Correction: Reproducible big data science: A case study in continuous FAIRness

[This corrects the article DOI: 10.1371/journal.pone.0213013.].

Midline suprapineal pseudocyst in brain of fetuses with open spina bifida

OBJECTIVES

Recently, it was noted that fetuses with open spina bifida (OSB) may have a midline cystic structure evident on ultrasound. Our aims were to determine the prevalence of this cystic structure, shed light on its pathophysiology and investigate the association between its presence and other characteristic brain findings in fetuses with OSB.

METHODS

This was a single-center retrospective study of all fetuses with OSB and available cineloop images in the axial plane referred to the Ontario Fetal Centre, Toronto, Canada, between June 2017 and May 2022. Ultrasound and magnetic resonance imaging (MRI) data obtained between 18 + 0 and 25 + 6 weeks were reviewed in search of a midline cystic structure. Pregnancy and lesion characteristics were collected. Transcerebellar diameter (TCD), clivus-supraocciput angle (CSA) and additional brain abnormalities (abnormal cavum septi pellucidi (CSP), abnormal corpus callosum (CC) and periventricular nodular heterotopia (PNH)) were assessed. In cases of in-utero repair, imaging findings were reviewed postoperatively. In cases of termination, neuropathological findings were reviewed, if available.

RESULTS

Of 76 fetuses with OSB, 56 (73.7%) had a suprapineal cystic structure on ultrasound. The percentage of agreement between ultrasound and MRI detection was 91.5% (Cohen's kappa coefficient, 0.78 (95% CI, 0.57-0.98)). Brain autopsy in terminated cases revealed a dilatation of the posterior third ventricle, with redundant tela choroidea and arachnoid forming the membranous roof of the third ventricle, anterior and superior to the pineal gland. A cyst wall could not be identified, indicating that the structure was a pseudocyst. The presence of the pseudocyst was associated with a smaller CSA (pseudocyst absent, 62.11 ± 9.60° vs pseudocyst present, 52.71 ± 8.22°; P = 0.04). When the pseudocyst was present, its area was correlated inversely with TCD (r, -0.28 (95% CI, -0.51 to -0.02); P = 0.04). Fetal surgery did not have any impact on the growth rate of the pseudocyst (fetal surgery, 5.07 ± 3.29 mm2 /week vs expectant management, 4.35 ± 3.17 mm2 /week; P = 0.58). The presence of the pseudocyst was not associated with abnormal CSP, CC or presence of PNH. None of the cases with available postnatal follow-up required surgical procedure related to the pseudocyst.

CONCLUSIONS

Approximately 75% of all OSB cases have a suprapineal pseudocyst. Its presence is associated with the degree of hindbrain herniation but not with abnormalities of the CSP and CC or presence of PNH. Thus, it should not be regarded as additional brain pathology and should not preclude fetuses from undergoing fetal surgery for OSB. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

cyjShiny: A cytoscape.js R Shiny Widget for network visualization and analysis

cyjShiny is an open-source R package that allows users to embed network visualization into Shiny apps and R Markdown documents. cyjShiny (https://github.com/cytoscape/cyjShiny) builds on the cytoscape.js Javascript graph library. Additionally, the package provides helper functions to convert common R data representations (e.g., data.frame) into forms compatible with cytoscape.js.

Comparative Evaluation of Pseudomonas aeruginosa Adhesion to a Poly-(2-Methacryloyloxyethyl Phosphorylcholine)-Modified Silicone Hydrogel Contact Lens

Pseudomonas aeruginosa is the most common causative agent associated with microbial keratitis. During contact lens wear, pathogens may be introduced into the ocular environment, which might cause adverse events. Lehfilcon A is a recently developed contact lens with a water gradient surface composed of polymeric 2-methacryloyloxyethyl phosphorylcholine (MPC). MPC is re-ported to impart anti-biofouling properties onto modified substrates. Therefore, in this in vitro experimental study, we tested the capability of lehfilcon A to resist adhesion by P. aeruginosa. Quantitative bacterial adhesion assays using five strains of P. aeruginosa were conducted to compare the adherence properties of lehfilcon A to five currently marketed silicone hydrogel (SiHy) contact lenses (comfilcon A, fanfilcon A, senofilcon A, senofilcon C, and samfilcon A). Compared to lehfilcon A, we observed 26.7 ± 8.8 times (p = 0.0028) more P. aeruginosa binding to comfilcon A, 30.0 ± 10.8 times (p = 0.0038) more binding to fanfilcon A, 18.2 ± 6.2 times (p = 0.0034) more binding to senofilcon A, 13.6 ± 3.9 times (p = 0.0019) more binding to senofilcon C, and 29.5 ± 11.8 times (p = 0.0057) more binding to samfilcon A. These results demonstrate that, for various strains of P. aeruginosa, lehfilcon A reduces bacterial adhesion compared to other contact lens materials.

Complete Recovery of Acanthamoeba Motility among Surviving Organisms after Contact Lens Care Disinfection

Acanthamoeba keratitis is a sight-threatening infection of the cornea which is extremely challenging to treat. Understanding this organism's responses during contact lens contact and disinfection could enhance our understanding of how Acanthamoebae colonize contact lens cases, better inform us on contact lens care solution (CLC) efficacy, and help us better understand the efficacy required of CLC products. To explore this gap in knowledge, we used Acanthamoeba ATCC 30461 and ATCC 50370 trophozoites to examine Acanthamoeba behavior during and after CLC disinfection. Amoebae were added to sterile aluminum flow cells and flow cell solutions were changed to Ringer's solution (control), or one of four CLCs based on biocides (PHMB, PAPB/Polyquad, Polyquad/Aldox, or Polyquad/Alexidine) for 6 h. Each flow cell solution was then changed to axenic culture media (AC6) for 12 h to determine the behavior of amoebae following disinfection. Distance, speed, and displacement were calculated for each organism. As compared to the control of one-quarter Ringer's solution, each CLC significantly impacted Acanthamoeba motility in both the CLC and AC6 conditions. However, the amoebae challenged with the PHMB CLC traveled a significantly greater total distance than with the other three CLCs, indicating differences in effectiveness between biocides. Furthermore, amoebae regaining motility post-disinfection by CLCs were observed to travel considerable distances and thus could be considered dangerous to ocular health. We determined that while all CLCs produced a substantial or complete cessation of movement vs. the control condition during disinfection, those which relied on the Polyquad biocides were the most effective, and that any amoebae which survived disinfection were able to recover motility. Future examinations of these findings should include direct correlations between motility and viability, and how infectivity and motility may be related.

Acanthamoeba spp. aggregate and encyst on contact lens material increasing resistance to disinfection

Introduction

Acanthamoeba keratitis is often caused when Acanthamoeba contaminate contact lenses and infect the cornea. Acanthamoeba is pervasive in the environment as a motile, foraging trophozoite or biocide-resistant and persistent cyst. As contact lens contamination is a potential first step in infection, we studied Acanthamoeba's behavior and interactions on different contact lens materials. We hypothesized that contact lenses may induce aggregation, which is a precursor to encystment, and that aggregated encystment would be more difficult to disinfect than motile trophozoites.

Methods

Six clinically and/or scientifically relevant strains of Acanthamoeba (ATCC 30010, ATCC 30461, ATCC 50370, ATCC 50702, ATCC 50703, and ATCC PRA-115) were investigated on seven different common silicone hydrogel contact lenses, and a no-lens control, for aggregation and encystment for 72 h. Cell count and size were used to determine aggregation, and fluorescent staining was used to understand encystment. RNA seq was performed to describe the genome of Acanthamoeba which was individually motile or aggregated on different lens materials. Disinfection efficacy using three common multi-purpose solutions was calculated to describe the potential disinfection resistance of trophozoites, individual cysts, or spheroids.

Results

Acanthamoeba trophozoites of all strains examined demonstrated significantly more aggregation on specific contact lens materials than others, or the no-lens control. Fluorescent staining demonstrated encystment in as little as 4 hours on contact lens materials, which is substantially faster than previously reported in natural or laboratory settings. Gene expression profiles corroborated encystment, with significantly differentially expressed pathways involving actin arrangement and membrane complexes. High disinfection resistance of cysts and spheroids with multi-purpose solutions was observed.

Discussion

Aggregation/encystment is a protective mechanism which may enable Acanthamoeba to be more disinfection resistant than individual trophozoites. This study demonstrates that some contact lens materials promote Acanthamoeba aggregation and encystment, and Acanthamoeba spheroids obstruct multi-purpose solutions from disinfecting Acanthamoeba.

Microbial Adherence to Contact Lenses and Pseudomonas aeruginosa as a Model Organism for Microbial Keratitis

Microbial keratitis (MK), the infection of the cornea, is a devastating disease and the fifth leading cause of blindness and visual impairment around the world. The overwhelming majority of MK cases are linked to contact lens wear combined with factors which promote infection such as corneal abrasion, an immunocompromised state, improper contact lens use, or failing to routinely disinfect lenses after wear. Contact lens-related MK involves the adherence of microorganisms to the contact lens. Therefore, this review discusses the information currently available regarding the disease pathophysiology, the common types of microorganisms causing MK, physical and organic mechanisms of adhesion, material properties which are involved in adhesion, and current antimicrobial strategies. This review also concludes that Pseudomonas aeruginosa is a model organism for the investigation of contact lens microbial adherence due to its prevalence in MK cases, its extremely robust adhesion, antimicrobial-resistant properties, and the severity of the disease it causes.

Reduction of disinfection efficacy of contact lens care products on the global market in the presence of contact lenses and cases

Objective

Sight-threatening infections can be caused by pathogenic micro-organisms colonising the cornea, leading to microbial keratitis (MK). These micro-organisms can be introduced to the eye via improper contact lens use and care. MK can also result from ineffective contact lens care solutions (CLCs), even if the patient is following best practice guidelines. Therefore, it is critical to understand the differences between the effectiveness of popular CLCs on the global market.

Methods and analysis

Following the International Standards Organisation standards 14 729 and 18259, bacteria (Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus), fungi (Candida albicans, Fusarium strains) and Acanthamoeba strains were inoculated into each CLC with and without contact lenses, and held for the manufacturer’s stated disinfection time. Plate counts were conducted to determine the number of surviving micro-organisms.

Results

All CLCs examined met the primary log reduction criteria during stand-alone testing for Pseudomonas, Staphylococcus, Candida and Fusarium. renu Multiplus, All Clean Soft, and Kombilösung Super did not meet the primary criteria when challenged with Serratia. Only OPTI-FREE Express exceeded 4 log reduction for both strains of Acanthamoeba tested. We noted a substantial reduction in disinfection efficacy when CLCs were challenged with Fusarium in the presence of lenses and cases versus stand-alone testing. OPTI-FREE Express demonstrated significantly less net log reduction loss than the other four CLCs tested.

Conclusion

Of the popular CLCs on the global market, the product which relies on dual biocides polyquaternium-1 and myristamidopropyl dimethylamine demonstrated the highest disinfection efficacy in microbial disinfection challenges in the absence and presence of contact lenses.

Differential Antimicrobial Efficacy of Preservative-Free Contact Lens Disinfection Systems against Common Ocular Pathogens

Microbial keratitis is a devastating disease that can cause eye damage and blindness and can be the result of infections by several common ocular pathogens. Importantly, some of these pathogens, such as Acanthamoeba, are particularly unsusceptible to biocides in common contact lens care solutions. Therefore, the disinfection efficacy of preservative-free (PF) disinfection systems against bacteria, fungi, and Acanthamoeba trophozoites and cysts should be assessed as products with the most potential to be efficacious against resistant organisms. PF disinfection systems were analyzed for antimicrobial efficacy. These were the one-step (hydrogen peroxide-based) Clear Care and Clear Care Plus systems and the two-step (povidone-iodine-based) Cleadew system. Stand-alone challenges using bacteria, fungi, and Acanthamoeba were prepared according to the International Standards Organization method 14729. These same challenges were also conducted in the presence of the following contact lenses: Boston RGP, Acuvue Oasys, Biofinity, Ultra, and 2-week PremiO. All challenges were performed at the manufacturer's recommended disinfection time. All preservative-free disinfection systems demonstrated similarly high rates of antimicrobial efficacy when challenged with bacteria or fungi, with or without lenses. However, both Clear Care and Clear Care Plus demonstrated significantly greater disinfection efficacy against Acanthamoeba trophozoites and cysts, with and without lenses (P < 0.05). Cleadew efficacy was impacted by the addition of contact lenses, whereas Clear Care/Clear Care Plus maintained similar efficacies in the absence or presence of lenses. While both hydrogen peroxide and povidone-iodine are highly effective against bacteria and fungi, hydrogen peroxide maintains significantly greater disinfection capabilities than povidone-iodine against all forms of Acanthamoeba. IMPORTANCE Understanding the most efficacious products will allow clinicians to best communicate to patients and consumers the safest products on the market to reduce adverse events, including microbial keratitis, during contact lens use.

Differential Antimicrobial Efficacy of Multipurpose Solutions against Acanthamoeba Trophozoites

SIGNIFICANCE

This investigation examines the effectiveness of several common contact lens solutions in the disinfection of Acanthamoeba, which causes a serious eye infection most often resulting from dysfunctional or improper use of contact lens products.

PURPOSE

Acanthamoeba keratitis is an eye infection caused by a free-living amoeba, which can lead to extensive corneal damage and frequently blindness. Acanthamoeba keratitis is linked with contact lens use combined with noncompliance with contact lens care cleaning regimens. The patient's choice and use of multipurpose solutions (MPSs) continue to be a risk factor for Acanthamoeba keratitis. Thus, it is critical that the Acanthamoeba disinfection efficacy of the popular MPSs be determined. Here we compare the efficacy of seven major MPSs on the global market.

METHODS

Using standard methods of Acanthamoeba disinfection and quantification, Acanthamoeba ATCC 30461, 30868, 50370, and 50676 trophozoites were inoculated into each MPS and held for the manufacturer's recommended disinfection time. Acanthamoeba recovery plates were incubated for 14 days, after which positive wells were identified and cell concentrations determined using the 50% endpoint method.

RESULTS

Members of the OPTI-FREE products (Express, Replenish, and Puremoist [Alcon, Fort Worth, TX]) demonstrated significantly higher percentages of antimicrobial activity compared with the renu Advanced Formula (Bausch + Lomb, Rochester, NY), Biotrue (Bausch + Lomb), Acuvue RevitaLens (Johnson & Johnson, Santa Ana, CA), and Lite products (Cooper Vision, Scottsville, NY) for four of the trophozoite strains tested.

CONCLUSIONS

Many of the popular MPS biocides maintain little or no antimicrobial activity against Acanthamoeba trophozoites, and the number of biocides in an MPS does not necessarily indicate its antimicrobial activity.

Antimicrobial Efficacy of Contact Lens Solutions Assessed by ISO Standards

Microbial keratitis (MK) is an eye infection caused by opportunistic bacteria or fungi, which may lead to sight-threatening corneal ulcers. These microorganisms can be introduced to the eye via improper contact lens usage or hygiene, or ineffective multipurpose solutions (MPSs) to disinfect daily wear contact lenses. Thus, the patient’s choice and use of these MPSs is a known risk factor for the development of MK. It is then critical to determine the efficacy of popular MPSs against ubiquitous ocular microorganisms. Therefore, we compare the efficacy of nine major MPSs on the global market against four different microorganism species, and with four different common contact lenses. In accordance with International Standards Organization protocol 14729 and 18259, the microorganisms were inoculated into each MPS with and without contact lenses, and held for the manufacturer’s disinfection time, 24 h, and 7 days after challenge with Serratia marcescens or Fusarium spp. Plates were incubated for 2–7 days and plate counts were conducted to determine the number of surviving microorganisms. The majority of MPSs demonstrated significantly higher disinfection efficacies without contact lenses. Broadly, among the microorganisms tested, the OPTI-FREE products (Puremoist, Express, and Replenish) maintained the highest disinfection efficacies at the manufacturer’s stated disinfection time when paired with any contact lens, compared with other MPSs. These were followed closely by RevitaLens and renu Advanced. MPSs containing dual biocides polyquaternium-1 and myristamidopropyl dimethylamine possessed the highest disinfection efficacy against multiple ocular pathogens.

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.

Variables Affecting the Recovery of Acanthamoeba Trophozoites

While the results of Acanthamoeba testing have been extensively published, laboratories conducting such testing are left to develop their own methods in the absence of a standardized methodology. The wide disparity of methods has resulted in equally inconsistent reported results for contact lens care (CLC) products. This study's objective was to determine the source of these discrepancies by evaluating basic Acanthamoeba biology and their impact on antimicrobial efficacy testing, including the ability of a recovery method to stimulate a single trophozoite to proliferate. Antimicrobial efficacy testing was conducted using well-published Acanthamoeba strains, storage conditions, and growth-based recovery methods. To identify variables that influence results, test solutions with low Acanthamoeba disinfection rates were utilized to prevent differences from being masked by high log reductions. In addition, single-cell proliferation assays were executed to understand the growth requirements to stimulate trophozoite propagation in two recovery methods. These studies indicated that both nutrient density (>106 CFU) and the length of plate incubation (at least 14 days) could significantly influence the accurate recovery of trophozoites. Together, this study emphasizes the need to understand how Acanthamoeba trophozoites biology can impact test methods to create divergent results.

Long-term postnatal outcome of fetuses with prenatally suspected septo-optic dysplasia

OBJECTIVES

Septo-optic dysplasia (SOD) is a clinical syndrome characterized by varying combinations of optic nerve hypoplasia, pituitary gland hypoplasia and abnormal cavum septi pellucidi. It is suspected on prenatal imaging when there is non-visualization or hypoplasia of the septal leaflets. Long-term postnatal outcomes of fetuses with prenatally suspected SOD have been documented poorly. The aims of this study were to describe the natural history of deficient septal leaflets, to quantify the incidence of postnatally confirmed SOD and to document the visual, endocrine and long-term neurodevelopmental outcomes of these infants.

METHODS

This was an observational retrospective study of all fetuses with prenatal imaging showing isolated septal agenesis, assessed at a single tertiary center over an 11-year period. Pregnancy, delivery and neonatal outcomes and pre- and postnatal imaging findings were reviewed. Neonatal evaluations or fetal autopsy reports were assessed for confirmation of SOD. Ophthalmologic, endocrine, genetic and long-term developmental evaluations were assessed. Imaging findings and outcome were compared between infants with and those without postnatally confirmed SOD.

RESULTS

Of 214 fetuses presenting with septal absence on prenatal ultrasound and magnetic resonance imaging (MRI), 18 (8.4%) were classified as having suspected isolated septal agenesis suspicious for SOD. Uniform prenatal MRI findings in cases with suspected SOD included remnants of the leaflets of the cavum septi pellucidi, fused forniceal columns, normal olfactory bulbs and tracts and a normal optic chiasm. Twelve fetuses were liveborn and five (27.8%) had postnatally confirmed SOD. Only two of these five fetuses had additional prenatal imaging features (pituitary cyst, microphthalmia and optic nerve hypoplasia) supporting a diagnosis of SOD. The other three confirmed SOD cases had no predictive prenatal or postnatal imaging findings that reliably differentiated them from cases without confirmed SOD. Visual and endocrine impairments were present in two (40%) and four (80%) cases with confirmed SOD, respectively. In those with visual and/or endocrine impairment, developmental delay (median age at follow-up, 2.5 (interquartile range, 2.5-7.0) years) was common (80%) and mostly severe. Neonates with isolated septal agenesis and a lack of visual or endocrine abnormalities to confirm SOD had normal development.

CONCLUSIONS

Only a quarter of fetuses with isolated septal agenesis suggestive of SOD will have postnatal confirmation of the diagnosis. Clinical manifestations of SOD are variable, but neurodevelopmental delay may be more prevalent than thought formerly. © 2020 Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis

Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.

Reproducible big data science: A case study in continuous FAIRness

Big biomedical data create exciting opportunities for discovery, but make it difficult to capture analyses and outputs in forms that are findable, accessible, interoperable, and reusable (FAIR). In response, we describe tools that make it easy to capture, and assign identifiers to, data and code throughout the data lifecycle. We illustrate the use of these tools via a case study involving a multi-step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive sites sequencing data. We show how the tools automate routine but complex tasks, capture analysis algorithms in understandable and reusable forms, and harness fast networks and powerful cloud computers to process data rapidly, all without sacrificing usability or reproducibility-thus ensuring that big data are not hard-to-(re)use data. We evaluate our approach via a user study, and show that 91% of participants were able to replicate a complex analysis involving considerable data volumes.

Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus

Investigators have long suspected that pathogenic microbes might contribute to the onset and progression of Alzheimer's disease (AD) although definitive evidence has not been presented. Whether such findings represent a causal contribution, or reflect opportunistic passengers of neurodegeneration, is also difficult to resolve. We constructed multiscale networks of the late-onset AD-associated virome, integrating genomic, transcriptomic, proteomic, and histopathological data across four brain regions from human post-mortem tissue. We observed increased human herpesvirus 6A (HHV-6A) and human herpesvirus 7 (HHV-7) from subjects with AD compared with controls. These results were replicated in two additional, independent and geographically dispersed cohorts. We observed regulatory relationships linking viral abundance and modulators of APP metabolism, including induction of APBB2, APPBP2, BIN1, BACE1, CLU, PICALM, and PSEN1 by HHV-6A. This study elucidates networks linking molecular, clinical, and neuropathological features with viral activity and is consistent with viral activity constituting a general feature of AD.

Analysis of tissue from products of conception and perinatal losses using QF-PCR and microarray: A three-year retrospective study resulting in an efficient protocol

OBJECTIVE

To evaluate the performance of a laboratory protocol for direct genetic analysis performed on tissues obtained from miscarriages, stillbirth and postnatal death.

METHODS

Samples were collected between July 1st, 2011 and June 30th, 2014. QF-PCR analysis was the initial test followed by aCGH analysis performed on the normal QF-PCR specimens.

RESULTS

Of the 1195 submitted specimens, a total of 1071 samples were confirmed as true fetal. The failure rate was 1.4%. Of those, 30.8% yielded abnormal results. Of the latter, 57.6% had abnormal QF-PCR and 42.4% had abnormal microarray result. Autosomal trisomies were detected in 61.2%, triploidy in 7.6%, monosomy X in 9.1%, sex-chromosome aneuploidy (apart from monosomy X) in 1.5%, molar pregnancies in 5.8% and copy number variants in 14.2% including microdeletions/microduplications and cryptic unbalanced rearrangements. The highest diagnostic yield was observed in the 1st trimester specimens at 67.6%. We confirmed that maternal age correlates with the likelihood of autosomal trisomies but not with triploidy, sex chromosome aneuploidies, molar pregnancy, or CNVs.

CONCLUSION

An efficient laboratory protocol, based on QF-PCR and aCGH of uncultured cells has replaced standard cytogenetic analysis in testing of tissue from all pregnancy losses in our center and resulted in reduced test failure rate and increased diagnostic yield.

Treatment satisfaction in cystic fibrosis: early patient experience with tobramycin inhalation powder

BACKGROUND

This study assessed treatment satisfaction of cystic fibrosis (CF) patients in a routine clinical setting for tobramycin inhalation powder (TIP), the first dry powder-inhaled antibiotic for Pseudomonas aeruginosa infection.

METHODS

CF patients aged 6 years or older treated with at least one cycle of TIP completed a web survey on experience with TIP, including the Treatment Satisfaction Questionnaire for Medication (TSQM). Regression analysis determined the factors associated with TSQM global satisfaction.

RESULTS

Eighty patients (mean age ± standard deviation: 24.4±9.4 years; 57.5% female; mean forced expiratory volume in 1 second ± standard deviation: 67.1%±27.3% predicted) completed the survey. The majority expressed satisfaction with TIP's administration time (100%), time to clean (97.1%), portability (97.1%), and ease of use (94.3%). Effectiveness was significantly associated with TSQM global satisfaction (regression R-squared: 0.54).

CONCLUSION

Patient preferences for TIP were based on administration time and ease of use. Global satisfaction was related to greater patient-perceived effectiveness.

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks.

In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines.

cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.

Development and validation of a cost-utility model for Type 1 diabetes mellitus

AIMS

To develop a health economic model to evaluate the cost-effectiveness of new interventions for Type 1 diabetes mellitus by their effects on long-term complications (measured through mean HbA1c ) while capturing the impact of treatment on hypoglycaemic events.

METHODS

Through a systematic review, we identified complications associated with Type 1 diabetes mellitus and data describing the long-term incidence of these complications. An individual patient simulation model was developed and included the following complications: cardiovascular disease, peripheral neuropathy, microalbuminuria, end-stage renal disease, proliferative retinopathy, ketoacidosis, cataract, hypoglycemia and adverse birth outcomes. Risk equations were developed from published cumulative incidence data and hazard ratios for the effect of HbA1c , age and duration of diabetes. We validated the model by comparing model predictions with observed outcomes from studies used to build the model (internal validation) and from other published data (external validation). We performed illustrative analyses for typical patient cohorts and a hypothetical intervention.

RESULTS

Model predictions were within 2% of expected values in the internal validation and within 8% of observed values in the external validation (percentages represent absolute differences in the cumulative incidence).

CONCLUSIONS

The model utilized high-quality, recent data specific to people with Type 1 diabetes mellitus. In the model validation, results deviated less than 8% from expected values.

Temporal lobe dysplasia: a characteristic sonographic finding in thanatophoric dysplasia

OBJECTIVE

To determine the incidence of temporal lobe dysplasia (TLD) detected on prenatal ultrasound in thanatophoric dysplasia (TD) over an 11-year period in a tertiary referral center.

METHODS

An 11-year retrospective review of perinatal autopsies from 2002 to 2013 was performed to identify cases of TD. The ultrasound images and corresponding reports of all TD cases were examined for the presence of TLD. The same set of images subsequently underwent a retrospective review by a perinatal radiologist with knowledge of the features of TLD to determine whether they could be identified.

RESULTS

Thirty-one cases of TD underwent perinatal autopsy, and prenatal ultrasound imaging was available for review in 24 (77%). Mean gestational age at diagnosis of TD was 21.3 (range, 18-36) weeks. TLD was identified and reported in 6/24 (25%) cases; all six cases occurred after 2007. Retrospective interpretation of the ultrasound images identified features of TLD in 10 additional cases. In total, 16/24 (67%) cases displayed sonographic evidence of TLD. Temporal trends showed that TLD features were present in 50% (5/10) of all TD cases between 2002 and 2006 and in 79% (11/14) of those detected between 2007 and 2013.

CONCLUSIONS

At present, the detection rate of TLD by ultrasound is low but may be increased by modified brain images that enhance visualization of the temporal lobes. Prenatal identification of TLD may help in the prenatal diagnosis of TD and thus provide more accurate prenatal counseling and guide molecular investigations to confirm the specific diagnosis of TD.

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing and filtering variant call format (VCF) files. VariantAnnotation allows ready access to additional R / Bioconductor facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.

AVAILABILITY AND IMPLEMENTATION

This package is implemented in R and available for download at the Bioconductor Web site (http://bioconductor.org/packages/2.13/bioc/html/VariantAnnotation.html). The package contains extensive help pages for individual functions and a 'vignette' outlining typical work flows; it is made available under the open source 'Artistic-2.0' license. Version 1.9.38 was used in this article.

Diffusion-weighted imaging of the cerebellum in the fetus with Chiari II malformation

BACKGROUND AND PURPOSE

Diffusion-weighted imaging can be used to characterize brain maturation. MR imaging of the fetus is used in cases of suspected Chiari II malformation when further evaluation of the posterior fossa is required. We sought to investigate whether there were any quantitative ADC abnormalities of the cerebellum in fetuses with this malformation.

MATERIALS AND METHODS

Measurements from ROIs acquired in each cerebellar hemisphere and the pons were obtained from calculated ADC maps performed on our Avanto 1.5T imaging system. Values in groups of patients with Chiari II malformations were compared with those from fetuses with structurally normal brains, allowing for the dependent variable of GA by using linear regression analysis.

RESULTS

There were 8 fetuses with Chiari II malformations and 23 healthy fetuses, ranging from 20 to 31 GW. There was a significant linear decline in the cerebellar ADC values with advancing gestation in our healthy fetus group, as expected. The ADC values of the cerebellum of fetuses with Chiari II malformation were higher [1820 (±100) × 10⁻⁶ mm²/s] than ADC values in the healthy fetuses (1370 ± 70) × 10⁻⁶ mm²/s. This was statistically significant, even when allowing for the dependent variable of GA (P = .0126). There was no significant difference between the pons ADC values in these groups (P = .645).

CONCLUSIONS

While abnormal white matter organization or early cerebellar degeneration could potentially contribute to our findings, the most plausible explanation pertains to abnormalities of CSF drainage in the posterior fossa, with increased extracellular water possibly accounting for this phenomenon.

Prenatal diagnosis and outcome of absent pulmonary valve syndrome: contemporary single-center experience and review of the literature

OBJECTIVE

To review the anomaly spectrum of prenatally detected absent pulmonary valve syndrome (APVS) and the outcome after diagnosis. Previous fetal studies reported survival rates of ≤ 25% for patients with intended postnatal care.

METHODS

Clinical data and echocardiograms of 12 cases with a fetal diagnosis of APVS between 2000 and 2010 were analyzed in this retrospective single-center study. Collected parameters included: gestational age at referral, associated fetal abnormalities, cardiothoracic ratio, maximum diameters of pulmonary annulus and main and branch pulmonary arteries, ventricular dimensions and function as well as ventricular Doppler flows. Karyotyping included fluorescence in-situ hybridization (FISH) analysis for microdeletion 22q11.2.

RESULTS

Median gestational age at diagnosis was 24 weeks. Three subtypes of APVS were observed: (1) with tetralogy of Fallot (TOF) and no arterial duct (n = 10; 83%); (2) isolated, with a large arterial duct (n = 1; 8%); and (3) with tricuspid atresia, right ventricular dysplasia and a restricted duct (n = 1; 8%). The cardiothoracic ratio and pulmonary artery dimensions were increased in all cases. The karyotype was abnormal in 70% of fetuses with TOF and their mortality rate was significantly higher due to pregnancy termination (n = 3) or perinatal demise (n = 2) (hazard ratio, 5; 95% CI, 0.87-28.9; P = 0.015). Of seven live births with active postnatal care, six children (86%) were alive without residual respiratory symptoms at a median follow-up of 4.7 (range, 2.1-10.6) years.

CONCLUSION

Outcome after fetal diagnosis of APVS was significantly better in this study compared with those of previous fetal series, with a low mortality rate for actively managed patients.

Clinical burden and incremental cost of fractures in postmenopausal women in the United Kingdom

This cohort study of postmenopausal women in the United Kingdom aged ≥50years determined the incremental cost of health care and clinical outcomes in the 12months following incident, selected fractures (non-vertebral non-hip [NVNHF], vertebral [VF] and multiple [MF]). Incremental costs and outcomes of the fracture cohorts were compared with those of cohorts comprised of women without fractures who were individually matched on age and comorbidity. Cohorts were identified from The Health Improvement Network database, a primary health care database, from 2001 to 2005. We estimated 1-year incremental costs (hospitalizations; general practice, accident/emergency, and referral visits; and prescription medications) associated with each fracture type. Descriptive analyses examined occurrence of subsequent fractures and death. No long-term health care costs or outcomes were assessed. Overall, 14,030 women had NVNHF, 1471 had VF, and 193 had MF. The risk of death was greater for women with fractures than for women in the non-fracture cohorts. Mean incremental cost for fractures compared with no fractures was £1152 for VF; £690 for NVNHF, and £2581 for MF. Of the total incremental cost, hospitalizations represented 54%-90% and medications represented 7%-29%. In all fracture cohorts, most of the total annual costs were concentrated in the 6months after the date of fracture. Fractures among postmenopausal women represent an important burden to the health system due to the increase in health resource utilization and related costs. In this study, hospitalizations were the main driver of the overall incremental cost during the 12months following the fracture. Mortality in women in the selected fracture cohorts was higher than in women in the non-fracture cohorts.

Myxopapillary ependymoma: correlation of clinical and imaging features with surgical resectability in a series with long-term follow-up

STUDY DESIGN

Retrospective case series.

OBJECTIVES

The objective of this study is to identify imaging and intraoperative characteristics that may predict surgical resection for myxopapillary ependymoma (MPE). The diffuse involvement in the conus-filum region makes complete resection challenging. The preoperative characteristics that may estimate the extent of resection has not been reported.

SETTING

Toronto, Canada.

METHODS

All MPE cases between 1972 and 2005 at a single institution were identified and reexamined by a neuropathologist. Neurological outcomes (Frankel scale), clinical features, operative findings, pre and postoperative imaging results were reviewed.

RESULTS

A total of 18 operations were performed on 15 MPE patients (8 females/7 males; age range: 18-71 years). Median postoperative follow-up was 56 months. Three patients (17%) developed tumor regrowth requiring reoperations. Preoperative magnetic resonance imaging (MRI; in 14/18 procedures) determined that tumors involved the conus in 70% of cases, which was significantly associated with intraoperative findings (P=0.02). Complete microsurgical resection was accomplished in 4 out of 7 cases where conus was not involved, but in only 1 out of 10 cases with conus involvement (P=0.056). The degree of conus involvement in one case was unclear. None of patients with total surgical resection developed recurrence. All patients survived at long-term follow-up.

CONCLUSION

Our series is the first to correlate MPE involvement to conus medullaris on preoperative MRI with intraoperative findings, and examine its significance on surgical resectability. This information could guide clinicians in preoperative planning and advising patients on treatment options and potential risks/benefits. MRI is very sensitive (100%) and moderately specific (67%) in detecting direct anatomical contact between conus and MPE tumors.

Study of the incremental cost and clinical burden of hip fractures in postmenopausal women in the United Kingdom

OBJECTIVE

To determine the incremental cost of healthcare and clinical outcomes in the 12 months following incident hip fractures among postmenopausal women in the UK.

METHODS

Retrospective cohort study of women aged 50 years or older hospitalized for an incident hip fracture within 1 week of the fracture date who were age- and comorbidity-matched to women without fracture. Cohorts were identified in the Health Improvement Network database, and followed up for 1 year.

RESULTS

Among 2,427 women who had a hip fracture and a recorded hospitalization, the mean [SD] age was 81 [9.3] years. About 18% of women without fractures were hospitalized during follow-up and 18% of women with hip fractures and 4% of women without fractures had at least one emergency admission (RR, 4.7; 95% CI, 3.8-5.8). There were no major differences in use of general practitioner visit, referral visits, or in prescription of medications. Mortality was 18% in the hip fracture cohort and 7% in the non-fracture cohort (RR, 2.5; 95% CI, 2.1-3.0). The overall 1-year mean incremental cost of hip fractures was £4,222 (95% CI, £4,105-4,339); most of this cost (97%) was for hospitalizations, with an increment of £4,095. About 98% of the incremental cost occurred in the first 6 months following hip fracture.

CONCLUSIONS

The results of this study indicate that the cost and clinical burden associated with hip fractures in postmenopausal women in the UK are considerable. The incremental cost is mostly related to the cost of hospitalization and treatment of the hip fracture. Key limitations were the inclusion of only those women with a recorded hospitalization, and that costs associated with rehabilitation services, social services, and long-term care were not recorded in this study, although these are important contributors to the total cost of fractures.

The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage

The Protein Information and Property Explorer 2 (PIPE2) is an enhanced software program and updated web application that aims at providing the proteomic researcher a simple, intuitive user interface through which to begin inquiry into the biological significance of a list of proteins typically produced by MS/MS proteomic processing software. PIPE2 includes an improved interface, new data visualization options, and new data analysis methods for combining disparate, but related, data sets. In particular, PIPE2 has been enhanced to handle multi-dimensional data such as protein abundance, gene expression, and/or interaction data. The current architecture of PIPE2, modeled after that of Gaggle (a programming infrastructure for interoperability between separately developed software tools), contains independent functional units that can be instantiated and pieced together at the user's discretion to form a pipelined analysis workflow. Among these functional units is the Network Viewer component, which adds rich network analysis capabilities to the suite of existing proteomic web resources. Additionally, PIPE2 implements a framework within which new analysis procedures can be easily deployed and distributed over the World Wide Web. PIPE2 is available as a web service at http://pipe2.systemsbiology.net/.

Corroboration of normal and abnormal fetal cerebral lamination on postmortem MR imaging with postmortem examination

BACKGROUND AND PURPOSE

The presence of normal fetal cerebral lamination of the germinal matrix, intermediate zone, subplate layer, and cortex can be used as a marker of normal fetal cerebral development. Our aim was to compare postmortem MR imaging assessment of normal and abnormal fetal cerebral lamination on T1- and T2-weighted images with histopathology.

MATERIALS AND METHODS

Fifty-five formalin-fixed brains from postmortem fetuses, ranging from 16 to 30 weeks' gestational age, mean of 23 weeks, underwent T1- and T2- weighted MR imaging and subsequent sectioning and histologic examination. The cerebral lamination was graded as normal or abnormal on T1- and T2-weighted imaging and compared with postmortem findings. The sensitivity, specificity, and positive and negative predictive values of T1 and T2 assessment of cerebral lamination were calculated.

RESULTS

Twenty-six fetuses had abnormal and 29 had normal cerebral lamination on histology. On T1, the overall sensitivity, specificity, and positive and negative predictive values of evaluating cerebral lamination were 96.15%(CI, 78.42%-99.80%), 89.66%(CI, 71.50%-97.29%), 89.29%(CI, 70.63%-97.19%), and 96.29%(CI, 79.11%-99.80%), respectively. On T2, the overall sensitivity, specificity, and positive and negative predictive values of evaluating cerebral lamination were 73.08%(CI, 51.95%-87.65%), 96.55%(CI, 80.37%-99.82%), 95.00%(CI, 73.06%-99.74%), and 80.00%(CI, 62.54%-90.94%), respectively.

CONCLUSIONS

Postmortem MR imaging has high sensitivity, specificity, and positive and negative predictive values in assessing fetal cerebral lamination compared with histology. T1-weighted imaging has a higher sensitivity and negative predictive value, while T2-weighted imaging has a higher specificity and positive predictive value.

Alteration of human fetal subplate layer and intermediate zone during normal development on MR and diffusion tensor imaging

BACKGROUND AND PURPOSE

The subplate layer and intermediate zone are the precursors for neonatal white matter. The aims of this study were to evaluate 1) T1 and T2 signal intensity, and 2) FA of subplate and intermediate zone in postmortem fetuses and correlate with histology, and 3) T2 signal intensity of subplate and intermediate zone on antenatal MR imaging.

MATERIALS AND METHODS

Fourteen immersion-fixed normal brains from 18 to 25 gestational weeks underwent 1.5T MR imaging, including DTI and histologic examination. The subplate and intermediate zone were graded on a scale of 1-5 on T1 and T2, and FAs were evaluated and then correlated with age. Seventeen antenatal MR images from 20 to 26 gestational weeks with normal brain were evaluated by using the same grading.

RESULTS

On T1 postmortem MR imaging, subplate has lower signal intensity compared with intermediate zone; subplate signal intensity correlated positively (r = 0.66, P = .012) with age, and intermediate zone signal intensity correlated negatively (r = -0.78, P = .001) with age. On T2 postmortem MR imaging, subplate has higher signal intensity compared with intermediate zone and remained persistently high in signal intensity; intermediate zone signal intensity showed moderate correlation (r = 0.48, P = .086) with age. FA of subplate correlated positively (r = 0.55, P < .001) with age; FA of intermediate zone correlated negatively (r = -0.64, P < .0001) with age. On histology, extracellular matrix decreased and cellularity increased in subplate layer, tangentially organized cellularity decreased, and projecting fibers became thicker in intermediate zone with increasing gestation. The findings on T2-weighted antenatal MR imaging were similar to T2-weighted postmortem MR imaging.

CONCLUSIONS

The changes in signal intensity and FA of subplate and intermediate zone in the second trimester reflect microstructural changes on histology.

Phase I dose escalation trial of tremelimumab plus sunitinib in patients (pts) with metastatic renal cell carcinoma (mRCC)

5115

Background: Sunitinib (SU) is an oral multitargeted tyrosine kinase inhibitor that has antitumor activity in mRCC. Recent data show sunitinib reduces levels of myeloid-derived suppressor cells and prevents T-cell suppression in pts with mRCC. CTLA4 blockade with tremelimumab is an immunotherapy that enhances T-cell activation and proliferation, and is associated with durable objective responses in metastatic melanoma. It was hypothesized that combination therapy could safely be administered. Methods: The primary endpoint was to assess maximum tolerated dose (MTD) of tremelimumab Q12W in combination with 2 schedules of SU (50 mg/day for 4 weeks followed by 2 weeks off or 37.5 mg QD continuous) in pts with ≤1 prior treatment. Tremelimumab doses were 6, 10, and 15 mg/kg. Secondary objectives included best overall response (RECIST), duration of response, safety, and pharmacokinetics. Results: Twenty-one pts were enrolled. Two of 5 pts in the SU 50 mg (4/2 schedule) plus tremelimumab 6 mg/kg cohort experienced dose-limiting toxicities (DLTs): 1) G5 ruptured diverticula; 2) prolonged G3 mucositis and fatigue. Further exploration of this schedule for SU was excluded. In the SU 37.5 mg QD continuous cohorts, no DLTs were observed at 6 mg/kg tremelimumab (n = 3), 1 of 6 pts treated with 10 mg/kg tremelimumab in the protocol-defined cohort suffered sudden death, and 3 of 6 pts treated with 15 mg/kg tremelimumab + SU experienced DLTs, including: 1 pt with G3 acute renal failure and G3 lymphopenia, 1 pt with G3 elevated creatinine, and 1 pt with worsening G3 dyspnea. Therefore, SU 37.5 QD + tremelimumab 10 mg/kg Q12W was considered the MTD. Five pts achieved partial response: 1 at SU 50 (4/2) + tremelimumab 6 mg/kg; 3 at SU 37.5 + tremelimumab 10 mg/kg; and 1 at SU 37.5 QD + tremelimumab 15 mg/kg. Six pts stayed on study ≥11 mo. An expansion cohort is enrolling another 12 patients at the MTD to further define toxicity and clinical activity. Conclusions: Tremelimumab 10 mg/kg Q12W + SU 37.5 mg QD was tolerable and associated with antitumor activity in pts with mRCC. Further exploration of this combination is warranted.

[Table: see text]

A phase I study of XL281, a selective oral RAF kinase inhibitor, in patients (Pts) with advanced solid tumors

3513

Background: XL281 is a potent and selective inhibitor of wild type and mutant RAF kinases showing anti-tumor activity in multiple xenograft models. Mutations in KRAS or BRAF can activate the RAF/MEK/ERK pathway in human tumors and may promote sensitivity to RAF kinase inhibitors. Methods: Pts were enrolled in successive cohorts of XL281 orally once daily on a 28-day cycle. Tumor response was assessed per RECIST every 8 wks. Plasma pharmacokinetic and pharmacodynamic samples were collected. The maximum tolerated dose (MTD) was expanded to 10 pts each with colorectal (CRC), melanoma, papillary thyroid (PTC) and NSCLC. Pre- and post-dose tumor and surrogate tissues were obtained. Biomarker and genotype analyses of pathway genes were performed. Results: The dose escalation phase is complete; 30 pts were treated with XL281. DLTs of fatigue, nausea, vomiting, and diarrhea were observed at the MAD (225 mg). The MTD is 150 mg. The most common related AEs included Grade 1/2, fatigue (48%), diarrhea (35%), nausea (35%), vomiting (35%) and anorexia (30%). Three pts had related AEs ≥G3: hypokalemia, nausea, and vomiting. One pt with an ocular melanoma demonstrated a cPR of 4 mos duration. Twelve pts had SD (3 -17+ mos), including 2 with I131-refractory PTC harboring BRAF V600E mutations (15+ and 17+ mos). Nine of these pts had decreases in target lesions (5–29%), including a pt with KRAS mutant CRC on study for 20 wks with marked symptomatic improvement. At the MTD, paired biopsies from 4 pts (3 melanoma, 1 NSCLC) show an average 72 % decrease in pMEK, 68 % decrease in pERK, 24 % decrease in Ki67 (proliferation) and 64 % increase in TUNEL (apoptosis). Three of 6 evaluable pts in the MTD cohort show SD at first assessment, including 1 melanoma pt with a NRAS Q61R mutation who showed a 20% decrease in target lesions. Conclusions: XL281 was generally well tolerated and the MTD was established at 150 mg. One cPR occurred in an ocular melanoma subject, and clinical benefit (PR or SD) occurred in 43% (13/30) of pts in the dose-escalation phase. XL281 demonstrates biological activity by modulation of the RAF pathway in tumor and surrogate tissue, with decreases in cell proliferation and increases in apoptosis.

[Table: see text]

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data

MOTIVATION

Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the protein information and property explorer (PIPE), the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server-side data storage using Hibernate.

AVAILABILITY

http://pipe.systemsbiology.net.

Rhombencephalosynapsis: prenatal imaging and autopsy findings

OBJECTIVES

Rhombencephalosynapsis is a rare, but increasingly recognized, brain malformation characterized by congenital fusion of the cerebellar hemispheres and absence of the vermis. Rhombencephalosynapsis is associated with significant developmental delay, seizures and involuntary head movements. We report four cases, with correlation of prenatal and postnatal imaging and autopsy findings.

METHODS

Over a 2-year period, four cases of rhombencephalosynapsis were diagnosed in the perinatal period, three in one center and one in another center. The clinical cases were reviewed, and correlation was made between the prenatal and postnatal imaging and autopsy findings where available.

RESULTS

All cases presented initially with ventriculomegaly on prenatal ultrasound examination. Subsequent magnetic resonance imaging (MRI) established the diagnosis in two cases and postnatal MRI established the diagnosis in a further two cases. Autopsy was available and confirmed the diagnosis in two cases. In one case the pregnancy was terminated, two infants died in the neonatal period and one died in infancy.

CONCLUSIONS

The cases in this perinatal series of rhombencephalosynapsis showed a very poor prognosis. The presence of ventriculomegaly on prenatal ultrasound imaging should alert the physician to consider rhombencephalosynapsis in the differential diagnosis. MRI appears to be the imaging modality of choice in establishing the diagnosis.

General transcription factor specified global gene regulation in archaea

Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria, sigma factors regulate much of this process, whereas in eukaryotes, four RNA polymerases and a multiplicity of generalized transcription factors (GTFs) are required. Here, by using a systems approach, we provide experimental evidence (including protein-coimmunoprecipitation, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of physiological functions. We are able to associate GTFs to nearly half of all putative promoters and show evidence for at least 7 of the possible 42 functional GTF pairs. This report represents a significant contribution toward closing the gap in our understanding of gene regulation by GTFs for all three domains of life and provides an example for how to use various experimental techniques to rapidly learn significant portions of a global gene regulatory network of organisms for which little has been previously known.