Loss of Diacylglycerol Kinase α Enhances Macrophage Responsiveness

The diacylglycerol kinases (DGKs) are a family of enzymes responsible for the conversion of diacylglycerol (DAG) to phosphatidic acid (PA). In addition to their primary function in lipid metabolism, DGKs have recently been identified as potential therapeutic targets in multiple cancers, including glioblastoma (GBM) and melanoma. Aside from its tumorigenic properties, DGKα is also a known promoter of T-cell anergy, supporting a role as a recently-recognized T cell checkpoint. In fact, the only significant phenotype previously observed in Dgka knockout (KO) mice is the enhancement of T-cell activity. Herein we reveal a novel, macrophage-specific, immune-regulatory function of DGKα. In bone marrow-derived macrophages (BMDMs) cultured from wild-type (WT) and KO mice, we observed increased responsiveness of KO macrophages to diverse stimuli that yield different phenotypes, including LPS, IL-4, and the chemoattractant MCP-1. Knockdown (KD) of Dgka in a murine macrophage cell line resulted in similar increased responsiveness. Demonstrating in vivo relevance, we observed significantly smaller wounds in Dgka^-/- mice with full-thickness cutaneous burns, a complex wound healing process in which macrophages play a key role. The burned area also demonstrated increased numbers of macrophages. In a cortical stab wound model, Dgka^-/- brains show increased Iba1⁺ cell numbers at the needle track versus that in WT brains. Taken together, these findings identify a novel immune-regulatory checkpoint function of DGKα in macrophages with potential implications for wound healing, cancer therapy, and other settings.

DUAL-PARTICLE DOSEMETER BASED ON ORGANIC SCINTILLATOR

Traditionally available handheld dosemeters are generally sensitive to only one type of radiation: neutrons or photons. Some dosemeters also rely on very specific attenuation correlations between response and dose, are not scalable in size and multiple dosemeters are required to characterise mixed-particle fields. The research presented here serves as a proof-of-concept for a method to simultaneously measure dose rates from neutrons and photons using a particle discriminating organic scintillation detector without the need for spectral deconvolution. The method was compared with traditional instruments and to simulation. Isotopic photon dose rates measured with this method were within 4% of simulated truth, whereas fission spectrum neutron dose rates were measured within 21%. Measurements of dose rates from both particles agree with simulated truth better than traditional instruments. This new method allows for measurement of dose equivalent from both neutrons and photons with a single instrument and no reliance on spectral deconvolution.

Body size data collected non-invasively from drone images indicate a morphologically distinct Chilean blue whale (Balaenoptera musculus) taxon

The blue whale Balaenoptera musculus (Linnaeus, 1758) was the target of intense commercial whaling in the 20th century, and current populations remain drastically below pre-whaling abundances. Reducing uncertainty in subspecific taxonomy would enable targeted conservation strategies for the recovery of unique intraspecific diversity. Currently, there are 2 named blue whale subspecies in the temperate to polar Southern Hemisphere: the Antarctic blue whale B. m. intermedia and the pygmy blue whale B. m. brevicauda. These subspecies have distinct morphologies, genetics, and acoustics. In 2019, the Society for Marine Mammalogy’s Committee on Taxonomy agreed that evidence supports a third (and presently unnamed) subspecies of Southern Hemisphere blue whale subspecies, the Chilean blue whale. Whaling data indicate that the Chilean blue whale is intermediate in body length between pygmy and Antarctic blue whales. We collected body size data from blue whales in the Gulfo Corcovado, Chile, during the austral summers of 2015 and 2017 using aerial photogrammetry from a remotely controlled drone to test the hypothesis that the Chilean blue whale is morphologically distinct from other Southern Hemisphere blue whale subspecies. We found the Chilean whale to be morphologically intermediate in both overall body length and relative tail length, thereby joining other diverse data in supporting the Chilean blue whale as a unique subspecific taxon. Additional photogrammetry studies of Antarctic, pygmy, and Chilean blue whales will help examine unique morphological variation within this species of conservation concern. To our knowledge, this is the first non-invasive small drone study to test a hypothesis for systematic biology.

A Serum Proteomic Signature Predicting Survival in Patients with Glioblastoma

Purpose

Glioblastoma (GBM) is the most common form of brain tumor and has a uniformly poor prognosis. Development of prognostic biomarkers in easily accessible serum samples have the potential to improve the outcomes of patients with GBM through personalized therapy planning.

Material/Methods

In this study pre-treatment serum samples from 30 patients newly diagnosed with GBM were evaluated using a 40-protein multiplex ELISA platform. Analysis of potentially relevant gene targets using The Cancer Genome Atlas database was done using the Glioblastoma Bio Discovery Portal (GBM-BioDP). A ten-biomarker subgroup of clinically relevant molecules was selected using a functional grouping analysis of the 40 plex genes with two genes selected from each group on the basis of degree of variance, lack of co-linearity with other biomarkers and clinical interest. A Multivariate Cox proportional hazard approach was used to analyze the relationship between overall survival (OS), gene expression, and resection status as covariates.

Results

Thirty of 40 of the MSD molecules mapped to known genes within TCGA and separated the patient cohort into two main clusters centered predominantly around a grouping of classical and proneural versus the mesenchymal subtype as classified by Verhaak. Using the values for the 30 proteins in a prognostic index (PI) demonstrated that patients in the entire cohort with a PI below the median lived longer than those patients with a PI above the median (HR 1.8, p=0.001) even when stratified by both age and MGMT status. This finding was also consistent within each Verhaak subclass and highly significant (range p=0.0001-0.011). Additionally, a subset of ten proteins including, CRP, SAA, VCAM1, VEGF, MDC, TNFA, IL7, IL8, IL10, IL16 were found to have prognostic value within the TCGA database and a positive correlation with overall survival in GBM patients who had received gross tumor resection followed by conventional radiation therapy and temozolomide treatment concurrent with the addition of valproic acid.

Conclusion

These findings demonstrate that proteomic approaches to the development of prognostic assays for treatment of GBM may hold potential clinical value.

A Framework for Climate Change-Related Research to Inform Environmental Protection

A critical charge for science to inform environmental protection is to characterize the risks associated with climate change, to support development of appropriate responses. The nature of climate change, however, presents significant challenges that must be overcome to do so, including the need for integration and synthesis across the many disciplines that contain knowledge relevant for achieving environmental protection goals. This paper describes an interdisciplinary research framework organized around three "Science Challenges" that directly respond to the needs of environmental protection organizations. Broadly, these Science Challenges refer to the research needed to: inform actions to enhance resilience across a broad range of environmental and social stresses to environmental management endpoints; actions to limit GHG emissions and slow the underlying rate of climate change; and the transition to sustainability across the full spectrum of climate change impacts and solutions; all as situated within an overarching risk management perspective. These Challenges span all media and systems critical to effective environmental protection, highlighting the cross-cutting nature of climate change and the need to address its impacts across systems and places. While this framework uses EPA's programs as an illustrative example, the research directions articulated herein are broadly applicable across the spectrum of environmental protection organizations. Going forward, we recommend that climate-related research to inform environmental protection efforts should accelerate its evolution toward research that is inherently cross-media and cross-scale; explicitly considers the social dimensions of change; and focuses on designing solutions to the specific risks climate change poses to the environment and society.

ClonEvol: clonal ordering and visualization in cancer sequencing

Background

Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation.

Materials and methods

ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution.

Results

ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones throughout metastatic progression observed in the tumors of a published breast cancer patient.

Conclusions

ClonEvol has broad applicability for longitudinal monitoring of clonal populations in tumor biopsies, or noninvasively, to guide precision medicine.

Availability

ClonEvol is written in R and is available at https://github.com/ChrisMaherLab/ClonEvol.

Preparation and Antibacterial Properties of Silver-Doped Nanoscale Hydroxyapatite Pastes for Bone Repair and Augmentation

The treatment of deep bone infections remains a significant challenge in orthopaedic and dental surgery. The relatively recent commercial manufacture of nanoscale hydroxyapatite has provided surgeons with an injectable biomaterial that promotes bone tissue regeneration, and with further modification it may be possible to incorporate antimicrobial properties into these devices. Silver-doped nanoscale hydroxyapatite pastes (0, 2, 5 and 10 mol.% silver) were prepared using a rapid mixing method. When the process was modified to prepare a 10 mol.% silver-doped material, silver phosphate was detected in addition to nanoscale hydroxyapatite. Thermal decomposition occurred more readily with greater silver content following calcination at 1000 °C for 2 h. Silver-doped nanoscale hydroxyapatite pastes showed antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa in a dose dependent manner using both agar diffusion assays and suspension cultures. It was concluded that the enhanced antibacterial activity of the silver-doped pastes was due to the action of diffusible silver ions. Based on these results, silver-doped nanoscale hydroxyapatite pastes represent a highly promising new biomaterial system for the prevention and treatment of deep infections in bone tissue.

Abstract P1-07-11: Tumor genomic profiling of triple negative breast cancer during neoadjuvant chemotherapy: Results from a prospective trial of carboplatin and docetaxel

Background-The clonal evolution and effect of neoadjuvant chemotherapy on the mutational landscape of triple negative breast cancer (TNBC) is unknown. Inability to eradicate TNBC may be due to clonal progression and selection of cells fundamentally resistant to chemotherapy.In this study, we sought to decipher the genomic architecture of TNBC serially during neoadjuvant chemotherapy to distinguish pre- versus post-chemotherapy genotypes.

Methods-Tumor specimens were obtained from patients with stages II and III TNBC enrolled on an ongoing prospective neoadjuvant co-clinical trial (NCT02124902). Patients have a research biopsy at baseline, cycle 1 day 3 (optional), and at definitive surgery for those with residual disease. Patients are treated with docetaxel 75mg/m2 and carboplatin AUC6 cycled every 3 weeks X six cycles. Definitive surgery is 3-5 weeks after chemotherapy. The primary endpoint is pathologic complete response rate. Correlative studies include development of patient derived xenografts, evaluation of genomic signatures of resistance and response, and comparison of chemotherapy responses between xenografts and host patients. Five patients' serial tumor samples and germline DNA were studied by exome and transcriptome sequencing. Three of these patients had an additional on-treatment sample at cycle 1 day 3. Two patients lacked residual disease samples- one was not banked and the other could not be accurately genotyped due to low cellularity. The median sequencing depth was 90.13x. Sequencing was performed on either fresh frozen or formalin-fixed paraffin-embedded samples with high cellularity (≥50%). After identifying somatic mutations in each tumor series, we evaluated whether each mutation was persistent, emergent, or cleared by comparing pre- and post-treatment (and when possible, on-treatment) samples.

Results-All five patients had response to neoadjuvant chemotherapy based on caliper-based and pathologic (residual cancer burden I or II) measurements. All residual disease remained TNBC by standard immunohistochemistry and all samples were basal-like from PAM50 gene expression analysis. We identified 908 somatic mutations, including the expected variants in TP53 which persisted in all post-treatment samples. Non-silent somatic variants were identified in other breast cancer-related genes, including GATA1, FBXO11, PIK3R1, AXIN2, ARID1B, BRCA2, and RBCC1. In spite of the clinico-pathologic evidence of response, we observed little change in clonal architecture, as derived from the purity-corrected variant allele fractions between baseline, cycle 1 day 3, and post-chemotherapy samples. Copy number alterations were likewise stable and transcriptional-based assessment indicated that patterns of mutant allele expression in driver genes were retained throughout the course of treatment.

Conclusion-In TNBC patients undergoing neoadjuvant platinum-based chemotherapy, there were no apparent shifts in the prevalence of known breast cancer specific somatic variants during or after chemotherapy. Despite pathologic response, core genomic features appear to be preserved in TNBC patients with residual disease following chemotherapy, likely accounting for high rates of relapse in these patients.

Citation Format: Ademuyiwa FO, Miller CA, Li T, Sanati S, Ma CX, Weilbaecher K, Ellis MJ, Mardis ER. Tumor genomic profiling of triple negative breast cancer during neoadjuvant chemotherapy: Results from a prospective trial of carboplatin and docetaxel [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-11.

Spatially weighted functional clustering of river network data

Incorporating spatial covariance into clustering has previously been considered for functional data to identify groups of functions which are similar across space. However, in the majority of situations that have been considered until now the most appropriate metric has been Euclidean distance. Directed networks present additional challenges in terms of estimating spatial covariance due to their complex structure. Although suitable river network covariance models have been proposed for use with stream distance, where distance is computed along the stream network, these models have not been extended for contexts where the data are functional, as is often the case with environmental data. The paper develops a method of calculating spatial covariance between functions from sites along a river network and applies the measure as a weight within functional hierarchical clustering. Levels of nitrate pollution on the River Tweed in Scotland are considered with the aim of identifying groups of monitoring stations which display similar spatiotemporal characteristics.

Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia

Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single-nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML.

Moderate drop in water table increases peatland vulnerability to post-fire regime shift

Northern and tropical peatlands represent a globally significant carbon reserve accumulated over thousands of years of waterlogged conditions. It is unclear whether moderate drying predicted for northern peatlands will stimulate burning and carbon losses as has occurred in their smaller tropical counterparts where the carbon legacy has been destabilized due to severe drainage and deep peat fires. Capitalizing on a unique long-term experiment, we quantify the post-wildfire recovery of a northern peatland subjected to decadal drainage. We show that the moderate drop in water table position predicted for most northern regions triggers a shift in vegetation composition previously observed within only severely disturbed tropical peatlands. The combined impact of moderate drainage followed by wildfire converted the low productivity, moss-dominated peatland to a non-carbon accumulating shrub-grass ecosystem. This new ecosystem is likely to experience a low intensity, high frequency wildfire regime, which will further deplete the legacy of stored peat carbon.

Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells

HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.

Measurement of the inclusive electron neutrino charged current cross section on carbon with the T2K near detector

The T2K off-axis near detector ND280 is used to make the first differential cross-section measurements of electron neutrino charged current interactions at energies ∼1  GeV as a function of electron momentum, electron scattering angle, and four-momentum transfer of the interaction. The total flux-averaged ν(e) charged current cross section on carbon is measured to be ⟨σ⟩(ϕ)=1.11±0.10(stat)±0.18(syst)×10⁻³⁸ cm²/nucleon. The differential and total cross-section measurements agree with the predictions of two leading neutrino interaction generators, NEUT and GENIE. The NEUT prediction is 1.23×10⁻³⁸ cm²/nucleon and the GENIE prediction is 1.08×10⁻³⁸ cm²/nucleon. The total ν(e) charged current cross-section result is also in agreement with data from the Gargamelle experiment.

Precise measurement of the neutrino mixing parameter θ23 from muon neutrino disappearance in an off-axis beam

New data from the T2K neutrino oscillation experiment produce the most precise measurement of the neutrino mixing parameter θ23. Using an off-axis neutrino beam with a peak energy of 0.6 GeV and a data set corresponding to 6.57×10(20) protons on target, T2K has fit the energy-dependent νμ oscillation probability to determine oscillation parameters. The 68% confidence limit on sin(2)(θ23) is 0.514(-0.056)(+0.055) (0.511±0.055), assuming normal (inverted) mass hierarchy. The best-fit mass-squared splitting for normal hierarchy is Δm32(2)=(2.51±0.10)×10(-3)  eV(2)/c(4) (inverted hierarchy: Δm13(2)=(2.48±0.10)×10(-3)  eV(2)/c(4)). Adding a model of multinucleon interactions that affect neutrino energy reconstruction is found to produce only small biases in neutrino oscillation parameter extraction at current levels of statistical uncertainty.

Mutual information as a measure of image quality for 3D dynamic lung imaging with EIT

We report on a pilot study of dynamic lung electrical impedance tomography (EIT) at the University of Manchester. Low-noise EIT data at 100 frames per second were obtained from healthy male subjects during controlled breathing, followed by magnetic resonance imaging (MRI) subsequently used for spatial validation of the EIT reconstruction. The torso surface in the MR image and electrode positions obtained using MRI fiducial markers informed the construction of a 3D finite element model extruded along the caudal-distal axis of the subject. Small changes in the boundary that occur during respiration were accounted for by incorporating the sensitivity with respect to boundary shape into a robust temporal difference reconstruction algorithm. EIT and MRI images were co-registered using the open source medical imaging software, 3D Slicer. A quantitative comparison of quality of different EIT reconstructions was achieved through calculation of the mutual information with a lung-segmented MR image. EIT reconstructions using a linear shape correction algorithm reduced boundary image artefacts, yielding better contrast of the lungs, and had 10% greater mutual information compared with a standard linear EIT reconstruction.

Observation of electron neutrino appearance in a muon neutrino beam

The T2K experiment has observed electron neutrino appearance in a muon neutrino beam produced 295 km from the Super-Kamiokande detector with a peak energy of 0.6 GeV. A total of 28 electron neutrino events were detected with an energy distribution consistent with an appearance signal, corresponding to a significance of 7.3σ when compared to 4.92±0.55 expected background events. In the Pontecorvo-Maki-Nakagawa-Sakata mixing model, the electron neutrino appearance signal depends on several parameters including three mixing angles θ12, θ23, θ13, a mass difference Δm(32)(2) and a CP violating phase δ(CP). In this neutrino oscillation scenario, assuming |Δm(32)(2)|=2.4×10(-3)  eV(2), sin(2)θ(23)=0.5, and Δm322>0 (Δm(32)(2)<0), a best-fit value of sin(2)2θ(13)=0.140(-0.032)(+0.038) (0.170(-0.037)(+0.045)) is obtained at δ(CP)=0. When combining the result with the current best knowledge of oscillation parameters including the world average value of θ(13) from reactor experiments, some values of δ(CP) are disfavored at the 90% C.L.

Measurement of neutrino oscillation parameters from muon neutrino disappearance with an off-axis beam

The T2K Collaboration reports a precision measurement of muon neutrino disappearance with an off-axis neutrino beam with a peak energy of 0.6 GeV. Near detector measurements are used to constrain the neutrino flux and cross section parameters. The Super-Kamiokande far detector, which is 295 km downstream of the neutrino production target, collected data corresponding to 3.01×10(20) protons on target. In the absence of neutrino oscillations, 205±17 (syst) events are expected to be detected while only 58 muon neutrino event candidates are observed. A fit to the neutrino rate and energy spectrum, assuming three neutrino flavors and normal mass hierarchy yields a best-fit mixing angle sin2(θ23)=0.514±0.082 and mass splitting |Δm(32)(2)|=2.44(-0.15)(+0.17)×10(-3) eV2/c4. Our result corresponds to the maximal oscillation disappearance probability.

The effect of denture design and fixatives on the retention of mandibular complete dentures tested on a novel in-vitro edentulous model

The aim of this study was to evaluate the effect of the design (extension and adaptation) of a mandibular complete acrylic denture and the use of denture adhesives using a novel in-vitro edentulous model. The model is a highly anatomically accurate replica based on a moderately resorbed human mandibular edentulous arch. The model has been designed and fabricated by means of an elaborate clinical and technical process that employs synthetic elastomeric materials with properties that attempts to reproduce in-vitro characteristics of the soft tissues overlying the ridges and immediate reflected tissues. This model was used to measure and compare the retention of mandibular dentures ofvarying designs (well-fitting, over- and under-extended) with and without the aid of denture fixatives. Retention tests were conducted with different volumes of artificial saliva at a cross head speed of 50 mm/min with 4 equidistant holding points on the denture occlusal surface, using a universal tensile testing machine in an axial pull direction. The effect of three denture adhesives on denture retention was also tested on the same denture types at different times over a period of 5 hours and beyond. The in-vitro model presented can be effectively used to test the retention of mandibular complete dentures. The speed of dislodgement force and amount of saliva are important variables in mandibular denture retention. The retention of well-fitting dentures was statistically higher than that of ill-fitting dentures. A significantly higher retention force was needed to dislodge mandibular dentures (well and ill-fitting dentures) when using a denture adhesive.

Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

Recent studies suggest that most cases of myelodysplastic syndrome (MDS) are clonally heterogeneous, with a founding clone and multiple subclones. It is not known whether specific gene mutations typically occur in founding clones or subclones. We screened a panel of 94 candidate genes in a cohort of 157 patients with MDS or secondary acute myeloid leukemia (sAML). This included 150 cases with samples obtained at MDS diagnosis and 15 cases with samples obtained at sAML transformation (8 were also analyzed at the MDS stage). We performed whole-genome sequencing (WGS) to define the clonal architecture in eight sAML genomes and identified the range of variant allele frequencies (VAFs) for founding clone mutations. At least one mutation or cytogenetic abnormality was detected in 83% of the 150 MDS patients and 17 genes were significantly mutated (false discovery rate ≤0.05). Individual genes and patient samples displayed a wide range of VAFs for recurrently mutated genes, indicating that no single gene is exclusively mutated in the founding clone. The VAFs of recurrently mutated genes did not fully recapitulate the clonal architecture defined by WGS, suggesting that comprehensive sequencing may be required to accurately assess the clonal status of recurrently mutated genes in MDS.

Endoscopic full-thickness biopsy of the gastric wall with defect closure by using an endoscopic suturing device: survival porcine study

BACKGROUND

The pathogenesis of several common gastric motility diseases and functional GI disorders remains essentially unexplained. Gastric wall biopsies that include the muscularis propria to evaluate the enteric nervous system, interstitial cells of Cajal, and immune cells can provide important insights for our understanding of the etiology of these disorders.

OBJECTIVES

To determine the technical feasibility, reproducibility, and safety of performing a full-thickness gastric biopsy (FTGB) by using a submucosal endoscopy with mucosal flap (SEMF) technique; the technical feasibility, reproducibility, and safety of tissue closure by using an endoscopic suturing device; the ability to identify myenteric ganglia in resected specimens; and the long-term safety.

DESIGN

Single center, preclinical survival study.

SETTING

Animal research laboratory, developmental endoscopy unit.

SUBJECTS

Twelve domestic pigs.

INTERVENTIONS

Animals underwent an SEMF procedure with gastric muscularis propria resection. The resultant offset mucosal entry site was closed by using an endoscopic suturing device. Animals were kept alive for 2 weeks.

MAIN OUTCOME MEASUREMENTS

The technical feasibility, reproducibility, and safety of the procedure; the clinical course of the animals; the histological and immunochemical evaluation of the resected specimen to determine whether myenteric ganglia were present in the sample.

RESULTS

FTGB was performed by using the SEMF technique in all 12 animals. The offset mucosal entry site was successfully closed by using the suturing device in all animals. The mean resected tissue specimen size was 11 mm. Mean total procedure time was 61 minutes with 2 to 4 interrupted sutures placed per animal. Histology showed muscularis propria and serosa, confirming full-thickness resections in all animals. Myenteric ganglia were visualized in 11 of 12 animals. The clinical course was uneventful. Repeat endoscopy and necropsy at 2 weeks showed absence of ulceration at both the mucosal entry sites and overlying the more distal muscularis propria resection sites. There was complete healing of the serosa in all animals with minimal single-band adhesions in 5 of 12 animals. Retained sutures were present in 10 of 12 animals.

LIMITATIONS

Animal experiment.

CONCLUSIONS

FTGB by using the SEMF technique and an endoscopic suturing device is technically feasible, reproducible, and safe. Larger tissue specimens will allow improved analysis of multiple cell types.

Indication of electron neutrino appearance from an accelerator-produced off-axis muon neutrino beam

The T2K experiment observes indications of ν(μ) → ν(e) appearance in data accumulated with 1.43×10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Δm(23)(2)| = 2.4×10(-3)  eV(2), sin(2)2θ(23) = 1 and sin(2)2θ(13) = 0, the expected number of such events is 1.5±0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7×10(-3), equivalent to 2.5σ significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2θ(13) < 0.28(0.34) for δ(CP) = 0 and a normal (inverted) hierarchy.

Observation of the naive-T-odd Sivers effect in deep-inelastic scattering

Azimuthal single-spin asymmetries of leptoproduced pions and charged kaons were measured on a transversely polarized hydrogen target. Evidence for a naive-T-odd, transverse-momentum-dependent parton distribution function is deduced from nonvanishing Sivers effects for pi(+), pi(0), and K(+/-), as well as in the difference of the pi(+) and pi(-) cross sections.

Double-hadron leptoproduction in the nuclear medium

The first measurements of double-hadron production in deep-inelastic scattering within the nuclear medium were made with the HERMES spectrometer at DESY HERA using a 27.6 GeV positron beam. By comparing data for deuterium, nitrogen, krypton, and xenon nuclei, the influence of the nuclear medium on the ratio of double-hadron to single-hadron yields was investigated. Nuclear effects on the additional hadron are clearly observed, but with little or no difference among nitrogen, krypton, or xenon, and with smaller magnitude than effects seen on previously measured single-hadron multiplicities. The data are compared with models based on partonic energy loss or prehadronic scattering and with a model based on a purely absorptive treatment of the final-state interactions. Thus, the double-hadron ratio provides an additional tool for studying modifications of hadronization in nuclear matter.

Measurement of the tensor structure function b1 of the deuteron

The Hermes experiment has investigated the tensor spin structure of the deuteron using the 27.6 GeV/c positron beam of DESY HERA. The use of a tensor-polarized deuteron gas target with only a negligible residual vector polarization enabled the first measurement of the tensor asymmetry A(d)zz and the tensor structure function b(d)1 for average values of the Bjorken variable 0.01< <x> <0.45 and of the negative of the squared four-momentum transfer 0.5 GeV2 < <Q2> <5 GeV2. The quantities A(d)zz and b(d)1 are found to be nonzero. The rise of b(d)1 for decreasing values of x can be interpreted to originate from the same mechanism that leads to nuclear shadowing in unpolarized scattering.

Frontotemporal dementia progresses to death faster than Alzheimer disease

BACKGROUND

Frontotemporal lobar degeneration (FTLD) is a common cause of non-Alzheimer dementia, but its natural history and the factors related to mortality in affected patients are not well understood.

METHODS

This retrospective, longitudinal study compared survival in FTLD (n = 177) with Alzheimer disease (AD; n = 395). Hazards analysis investigated the contribution of various demographic, neuropsychiatric, and neuropsychological variables and associated neurologic and neuropathologic findings.

RESULTS

The frontotemporal dementia (FTD) subtype of FTLD progressed faster than AD (median survival from retrospectively determined symptom onset, 8.7 +/- 1.2 vs 11.8 +/- 0.6 years, p < 0.0001; median survival from initial clinic presentation, 3.0 +/- 0.5 vs 5.7 +/- 0.1 years, p < 0.0001). Survival was similarly reduced in the related conditions corticobasal degeneration and progressive supranuclear palsy. Survival in the semantic dementia subtype of FTLD (11.9 +/- 0.2 years from onset and 5.3 +/- 0.4 years from presentation), however, was significantly longer than in FTD and did not differ from AD. Hazards analysis to determine factors affecting survival in FTLD showed no effect of age at onset, sex, education, family history, or neuropsychiatric profile. Among neuropsychological measures examined, impaired letter fluency had a significant association with reduced survival. Associated ALS significantly reduced survival in FTLD. The presence of tau-positive inclusions was associated with the slowest progression.

CONCLUSIONS

Frontotemporal lobar degeneration progresses more rapidly than Alzheimer disease, and the fastest-progressing cases are those with the frontotemporal dementia clinical subtype, coexisting motor neuron disease, or tau-negative neuropathology.

Single-spin asymmetries in semi-inclusive deep-inelastic scattering on a transversely polarized hydrogen target

Single-spin asymmetries for semi-inclusive electroproduction of charged pions in deep-inelastic scattering of positrons are measured for the first time with transverse target polarization. The asymmetry depends on the azimuthal angles of both the pion (phi) and the target spin axis (phi(S)) about the virtual-photon direction and relative to the lepton scattering plane. The extracted Fourier component sin((phi+phi(S))(pi)(UT) is a signal of the previously unmeasured quark transversity distribution, in conjunction with the Collins fragmentation function, also unknown. The component sin((phi-phi(S)(pi)(UT) arises from a correlation between the transverse polarization of the target nucleon and the intrinsic transverse momentum of quarks, as represented by the previously unmeasured Sivers distribution function. Evidence for both signals is observed, but the Sivers asymmetry may be affected by exclusive vector meson production.

Emissions of sulfur trioxide from coal-fired power plants

Emissions of sulfur trioxide (SO3) are a key component of plume opacity and acid deposition. Consequently, these emissions need to be low enough to not cause opacity violations and acid deposition. Generally, a small fraction of sulfur (S) in coal is converted to SO3 in coal-fired combustion devices such as electric utility boilers. The emissions of SO3 from such a boiler depend on coal S content, combustion conditions, flue gas characteristics, and air pollution devices being used. It is well known that the catalyst used in the selective catalytic reduction (SCR) technology for nitrogen oxides control oxidizes a small fraction of sulfur dioxide in the flue gas to SO3. The extent of this oxidation depends on the catalyst formulation and SCR operating conditions. Gas-phase SO3 and sulfuric acid, on being quenched in plant equipment (e.g., air preheater and wet scrubber), result in fine acidic mist, which can cause increased plume opacity and undesirable emissions. Recently, such effects have been observed at plants firing high-S coal and equipped with SCR systems and wet scrubbers. This paper investigates the factors that affect acidic mist production in coal-fired electric utility boilers and discusses approaches for mitigating emission of this mist.

Flavor decomposition of the sea-quark helicity distributions in the nucleon from semiinclusive deep inelastic scattering

Double-spin asymmetries of semiinclusive cross sections for the production of identified pions and kaons have been measured in deep inelastic scattering of polarized positrons on a polarized deuterium target. Five helicity distributions including those for three sea quark flavors were extracted from these data together with reanalyzed previous data for identified pions from a hydrogen target. These distributions are consistent with zero for all three sea flavors. A recently predicted flavor asymmetry in the polarization of the light quark sea appears to be disfavored by the data.

Devitrification of ionomer glass and its effect on the in vitro biocompatibility of glass-ionomer cements

The effects of devitrification of an ionomer glass with a molar composition 4.5SiO(2).3Al(2)O(3).1.5P(2)O(5).3CaO.2CaF(2) on cement formation and in vitro biocompatibility were investigated. Differential thermal analysis was used to study the phase evolution in the glass, and to determine the heat treatments for production of glass-ceramics. X-ray diffraction patterns from glass frit heat-treated at 750 degrees C for 2h contained peaks corresponding to apatite (JCPDS 15-876), whereas for samples heat-treated at 950 degrees C for 2h apatite and mullite (JCPDS 15-776) were the major phases detected. Transmission electron microscopy (TEM) confirmed that apatite and apatite-mullite phases were present after heat treatments at 750 degrees C and 950 degrees C respectively. Glass and glass-ceramics were ground to prepare <45microm powders and glass ionomer cements were produced using a ratio of 1g powder: 0.2g PAA: 0.3g 10% m/v tartaric acid solution in water. In vitro biocompatibility was evaluated using cultured rat osteosarcoma (ROS) cells. Scanning electron microscopy (SEM) showed that cells colonised the surfaces of cements prepared using untreated ionomer glass and glass crystallised to form apatite (750 degrees C/2h). However, quantitative evaluation using MTT and total protein assays indicated that more cell growth occurred in the presence of cements prepared using ionomer glasses crystallised to apatite than cements prepared using untreated glass. The least cell growth and respiratory activity was observed on cements made with crystallised glass containing both apatite and mullite. It was concluded that the controlled devitrification of ionomer glasses could be used to produce GIC bone cements with improved biocompatibility.

Evidence for quark-hadron duality in the proton spin asymmetry A1

Spin-dependent lepton-nucleon scattering data have been used to investigate the validity of the concept of quark-hadron duality for the spin asymmetry A1. Longitudinally polarized positrons were scattered off a longitudinally polarized hydrogen target for values of Q2 between 1.2 and 12 GeV2 and values of W2 between 1 and 4 GeV2. The average double-spin asymmetry in the nucleon resonance region is found to agree with that measured in deep-inelastic scattering at the same values of the Bjorken scaling variable x. This finding implies that the description of A1 in terms of quark degrees of freedom is valid also in the nucleon resonance region for values of Q2 above 1.6 GeV2.

Identification of a mutation associated with erythromycin resistance in Bordetella pertussis: implications for surveillance of antimicrobial resistance

Erythromycin treatment failures and in vitro resistance of Bordetella pertussis have been reported on several occasions in the past few years, but the mechanism of resistance has not been described. One potential mechanism, genetic modification of the erythromycin-binding site on the 23S rRNA of the 50S ribosomal subunit, has been observed in other bacteria. To explore this possibility, we amplified the portion of the 23S rRNA gene encoding the central loop of domain V. DNA sequencing and restriction fragment length polymorphism of the PCR products showed that each of the four erythromycin-resistant B. pertussis strains tested contained an A-to-G transition mutation at position 2058 (Escherichia coli numbering) of the 23S rRNA gene. The mutation was not found in seven erythromycin-susceptible isolates tested. Two of the resistant isolates were heterozygous, containing at least one mutant copy and one wild-type copy of the 23S rRNA gene. These results indicate that erythromycin resistance in these strains is likely due to a mutation of the erythromycin-binding site in the 23S rRNA gene. Identification of the resistance mechanism will facilitate development of molecular susceptibility testing methods that can be used directly on clinical specimens in the absence of an isolate.

Q2 dependence of nuclear transparency for exclusive rho0 production

Exclusive coherent and incoherent electroproduction of the rho(0) meson from 1H and 14N targets has been studied at the HERMES experiment as a function of coherence length (l(c)), corresponding to the lifetime of hadronic fluctuations of the virtual photon, and squared four-momentum of the virtual photon (-Q2). The ratio of 14N to 1H cross sections per nucleon, called nuclear transparency, was found to increase (decrease) with increasing l(c) for coherent (incoherent) rho(0) electroproduction. For fixed l(c), a rise of nuclear transparency with Q2 is observed for both coherent and incoherent rho(0) production, which is in agreement with theoretical calculations of color transparency.

Comparison of screening methods for TEM- and SHV-derived extended-spectrum beta-lactamase detection

OBJECTIVE

To compare common extended-spectrum beta-lactamase (ESBL) screening methods and beta-lactams for their ability to detect TEM- and SHV-related ESBL enzymes.

METHODS

This study compared disk diffusion testing by NCCLS methodology, the Jarlier double disk test, a disk-on-disk test, a modified three-dimensional test and the E test method for their sensitivity and specificity in detecting TEM- and SHV-related ESBL producers. Three negative and 22 positive controls were studied. These were two Klebsiella pneumoniae and 23 Escherichia coli transconjugants. Seventeen beta-lactam antibiotics were tested: cefamandole, cefotetan, cefoxitin, cefuroxime, cefixime, cefoperazone, cefotaxime, cefpodoxime, cefsulodin, ceftazidime, ceftibuten, ceftizoxime, ceftriaxone, moxalactam, cefepime, cefpirome and aztreonam.

RESULTS

NCCLS disk diffusion was 14% sensitive with ceftriaxone, 36% with cefotaxime, 64% with aztreonam, 68% with cefpodoxime, and 73% with ceftazidime. Cefoperazone, cefamandole, cefpodoxime and cefpirome showed 91% sensitivity using the Jarlier test. Using the disk-on-disk test, cefsulodin showed 95% sensitivity, and cefoperazone, cefepime and cefamandole showed 91% sensitivity. With the modified three-dimensional test, cefoperazone, cefpodoxime and cefpirome showed 91% sensitivity.

CONCLUSIONS

For practical reasons, we would recommend use of either the Jarlier test or the commercial cephalosporin disks containing clavulanic acid to screen for ESBL producers. Cefoperazone, cefamandole, cefpodoxime and cefpirome showed good sensitivity across the methods tested.

Formation of apatite layers on modified canasite glass-ceramics in simulated body fluid

Canasite glass-ceramics were modified by either increasing the concentration of calcium in the glass, or by the addition of P2O5. Samples of these novel materials were placed in simulated body fluid (SBF), along with a control material (commercial canasite), for periods ranging from 12 h to 28 days. After immersion, surface analysis was performed using thin film X-ray diffraction, Fourier transform infrared reflection spectroscopy, and scanning electron microscopy equipped with energy dispersive X-ray detectors. The concentrations of sodium, potassium, calcium, silicon, and phosphorus in the SBF solution were measured using inductively coupled plasma emission spectroscopy. No apatite was detected on the surface of commercial canasite, even after 28 days of immersion in SBF. A crystalline apatite layer was formed on the surface of a P2O5-containing canasite after 5 days, and after 3 days for calcium-enriched canasite. Ion release data suggested that the mechanism for apatite deposition was different for P2O5 and non-P2O5-containing glass-ceramics.

Performance assessment of NAPL remediation in heterogeneous alluvium

Over the last few years, more than 40 partitioning interwell tracer tests (PITTs) have been conducted at many different sites to measure nonaqueous phase liquid (NAPL) saturations in the subsurface. While the main goal of these PITTs was to estimate the NAPL volume in the subsurface, some were specifically conducted to assess the performance of remedial actions involving NAPL removal. In this paper, we present a quantitative approach to assess the performance of remedial actions to recover NAPL that can be used to assess any NAPL removal technology. It combines the use of PITTs (to estimate the NAPL volume in the swept pore volume between injection and extraction wells of a test area) with the use of several cores to determine the vertical NAPL distribution in the subsurface. We illustrate the effectiveness of such an approach by assessing the performance of a surfactant/foam flood conducted at Hill Air Force Base, UT, to remove a TCE-rich NAPL from alluvium with permeability contrasts as high as one order of magnitude. In addition, we compare the NAPL volumes determined by the PITTs with volumes estimated through geostatistical interpolation of aquifer sediment core data collected with a vertical frequency of 5-10 cm and a lateral borehole spacing of 0.15 m. We demonstrate the use of several innovations including the explicit estimation of not only the errors associated with NAPL volumes and saturations derived from PITTs but also the heterogeneity of the aquifer sediments based upon permeability estimates. Most importantly, we demonstrate the reliability of the

Continuity of care for short-stay neurosurgery patients: a quality improvement initiative

Decreases in the length of hospital stay for patients undergoing spinal surgery prompted this evaluation of the post-discharge needs of patients and the strategies that patients and their families employ to meet these needs. The nature and extent of post-discharge problems experienced by newly discharged patients was required as a baseline for the evaluation and improvement of discharge planning. Forty patients were interviewed following discharge, 20 patients within the first week of discharge, and 20 different patients between three and four weeks after discharge. Most patients reported that they had been well-informed about pain management and the majority of patients reported that pain was well-controlled. There was a subset of patients, however, who continued to report high levels of pain, even at one month after discharge. Less than one in three patients stated that they had received information about wound care and the information received was not consistent among health professionals. Given the limited time to prepare patients for discharge, this project highlights the need for written materials and for systematic follow-up after discharge.

Analysis of monophasic and biphasic electrical stimulation of nerve

In an earlier study, biphasic and monphasic electrical stimulation of the auditory nerve was performed in cats with a cochlear implant. Single-unit recordings demonstrated that spikes resulting from monophasic and biphasic stimuli have different thresholds and latencies. Monophasic thresholds are lower and latencies are shorter under cathodic stimulation. Results from stochastic simulations of a biophysical model of electrical stimulation are similar. A simple analysis of a linear, "integrate to threshold" membrane model accounts for the threshold and latency differences observed experimentally and computationally. Since biphasic stimuli are used extensively in functional electrical stimulation, this analysis greatly simplifies the biophysical interpretation of responses to clinically relevant stimuli by relating them to the responses obtained with monophasic stimuli.

Response properties of the refractory auditory nerve fiber

The refractory characteristics of auditory nerve fibers limit their ability to accurately encode temporal information. Therefore, they are relevant to the design of cochlear prostheses. It is also possible that the refractory property could be exploited by prosthetic devices to improve information transfer, as refractoriness may enhance the nerve's stochastic properties. Furthermore, refractory data are needed for the development of accurate computational models of auditory nerve fibers. We applied a two-pulse forward-masking paradigm to a feline model of the human auditory nerve to assess refractory properties of single fibers. Each fiber was driven to refractoriness by a single (masker) current pulse delivered intracochlearly. Properties of firing efficiency, latency, jitter, spike amplitude, and relative spread (a measure of dynamic range and stochasticity) were examined by exciting fibers with a second (probe) pulse and systematically varying the masker-probe interval (MPI). Responses to monophasic cathodic current pulses were analyzed. We estimated the mean absolute refractory period to be about 330 micros and the mean recovery time constant to be about 410 micros. A significant proportion of fibers (13 of 34) responded to the probe pulse with MPIs as short as 500 micros. Spike amplitude decreased with decreasing MPI, a finding relevant to the development of computational nerve-fiber models, interpretation of gross evoked potentials, and models of more central neural processing. A small mean decrement in spike jitter was noted at small MPI values. Some trends (such as spike latency-vs-MPI) varied across fibers, suggesting that sites of excitation varied across fibers. Relative spread was found to increase with decreasing MPI values, providing direct evidence that stochastic properties of fibers are altered under conditions of refractoriness.

Indirubin and indigo are potent aryl hydrocarbon receptor ligands present in human urine

Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that regulates genes involved in xenobiotic metabolism, cellular proliferation, and differentiation. Numerous xenobiotic and biological compounds are known to interact with AhR, but it remains an orphan receptor, because its physiological ligand is unknown. We identified AhR ligands in human urine using a yeast AhR signaling assay and then characterized their properties. Two ligands, indirubin and indigo, were both present at average concentrations of approximately 0.2 nm in the urine of normal donors. Indirubin was also detected in fetal bovine serum and contributed half of the total AhR ligand activity. The activities of indirubin and indigo were comparable with or more potent than that of the archetypal ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin, in yeast AhR activation assays. We suggest that the endogenous levels and potencies of indirubin and indigo are such that they activate AhR-mediated signaling mechanisms in vivo.