Improving the representation of stream water sources in surrogate nutrient models with water isotope data

An important part of meeting nutrient reduction goals in the lower Great Lakes basin and assessing the success of different land management strategies is modeling nutrient losses from agricultural land. This study aimed to improve the representation of water source contributions to streamflow in generalized additive models for predicting nutrient fluxes from three headwater agricultural streams in southern Ontario monitored during the Multi-Watershed Nutrient Study (MWNS). The previous development of these models represented baseflow contributions to streamflow using the baseflow proportion derived using an uncalibrated recursive digital filter. Recursive digital filters are commonly used to partition stream discharge into separate components from slower and faster pathways. In this study, we calibrated the recursive digital filter using stream water source information from stable isotopes of oxygen in water. Across sites, optimization of the filter parameters reduced bias in baseflow estimates by as much as 68 %. In most cases, calibrating the filter also improved agreement between filter-derived baseflow and baseflow calculated from isotope and streamflow data: the average Kling-Gupta Efficiencies using default and calibrated parameters were 0.44 and 0.82, respectively. When incorporated into the generalized additive models, the revised baseflow proportion predictor was more often statistically significant, improved model parsimony, and reduced prediction uncertainty. Moreover, this information allowed for a more rigorous interpretation of how different stream water sources influence nutrient losses from the agricultural MWNS watersheds.

Total and dissolved phosphorus losses from agricultural headwater streams during extreme runoff events

Eutrophication continues to be a concerning global water quality issue. Managing and mitigating harmful algal blooms demands clear information on the conditions promoting large phosphorus losses from contributing watersheds. Of particular concern is the amount and form of phosphorus loading to receiving water bodies during extreme runoff events, which are expected to increase in frequency due to climate change. Five years (2015 to 2020) of water quantity and quality data from 11 agricultural watersheds in the lower Great Lakes basin were analyzed and used to model total and dissolved phosphorus losses. This study aimed to assess temporal dynamics in phosphorus concentrations and losses over runoff events covering a wide range of hydrologic conditions and to quantify their relative importance on annual phosphorus losses. Event concentration-discharge relationships for total and dissolved phosphorus were hysteretic and had contrasting dominant patterns across watersheds. The proportion of annual phosphorus losses during events was highly variable between watersheds, accounting for 47-94 %. Extreme events were particularly impactful: as few as three events per year were found to be responsible for nearly half of total phosphorus (20-50 %) and total dissolved phosphorus (14-44 %) losses. Variability in total and dissolved phosphorus losses and concentrations over a wide range of flow conditions suggests that event magnitude is an important control on the relative mobility of particulate and dissolved phosphorus fractions. This study showed that insights into nutrient dynamics and phosphorus budgets in the lower Great Lakes basin and agriculture dominated environments more broadly can be gained by assessing event nutrient losses with respect to flow conditions and patterns in concentration-discharge relationships.

Novel predictors related to hysteresis and baseflow improve predictions of watershed nutrient loads: An example from Ontario's lower Great Lakes basin

Eutrophication has re-emerged in the lower Great Lakes basin resulting in critical water quality issues. Models that accurately predict nutrient loading from streams are needed to inform appropriate nutrient management decisions. Generalized additive models (GAMs) that use surrogate data from sensors to predict nutrient loads offer an alternative to commonly applied linear regression and may better handle relationship non-linearities and skewed water quality data. Five years (2015-2020) of water quantity and quality data from 11 agricultural watersheds in southern Ontario were used to develop GAMs to predict total phosphorus (TP) and nitrate (NO₃^-) loads. This study aimed to 1) use GAMs to predict nutrient loads using both common and novel predictors and 2) quantify and examine the variability in seasonal and annual nutrient loads. Along with routine surrogate model predictors (i.e., flow, turbidity, and seasonality), the addition of the baseflow proportion and the hydrograph position of flow observations improved model performance. Conversely, including the antecedent precipitation index minimally affected model performance, regardless of constituent. Seasonal and annual patterns in TP and NO₃^- load predictions mirrored that of the hydrologic regime. This study showed that parsimonious GAMs featuring novel model predictors can be used to predict nutrient loads while accounting for the partitioning of surface and subsurface flow paths and hysteresis between streamflow and water quality parameters that are frequently observed in a wide range of environments.

SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA

Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a small number of fusions are clinically actionable, targeted polymerase chain reaction (PCR)-based NGS chemistries, such as the QIAseq RNAscan assay, aim to improve accuracy compared to standard RNA sequencing. Existing informatics methods for gene fusion detection in NGS-based RNA sequencing assays traditionally use a transcriptome-based spliced alignment approach or a de-novo assembly approach. Transcriptome-based spliced alignment methods face challenges with short read mapping yielding low quality alignments. De-novo assembly-based methods yield longer contigs from short reads that can be more sensitive for genomic rearrangements, but face performance and scalability challenges. Consequently, there exists a need for a method to efficiently and accurately detect fusions in targeted PCR-based NGS chemistries. We describe SeekFusion, a highly accurate and computationally efficient pipeline enabling identification of gene fusions from PCR-based NGS chemistries. Utilizing biological samples processed with the QIAseq RNAscan assay and in-silico simulated data we demonstrate that SeekFusion gene fusion detection accuracy outperforms popular existing methods such as STAR-Fusion, TOPHAT-Fusion and JAFFA-hybrid. We also present results from 4,484 patient samples tested for neurological tumors and sarcoma, encompassing details on some novel fusions identified.

Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance

Acquired PARP inhibitor (PARPi) resistance in BRCA1- or BRCA2-mutant ovarian cancer often results from secondary mutations that restore expression of functional protein. RAD51C is a less commonly studied ovarian cancer susceptibility gene whose promoter is sometimes methylated, leading to homologous recombination (HR) deficiency and PARPi sensitivity. For this study, the PARPi-sensitive patient-derived ovarian cancer xenograft PH039, which lacks HR gene mutations but harbors RAD51C promoter methylation, was selected for PARPi resistance by cyclical niraparib treatment in vivo. PH039 acquired PARPi resistance by the third treatment cycle and grew through subsequent treatment with either niraparib or rucaparib. Transcriptional profiling throughout the course of resistance development showed widespread pathway level changes along with a marked increase in RAD51C mRNA, which reflected loss of RAD51C promoter methylation. Analysis of ovarian cancer samples from the ARIEL2 Part 1 clinical trial of rucaparib monotherapy likewise indicated an association between loss of RAD51C methylation prior to on-study biopsy and limited response. Interestingly, the PARPi resistant PH039 model remained platinum sensitive. Collectively, these results not only indicate that PARPi treatment pressure can reverse RAD51C methylation and restore RAD51C expression, but also provide a model for studying the clinical observation that PARPi and platinum sensitivity are sometimes dissociated.

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The Genome Analysis Toolkit (GATK), maintained by the Broad Institute, is currently the widely accepted standard for variant calling software. However, alternative solutions may provide faster variant calling without sacrificing accuracy. One such alternative is Sentieon DNASeq, a toolkit analogous to GATK but built on a highly optimized backend. We conducted an independent evaluation of the DNASeq single-sample variant calling pipeline in comparison to that of GATK. Our results support the near-identical accuracy of the two software packages, showcase optimal scalability and great speed from Sentieon, and describe computational performance considerations for the deployment of DNASeq.

Author Correction: ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

In the version of this Article originally published, Supplementary Fig. 6j showed incorrect values for the LS and AG4 glutathione samples, and Fig. 5c and Supplementary Fig. 6j did not include all n = 6 samples for the hESC, Y-hiPSC and AG4-ZSCAN10 groups as was stated in the legend. In addition, the bars for hESC, Y-hiPSC, AG4-ZCNAN10, AG4 and LS in Supplementary Fig. 6i and j have been reproduced from Fig. 5b and c, respectively. Fig. 6e was also reproduced in the lower panel of Supplementary Fig. 6h, to enable direct comparison of the data, however this was not explained in the original figure legends. The correct versions of these figures and their legends are shown below, and Supplementary Table 5 has been updated with the source data for all numerical data in the manuscript.

Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

Metabolism is an emerging stem cell hallmark tied to cell fate, pluripotency, and self-renewal, yet systems-level understanding of stem cell metabolism has been limited by the lack of genome-scale network models. Here, we develop a systems approach to integrate time-course metabolomics data with a computational model of metabolism to analyze the metabolic state of naive and primed murine pluripotent stem cells. Using this approach, we find that one-carbon metabolism involving phosphoglycerate dehydrogenase, folate synthesis, and nucleotide synthesis is a key pathway that differs between the two states, resulting in differential sensitivity to anti-folates. The model also predicts that the pluripotency factor Lin28 regulates this one-carbon metabolic pathway, which we validate using metabolomics data from Lin28-deficient cells. Moreover, we identify and validate metabolic reactions related to S-adenosyl-methionine production that can differentially impact histone methylation in naive and primed cells. Our network-based approach provides a framework for characterizing metabolic changes influencing pluripotency and cell fate.

RNA Exosome Complex-Mediated Control of Redox Status in Pluripotent Stem Cells

The RNA exosome complex targets AU-rich element (ARE)-containing mRNAs in eukaryotic cells. We identified a transcription factor, ZSCAN10, which binds to the promoters of multiple RNA exosome complex subunits in pluripotent stem cells to maintain subunit gene expression. We discovered that induced pluripotent stem cell clones generated from aged tissue donors (A-iPSC) show poor expression of ZSCAN10, leading to poor RNA exosome complex expression, and a subsequent elevation in ARE-containing RNAs, including glutathione peroxidase 2 (Gpx2). Excess GPX2 leads to excess glutathione-mediated reactive oxygen species scavenging activity that blunts the DNA damage response and apoptosis. Expression of ZSCAN10 in A-iPSC recovers RNA exosome gene expression, the DNA damage response, and apoptosis. These findings reveal the central role of ZSCAN10 and the RNA exosome complex in maintaining pluripotent stem cell redox status to support a normal DNA damage response.

Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease

We previously found C9orf72-associated (c9ALS) and sporadic amyotrophic lateral sclerosis (sALS) brain transcriptomes comprise thousands of defects, among which, some are likely key contributors to ALS pathogenesis. We have now generated complementary methylome data and combine these two data sets to perform a comprehensive "multi-omic" analysis to clarify the molecular mechanisms initiating RNA misregulation in ALS. We found that c9ALS and sALS patients have generally distinct but overlapping methylome profiles, and that the c9ALS- and sALS-affected genes and pathways have similar biological functions, indicating conserved pathobiology in disease. Our results strongly implicate SERPINA1 in both C9orf72 repeat expansion carriers and non-carriers, where expression levels are greatly increased in both patient groups across the frontal cortex and cerebellum. SERPINA1 expression is particularly pronounced in C9orf72 repeat expansion carriers for both brain regions, where SERPINA1 levels are strictly down regulated across most human tissues, including the brain, except liver and blood, and are not measurable in E18 mouse brain. The altered biological networks we identified contain critical molecular players known to contribute to ALS pathology, which also interact with SERPINA1. Our comprehensive combined methylation and transcription study identifies new genes and highlights that direct genetic and epigenetic changes contribute to c9ALS and sALS pathogenesis.

ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors

Induced pluripotent stem cells (iPSCs), which are used to produce transplantable tissues, may particularly benefit older patients, who are more likely to suffer from degenerative diseases. However, iPSCs generated from aged donors (A-iPSCs) exhibit higher genomic instability, defects in apoptosis and a blunted DNA damage response compared with iPSCs generated from younger donors. We demonstrated that A-iPSCs exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and permits survival of cells with genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSCs and addition of ZSCAN10 to the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) during A-iPSC reprogramming normalizes ROS-glutathione homeostasis and the DNA damage response, and recovers genomic stability. Correcting the genomic instability of A-iPSCs will ultimately enhance our ability to produce histocompatible functional tissues from older patients' own cells that are safe for transplantation.

Morphology, directed self-assembly and pattern transfer from a high molecular weight polystyrene-block-poly(dimethylsiloxane) block copolymer film

The self-assembly of block copolymers with large feature sizes is inherently challenging as the large kinetic barrier arising from chain entanglement of high molecular weight (MW) polymers limits the extent over which long-range ordered microdomains can be achieved. Here, we illustrate the evolution of thin film morphology from a diblock copolymer of polystyrene-block-poly(dimethylsiloxane) exhibiting total number average MW of 123 kg mol^-1, and demonstrate the formation of layers of well-ordered cylindrical microdomains under appropriate conditions of binary solvent mix ratio, commensurate film thickness, and solvent vapor annealing time. Directed self-assembly of the block copolymer within lithographically patterned trenches occurs with alignment of cylinders parallel to the sidewalls. Fabrication of ordered cobalt nanowire arrays by pattern transfer was also implemented, and their magnetic properties and domain wall behavior were characterized.

Interface electronic structure at the topological insulator-ferrimagnetic insulator junction

An interface electron state at the junction between a three-dimensional topological insulator film, Bi₂Se₃, and a ferrimagnetic insulator film, Y₃Fe₅O₁₂ (YIG), was investigated by measurements of angle-resolved photoelectron spectroscopy and x-ray absorption magnetic circular dichroism. The surface state of the Bi₂Se₃ film was directly observed and localized 3d spin states of the Fe³⁺ in the YIG film were confirmed. The proximity effect is likely described in terms of the exchange interaction between the localized Fe 3d electrons in the YIG film and delocalized electrons of the surface and bulk states in the Bi₂Se₃ film.

UV-solvent annealing of PDMS-majority and PS-majority PS-b-PDMS block copolymer films

The response of polystyrene-block-poly(dimethylsiloxane) (PS-b-PDMS) thin films to UV exposure during solvent vapor annealing is described, in order to improve their applicability in nanolithography and nanofabrication. Two BCPs were examined, one with the PS block as majority (f _PS = 68%, M _n = 53 kg mol^-1), the other with PDMS block as majority (f _PDMS = 67%, M _n = 44 kg mol^-1). A 5 min UV irradiation was applied during solvent vapor annealing which led to both partial crosslinking of the polymer and a small increase in the temperature of the annealing chamber. This approach was effective for improving the correlation length of the self-assembled microdomain arrays and in limiting subsequent flow of the PDMS in the PDMS-majority BCP to preserve the post-anneal morphology. Ordering and orientation of microdomains were controlled by directed self-assembly of the BCPs in trench substrates. Highly-ordered perpendicular nanochannel arrays were obtained in the PDMS-majority BCP.

HDQLIFE: development and assessment of health-related quality of life in Huntington disease (HD)

PURPOSE

Huntington disease (HD) is a chronic, debilitating genetic disease that affects physical, emotional, cognitive, and social health. Existing patient-reported outcomes (PROs) of health-related quality of life (HRQOL) used in HD are neither comprehensive, nor do they adequately account for clinically meaningful changes in function. While new PROs examining HRQOL (i.e., Neuro-QoL-Quality of Life in Neurological Disorders and PROMIS-Patient-Reported Outcomes Measurement Information System) offer solutions to many of these shortcomings, they do not include HD-specific content, nor have they been validated in HD. HDQLIFE addresses this by validating 12 PROMIS/Neuro-QoL domains in individuals with HD and by using established PROMIS methodology to develop new, HD-specific content.

METHODS

New item pools were developed using cognitive debriefing with individuals with HD, and expert, literacy, and translatability reviews. Existing item banks and new item pools were field tested in 536 individuals with prodromal, early-, or late-stage HD.

RESULTS

Moderate to strong relationships between Neuro-QoL/PROMIS measures and generic self-report measures of HRQOL, and moderate relationships between Neuro-QoL/PROMIS and clinician-rated measures of similar constructs supported the validity of Neuro-QoL/PROMIS in individuals with HD. Exploratory and confirmatory factor analysis, item response theory, and differential item functioning analyses were utilized to develop new item banks for Chorea, Speech Difficulties, Swallowing Difficulties, and Concern with Death and Dying, with corresponding six-item short forms. A four-item short form was developed for Meaning and Purpose.

CONCLUSIONS

HDQLIFE encompasses both validated Neuro-QoL/PROMIS measures, as well as five new scales in order to provide a comprehensive assessment of HRQOL in HD.

Plasma 8-hydroxy-2'-deoxyguanosine Levels in Huntington Disease and Healthy Controls Treated with Coenzyme Q10

We analyzed plasma 8OHdG concentrations in 20 individuals enrolled in the Pre-2CARE study before and after treatment with CoQ. Treatment resulted in a mean reduction in 8OHdG of 2.9 ± 2.9 pg/ml for the cohort (p = 0.0003) and 3.0 ± 2.6 pg/ml, for the HD group (p = 0.002). Baseline 8OHdG levels were not different between individuals with HD and controls (19.3 ± 3.2 pg/ml vs. 19.5 ± 4.7 pg/ml, p = 0.87) though baseline CoQ levels were elevated in HD compared with controls (p < 0.001). CoQ treatment reduces plasma 8OHdG and this reduction may serve as a marker of pharmacologic activity of CoQ in HD.

Quantitative Susceptibility Mapping Suggests Altered Brain Iron in Premanifest Huntington Disease

BACKGROUND AND PURPOSE

In patients with premanifest (nonsymptomatic) and advanced Huntington disease, changes in brain iron levels in the basal ganglia have been previously reported, especially in the striatum. Quantitative susceptibility mapping by using MR phase imaging allows in vivo measurements of tissue magnetic susceptibility, which has been shown to correlate well with iron levels in brain gray matter and is believed to be more specific than other imaging-based iron measures. The purpose of this study was to investigate the use of magnetic susceptibility as a biomarker of disease progression.

MATERIALS AND METHODS

Fifteen subjects with premanifest Huntington disease and 16 age-matched healthy controls were scanned at 7T. Magnetic susceptibility, effective relaxation, and tissue volume in deep gray matter structures were quantified and compared with genetic and clinical measures.

RESULTS

Subjects with premanifest Huntington disease showed significantly higher susceptibility values in the caudate nucleus, putamen, and globus pallidus, indicating increased iron levels in these structures. Significant decreases in magnetic susceptibility were found in the substantia nigra and hippocampus. In addition, significant volume loss (atrophy) and an increase effective relaxation were observed in the caudate nucleus and putamen. Susceptibility values in the caudate nucleus and putamen were found to be inversely correlated with structure volumes and directly correlated with the genetic burdens, represented by cytosine-adenine-guanine repeat age-product-scaled scores.

CONCLUSIONS

The significant magnetic susceptibility differences between subjects with premanifest Huntington disease and controls and their correlation with genetic burden scores indicate the potential use of magnetic susceptibility as a biomarker of disease progression in premanifest Huntington disease.

Magnetophotonic crystal with cerium substituted yttrium iron garnet and enhanced Faraday rotation angle

Magnetophotonic crystals (MPCs) comprising cerium-substituted yttrium iron garnet (CeYIG) sandwiched by two Bragg mirrors were fabricated by vacuum annealing. CeYIG was deposited on Bragg mirrors at room temperature and annealed in 5 Pa of residual air. No ceria or other non-garnet phases were detected. Cerium 3 + ions substituted on the yttrium sites and no cerium 4 + ions were found. The Faraday rotation angle of the MPC was -2.92° at a wavelength of λ = 1570 nm was 30 times larger than that of the CeYIG film. These results showed good agreement with calculated values derived using a matrix approach.

Geometrically frustrated Fe2P-like systems: beyond the Fe-trimer approximation

Fe(2)P-like structures can be strongly frustrated magnets due to their Kagome/triangular intercalated-layer structure. A complete magnetic solution of the complex spin architecture, and hence the full potential of the magnetic phenomena in Fe(2)P-like material prototypes, is yet to be found. A previous magnetic model for a representative FeCrAs-like system used a mean-field effective-spin to describe the 3g-Wyckoff located Fe-triangles. Such an approach demonstrated the outstanding magnetocaloric properties of the material but left the question of whether the intra-trimer interaction could lead to new physical phenomena and therefore more potentially useful properties. In this work Monte Carlo simulations are employed in order to understand both the influence of the additional degrees of freedom introduced by the Fe-trimers and the changes caused by all the possible exchange couplings between them. Complex scenarios arise, in which FM coupling in the trimers gives rise to both in-plane and out-of-plane inter-layer AFM states; whereas AFM exchange in the trimers gives rise to three distinct states, i.e. AFM-canted layers, a non-collinear superposition of ferromagnetic Kagome/triangular orderings, and tilted inter-planar AFM order. These last three configurations generate a double bifurcated magnetic phase diagram while the first one mimics the behavior seen in a model that treats the trimer as an effective-spin under an applied magnetic field.

Simulation methods for solvent vapor annealing of block copolymer thin films

Recent progress in modelling the solvent vapor annealing of thin film block copolymers is examined in the context of a self-consistent field theory framework. Key control variables in determining the final microdomain morphologies include swelling ratio or swollen film solvent volume fraction, swollen film thickness, substrate and vapor atmosphere surface energies, effective volume fraction, and effective Flory-Huggins interaction parameter. The regime of solvent vapor annealing studied is where the block copolymer has a high enough Flory-Huggins parameter that ordered structures form during swelling and are then trapped in the system through quenching. Both implicit and explicit consideration of the solvent vapor is considered to distinguish the cases in which solvent vapor leads to a non-bulk morphology. Block-selective solvents are considered based on the experimental systems of polystyrene-b-polydimethylsiloxane annealed with toluene and heptane. The results of these simulations are compared with these experiments.

Oxygen partial pressure dependence of magnetic, optical and magneto-optical properties of epitaxial cobalt-substituted SrTiO₃ films

Cobalt-substituted SrTiO3 films (SrTi0.70Co0.30O(3-δ)) were grown on SrTiO3 substrates using pulsed laser deposition under oxygen pressures ranging from 1 μTorr to 20 mTorr. The effect of oxygen pressure on structural, magnetic, optical, and magneto-optical properties of the films was investigated. The film grown at 3 μTorr has the highest Faraday rotation (FR) and magnetic saturation moment (M(s)). Increasing oxygen pressure during growth reduced M(s), FR and optical absorption in the near-infrared. This trend is attributed to decreasing Co2+ ion concentration and oxygen vacancy concentration with higher oxygen partial pressure during growth.

SrGa(0.7)Co(0.3)O(3-δ) perovskite-cobalt oxide-metal nanocomposite films: magnetic and optical properties

Two-phase nanocomposite films consisting of metallic Co nanoparticles below 50 nm diameter in a perovskite matrix were grown by pulsed laser deposition onto (LaAlO3)0.3(Sr2AlTaO6)0.7 (LSAT) and silicon substrates from a target of SrGa0.73Co0.27O3. The particles made up about 6% by volume of the film and were present within the film and at the substrate interface. The saturation magnetization of the film was up to 85 emu cm(-3) at 80 nm thickness and the Faraday rotation (FR) tracked the out-of-plane hysteresis loop, reaching 3000 deg cm(-1) at 10 kOe for 1550 nm wavelength. The magneto-optical figure of merit defined as FR divided by optical absorption was 0.04-0.06 deg dB(-1) due to the high optical absorption of the Co particles.

Multiferroic behavior of templated BiFeO3-CoFe2O4 self-assembled nanocomposites

Self-assembled BiFeO3-CoFe2O4 nanocomposites were templated into ordered structures in which the ferrimagnetic CoFe2O4 pillars form square arrays of periods 60-100 nm in a ferroelectric BiFeO3 matrix. The ferroelectricity, magnetism, conductivity, and magnetoelectric coupling of the ordered nanocomposites were characterized by scanning probe microscopy. The insulating BiFeO3 matrix exhibited ferroelectric domains, whereas the resistive CoFe2O4 pillars exhibited single-domain magnetic contrast with high anisotropy due to the magnetoelasticity of the spinel phase. Magnetoelectric coupling was observed in which an applied voltage led to reversal of the magnetic pillars.

Cardiac transcriptome and dilated cardiomyopathy genes in zebrafish

BACKGROUND

Genetic studies of cardiomyopathy and heart failure have limited throughput in mammalian models. Adult zebrafish have been recently pursued as a vertebrate model with higher throughput, but genetic conservation must be tested.

METHODS AND RESULTS

We conducted transcriptome analysis of zebrafish heart and searched for fish homologues of 51 known human dilated cardiomyopathy-associated genes. We also identified genes with high cardiac expression and genes with differential expression between embryonic and adult stages. Among tested genes, 30 had a single zebrafish orthologue, 14 had 2 homologues, and 5 had ≥3 homologues. By analyzing the expression data on the basis of cardiac abundance and enrichment hypotheses, we identified a single zebrafish gene for 14 of 19 multiple-homologue genes and 2 zebrafish homologues of high priority for ACTC1. Of note, our data suggested vmhc and vmhcl as functional zebrafish orthologues for human genes MYH6 and MYH7, respectively, which are established molecular markers for cardiac remodeling.

CONCLUSIONS

Most known genes for human dilated cardiomyopathy have a corresponding zebrafish orthologue, which supports the use of zebrafish as a conserved vertebrate model. Definition of the cardiac transcriptome and fetal gene program will facilitate systems biology studies of dilated cardiomyopathy in zebrafish.

Integration of bulk-quality thin film magneto-optical cerium-doped yttrium iron garnet on silicon nitride photonic substrates

Cerium substituted yttrium iron garnet (Ce:YIG) films were grown on yttrium iron garnet (YIG) seed layers on silicon nitride films using pulsed laser deposition. Optimal process conditions for forming garnet films on silicon nitride are presented. Bulk or near-bulk magnetic and magneto-optical properties were observed for 160 nm thick Ce:YIG films grown at 640 °C on rapid thermal annealed 40 nm thick YIG grown at 640 °C and 2 Hz pulse rate. The effect of growth temperature and deposition rate on structural, magnetic and magneto-optical properties has been investigated.

A nonreciprocal racetrack resonator based on vacuum-annealed magnetooptical cerium-substituted yttrium iron garnet

Vacuum annealed polycrystalline cerium substituted yttrium iron garnet (CeYIG) films deposited by radio frequency magnetron sputtering on non-garnet substrates were used in nonreciprocal racetrack resonators. CeYIG annealed at 800°C for 30 min provided a large Faraday rotation angle, close to the single crystal value. Crystallinity, magnetic properties, refractive indices and absorption coefficients were measured. The resonant transmission peak of the racetrack resonator covered with CeYIG was non-reciprocally shifted by applying an in-plane magnetic field.

The Geogenomic Mutational Atlas of Pathogens (GoMAP) web system

We present a new approach for pathogen surveillance we call Geogenomics. Geogenomics examines the geographic distribution of the genomes of pathogens, with a particular emphasis on those mutations that give rise to drug resistance. We engineered a new web system called Geogenomic Mutational Atlas of Pathogens (GoMAP) that enables investigation of the global distribution of individual drug resistance mutations. As a test case we examined mutations associated with HIV resistance to FDA-approved antiretroviral drugs. GoMAP-HIV makes use of existing public drug resistance and HIV protein sequence data to examine the distribution of 872 drug resistance mutations in ∼ 502,000 sequences for many countries in the world. We also implemented a broadened classification scheme for HIV drug resistance mutations. Several patterns for geographic distributions of resistance mutations were identified by visual mining using this web tool. GoMAP-HIV is an open access web application available at http://www.bio-toolkit.com/GoMap/project/

Protocol for an HTA report: Does therapeutic writing help people with long-term conditions? Systematic review, realist synthesis and economic modelling

INTRODUCTION

Long-term medical conditions (LTCs) cause reduced health-related quality of life and considerable health service expenditure. Writing therapy has potential to improve physical and mental health in people with LTCs, but its effectiveness is not established. This project aims to establish the clinical and cost-effectiveness of therapeutic writing in LTCs by systematic review and economic evaluation, and to evaluate context and mechanisms by which it might work, through realist synthesis.

METHODS

Included are any comparative study of therapeutic writing compared with no writing, waiting list, attention control or placebo writing in patients with any diagnosed LTCs that report at least one of the following: relevant clinical outcomes; quality of life; health service use; psychological, behavioural or social functioning; adherence or adverse events. Searches will be conducted in the main medical databases including MEDLINE, EMBASE, PsycINFO, The Cochrane Library and Science Citation Index. For the realist review, further purposive and iterative searches through snowballing techniques will be undertaken. Inclusions, data extraction and quality assessment will be in duplicate with disagreements resolved through discussion. Quality assessment will include using Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria. Data synthesis will be narrative and tabular with meta-analysis where appropriate. De novo economic modelling will be attempted in one clinical area if sufficient evidence is available and performed according to the National Institute for Health and Care Excellence (NICE) reference case.

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters, and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly-complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name ‘Atribacteria’. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden-Meyerhof glycolysis with production of hydrogen, acetate, and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the ‘Atribacteria’.

Solvothermal annealing of block copolymer thin films

A two-stage annealing process for block copolymer films was introduced consisting of a solvent vapor exposure followed by a thermal cycle. By heating the film but not the chamber, changes in the ambient vapor pressure of the solvent were avoided. Films of block copolymers and homopolymers showed transient nonmonotonic swelling behavior immediately after solvent exposure that was dependent on how the thin film was cast before the anneal. Thermal cycling of the solvent-swelled block copolymer films during the solvent vapor anneal (SVA) caused the films to deswell in 1-10 s and produced well-ordered microdomains in templated 45.5 and 51.5 kg/mol polystyrene-block-polydimethylsiloxane films annealed in toluene and n-heptane vapors for total process times of 30 s to 5 min.

Magnetic entropy change plateau in a geometrically frustrated layered system: FeCrAs-like iron-pnictide structure as a magnetocaloric prototype

Monte Carlo modeling suggests that the magnetothermal features of the Fe2P-structured FeCrAs-like compound offer a promising route for the design of magnetocaloric materials. The prototype structure is modeled as antiferromagnetically coupled layered Heisenberg systems mimicking the distorted Kagome/triangular stacked architecture of FeCrAs iron-pnictide. The magnetic entropy change ΔSm(T) presents a plateau-like behavior which can be tailored by tuning either the JCr-Fe/JCr-Cr exchange energy ratio or the magnetic field. The plateau is defined by cooperative spin ordering within a ferrimagnetic region which exists between two critical temperatures separating at the lower bound (Tac) a canted antiferromagnetic phase and at the upper bound (Tdc) the thermally disordered phase. The refrigerant capacity and adiabatic change of temperature are A(H)(Tdc - Tac) and A(H)Tp/Cm respectively, with Tac < Tp < Tdc, A(H) an increasing positive function of the field defining the height of the plateau and Cm the magnetic specific heat, whose critical behavior is related to the T(a,d)(c) values.

Self-assembled incorporation of modulated block copolymer nanostructures in phase-change memory for switching power reduction

Phase change memory (PCM), which exploits the phase change behavior of chalcogenide materials, affords tremendous advantages over conventional solid-state memory due to its nonvolatility, high speed, and scalability. However, high power consumption of PCM poses a critical challenge and has been the most significant obstacle to its widespread commercialization. Here, we present a novel approach based on the self-assembly of a block copolymer (BCP) to form a thin nanostructured SiOx layer that locally blocks the contact between a heater electrode and a phase change material. The writing current is decreased 5-fold (corresponding to a power reduction by 1/20) as the occupying area fraction of SiOx nanostructures is increased from a fill factor of 9.1% to 63.6%. Simulation results theoretically explain the current reduction mechanism by localized switching of BCP-blocked phase change materials.

Magnetostriction in epitaxial SrTi(1-x)Fe(x)O(3-δ) perovskite films with x = 0.13 and 0.35

The crystal structure, magnetic anisotropy and magnetoelasticity of epitaxial SrTi(0.87)Fe(0.13)O(3-δ) (STF13) and SrTi(0.65)Fe(0.35)O(3-δ) (STF35) films grown on (001), (011), and (111) oriented SrTiO(3) substrates were investigated. The films grew with compressive in-plane strain and underwent tetragonal, monoclinic, and rhombohedral distortions on the (001), (011), and (111) substrates, respectively. All samples showed room temperature magnetic hysteresis loops with strong out-of-plane anisotropy. The resulting magnetoelastic anisotropy was an order of magnitude greater than the magnetocrystalline and shape anisotropies. Magnetoelastic coefficients of B(1) =- 6.7 × 10(6) and B(2) =- 28 to -26 × 10(6) erg cm(-3) for STF13 and B(1) =- 2.0 × 10(6) and B(2) =- 5.4 to -3.9 × 10(6) erg cm(-3) for STF35 were determined from the magnetic anisotropy and lattice strain, corresponding to magnetostriction constants of λ(100) = 2.09 × 10(-6) and λ(111) = 7.68 × 10(-6) for STF13, and λ(100) = 0.62 × 10(-6) and λ(111) = 1.07 × 10(-6) for STF35.

Magneto-optical properties of cerium substituted yttrium iron garnet films with reduced thermal budget for monolithic photonic integrated circuits

Thin films of polycrystalline cerium substituted yttrium iron garnet (CeYIG) were grown on an yttrium iron garnet (YIG) seed layer on Si and Si-on-insulator substrates by pulsed laser deposition, and their optical and magneto-optical properties in the near-IR region were measured. A YIG seed layer of ~30 nm thick processed by rapid thermal anneal at 800°C provided a virtual substrate to promote crystallization of the CeYIG. The effect of the thermal budget of the YIG/CeYIG growth process on the film structure, magnetic and magnetooptical properties was determined.

Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning

Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7–8.5 at concentrations up to 6.6×10⁶ 16S rRNA gene copies g⁻¹ wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.

CAG repeat expansion in Huntington disease determines age at onset in a fully dominant fashion

OBJECTIVE

Age at onset of diagnostic motor manifestations in Huntington disease (HD) is strongly correlated with an expanded CAG trinucleotide repeat. The length of the normal CAG repeat allele has been reported also to influence age at onset, in interaction with the expanded allele. Due to profound implications for disease mechanism and modification, we tested whether the normal allele, interaction between the expanded and normal alleles, or presence of a second expanded allele affects age at onset of HD motor signs.

METHODS

We modeled natural log-transformed age at onset as a function of CAG repeat lengths of expanded and normal alleles and their interaction by linear regression.

RESULTS

An apparently significant effect of interaction on age at motor onset among 4,068 subjects was dependent on a single outlier data point. A rigorous statistical analysis with a well-behaved dataset that conformed to the fundamental assumptions of linear regression (e.g., constant variance and normally distributed error) revealed significance only for the expanded CAG repeat, with no effect of the normal CAG repeat. Ten subjects with 2 expanded alleles showed an age at motor onset consistent with the length of the larger expanded allele.

CONCLUSIONS

Normal allele CAG length, interaction between expanded and normal alleles, and presence of a second expanded allele do not influence age at onset of motor manifestations, indicating that the rate of HD pathogenesis leading to motor diagnosis is determined by a completely dominant action of the longest expanded allele and as yet unidentified genetic or environmental factors.

The role of deprivation, abuse, and trauma in pediatric catatonia without a clear medical cause

OBJECTIVE

Catatonia is considered a unique syndrome of motor signs, at times life-threatening when aggravated by autonomic dysfunction and fever, but eminently treatable with specific medical treatments, if recognized early. Catatonia commonly occurs in children and adolescents with a wide range of associated disorders. The role of deprivation, abuse, or trauma in the development of pediatric catatonia is examined.

METHOD

Reports considering deprivation, abuse, or trauma as precipitants of catatonia in pediatric cases are culled from the classic writings on catatonia and from a selective review of modern contributions.

RESULTS

Kahlbaum gave trauma a central role in catatonia in many young adult cases. Kanner described children with psychogenic catalepsy. Anaclitic depression, a condition found by Spitz in deprived institutionalized children, strongly resembles stuporous catatonia. Leonhard considered lack of communication with the mother or substitute mother as an important risk factor for childhood catatonia. Children including those with autism who experience emotional and physical trauma sometimes develop catatonia. The clinical descriptions of children with classic catatonic syndromes and those of contemporary refugee children with a syndrome labeled Pervasive Refusal Syndrome are similar.

CONCLUSION

The literature supports the view that deprivation, abuse, and trauma can precipitate catatonia in children and adolescents.

Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences

Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease.

A novel obesity model: synphilin-1-induced hyperphagia and obesity in mice

Aims

The pathogenesis of obesity remains incompletely understood and the exploration of the role of novel proteins in obesity may provide important insights into its causes and treatments. Here we report a previously unidentified role for synphilin-1 in the controls of food intake and body weight. Synphilin-1, a cytoplasmic protein, was initially identified as an interaction partner of alpha-synuclein, and has implications in Parkinson's disease pathogenesis related to protein aggregation.

Subjects and methods

To study the in vivo role of synphilin-1, we characterized a human synphilin-1 transgenic mouse (SP1) by assessing synphilin-1 expression, plasma parameters, food intake and spontaneous activity to determine the major behavioral changes and their consequences in the development of the obesity phenotype.

Results

Expression of human synphilin-1 in brain neurons in SP1 mice resulted in increased food intake, body weight and body fat. SP1 mice also displayed hyperinsulinemia, hyperleptinemia and impaired glucose tolerance. Pair-feeding SP1 mice to amounts consumed by non-transgenic mice prevented the increased body weight, adiposity, hyperinsulinemia and hyperleptinemia demonstrating that these were all the consequences of increased food intake. Transgenic expression of synphilin-1 was enriched in hypothalamic nuclei involved in feeding control, and fasting induced elevated endogenous synphilin-1 levels at these sites, suggesting that synphilin-1 is an important player in the hypothalamic energy balance regulatory system.

Conclusion

These studies identify a novel function of synphilin-1 in controlling food intake and body weight, and may provide a unique obesity model for future studies of obesity pathogenesis and therapeutics.

Highly tunable self-assembled nanostructures from a poly(2-vinylpyridine-b-dimethylsiloxane) block copolymer

An extraordinarily large degree of tunability in geometry and dimension is demonstrated in films of a self-assembled block copolymer. A poly(2-vinylpyridine-b-dimethylsiloxane) block copolymer with highly incompatible blocks was spun-cast on patterned substrates and treated with various solvent vapors. The degree of selective swelling in the poly(2-vinylpyridine) matrix block could be controlled over an extensive range, leading to the formation of various microdomain morphologies such as spheres, cylinders, hexagonally perforated lamellae, and lamellae from the same block copolymer. The systematic control of swelling ratio and the choice of solvent vapors offer the unusual ability to control the width of very well-ordered linear features within a range between 6 and 31 nm. This methodology is particularly useful for nanolithography based on directed self-assembly in that a single block copolymer film can form microdomains with a broad range of geometries and sizes without the need to change molecular weight or volume fraction.

Preparation and magnetic properties of cylindrical NiFe films and antidot arrays

Continuous NiFe (Permalloy) cylindrical films and arrays of cylindrical NiFe antidots 7 nm thick have been prepared by sputtering onto cylindrical aluminum wires and onto wires anodized to form a porous anodic alumina layer. The antidots are arranged in a close-packed pattern determined by the hexagonal pore arrangement in the porous alumina, with period 103 nm and diameter 42 nm. Hysteresis loops were measured at different angles with respect to the cylinder axis and indicate an easy plane normal to the radius of the wire. The antidots enhance the coercivity compared to the continuous cylindrical film.

Guidelines for nomenclature assignment of Ger receptors

Some members of the orders Bacillales and Clostridiales form dormant spores when subjected to environmental stress. These resistant spores return to normal vegetative growth upon encountering nutrients. A family of membrane-bound proteins called germination (Ger) receptors is tasked with detecting metabolites that serve as germination signals. During the characterization of tripartite Ger receptor proteins from the genera Bacillus and Clostridium, we found numerous nomenclature inconsistencies. In this work, we issued guidelines to remediate this problem. We generated a sample of sequenced Bacillus, Clostridium and related endospore-forming genera. Ger receptor proteins were recovered from these genomes by PSI-BLAST. The resulting Ger receptor protein sequences were then clustered by neighbor-joining based on sequence alignment. Inconsistencies in Ger receptor labeling were noted and new names proposed. Finally, a systematic approach for naming of new Ger receptors was designed.

Fabrication of diverse metallic nanowire arrays based on block copolymer self-assembly

Metallic nanowires are useful for fabricating highly integrated nanoscale electrical, magnetic, and photonic devices. However, conventional methods based on bottom-up growth techniques are subject to concerns such as broad distributions in their dimension as well and difficulties in precise placement of the nanowires. These issues can be solved by the guided self-assembly of block copolymer thin films that can produce periodic arrays of monodisperse nanoscale features with excellent positional accuracy. Here, we report transfer of high-quality linear block copolymer patterns into various metals, Ti, W, Pt, Co, Ni, Ta, Au, and Al, to fabricate highly ordered nanowire arrays with widths down to 9 nm. This novel patterning process does not require specific film deposition techniques or etch-chemistries. We also describe their structural, magnetic, and electrical properties.

Complex self-assembled patterns using sparse commensurate templates with locally varying motifs

Templated self-assembly of block copolymer thin films can generate periodic arrays of microdomains within a sparse template, or complex patterns using 1:1 templates. However, arbitrary pattern generation directed by sparse templates remains elusive. Here, we show that an array of carefully spaced and shaped posts, prepared by electron-beam patterning of an inorganic resist, can be used to template complex patterns in a cylindrical-morphology block copolymer. We use two distinct methods: making the post spacing commensurate with the equilibrium periodicity of the polymer, which controls the orientation of the linear features, and making local changes to the shape or distribution of the posts, which direct the formation of bends, junctions and other aperiodic features in specific locations. The first of these methods permits linear patterns to be directed by a sparse template that occupies only a few percent of the area of the final self-assembled pattern, while the second method can be used to selectively and locally template complex linear patterns.

A path to ultranarrow patterns using self-assembled lithography

The templated self-assembly of block copolymer (BCP) thin films can generate regular arrays of 10-50 nm scale features with good positional and orientational accuracy, but the ordering, registration and pattern transfer of sub-10-nm feature sizes is not well established. Here, we report solvent-annealing and templating methods that enable the formation of highly ordered grating patterns with a line width of 8 nm and period 17 nm from a self-assembled poly(styrene-b-dimethylsiloxane) (PS-PDMS) diblock copolymer. The BCP patterns can be registered hierarchically on a larger-period BCP pattern, which can potentially diversify the available pattern geometries and enables precise pattern registration at small feature sizes. Sub-10-nm-wide tungsten nanowires with excellent order and uniformity were fabricated from the self-assembled patterns using a reactive ion etching process.

Synphilin-1 exhibits trophic and protective effects against Rotenone toxicity

Synphilin-1 is a cytoplasmic protein with unclear function. Synphilin-1 has been identified as an interaction partner of alpha-synuclein. The interaction between synphilin-1 and alpha-synuclein has implications in Parkinson's disease. In this study, we stably overexpressed human synphilin-1 in mouse N1E-115 neuroblastoma cells. We found that overexpression of synphilin-1 shortened cell growth doubling time and increased neurite outgrowth. Knockdown of endogenous synphilin-1 caused neuronal toxicity and shortened neurite outgrowth. We further found that synphilin-1 increased activation of the extracellular signal-regulated kinases (ERK1/2) and mediated neurite outgrowth. Rotenone, mitochondrial complex I inhibitor, has been shown previously to induce dopaminergic neurodegeneration and Parkinsonism in rats and Drosophila. We found that Rotenone induced apoptotic cell death in N1E-115 cells via caspase-3 activation and poly (ADP-ribose) polymerase (PARP) cleavage. Overexpression of synphilin-1 significantly reduced Rotenone-induced cell death, caspase-3 activation and PARP cleavage. The results indicate that synphilin-1 displays trophic and protective effects in vitro, suggesting that synphilin-1 may play a protective role in Parkinson's disease (PD) pathogenesis and may lead to a potential therapeutic target for PD intervention.

Stigma, negative attitudes and discrimination towards mental illness within the nursing profession: a review of the literature

The aim of this paper was to review the existing literature pertaining to stigma, negative attitudes and discrimination towards mental illness, specifically as viewed through the lens of the nursing profession. The results of the literature review were synthesized and analysed, and the major themes drawn from this were found to correspond with Schulze's model identifying three positions that healthcare workers may assume in relation to stigma of mental illness: 'stigmatizers', 'stigmatized' and 'de-stigmatizers'. In this paper, the nursing profession is examined from the perspectives of the first two major themes: the 'stigmatizers' and 'stigmatized'. Their primary sub-themes are identified and discussed: (1) Nurses as 'the stigmatizers': (a) nurses' attitudes in general medical settings towards patients with psychiatric illness and (b) psychiatric nurses; (2) Nurses as 'the stigmatized': (a) nurses who have mental illness and (b) stigma within the profession against psychiatric nurses and/or psychiatry in general. The secondary and tertiary sub-themes are also identified and reviewed.