Distribution control enables efficient reduced-dimensional perovskite LEDs.

Light-emitting diodes (LEDs) based on perovskite quantum dots have shown external quantum efficiencies (EQEs) of over 23% and narrowband emission, but suffer from limited operating stability1. Reduced-dimensional perovskites (RDPs) consisting of quantum wells (QWs) separated by organic intercalating cations show high exciton binding energies and have the potential to increase the stability and the photoluminescence quantum yield2,3. However, until now, RDP-based LEDs have exhibited lower EQEs and inferior colour purities4-6. We posit that the presence of variably confined QWs may contribute to non-radiative recombination losses and broadened emission. Here we report bright RDPs with a more monodispersed QW thickness distribution, achieved through the use of a bifunctional molecular additive that simultaneously controls the RDP polydispersity while passivating the perovskite QW surfaces. We synthesize a fluorinated triphenylphosphine oxide additive that hydrogen bonds with the organic cations, controlling their diffusion during RDP film deposition and suppressing the formation of low-thickness QWs. The phosphine oxide moiety passivates the perovskite grain boundaries via coordination bonding with unsaturated sites, which suppresses defect formation. This results in compact, smooth and uniform RDP thin films with narrowband emission and high photoluminescence quantum yield. This enables LEDs with an EQE of 25.6% with an average of 22.1 ±1.2% over 40 devices, and an operating half-life of two hours at an initial luminance of 7,200 candela per metre squared, indicating tenfold-enhanced operating stability relative to the best-known perovskite LEDs with an EQE exceeding 20%1,4-6.

Antimicrobial Peptide LL37 and MAVS Signaling Drive Interferon-ß Production by Epidermal Keratinocytes during Skin Injury.

Type 1 interferons (IFNs) promote inflammation in the skin but the mechanisms responsible for inducing these cytokines are not well understood. We found that IFN-ß was abundantly produced by epidermal keratinocytes (KCs) in psoriasis and during wound repair. KC IFN-ß production depended on stimulation of mitochondrial antiviral-signaling protein (MAVS) by the antimicrobial peptide LL37 and double stranded-RNA released from necrotic cells. MAVS activated downstream TBK1 (TANK-Binding Kinase 1)-AKT (AKT serine/threonine kinase 1)-IRF3 (interferon regulatory factor 3) signaling cascade leading to IFN-ß production and then promoted maturation of dendritic cells. In mice, the production of epidermal IFN-ß by LL37 required MAVS, and human wounded and/or psoriatic skin showed activation of MAVS-associated IRF3 and induction of MAVS and IFN-ß gene signatures. These findings show that KCs are an important source of IFN-ß and MAVS is critical to this function, and demonstrates how the epidermis triggers unwanted skin inflammation under disease conditions.

Understanding cancer patient cohorts in virtual reality environment for better clinical decisions: a usability study.

BACKGROUND: Visualising patient genomic data in a cohort with embedding data analytics models can provide relevant and sensible patient comparisons to assist a clinician with treatment decisions. As immersive technology is actively used around the medical world, there is a rising demand for an efficient environment that can effectively display genomic data visualisations on immersive devices such as a Virtual Reality (VR) environment. The VR technology will allow clinicians, biologists, and computer scientists to explore a cohort of individual patients within the 3D environment. However, demonstrating the feasibility of the VR prototype needs domain users' feedback for future user-centred design and a better cognitive model of human-computer interactions. There is limited research work for collecting and integrating domain knowledge into the prototype design. OBJECTIVE: A usability study for the VR prototype--Virtual Reality to Observe Oncology data Models (VROOM) was implemented. VROOM was designed based on a preliminary study among medical users. The goals of this usability study included establishing a baseline of user experience, validating user performance measures, and identifying potential design improvements that are to be addressed to improve efficiency, functionality, and end-user satisfaction. METHODS: The study was conducted with a group of domain users (10 males, 10 females) with portable VR devices and camera equipment. These domain users included medical users such as clinicians and genetic scientists and computing domain users such as bioinformatics and data analysts. Users were asked to complete routine tasks based on a clinical scenario. Sessions were recorded and analysed to identify potential areas for improvement to the data visual analytics projects in the VR environment. The one-hour usability study included learning VR interaction gestures, running visual analytics tool, and collecting before and after feedback. The feedback was analysed with different methods to measure effectiveness. The statistical method Mann-Whitney U test was used to analyse various task performances among the different participant groups, and multiple data visualisations were created to find insights from questionnaire answers. RESULTS: The usability study investigated the feasibility of using VR for genomic data analysis in domain users' daily work. From the feedback, 65% of the participants, especially clinicians (75% of them), indicated that the VR prototype is potentially helpful for domain users' daily work but needed more flexibility, such as allowing them to define their features for machine learning part, adding new patient data, and importing their datasets in a better way. We calculated the engaged time for each task and compared them among different user groups. Computing domain users spent 50% more time exploring the algorithms and datasets than medical domain users. Additionally, the medical domain users engaged in the data visual analytics parts (approximately 20%) longer than the computing domain users.

Rigid Conjugated Diamine Templates for Stable Dion-Jacobson-Type Two-Dimensional Perovskites.

Hybrid organic-inorganic perovskites (HOIPs) have garnered widespread interest, yet stability remains a critical issue that limits their further application. Compared to their three-dimensional (3D) counterparts, two-dimensional (2D)-HOIPs exhibit improved stability. 2D-HOIPs are also appealing because their structural and optical properties can be tuned according to the choice of organic ligand, with monovalent or divalent ligands forming Ruddlesden-Popper (RP) or Dion-Jacobson (DJ)-type 2D perovskites, respectively. Unlike RP-type 2D perovskites, DJ-type 2D perovskites do not contain a van der Waals gap between the 2D layers, leading to improved stability. However, bifunctional organic ligands currently used to develop DJ-type 2D perovskites are limited to commercially available aliphatic and single-ring aromatic ammonium cations. Large conjugated organic ligands are in demand for their semiconducting properties and their potential to improve materials stability further. In this manuscript, we report the design and synthesis of a new set of larger conjugated diamine ligands and their incorporation into DJ-type 2D perovskites. Compared with analogous RP-type 2D perovskites, DJ 2D perovskites reported here show blue-shifted, narrower emissions and significantly improved stability. By changing the structure of rings (benzene vs thiophene) and substituents, we develop structure-property relationships, finding that fluorine substitution enhances crystallinity. Single-crystal structure analysis and density functional theory calculations indicate that these changes are due to strong electrostatic interactions between the organic templates and inorganic layers as well as the rigid backbone and strong π-π interaction between the organic ligands themselves. These results illustrate that targeted engineering of the diamine ligands can enhance the stability of DJ-type 2D perovskites.

Whole-genome bisulfite sequencing with improved accuracy and cost.

DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%-2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with transposase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression. Using these transposase-accessible loci to represent the cis-regulatory loci in the genome, we compared the representation of these loci between WGBS and other genome-wide DNA methylation assays, showing WGBS to outperform substantially all of the alternatives. We conclude that it is now technologically and financially feasible to perform WGBS in larger numbers of samples with greater accuracy than previously possible.

Multi-cation perovskites prevent carrier reflection from grain surfaces.

The composition of perovskite has been optimized combinatorially such that it often contains six components (AxByC1-x-yPbXzY3-z) in state-of-art perovskite solar cells. Questions remain regarding the precise role of each component, and the lack of a mechanistic explanation limits the practical exploration of the large and growing chemical space. Here, aided by transient photoluminescence microscopy, we find that, in perovskite single crystals, carrier diffusivity is in fact independent of composition. In polycrystalline thin films, the different compositions play a crucial role in carrier diffusion. We report that methylammonium (MA)-based films show a high carrier diffusivity of 0.047 cm2 s-1, while MA-free mixed caesium-formamidinium (CsFA) films exhibit an order of magnitude lower diffusivity. Elemental composition studies show that CsFA grains display a graded composition. This curtails electron diffusion in these films, as seen in both vertical carrier transport and surface potential studies. Incorporation of MA leads to a uniform grain core-to-edge composition, giving rise to a diffusivity of 0.034 cm2 s-1 in CsMAFA films. A model that invokes competing crystallization processes allows us to account for this finding, and suggests further strategies to achieve homogeneous crystallization for the benefit of perovskite optoelectronics.

Functional Genomics of the Pediatric Obese Asthma Phenotype Reveal Enrichment of Rho-GTPase Pathways.

Rationale: Obesity-related asthma disproportionately affects minority children and is associated with nonatopic T-helper type 1 (Th1) cell polarized inflammation that correlates with pulmonary function deficits. Its underlying mechanisms are poorly understood.Objectives: To use functional genomics to identify cellular mechanisms associated with nonatopic inflammation in obese minority children with asthma.Methods: CD4+ (cluster of differentiation 4-positive) Th cells from 59 obese Hispanic and African American children with asthma and 61 normal-weight Hispanic and African American children with asthma underwent quantification of the transcriptome and DNA methylome and genotyping. Expression and methylation quantitative trait loci revealed the contribution of genetic variation to transcription and DNA methylation. Adjusting for Th-cell subtype proportions discriminated loci where transcription or methylation differences were driven by differences in subtype proportions from loci that were independently associated with obesity-related asthma.Measurements and Main Results: Obese children with asthma had more memory and fewer naive Th cells than normal-weight children with asthma. Differentially expressed and methylated genes and methylation quantitative trait loci in obese children with asthma, independent of Th-cell subtype proportions, were enriched in Rho-GTPase pathways. Inhibition of CDC42 (cell division cycle 42), one of the Rho-GTPases associated with Th-cell differentiation, was associated with downregulation of the IFNγ, but not the IL-4, gene. Differential expression of the RPS27L (40S ribosomal protein S27-like) gene, part of the p53/mammalian target of rapamycin pathway, was due to nonrandom distribution of expression quantitative trait loci variants between groups. Differentially expressed and/or methylated genes, including RPS27L, were associated with pulmonary function deficits in obese children with asthma.Conclusions: We found enrichment of Rho-GTPase pathways in obese asthmatic Th cells, identifying them as a novel therapeutic target for obesity-related asthma, a disease that is suboptimally responsive to current therapies.

All-Inorganic Quantum-Dot LEDs Based on a Phase-Stabilized α-CsPbI3 Perovskite.

The all-inorganic nature of CsPbI3 perovskites allows to enhance stability in perovskite devices. Research efforts have led to improved stability of the black phase in CsPbI3 films; however, these strategies-including strain and doping-are based on organic-ligand-capped perovskites, which prevent perovskites from forming the close-packed quantum dot (QD) solids necessary to achieve high charge and thermal transport. We developed an inorganic ligand exchange that leads to CsPbI3 QD films with superior phase stability and increased thermal transport. The atomic-ligand-exchanged QD films, once mechanically coupled, exhibit improved phase stability, and we link this to distributing strain across the film. Operando measurements of the temperature of the LEDs indicate that KI-exchanged QD films exhibit increased thermal transport compared to controls that rely on organic ligands. The LEDs exhibit a maximum EQE of 23 % with an electroluminescence emission centered at 640 nm (FWHM: ≈31 nm). These red LEDs provide an operating half-lifetime of 10 h (luminance of 200 cd m-2 ) and an operating stability that is 6× higher than that of control devices.

Abernethy Malformations: Evaluation and Management of Congenital Portosystemic Shunts.

PURPOSE: To assess the utility of preoperative venography in evaluating and managing patients with congenital portosystemic shunts (CPSSs). MATERIALS AND METHODS: A retrospective study was performed of 42 patients (62% female; median age, 4.1 years) diagnosed with a CPSS from 2005 to 2018. Preoperative venography (n = 39) and balloon occlusive pressure measurements (n = 33) within the mesenteric venous system guided treatment. Primary outcome was serum ammonia levels at 1 month after shunt closure. Management strategies included single (n = 12) or staged (n = 18) operative ligation, endovascular occlusion (n = 8), combined surgical and endovascular closure (n = 2), and observation (n = 2). RESULTS: At 1 month, serum ammonia levels decreased from 82.5 ± 10.3 µmol/L to 38.4 ± 4.6 µmol/L (P < .001). No difference was observed in the decrease between patients treated surgically or endovascularly (P = .91). Mean occluded to non-occluded pressure gradients were significantly lower for endovascular closure (5.3 ± 1.8 mmHg) than for surgical closure (12.3 ± 3.3 mmHg, P = .02). Shunts were classified as extrahepatic in 29 patients and as intrahepatic in 13 patients; all shunts demonstrated filling of the portal system with occlusive venography. Broad and short shunts were closed surgically; narrow and long shunts were closed endovascularly. Shunts were closed in a single session (n = 20) if the pressure gradient was less than 10 mmHg and the occluded mesenteric pressure was less than 25 mmHg. CONCLUSIONS: Preoperative venography delineates shunt morphology, and balloon occlusion simulates closure hemodynamics. This information is necessary to determine whether definitive closure should be performed through endovascular or surgical methods and whether closure should be performed in a single or staged setting.

High-dose, high-frequency infliximab: A novel treatment paradigm for hidradenitis suppurativa.

BACKGROUND: The permanent disfigurement associated with hidradenitis suppurativa (HS) necessitates early aggressive disease intervention. Although limited data support the use of infliximab (IFX) in HS, the efficacy of high-dose, high-frequency IFX has yet to be defined. OBJECTIVE: To evaluate the efficacy of IFX 7.5 to 10 mg/kg, with a maintenance frequency every 4 weeks. METHODS: Prospective analysis of 42 patients initiating IFX 7.5 mg/kg every 4 weeks (IFX 7.5) and 16 patients receiving dose escalation to IFX 10 mg/kg every 4 weeks (IFX 10) between March 1, 2018, and February 28, 2019. The primary outcome measure (clinical response) was the proportion of patients with Physician Global Assessment of clear, minimal, or mild (score of 0-2) HS with at least a 2-grade improvement from baseline scores. RESULTS: The proportion of patients achieving a clinical response after initiating IFX 7.5 was 20 of 42 (47.6%) at week 4 and 17 of 24 (70.8%) at week 12. For patients receiving dose escalation to IFX 10 because of incomplete initial response, 6 of 16 (37.5%) achieved clinical response at week 4 and 6 of 12 (50%) at week 12. CONCLUSIONS: Initiation of IFX 7.5 every 4 weeks, with possible dose escalation to IFX 10, if needed, provides optimal mitigation of HS-related disease activity.

Thiophene Cation Intercalation to Improve Band-Edge Integrity in Reduced-Dimensional Perovskites.

The insertion of large organic cations in metal halide perovskites with reduced-dimensional (RD) crystal structures increases crystal formation energy and regulates the growth orientation of the inorganic domains. However, the power conversion performance is curtailed by the insulating nature of the bulky cations. Now a series of RD perovskites with 2-thiophenmethylammonium (TMA) as the intercalating cation are investigated. Compared with traditional ligands, TMA demonstrates improved electron transfer in the inorganic framework. TMA modifies the near-band-edge integrity of the RD perovskite, improving hole transport. A power conversion efficiency of 19 % is achieved, the highest to date for TMA-based RD perovskite photovoltaics; these TMA devices provide a 12 % relative increase in PCE compared to control RD perovskite devices that use PEA as the intercalating ligand, a result of the improved charge transfer from the inorganic layer to the organic ligands.

Learning-in-Templates Enables Accelerated Discovery and Synthesis of New Stable Double Perovskites.

In the past three years, machine learning (ML) in combination with density functional theory (DFT) has enabled computational screening of compounds with the goal of accelerated materials discovery. Unfortunately, DFT+ML has, until now, either relied on knowledge of the atomic positions at DFT energy minima, which are a priori unknown, or been limited to chemical spaces of modest size. Here we report a strategy that we term learning-in-templates (LiT), wherein we first define a series of space group and stoichiometry templates corresponding to hypothesized compounds and, orthogonally, we allow any list of atoms to take on any template. The LiT approach is deployed in combination with previously established position-dependent representations and performs best with the representations that rely least on the atomic positions. Since the positions of the atoms in templates are known and do not change, LiT enables us to infer the properties of interest directly; additionally, LiT allows working with increased chemical spaces, since the same elements can take on a large number of templates. Only by using LiT were we able to span 5 × 106 double-perovskite compounds and achieve an acceleration factor of 700 compared to brute-force DFT, allowing us to predict never-before-screened compounds. Our findings motivated us to synthesize a new BaCu yTa(1- y)S3 perovskite, which we show using an electron probe microanalyzer has a 5:3 molar ratio of Cu to Ta and, using powder X-ray diffraction (XRD) analysis combined with a DFT-based XRD simulation and fitting, indicate a new phase having an I4/ m space group.

CDC42-related genes are upregulated in helper T cells from obese asthmatic children.

BACKGROUND: Pediatric obesity-related asthma is more severe and less responsive to medications than asthma in normal-weight children. Obese asthmatic children have nonatopic TH1-polarized systemic inflammation that correlates with pulmonary function deficits, but the pathways underlying TH1-polarized inflammation are not well understood. OBJECTIVE: We compared the CD4+ T-cell transcriptome in obese children with asthma with that in normal-weight children with asthma to identify key differentially expressed genes associated with TH1-polarized inflammation. METHODS: CD4+ T-cell transcriptome-wide differential gene expression was compared between 21 obese and 21 normal-weight children by using directional RNA sequencing. High-confidence differentially expressed genes were verified in the first cohort and validated in a second cohort of 20 children (10 obese and 10 normal-weight children) by using quantitative RT-PCR. RESULTS: Transcriptome-wide differential gene expression among obese asthmatic children was enriched for genes, including VAV2, DOCK5, PAK3, PLD1, CDC42EP4, and CDC42PBB, which are associated with CDC42, a small guanosine triphosphate protein linked to T-cell activation. Upregulation of MLK3 and PLD1, genes downstream of CDC42 in the mitogen-activated protein kinase and mammalian target of rapamycin pathways and the inverse correlation of CDC42EP4 and DOCK5 transcript counts with FEV1/FVC ratio together support a role of CDC42 in the TH1 polarization and pulmonary function deficits found in patients with obesity-related asthma. CONCLUSIONS: Our study identifies the CDC42 pathway as a novel target that is upregulated in TH cells of obese asthmatic children, suggesting its role in nonatopic TH1-polarized systemic inflammation and pulmonary function deficits found in patients with pediatric obesity-related asthma.

IL-1 and IL-36 are dominant cytokines in generalized pustular psoriasis.

BACKGROUND: Generalized pustular psoriasis (GPP) is a rare, debilitating, and often life-threatening inflammatory disease characterized by episodic infiltration of neutrophils into the skin, pustule development, and systemic inflammation, which can manifest in the presence or absence of chronic plaque psoriasis (PV). Current treatments are unsatisfactory and warrant a better understanding of GPP pathogenesis. OBJECTIVE: We sought to understand better the disease mechanism of GPP to allow improved targeted therapies. METHODS: We performed a gene expression study on formalin-fixed paraffin-embedded GPP (n = 28) and PV (n = 12) lesional biopsies and healthy control (n = 20) skin. Differential gene expression was analyzed using gene ontology and enrichment analysis. Gene expression was validated with quantitative RT-PCR and immunohistochemistry, and a potential disease mechanism was investigated using primary human cell culture. RESULTS: Compared with healthy skin, GPP lesions yielded 479 and PV 854 differentially expressed genes, respectively, with 184 upregulated in both diseases. We detected significant contributions of IL-17A, TNF, IL-1, IL-36, and interferons in both diseases; although GPP lesions furnished higher IL-1 and IL-36 and lower IL-17A and IFN-γ mRNA expression than PV lesions did. We detected prominent IL-36 expression by keratinocytes proximal to neutrophilic pustules, and we show that both neutrophils and neutrophil proteases activate IL-36. Suggesting another mechanism regulating IL-36 activity, the protease inhibitors serpin A1 and A3, which inhibit elastase and cathepsin G, respectively, were upregulated in both diseases and inhibited activation of IL-36. CONCLUSIONS: Our data indicate sustained activation of IL-1 and IL-36 in GPP, inducing neutrophil chemokine expression, infiltration, and pustule formation, suggesting that the IL-1/IL-36 inflammatory axis is a potent driver of disease pathology in GPP.

Six-transmembrane epithelial antigens of the prostate comprise a novel inflammatory nexus in patients with pustular skin disorders.

BACKGROUND: Pustular skin disorders are a category of difficult-to-treat and potentially life-threatening conditions that involve the appearance of neutrophil-rich pustules. The molecular basis of most pustular skin conditions has remained unknown. OBJECTIVE: We sought to investigate the molecular basis of 3 pustular skin disorders: generalized pustular psoriasis (GPP), palmoplantar pustulosis (PPP), and acute generalized exanthematous pustulosis (AGEP). METHODS: Microarray analyses were performed to profile genome-wide gene expression of skin biopsy specimens obtained from patients with GPP, PPP, or AGEP and healthy control subjects. Functional enrichment, gene network, and k-means clustering analyses were used to identify molecular pathways dysregulated in patients with these disorders. Immunohistochemistry and immunofluorescence were used to determine protein localization. Quantitative RT-PCR and ELISA were used to determine transcript and secreted cytokine levels. Small interfering RNA was used to decrease transcript levels. RESULTS: Molecules and pathways related to neutrophil chemotaxis emerged as common alterations in patients with GPP, PPP, and AGEP, which is consistent with the pustular phenotypes. Expression of two 6-transmembrane epithelial antigens of the prostate (STEAP) proteins, STEAP1 and STEAP4, was increased in patients' skin and colocalized with IL-36γ around neutrophilic pustules. STEAP1/4 expression clustered with and positively correlated with that of IL-1, the IL-36 family proteins, and CXCL1/8. STEAP4 expression was activated by cytokines and suppressed by inhibition of mitogen-activated protein kinase kinase 1/2, whereas STEAP1 expression appeared less prone to such dynamic regulation. Importantly, STEAP1/4 knockdown resulted in impaired induction of a broad spectrum of proinflammatory cytokines, including IL-1, IL-36, and the neutrophil chemotaxins CXCL1 and CXCL8. STEAP1/4 knockdown also reduced the ability of keratinocytes to induce neutrophil chemotaxis. CONCLUSION: Transcriptomic changes in 3 pustular skin disorders, GPP, PPP, and AGEP, converged on neutrophil chemotaxis and diapedesis and cytokines known to drive neutrophil-rich inflammatory processes, including IL-1 and members of the IL-36 family. STEAP1 and STEAP4 positively regulate the induction of proinflammatory neutrophil-activating cytokines.

A study of the intermolecular interactions of lipid components from analogue fingerprint residues.

A compositionally simplified analogue of a latent fingermark was created by combining single representatives of each major component of a natural fingermark. Further modified analogues were also produced each having one component removed. The aim of this study was to investigate the intermolecular interactions that occurred within these analogue samples using Fourier Transform Infrared (FT-IR) Microspectroscopy. FT-IR microspectroscopy showed that the absence of squalene and cholesterol significantly restricted the interactions between the other organic constituents within the analogue samples. Investigating the intermolecular interactions of organic compounds within a simplified analogue solution could indicate corresponding interactions that occur within natural fingermarks. These potential interactions could go on to be the target of further investigation of latent fingermark chemistry, and ultimately contribute to a better understanding of the aging processes and degradation mechanisms that take place post-deposition.

SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information.

BACKGROUND: The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight into the state of the cells tested. What should be possible is to add the information derived from separate, complementary assays to gain higher-confidence insights into cellular states. At present, the analysis of multi-dimensional, massive genome-wide data requires an initial pruning step to create manageable subsets of observations that are then used for integration, which decreases the sizes of the intersecting data sets and the potential for biological insights. Our Significance-based Modules Integrating the Transcriptome and Epigenome (SMITE) approach was developed to integrate transcriptional and epigenetic regulatory data without a loss of resolution. RESULTS: SMITE combines p-values by accounting for the correlation between non-independent values within data sets, allowing genes and gene modules in an interaction network to be assigned significance values. The contribution of each type of genomic data can be weighted, permitting integration of individually under-powered data sets, increasing the overall ability to detect effects within modules of genes. We apply SMITE to a complex genomic data set including the epigenomic and transcriptomic effects of Toxoplasma gondii infection on human host cells and demonstrate that SMITE is able to identify novel subnetworks of dysregulated genes. Additionally, we show that SMITE outperforms Functional Epigenetic Modules (FEM), the current paradigm of using the spin-glass algorithm to integrate gene expression and epigenetic data. CONCLUSIONS: SMITE represents a flexible, scalable tool that allows integration of transcriptional and epigenetic regulatory data from genome-wide assays to boost confidence in finding gene modules reflecting altered cellular states.

Simvastatin in the acute respiratory distress syndrome.

BACKGROUND: Studies in animals and in vitro and phase 2 studies in humans suggest that statins may be beneficial in the treatment of the acute respiratory distress syndrome (ARDS). This study tested the hypothesis that treatment with simvastatin would improve clinical outcomes in patients with ARDS. METHODS: In this multicenter, double-blind clinical trial, we randomly assigned (in a 1:1 ratio) patients with an onset of ARDS within the previous 48 hours to receive enteral simvastatin at a dose of 80 mg or placebo once daily for a maximum of 28 days. The primary outcome was the number of ventilator-free days to day 28. Secondary outcomes included the number of days free of nonpulmonary organ failure to day 28, mortality at 28 days, and safety. RESULTS: The study recruited 540 patients, with 259 patients assigned to simvastatin and 281 to placebo. The groups were well matched with respect to demographic and baseline physiological variables. There was no significant difference between the study groups in the mean (±SD) number of ventilator-free days (12.6±9.9 with simvastatin and 11.5±10.4 with placebo, P=0.21) or days free of nonpulmonary organ failure (19.4±11.1 and 17.8±11.7, respectively; P=0.11) or in mortality at 28 days (22.0% and 26.8%, respectively; P=0.23). There was no significant difference between the two groups in the incidence of serious adverse events related to the study drug. CONCLUSIONS: Simvastatin therapy, although safe and associated with minimal adverse effects, did not improve clinical outcomes in patients with ARDS. (Funded by the U.K. National Institute for Health Research Efficacy and Mechanism Evaluation Programme and others; HARP-2 Current Controlled Trials number, ISRCTN88244364.).