sendigR: an R package to leverage the value of CDISC SEND datasets for cross-study analysis.

The CDISC Standard for Exchange of Nonclinical Data (SEND) data standard has created new opportunities for collaborative development of open-source software solutions to facilitate cross-study analyses of toxicology study data. A public-private partnership between BioCelerate and the FDA/Center for Drug Evaluation and Research (CDER) was established in part to develop and publicize novel methods to facilitate cross-study analysis of SEND datasets. As part of this work in collaboration with the Pharmaceutical Users Software Exchange (PHUSE), an R package sendigR has been developed to enable users to construct a relational database from a collection of SEND datasets and then query that database to perform cross-study analyses. The sendigR package also includes an integrated Python package, xptcleaner, which can be used to harmonize the terminology used in SEND datasets by mapping to CDISC controlled terminologies. The sendigR R package is freely available on the comprehensive R Archive Network (CRAN) and at https://github.com/phuse-org/sendigR. An R Shiny web application was included in the R package to enable toxicologists with no coding experience to perform historical control analyses. Experienced R programmers will be able to integrate the package functions into their own custom scripts/packages and potentially contribute improvements to the functionality of sendigR. sendigR reference manual: https://phuse-org.github.io/sendigR/. sendigR R Shiny demo app: https://phuse-org.shinyapps.io/sendigR/.

Persistent Proclivity to a Proinflammatory State in a Human Enteroid Model of Necrotizing Enterocolitis.

Background: Necrotizing enterocolitis (NEC) is a devastating disease of premature neonates with substantial morbidity and mortality. Necrotizing enterocolitis is associated with prematurity, a hyperinflammatory response, and dysregulation of intestinal barrier function. We hypothesize that patients with NEC will have an increased hyperinflammatory intestinal response compared with those without NEC. Patients and Methods: Enteroids were generated from intestinal tissue from neonates undergoing resection. They were treated with 100 mcg/mL lipopolysaccharide (LPS), subjected to 24 hours of hypoxia inducing experimental NEC, then compared with untreated controls. Expression of tumor necrosis factor (TNF-α) and interleukin 8 (IL-8) were evaluated via reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA) to measure inflammatory response. Analysis of variance (ANOVA) determined statistical significance (p < 0.05). Results: Treated NEC-derived enteroids expressed significantly higher levels of IL-8 (RT-qPCR, p = 0.003; ELISA, p = 0.0002) compared with untreated NEC-derived enteroids with an increase in inflammatory marker concentration in those with a greater degree of prematurity (ELISA, p = 0.0015). A higher level of IL-8 was seen in NEC-derived enteroids compared with control after treatment (RT-qPCR, p = 0.024). Tumor necrosis factor-α levels were elevated in treated NEC-derived enteroids compared with untreated NEC-derived enteroids (RT-qPCR, p = 0.006; ELISA, p = 0.002) and compared with treated non-NEC-derived enteroids (RT-qPCR, p = 0.025; ELISA, p < 0.0001). Conclusions: Enteroids generated from neonates with NEC have an elevated hyperinflammatory response in response to NEC-inducing stimuli compared with controls. Enteroids generated from neonates with NEC with a greater degree of prematurity have a larger increase in inflammatory markers. This tendency toward a hyperinflammatory state may be correlated with an infant's proclivity to develop NEC and further demonstrates the hyperinflammatory state of prematurity.

Bugs and the barrier: A review of the gut microbiome and intestinal barrier in necrotizing enterocolitis.

Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease that affects premature neonates. It frequently results in significant morbidity and mortality for those affected. Years of research into the pathophysiology of NEC have revealed it to be a variable and multifactorial disease. However, there are risk factors associated with NEC including low birth weight, prematurity, intestinal immaturity, alterations in microbial colonization, and history of rapid or formula based enteral feeds (Fig. 1).1-3 An accepted generalization of the pathogenesis of NEC includes a hyperresponsive immune reaction to insults such as ischemia, starting formula feeds, or alterations in the microbiome with pathologic bacterial colonization and translocation. This reaction causes a hyperinflammatory response disrupting the normal intestinal barrier, allowing abnormal bacterial translocation and ultimately sepsis.1,2,4 This review will focus specifically on the interactions with the microbiome and intestinal barrier function in NEC.

Hormonal correlates of male dominance rank, age, and genital colouration in vervet monkey (Chlorocebus pygerythrus).

Primates are the most colourful members of the Mammalian clade. In vervet monkeys (Chlorocebus pygerythrus), males are characterized by their red penis and blue scrotum. Such colour signals are often used in conspecific communication, and thus could be used to convey signaller condition. We quantified scrotal and penile colour characteristics using digital photographs between May-June 2016 from males in two neighboring groups along the shores of Lake Nabugabo, Uganda. We examined the relationship between fecal hormones, male dominance rank, age (adult vs. immature), and colour. Adult males were higher ranking than immatures, but there were no rank or age differences in fecal hormone levels. Glucocorticoids and androgens were positively correlated in immature, but not adult males. All scrotal characteristics were predicted by age, with adult males having more teal (i.e., less blue, more green) and more luminant scrota. Within adult males, those with higher androgens levels had more saturated blue scrotal colouration and higher-ranking males were more luminant. Penile colouration was also associated with age and rank. High-ranking males had a more saturated red penis, and adult male penile colour was more luminant and bluer than in immature males. Our findings are consistent with previous reports that scrotal colouration advertises sexual or reproductive maturity (i.e., age), but we also find that within adult males, colour also advertises dominance rank and may be mediated by androgen levels. Penile colouration also appears to signal information about male age and dominance rank but does not appear to be mediated by hormones.

Increased Perviousness on CT for Acute Ischemic Stroke is Associated with Fibrin/Platelet-Rich Clots.

BACKGROUND AND PURPOSE: Clot perviousness in acute ischemic stroke is a potential CT imaging biomarker for mechanical thrombectomy efficacy. We investigated the association among perviousness, clot cellular composition, and first-pass effect. MATERIALS AND METHODS: In 40 mechanical thrombectomy-treated cases of acute ischemic stroke, we calculated perviousness as the difference in clot density on CT angiography and noncontrast CT. We assessed the proportion of fibrin/platelet aggregates, red blood cells, and white blood cells on clot histopathology. We tested for linear correlation between histologic components and perviousness, differences in components between "high" and "low" pervious clots defined by median perviousness, and differences in perviousness/composition between cases that did and did not achieve a first-pass effect. RESULTS: Perviousness significantly positively and negatively correlated with the percentage of fibrin/platelet aggregates (P = .001) and the percentage of red blood cells (P = .001), respectively. Higher pervious clots had significantly greater fibrin/platelet aggregate content (P = .042). Cases that achieved a first-pass effect (n = 14) had lower perviousness, though not significantly (P = .055). The percentage of red blood cells was significantly higher (P = .028) and the percentage of fibrin/platelet aggregates was significantly lower (P = .016) in cases with a first-pass effect. There was no association between clot density on NCCT and clot composition or first-pass effect. Receiver operating characteristic analysis indicated that clot composition was the best predictor of first-pass effect (area under receiver operating characteristic curve: percentage of fibrin/platelet aggregates = 0.731, percentage of red blood cells = 0.706, perviousness = 0.668). CONCLUSIONS: Clot perviousness on CT is associated with a higher percentage of fibrin/platelet aggregate content. Histologic data and, to a lesser degree, perviousness may have value in predicting first-pass outcome. Imaging metrics that more strongly reflect clot biology than perviousness may be needed to predict a first-pass effect with high accuracy.

Approaches to training multiclass semantic image segmentation of damage in concrete.

This paper addresses the problem of creating a large quantity of high-quality training segmentation masks from scanning electron microscopy (SEM) images. The images are acquired from concrete samples that exhibit progressive amounts of degradation resulting from alkali-silica reaction (ASR), a leading cause of deterioration, cracking and loss of capacity in much of the nation's infrastructure. The target damage classes in concrete SEM images are defined as paste damage, aggregate damage, air voids and no damage. We approached the SEM segmentation problem by applying convolutional neural network (CNN)-based methods to predict the damage classes due to ASR for each image pixel. The challenges in using the CNN-based methods lie in preparing large numbers of high-quality training labelled images while having limited human resources. To address these challenges, we designed damage- and context-assisted approaches to lower the requirements on human resources. We then evaluated the accuracy of CNN-based segmentation methods using the datasets prepared with these two approaches. LAY DESCRIPTION: This work is about automated segmentation of Scanning Electron Microscopy (SEM) images taken from core and prism samples of concrete. The segmentation must detect several damage classes in each image in order to understand properties of concrete-made structures over time. The segmentation problem is approached with an artificial network (AI) based model. The training data for the AI model are created using damage- and context-assisted approaches to lower the requirements on human resources. The access to all training data and to a web-based validation system for scoring segmented images is available at https://isg.nist.gov/deepzoomweb/data/concreteScoring.

Assessment of a Bayesian Vitrea CT Perfusion Analysis to Predict Final Infarct and Penumbra Volumes in Patients with Acute Ischemic Stroke: A Comparison with RAPID.

BACKGROUND AND PURPOSE: Brain CTP is used to estimate infarct and penumbra volumes to determine endovascular treatment eligibility for patients with acute ischemic stroke. We aimed to assess the accuracy of a Bayesian CTP algorithm in determining penumbra and final infarct volumes. MATERIALS AND METHODS: Data were retrospectively collected for 105 patients with acute ischemic stroke (55 patients with successful recanalization [TICI 2b/2c/3] and large-vessel occlusions and 50 patients without interventions). Final infarct volumes were calculated using DWI and FLAIR 24 hours following CTP imaging. RAPID and the Vitrea Bayesian CTP algorithm (with 3 different settings) predicted infarct and penumbra volumes for comparison with final infarct volumes to assess software performance. Vitrea settings used different combinations of perfusion maps (MTT, TTP, CBV, CBF, delay time) for infarct and penumbra quantification. Patients with and without interventions were included for assessment of predicted infarct and penumbra volumes, respectively. RESULTS: RAPID and Vitrea default setting had the most accurate final infarct volume prediction in patients with interventions ([Spearman correlation coefficient, mean infarct difference] default versus FLAIR: [0.77, 4.1 mL], default versus DWI: [0.72, 4.7 mL], RAPID versus FLAIR: [0.75, 7.5 mL], RAPID versus DWI: [0.75, 6.9 mL]). Default Vitrea and RAPID were the most and least accurate in determining final infarct volume for patients without an intervention, respectively (default versus FLAIR: [0.76, -0.4 mL], default versus DWI: [0.71, -2.6 mL], RAPID versus FLAIR: [0.68, -49.3 mL], RAPID versus DWI: [0.65, -51.5 mL]). CONCLUSIONS: Compared with RAPID, the Vitrea default setting was noninferior for patients with interventions and superior in penumbra estimation for patients without interventions as indicated by mean infarct differences and correlations with final infarct volumes.

Flow-Pattern Details in an Aneurysm Model Using High-Speed 1000-Frames-per-Second Angiography.

Traditional digital subtraction angiography provides rather limited evaluation of contrast flow dynamics when studying and treating intracranial brain aneurysms. A 1000-frames-per-second photon-counting x-ray detector was used to image detailed iodine-contrast flow patterns in an internal carotid artery aneurysm of a 3D-printed vascular phantom. High-speed imaging revealed differences in vortex and inflow patterns with and without a Pipeline Embolization Device flow diverter in more detail and clarity than could be seen in standard pulsed angiography. Improved temporal imaging has the potential to impact the outcomes of endovascular interventions by allowing clinicians to better understand and act on flow dynamics in real-time.

Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor.

Migration of human glioma cells (hGCs) within the brain parenchyma makes glioblastoma one of the most aggressive and lethal tumors. Studies of the cellular and molecular mechanisms underlying hGC migration are hindered by the limitations of existing glioma models. Here we developed a dorsal root ganglion axon-oligodendrocyte-hGC co-culture to study in real time the migration and interaction of hGCs with their microenvironment. hGCs interact with myelinated and non-myelinated axons through the formation of pseudopodia. Isolation of pseudopodia-localized polysome-bound RNA reveals transcripts of Lck, Paxillin, Crk-II, and Rac1 that undergo local translation. Inhibition of Lck phosphorylation using a small-molecule inhibitor (Lck-I), blocks the phosphorylation of Paxillin and Crk-II, the formation of pseudopodia and the migration of hGCs. In vivo intraventricular administration of the Lck-I using an orthotopic xenograft glioma model, results in statistically significant inhibition of tumor size and significant down-regulation of Nanog-targeted genes, which are associated with glioblastoma patient survival. Moreover, treatment of human glioma stem cells (hGSCs) with Lck-I, results in significant inhibition of self-renewal and tumor-sphere formation. The involvement of Lck in different levels of glioma malignant progression, such as migration, tumor growth, and regulation of cancer stemness, makes Lck a potentially important therapeutic target for human glioblastomas.

Development and Pilot Testing of a Coping Kit for Parents of Hospitalized Children.

OBJECTIVE: Serious pediatric illness places great stress on families. Parents who learn coping skills may better manage these stressors. This study sought to develop and refine a stress coping intervention for parents of hospitalized children, assess the intervention acceptability among these parents, and gather preliminary data on stress, negative and positive affect, anxiety, depression, and self-efficacy. METHODS: We conducted an observational study in 2 phases, enrolling parents of children who were inpatients with serious illness, 10 in Phase 1 and 40 in Phase 2. All parents completed at baseline measures of stress and psychological well-being and were introduced to the Coping Kit for Parents. Follow-up interviews were conducted at 1 week (all parents) and 1 month (Phase 2 parents only) regarding the acceptability of the intervention. RESULTS: At baseline, parents reported that stressful situations were frequent (mean = 30.6, standard deviation [SD] = 6.8) and difficult (mean = 26.2, SD = 7.1) and revealed elevated levels of negative affect (mean = 27.3, SD = 7.7), depression (mean = 8.5, SD = 3.7), and anxiety (mean = 11.3, SD = 3.1) and moderate levels of self-efficacy related to their child's illness (mean = 3.3, SD = 0.5). The majority of parents used the kit regularly and on a scale of 1 to 7 agreed that the kit was helpful (mean = 6.0, SD = 0.9), interesting (mean = 5.7, SD = 1.3), practical (mean = 5.7, SD = 1.4), enjoyable (mean = 6.0, SD = 1.3), and they would recommend it to other parents (mean = 6.4, SD = 0.9). CONCLUSIONS: The Coping Kit for Parents is an acceptable stress management intervention that could be made available to parents of children with serious illness at pediatric hospitals with minimal staff training or time commitment.

Laparoscopy reduces iatrogenic splenic injuries during colorectal surgery.

BACKGROUND: Splenic injury can occur during colorectal surgery especially in cases, where the splenic flexure is mobilized. The aim of this study was to analyze whether the operative approach (laparoscopic vs. open) was associated with an increased risk for splenic injury during colorectal surgery and to compare the outcomes of different management options. METHODS: All accidental injuries that occurred during colorectal resections performed in our department between January 2010 and June 2013 were identified from an administrative database. All patients with iatrogenic splenic injuries were classified into two groups according to the operative approach. Only procedures that required splenic flexure mobilization were included. Splenic injury management options and outcomes were compared. RESULTS: There were 2336 colorectal resections (1520 open, 816 laparoscopic) performed during the study period. There were 25 (1.1%) iatrogenic splenic injuries. 23 out of 25 splenic injuries occurred during open colorectal surgery. Overall, 16 (64%) patients were managed with topical hemostatic methods, 5 (20%) with splenectomy, and 4 (16%) with splenorrhaphy. It was possible to salvage the spleen in both laparoscopic patients. The laparoscopic approach was associated with a lower splenic injury rate (0.25% vs. 1.5%, p = 0.005) and a lower need for splenectomy/splenorrhaphy (p = 0.03). CONCLUSIONS: Our data suggest that laparoscopic colorectal surgery may be associated with a lower risk of iatrogenic splenic injury, and that most splenic injuries can be managed with spleen-preserving approaches.

A Patient Dose-Reduction Technique for Neuroendovascular Image-Guided Interventions: Image-Quality Comparison Study.

BACKGROUND AND PURPOSE: The ROI-dose-reduced intervention technique represents an extension of ROI fluoroscopy combining x-ray entrance skin dose reduction with spatially different recursive temporal filtering to reduce excessive image noise in the dose-reduced periphery in real-time. The aim of our study was to compare the image quality of simulated neurointerventions with regular and reduced radiation doses using a standard flat panel detector system. MATERIALS AND METHODS: Ten 3D-printed intracranial aneurysm models were generated on the basis of a single patient vasculature derived from intracranial DSA and CTA. The incident dose to each model was reduced using a 0.7-mm-thick copper attenuator with a circular ROI hole (10-mm diameter) in the middle mounted inside the Infinix C-arm. Each model was treated twice with a primary coiling intervention using ROI-dose-reduced intervention and regular-dose intervention protocols. Eighty images acquired at various intervention stages were shown twice to 2 neurointerventionalists who independently scored imaging qualities (visibility of aneurysm-parent vessel morphology, associated vessels, and/or devices used). Dose-reduction measurements were performed using an ionization chamber. RESULTS: A total integral dose reduction of 62% per frame was achieved. The mean scores for regular-dose intervention and ROI dose-reduced intervention images did not differ significantly, suggesting similar image quality. Overall intrarater agreement for all scored criteria was substantial (Kendall τ = 0.62887; P < .001). Overall interrater agreement for all criteria was fair (κ = 0.2816; 95% CI, 0.2060-0.3571). CONCLUSIONS: Substantial dose reduction (62%) with a live peripheral image was achieved without compromising feature visibility during neuroendovascular interventions.

Leaching of Conductive Species: Implications to Measurements of Electrical Resistivity.

Electrical tests have been used to characterize the microstructure of porous materials, the measured electrical response being determined by the contribution of the microstructure (porosity and tortuosity) and the electrical properties of the solution (conductivity of the pore solution) inside the pores of the material. This study has shown how differences in concentration between the pore solution (i.e., the solution in the pores) and the storage solution surrounding the test specimen leads to significant transport (leaching) of the conductive ionic species between the pore solution and the storage solution. Leaching influences the resistivity of the pore solution, thereby influencing electrical measurements on the bulk material from either a surface or uniaxial bulk resistance test. This paper has three main conclusions: 1.) Leaching of conductive species does occur with concentration gradients and that a diffusion based approach can be used to estimate the time scale associated with this change. 2.) Leaching of ions in the pore solution can influence resistivity measurements, and the ratio of surface to uniaxial resistivity can be used as a method to assess the presence of leaching and 3.) An estimation of the magnitude of leaching for standardized tests of cementitious materials.

Technical Note: Evaluation of the systematic accuracy of a frameless, multiple image modality guided, linear accelerator based stereotactic radiosurgery system.

PURPOSE: To evaluate the total systematic accuracy of a frameless, image guided stereotactic radiosurgery system. METHODS: The localization accuracy and intermodality difference was determined by delivering radiation to an end-to-end prototype phantom, in which the targets were localized using optical surface monitoring system (OSMS), electromagnetic beacon-based tracking (Calypso®), cone-beam CT, "snap-shot" planar x-ray imaging, and a robotic couch. Six IMRT plans with jaw tracking and a flattening filter free beam were used to study the dosimetric accuracy for intracranial and spinal stereotactic radiosurgery treatment. RESULTS: End-to-end localization accuracy of the system evaluated with the end-to-end phantom was 0.5 ± 0.2 mm with a maximum deviation of 0.9 mm over 90 measurements (including jaw, MLC, and cone measurements for both auto and manual fusion) for single isocenter, single target treatment, 0.6 ± 0.4 mm for multitarget treatment with shared isocenter. Residual setup errors were within 0.1 mm for OSMS, and 0.3 mm for Calypso. Dosimetric evaluation based on absolute film dosimetry showed greater than 90% pass rate for all cases using a gamma criteria of 3%/1 mm. CONCLUSIONS: The authors' experience demonstrates that the localization accuracy of the frameless image-guided system is comparable to robotic or invasive frame based radiosurgery systems.

Endovascular intracranial treatment of acute ischemic strokes.

Acute ischemic stroke (AIS) is the leading cause of long-term disability and the second cause of death worldwide. Intravenous (IV) tissue plasminogen activator (tPA) remains the only FDA-approved treatment for AIS. The use of IV tPA in AIS related to large-vessel occlusion (LVO) has shown low recanalization rates and poor clinical outcomes. Over the last decade, endovascular treatment has demonstrated safety and effectiveness in the management of LVO-associated AIS due to the evolution of endovascular techniques and technologies, beginning with intraarterial thrombolysis, aspiration, self- expanding intracranial stents, and now retrievable stents. With the recent publication of the results of 5 randomized controlled studies, mechanical thrombectomy in combination with IV tPA demonstrated significant radiographic and clinical benefit over traditional strategies with IV tPA alone. In light of these results, endovascular therapy has been placed at the forefront of stroke treatment, redefining the standard of care. This review presents the evolution of endovascular treatment of AIS resulting from LVO; provides an analysis of the initial and latest RCTs; and discusses the association between endovascular mechanical thrombectomy and clinical outcomes, functional outcomes, and rates of revascularization, intracranial hemorrhage, morbidity, and mortality. Finally, shortcomings of the recent technological advances, such as clot fragmentation, and potential solutions to overcome these drawbacks are presented.

Extracting the normal lung dose-response curve from clinical DVH data: a possible role for low dose hyper-radiosensitivity, increased radioresistance.

In conventionally fractionated radiation therapy for lung cancer, radiation pneumonitis' (RP) dependence on the normal lung dose-volume histogram (DVH) is not well understood. Complication models alternatively make RP a function of a summary statistic, such as mean lung dose (MLD). This work searches over damage profiles, which quantify sub-volume damage as a function of dose. Profiles that achieve best RP predictive accuracy on a clinical dataset are hypothesized to approximate DVH dependence.Step function damage rate profiles R(D) are generated, having discrete steps at several dose points. A range of profiles is sampled by varying the step heights and dose point locations. Normal lung damage is the integral of R(D) with the cumulative DVH. Each profile is used in conjunction with a damage cutoff to predict grade 2 plus (G2+) RP for DVHs from a University of Michigan clinical trial dataset consisting of 89 CFRT patients, of which 17 were diagnosed with G2+ RP.Optimal profiles achieve a modest increase in predictive accuracy--erroneous RP predictions are reduced from 11 (using MLD) to 8. A novel result is that optimal profiles have a similar distinctive shape: enhanced damage contribution from low doses (<20 Gy), a flat contribution from doses in the range ~20-40 Gy, then a further enhanced contribution from doses above 40 Gy. These features resemble the hyper-radiosensitivity / increased radioresistance (HRS/IRR) observed in some cell survival curves, which can be modeled using Joiner's induced repair model.A novel search strategy is employed, which has the potential to estimate RP dependence on the normal lung DVH. When applied to a clinical dataset, identified profiles share a characteristic shape, which resembles HRS/IRR. This suggests that normal lung may have enhanced sensitivity to low doses, and that this sensitivity can affect RP risk.

CFD: computational fluid dynamics or confounding factor dissemination? The role of hemodynamics in intracranial aneurysm rupture risk assessment.

Image-based computational fluid dynamics holds a prominent position in the evaluation of intracranial aneurysms, especially as a promising tool to stratify rupture risk. Current computational fluid dynamics findings correlating both high and low wall shear stress with intracranial aneurysm growth and rupture puzzle researchers and clinicians alike. These conflicting findings may stem from inconsistent parameter definitions, small datasets, and intrinsic complexities in intracranial aneurysm growth and rupture. In Part 1 of this 2-part review, we proposed a unifying hypothesis: both high and low wall shear stress drive intracranial aneurysm growth and rupture through mural cell-mediated and inflammatory cell-mediated destructive remodeling pathways, respectively. In the present report, Part 2, we delineate different wall shear stress parameter definitions and survey recent computational fluid dynamics studies, in light of this mechanistic heterogeneity. In the future, we expect that larger datasets, better analyses, and increased understanding of hemodynamic-biologic mechanisms will lead to more accurate predictive models for intracranial aneurysm risk assessment from computational fluid dynamics.

Pharmacogenomics of selective serotonin reuptake inhibitor treatment for major depressive disorder: genome-wide associations and functional genomics.

A genome-wide association (GWA) study of treatment outcomes (response and remission) of selective serotonin reuptake inhibitors (SSRIs) was conducted using 529 subjects with major depressive disorder. While no SNP associations reached the genome-wide level of significance, 14 SNPs of interest were identified for functional analysis. The rs11144870 SNP in the riboflavin kinase (RFK) gene on chromosome 9 was associated with 8-week treatment response (odds ratio (OR)=0.42, P=1.04 × 10⁻6). The rs915120 SNP in the G protein-coupled receptor kinase 5 (GRK5) gene on chromosome 10 was associated with 8-week remission (OR=0.50, P=1.15 × 10⁻5). Both SNPs were shown to influence transcription by a reporter gene assay and to alter nuclear protein binding using an electrophoretic mobility shift assay. This report represents an example of joining functional genomics with traditional GWA study results derived from a GWA analysis of SSRI treatment outcomes. The goal of this analytical strategy is to provide insights into the potential relevance of biologically plausible observed associations.

Using a pharmacogenomic algorithm to guide the treatment of depression.

The objective of this study was to evaluate the potential benefit of utilizing a pharmacogenomic testing report to guide the selection and dosing of psychotropic medications in an outpatient psychiatric practice. The non-randomized, open label, prospective cohort study was conducted from September 2009 to July 2010. In the first cohort, depressed patients were treated without the benefit of pharmacogenomic testing (the unguided group). A DNA sample was obtained from patients in the unguided group, but the results were not shared with either the physicians or patients until the end of the 8-week study period. In the second cohort (the guided group), testing results were provided at the beginning of the 8-week treatment period. Depression ratings were collected at baseline and after 2 weeks, 4 weeks and 8 weeks of treatment using the Quick Inventory of Depressive Symptomatology, Clinician Rated (QIDS-C16) and the 17-item Hamilton Rating Scale for Depression (HAM-D17). Clinician and patient satisfaction was also assessed. The reduction in depressive symptoms achieved within the guided treatment group was greater than the reduction of depressive symptoms in the unguided treatment group using either the QIDS-C16 (P=0.002) or HAM-D17 (P=0.04). We concluded that a rapidly available pharmacogenomic interpretive report provided clinical guidance that was associated with improved clinical outcomes for depressed patients treated in an outpatient psychiatric clinic setting.

Myeloid cell-specific expression of Ship1 regulates IL-12 production and immunity to helminth infection.

Helminth infection leads to the local proliferation and accumulation of macrophages in tissues. However, the function of macrophages during helminth infection remains unclear. SH2-containing inositol 5'-phosphatase 1 (Ship1, Inpp5d) is a lipid phosphatase that has been shown to play a critical role in macrophage function. Here, we identify a critical role for Ship1 in the negative regulation of interleukin (IL)-12/23p40 production by macrophages during infection with the intestinal helminth parasite Trichuris muris. Mice with myeloid cell-specific deletion of Ship1 (Ship1(ΔLysM) mice) develop a non-protective T-helper type 1 cell response and fail to expel parasites. Ship1-deficient macrophages produce heightened levels of IL-12/23p40 in vitro and in vivo and antibody blockade of IL-12/23p40 renders Ship1(ΔLysM) mice resistant to Trichuris infection. Our results identify a critical role for the negative regulation of IL-12/23p40 production by macrophages in the development of a protective T(H)2 cell response.