with multilevel modeling

Background

Surgical site infection (SSI) surveillance is a key factor in the elaboration of strategies to reduce SSI occurrence and in providing surgeons with appropriate data feedback (risk indicators, clinical prediction rule).

Aim

To improve the predictive performance of an individual-based SSI risk model by considering a multilevel hierarchical structure.

Patients and Methods

Data were collected anonymously by the French SSI active surveillance system in 2011. An SSI diagnosis was made by the surgical teams and infection control practitioners following standardized criteria. A random 20% sample comprising 151 hospitals, 502 wards and 62280 patients was used. Three-level (patient, ward, hospital) hierarchical logistic regression models were initially performed. Parameters were estimated using the simulation-based Markov Chain Monte Carlo procedure.

Results

A total of 623 SSI were diagnosed (1%). The hospital level was discarded from the analysis as it did not contribute to variability of SSI occurrence (p  = 0.32). Established individual risk factors (patient history, surgical procedure and hospitalization characteristics) were identified. A significant heterogeneity in SSI occurrence between wards was found (median odds ratio [MOR] 3.59, 95% credibility interval [CI] 3.03 to 4.33) after adjusting for patient-level variables. The effects of the follow-up duration varied between wards (p<10⁻⁹), with an increased heterogeneity when follow-up was <15 days (MOR 6.92, 95% CI 5.31 to 9.07]). The final two-level model significantly improved the discriminative accuracy compared to the single level reference model (p<10⁻⁹), with an area under the ROC curve of 0.84.

Conclusion

This study sheds new light on the respective contribution of patient-, ward- and hospital-levels to SSI occurrence and demonstrates the significant impact of the ward level over and above risk factors present at patient level (i.e., independently from patient case-mix).

Effect of a Mediterranean diet during pregnancy on fetal growth and preterm delivery: results from a French Caribbean Mother-Child Cohort Study (TIMOUN)

BACKGROUND

Recent studies suggest that a Mediterranean dietary pattern during pregnancy may influence pregnancy outcomes. The aim of this study was to evaluate the effect of adherence to a Mediterranean diet (MD) during pregnancy on fetal growth restriction (FGR) and preterm delivery (PTD) in a French Caribbean island where the population is largely of African descent and presents dietary patterns similar to MD.

METHODS

Using data from the TIMOUN Mother-Child Cohort Study conducted in Guadeloupe (French West Indies) between 2004 and 2007, we analysed data for 728 pregnant women who delivered liveborn singletons without any major congenital malformations. Degree of adherence to MD during pregnancy was evaluated with a semi-quantitative food frequency questionnaire based on nine dietary criteria. Multiple logistic regression models were used to analyse birth outcomes while taking potential confounders into account.

RESULTS

Overall there was no association between MD adherence during pregnancy and the risk of PTD or FGR. However, pre-pregnancy body mass index was a strong effect modifier, and MD adherence was associated with a decreased risk of PTD specifically in overweight and obese women (adjusted odds ratio 0.7, 95% confidence interval 0.6, 0.9) (P heterogeneity <0.01).

CONCLUSIONS

These results suggest that Caribbean diet during pregnancy may carry some benefits of MD and may contribute to reduce the risk of PTD in overweight and obese pregnant women.

Iterative thoracentesis as first-line treatment of complicated parapneumonic effusion

Rationale

Optimal management of complicated parapneumonic effusions (CPPE) remains controversial.

Objectives

to assess safety and efficacy of iterative therapeutic thoracentesis (ITTC), the first-line treatment of CPPE in Rennes University Hospital.

Methods

Patients with CPPE were identified through our computerized database. We retrospectively studied all cases of CPPE initially managed with ITTC in our institution between 2001 and 2010. ITTC failure was defined by the need for additional treatment (i.e. surgery or percutaneous drainage), or death.

Results

Seventy-nine consecutive patients were included. The success rate was 81% (n = 64). Only 3 patients (4%) were referred to thoracic surgery. The one-year survival rate was 88%. On multivariate analysis, microorganisms observed in pleural fluid after Gram staining and first thoracentesis volume ≥450 mL were associated with ITTC failure with adjusted odds-ratios of 7.65 [95% CI, 1.44–40.67] and 6.97 [95% CI, 1.86–26.07], respectively. The main complications of ITTC were iatrogenic pneumothorax (n = 5, 6%) and vasovagal reactions (n = 3, 4%). None of the pneumothoraces required chest tube drainage, and no hemothorax or re-expansion pulmonary edema was observed.

Conclusions

Although not indicated in international recommendations, ITTC is safe and effective as first-line treatment of CPPE, with limited invasiveness.

Risk factors for neurosurgical site infection after neurosurgery in Rennes, France: comparison of logistic and Cox models

The logistic model is widely used to assess the risk factors for surgical site infections (SSIs). An alternative to the logistic model is the Cox model. The objective of this study was to compare these 2 models to identify the risk factors of SSIs in neurosurgery. The Cox model is a valid alternative for assessing the risk factors of SSIs.

The high cost to health and social care of managing falls in older adults living in the community in Scotland

Background and aims

Estimate costs for health and social care services in managing older people in the community who fall.

Method and results

Analyses of predominantly national databases using cost of illness methodologies. In Scotland, 294,000 (34%) of people over 65 years and living in the community fall at least once a year. Of these 20%, almost 60,000 people contacted a medical service for assistance. There were almost 30,000 attendances at GP practices, over 36,100 calls to the Scottish Ambulance Service and 46,816 people presenting at A&E, with 16,549 admitted, 30% with a hip fracture. Mortality was high, 7% during the hospital stay, rising to over 12% at 1 year. Over 20% of patients were unable to return to their homes. Associated costs were over £470 million, with 60% incurred by social services, mainly providing long-term care. Cost per person falling was over £1720, rising to over £8600 for those seeking medical assistance. A hip fracture admission cost £39,490, compared with £21,960 for other falls-related admissions.

Conclusions

Transparent, robust cost information demonstrates the substantial burden of falls for health and social care services and should be a driver for implementing evidence-based interventions to reduce falls.

Erythrocyte pyruvate kinase deficiency in an old-order Amish cohort: longitudinal risk and disease management

Pyruvate kinase deficiency is a chronic illness with age specific consequences. Newborns suffer life-threatening hemolytic crisis and hyperbilirubinemia. Adults are at risk for infections because of asplenia, pregnancy-related morbidity, and may suffer organ damage because of systemic iron overload. We describe 27 Old Order Amish patients (ages 8 months-52 years) homozygous for c.1436G>A mutations in PKLR. Each subject had a predictable neonatal course requiring packed red blood cell transfusions (30 ± 5 mL/kg) to control hemolytic disease and intensive phototherapy to prevent kernicterus. Hemochromatosis affected 29% (n = 4) of adult patients, who had inappropriately normal serum hepcidin (34.5 ± 12.7 ng/mL) and GDF-15 (595 ± 335pg/mL) relative to hyperferritinemia (769 ± 595 mg/dL). A high prevalence of HFE gene mutations exists in this population and may contribute to iron-related morbidity. Based on our observations, we present a strategy for long-term management of pyruvate kinase deficiency.

A Light-Scattering Study of Lysolecithin Sols

Sols of four samples of lysolecithin have been studied by means of a light-scattering apparatus. The results of a large number of measurements have been analysed statistically. They indicate that the mean molecular weight of the micelles in the sols is 92,400, the experimental error in this estimate being 7 per cent.

Implementation of response to intervention: a snapshot of progress

This article provides a snapshot of how all 50 states are progressing with the development and implementation of response-to-intervention (RtI) models 1 year after the final regulations for the Individuals with Disabilities Education Act were passed. Data were collected through a review of existing state department of education Web sites and conversations with representatives in each state department of education. Information related to RtI model type, implementation status, professional development, criteria for eligibility, and specific features of individual state RtI models are presented. Findings indicate that most states are in some phase of RtI development, although approaches vary widely throughout the country. Implications for research and practice are discussed.

Predictors of in-hospital mortality following operative management of hip fractures

OBJECTIVE

To identify predictors of in-hospital mortality and hospital stay following hip fractures.

DESIGN

Retrospective cohort study of 185 consecutive patients.

SETTING

Tertiary Care University Hospital.

PARTICIPANTS

Individuals requiring operative treatment of a proximal femoral fracture excluding those individuals < 50 years old, with femoral head or subtrochanteric fractures, and significant co-morbidity.

OUTCOMES

In-hospital mortality and length of hospital stay (days).

RESULTS

116 patients met the inclusion criteria. Predictors of in-hospital mortality from logistic regression analysis included male gender (odds ratio with 95% CI: 5.5, 1.5-20.5), admission from a long term care facility (5.5, 1.4-22.6), age greater than 90 years (4.5, 0.9-22.1), and living at home with support (0.2, 0.03-0.9). Predictors of hospital stay from multivariate regression analysis in order of magnitude included presence of a post-operative complication (odds ratio with 95% CI: 14.1, 4.7-44), living at home with support (3.4, 1.3-8.9) and older age (> 85 years) (2.7, 1.0-7.3). Moreover, confusion, urinary tract infections and decubitus ulcers accounted for greater than 50% of all complications encountered. A trend between the number of positive predictors and length of hospital stay was observed.

CONCLUSIONS

Elderly individuals admitted from a long term care facility are at high risk of mortality following operative fixation of hip fractures. Early recognition and aggressive management of post-operative complications such as confusion, urinary tract infections and decubitus ulcers through careful patient monitoring may decrease hospital stays in those that survive.

An investigation of condom use by frequency of sex

OBJECTIVES

To examine the association between condom use and frequency of sex across sexual partner types.

METHODS

Data were collected from African American drug users residing in Washington, DC. Participants were asked to provide the first name of the last three partners with whom they had had vaginal sex, to define the type of relationship, the number of times they had had vaginal sex in the last 30 days with each partner, and whether they had used a condom during their last sexual encounter with each partner. Condom use was examined by frequency of sex in the past 30 days controlling for partner type.

RESULTS

Frequency of sexual encounters varied by partner type. The largest number of sexual encounters was with casual partners, followed by commercial and primary partners, respectively. Within partner types, participants had sex most frequently with primary partners. Condom use was lowest within primary partner relationships. Regardless of partner type, condom use varied consistently depending on the frequency of sex with the same partner.

CONCLUSIONS

Condom use is related to the frequency of sex between partners when partner type is controlled. The association between frequency of sex and condom use is independent of partner type, suggesting that partner type may become less influential in determining condom use as the frequency of sex increases. This finding suggests that contextual factors determining condom use go beyond partner type designations and include other relationship variables.

The acceptability of a computer HIV/AIDS risk assessment to not-in-treatment drug users

The purpose of this paper is to report the results of a study assessing the acceptability of a computer HIV risk assessment instrument administered to not-in-treatment drug users. The study asked three questions related to acceptability: (1) are drug users comfortable responding to HIV risk questions using the computer assessment; (2) do drug users feel that they possess the requisite skill to respond to questions using a computer; and (3) do drug users believe that the responses they provide using the computer assessment will remain private and confidential. This study differs from other assessments of the acceptability of computer assisted data collection in that the population of interest has only limited education and interaction with computers. Furthermore, the study was implemented under field conditions. To conduct the study, an existing HIV risk assessment instrument was adapted for use with the computer. Only slight modifications were made to the content of the instrument. To facilitate data collection with this population, audio enhancement and touch screen were used. Three scales measuring comfort, skill and perceived privacy were developed. Results of analysis showed that drug users are comfortable responding to an HIV risk assessment using computer assisted interviewing. Drug users also perceived that they possessed the requisite skill to successfully complete the interview. And, study participants reported that they believed that their responses using the computer interview would remain private and confidential. Only minor differences in scale scores based on sociodemographic characteristics were found among study participants. Implications of the findings are discussed.