Stable Solid Molecular Hydrogen above 900 K from a Machine-Learned Potential Trained with Diffusion Quantum Monte Carlo.

We survey the phase diagram of high-pressure molecular hydrogen with path integral molecular dynamics using a machine-learned interatomic potential trained with quantum Monte Carlo forces and energies. Besides the HCP and C2/c-24 phases, we find two new stable phases both with molecular centers in the Fmmm-4 structure, separated by a molecular orientation transition with temperature. The high temperature isotropic Fmmm-4 phase has a reentrant melting line with a maximum at higher temperature (1450 K at 150 GPa) than previously estimated and crosses the liquid-liquid transition line around 1200 K and 200 GPa.

X-ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates.

Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal-ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kß emission optimized for analysis of dilute biological samples. We further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.

Assessment of biogeographic variation in traits of Lewis flax (Linum lewisii) for use in restoration and agriculture.

Lewis flax (Linum lewisii) is widely distributed across western North America and is currently used in native ecosystem restoration. There is also growing interest in de novo domestication of Lewis flax as a perennial oilseed crop. To better understand this species and facilitate both restoration and domestication, we used common gardens to assess biogeographical variation in a variety of seed and growth traits from 37 flax accessions, consisting of 35 wild populations from the Intermountain West region, the pre-variety germplasm Maple Grove (L. lewisii) and the cultivar 'Appar' (L. perenne) and related this variation to collection site geography and climate. Results from linear mixed models suggest there is extensive phenotypic variation among populations of Lewis flax within the Intermountain West. Using a multivariate approach, we identify a key suite of traits that are related to latitude and climate and may facilitate adaptation, including flowering indeterminacy, seed mass and stem number. These traits should be taken into account when considering the release of new germplasm for restoration efforts. We also find that Lewis flax seed contains desirably high amounts of alpha-linolenic acid and is otherwise mostly indistinguishable in fatty acid composition from oil-type varieties of domesticated flax (L. usitatissimum), making it a strong candidate for domestication. This study provides fundamental knowledge for future research into the ecology and evolution of Lewis flax, which will inform its use in both restoration and agriculture.

Early Binding of Substrate Oxygen Is Responsible for a Spectroscopically Distinct S2 State in Photosystem II.

The biological generation of oxygen by the oxygen-evolving complex (OEC) in photosystem II (PS II) is one of nature's most important reactions. The OEC is a Mn4Ca cluster that has multiple Mn-O-Mn and Mn-O-Ca bridges and binds four water molecules. Previously, binding of an additional oxygen was detected in the S2 to S3 transition. Here we demonstrate that early binding of the substrate oxygen to the five-coordinate Mn1 center in the S2 state is likely responsible for the S2 high-spin EPR signal. Substrate binding in the Mn1-OH form explains the prevalence of the high-spin S2 state at higher pH and its low-temperature conversion into the S3 state. The given interpretation was confirmed by X-ray absorption spectroscopic measurements, DFT, and broken symmetry DFT calculations of structures and magnetic properties. Structural, electronic, and spectroscopic properties of the high-spin S2 state model are provided and compared with the available S3 state models. New interpretation of the high-spin S2 state opens opportunity for analysis of factors controlling the oxygen substrate binding in PS II.

DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system.

The application of X-ray emission spectroscopy (XES) has grown substantially with the development of X-ray free electron lasers, third and fourth generation synchrotron sources and high-power benchtop sources. By providing the high X-ray flux required for XES, these sources broaden the availability and application of this method of probing electronic structure. As the number of sources increase, so does the demand for X-ray emission detection and sample delivery systems that are cost effective and customizable. Here, we present a detailed fabrication protocol for von Hamos X-ray optics and give details for a 3D-printed spectrometer design. Additionally, we outline an automated, externally triggered liquid sample delivery system that can be used to repeatedly deliver nanoliter droplets onto a plastic substrate for measurement. These systems are both low cost, efficient and easy to recreate or modify depending on the application. A low cost multiple X-ray analyzer system enables measurement of dilute samples, whereas the sample delivery limits sample loss and replaces spent sample with fresh sample in the same position. While both systems can be used in a wide range of applications, the design addresses several challenges associated specifically with time-resolved XES (TRXES). As an example application, we show results from TRXES measurements of photosystem II, a dilute, photoactive protein.

X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis.

X-ray free electron lasers (XFELs) provide ultrashort intense X-ray pulses suitable to probe electron dynamics but can also induce a multitude of nonlinear excitation processes. These affect spectroscopic measurements and interpretation, particularly for upcoming brighter XFELs. Here we identify and discuss the limits to observing classical spectroscopy, where only one photon is absorbed per atom for a Mn2+ in a light element (O, C, H) environment. X-ray emission spectroscopy (XES) with different incident photon energies, pulse intensities, and pulse durations is presented. A rate equation model based on sequential ionization and relaxation events is used to calculate populations of multiply ionized states during a single pulse and to explain the observed X-ray induced spectral lines shifts. This model provides easy estimation of spectral shifts, which is essential for experimental designs at XFELs and illustrates that shorter X-ray pulses will not overcome sequential ionization but can reduce electron cascade effects.

Parameters of Time-out: Research Update and Comparison to Parenting Programs, Books, and Online Recommendations.

In reviews published more than 30 years ago, eight parameters important to the use of time-out were identified and available research was summarized. The purpose of the current paper is to provide an updated summary of existing research for each parameter of time-out. Within each parameter, we conducted a thorough review of the published literature and identified all peer-reviewed articles addressing each parameter. We identified and summarized a total of 46 articles across the eight parameters, including 32 not cited in previous reviews. Sufficient findings were available to draw conclusions regarding time-out warning, schedule of time-out, contingent versus noncontingent release, and duration. Tentative conclusions based on only a few studies could be drawn in regard to instructional versus physical administration and verbalized reason for time-out. No conclusions could be drawn regarding time-out signal and specific time-out location. While we know much more today regarding effective implementation of time-out, there is a clear need for further exploration within these identified parameters. In addition to summarizing the literature, we reviewed recommendations made by behavioral parent training programs, parenting books, and parenting Web sites, and compared how well their recommendations matched current research based on the conclusions drawn from our review. We found that parenting sources made strong and specific recommendations on several of the parameters that were either not consistent with available research or simply lacked a sufficient research base.

Structured Feedback Training for Time-Out: Efficacy and Efficiency in Comparison to a Didactic Method.

Although time-out has been demonstrated to be effective across multiple settings, little research exists on effective methods for training others to implement time-out. The present set of studies is an exploratory analysis of a structured feedback method for training time-out using repeated role-plays. The three studies examined (a) a between-subjects comparison to more a traditional didactic/video modeling method of time-out training, (b) a within-subjects comparison to traditional didactic/video modeling training for another skill, and (c) the impact of structured feedback training on in-home time-out implementation. Though findings are only preliminary and more research is needed, the structured feedback method appears across studies to be an efficient, effective method that demonstrates good maintenance of skill up to 3 months post training. Findings suggest, though do not confirm, a benefit of the structured feedback method over a more traditional didactic/video training model. Implications and further research on the method are discussed.

Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field.

Despite years of research into microbial activity at diffuse flow hydrothermal vents, the extent of microbial niche diversity in these settings is not known. To better understand the relationship between microbial activity and the associated physical and geochemical conditions, we obtained co-registered metatranscriptomic and geochemical data from a variety of different fluid regimes within the ASHES vent field on the Juan de Fuca Ridge. Microbial activity in the majority of the cool and warm fluids sampled was dominated by a population of Gammaproteobacteria (likely sulfur oxidizers) that appear to thrive in a variety of chemically distinct fluids. Only the warmest, most hydrothermally-influenced flows were dominated by active populations of canonically vent-endemic Epsilonproteobacteria. These data suggest that the Gammaproteobacteria collected during this study may be generalists, capable of thriving over a broader range of geochemical conditions than the Epsilonproteobacteria. Notably, the apparent metabolic activity of the Gammaproteobacteria-particularly carbon fixation-in the seawater found between discrete fluid flows (the intra-field water) suggests that this area within the Axial caldera is a highly productive, and previously overlooked, habitat. By extension, our findings suggest that analogous, diffuse flow fields may be similarly productive and thus constitute a very important and underappreciated aspect of deep-sea biogeochemical cycling that is occurring at the global scale.

X-ray Emission Spectroscopy of Biomimetic Mn Coordination Complexes.

Understanding the function of Mn ions in biological and chemical redox catalysis requires precise knowledge of their electronic structure. X-ray emission spectroscopy (XES) is an emerging technique with a growing application to biological and biomimetic systems. Here, we report an improved, cost-effective spectrometer used to analyze two biomimetic coordination compounds, [MnIV(OH)2(Me2EBC)]2+ and [MnIV(O)(OH)(Me2EBC)]+, the second of which contains a key MnIV═O structural fragment. Despite having the same formal oxidation state (MnIV) and tetradentate ligands, XES spectra from these two compounds demonstrate different electronic structures. Experimental measurements and DFT calculations yield different localized spin densities for the two complexes resulting from MnIV-OH conversion to MnIV═O. The relevance of the observed spectroscopic changes is discussed for applications in analyzing complex biological systems such as photosystem II. A model of the S3 intermediate state of photosystem II containing a MnIV═O fragment is compared to recent time-resolved X-ray diffraction data of the same state.

Measurement Issues: Large effect sizes do not mean most people get better - clinical significance and the importance of individual results.

BACKGROUND: This paper seeks to compare group statistical analysis with effect size, group measures of clinical significance (Reliable Change Index and normative comparison), and individual analysis of clinical significance. METHOD: Measures of variables important to parenting and child behavior improvement (Parenting Scale, Eyberg Child Behavior Inventory, and Parenting Stress Index [PSI]) were administered pre and post for a 9- to 10-week group Behavioral Parent Training Intervention. Analysis compares traditional group statistical significance testing with group measure of clinical significance and individual analysis of clinical significance. RESULTS: All three measures demonstrated statistically significant differences from pre to post, with large effect sizes. Group measures of clinical significance, however, demonstrated meaningful change only on the PSI, while individual analysis showed improvements of 54% of participants at best and 0% at worst. CONCLUSIONS: Individual analysis of clinical significance provides valuable information in treatment outcomes and should be included as a standard practice in outcomes research.

Engagement in Behavioral Parent Training: Review of the Literature and Implications for Practice.

Engagement in behavioral parent training (BPT), including enrollment, attrition, attendance, within-session engagement, and homework completion, has long been a critical issue in the literature. Several estimates of various aspects of engagement have been suggested in the literature, but a systematic review of the available literature has never been accomplished. This review examines engagement data across 262 studies of BPT. Recruitment attrition, program attrition, attendance, and within-session engagement are examined across studies, with particular emphasis on the impact that SES, study purpose (efficacy vs. effectiveness), treatment format (individual vs. group), and age of child may have on those rates. Results of this review suggest that the significant amount of attrition occurs prior to enrollment in BPT, with at least 25 % of those identified as appropriate for BPT not enrolling in such programs. An additional 26 % begin, but drop out before completing treatment. Still the combined dropout rate of at least 51 % leaves at best half of identified parents completing treatment. While SES status had a small effect on attrition, other variables were not found to meaningfully impact engagement. Information on within-session engagement (homework and ratings of participation) was not often reported in studies. Key issues in this literature (e.g., varying definitions of engagement, limited attention to reporting key aspects of engagement) are discussed, and recommendations are made to further improve this important area of research and clinical practice.

Autonomous application of quantitative PCR in the deep sea: in situ surveys of aerobic methanotrophs using the deep-sea environmental sample processor.

Recent advances in ocean observing systems and genomic technologies have led to the development of the deep-sea environmental sample processor (D-ESP). The D-ESP filters particulates from seawater at depths up to 4000 m and applies a variety of molecular assays to the particulates, including quantitative PCR (qPCR), to identify particular organisms and genes in situ. Preserved samples enable laboratory-based validation of in situ results and expanded studies of genomic diversity and gene expression. Tests of the D-ESP at a methane-rich mound in the Santa Monica Basin centered on detection of 16S rRNA and particulate methane monooxygenase (pmoA) genes for two putative aerobic methanotrophs. Comparison of in situ qPCR results with laboratory-based assays of preserved samples demonstrates the D-ESP generated high-quality qPCR data while operating autonomously on the seafloor. Levels of 16S rRNA and pmoA cDNA detected in preserved samples are consistent with an active community of aerobic methanotrophs near the methane-rich mound. These findings are substantiated at low methane sites off Point Conception and in Monterey Bay where target genes are at or below detection limits. Successful deployment of the D-ESP is a major step toward developing autonomous systems to facilitate a wide range of marine microbiological investigations.

Payment schedules do not affect attendance/completion of group behavioral parent training.

Though previous research suggests that attendance at individual therapy is not impacted by amount or source of payment for services, such research is relatively sparse and clinician concerns remain. The present study explores the connection between payment of fees and attendance at group treatments--a previously unexplored area. Participants in a 10-week behavioral parent training (BPT) program varied in timing of payment of fees as well as amount of fees based on income. The varying payment schedules did not affect attendance to sessions at which payments were due nor did payment schedules affect completion of the program. A small relationship was found between income group and attendance. The results are discussed in their relation to the larger literature on fees and attendance at psychotherapy.

High-frequency ultrasound for intraoperative margin assessments in breast conservation surgery: a feasibility study.

BACKGROUND: In addition to breast imaging, ultrasound offers the potential for characterizing and distinguishing between benign and malignant breast tissues due to their different microstructures and material properties. The aim of this study was to determine if high-frequency ultrasound (20-80 MHz) can provide pathology sensitive measurements for the ex vivo detection of cancer in margins during breast conservation surgery. METHODS: Ultrasonic tests were performed on resected margins and other tissues obtained from 17 patients, resulting in 34 specimens that were classified into 15 pathology categories. Pulse-echo and through-transmission measurements were acquired from a total of 57 sites on the specimens using two single-element 50-MHz transducers. Ultrasonic attenuation and sound speed were obtained from time-domain waveforms. The waveforms were further processed with fast Fourier transforms to provide ultrasonic spectra and cepstra. The ultrasonic measurements and pathology types were analyzed for correlations. The specimens were additionally re-classified into five pathology types to determine specificity and sensitivity values. RESULTS: The density of peaks in the ultrasonic spectra, a measure of spectral structure, showed significantly higher values for carcinomas and precancerous pathologies such as atypical ductal hyperplasia than for normal tissue. The slopes of the cepstra for non-malignant pathologies displayed significantly greater values that differentiated them from the normal and malignant tissues. The attenuation coefficients were sensitive to fat necrosis, fibroadenoma, and invasive lobular carcinoma. Specificities and sensitivities for differentiating pathologies from normal tissue were 100% and 86% for lobular carcinomas, 100% and 74% for ductal carcinomas, 80% and 82% for benign pathologies, and 80% and 100% for fat necrosis and adenomas. Specificities and sensitivities were also determined for differentiating each pathology type from the other four using a multivariate analysis. The results yielded specificities and sensitivities of 85% and 86% for lobular carcinomas, 85% and 74% for ductal carcinomas, 100% and 61% for benign pathologies, 84% and 100% for fat necrosis and adenomas, and 98% and 80% for normal tissue. CONCLUSIONS: Results from high-frequency ultrasonic measurements of human breast tissue specimens indicate that characteristics in the ultrasonic attenuation, spectra, and cepstra can be used to differentiate between normal, benign, and malignant breast pathologies.

Greenhouse Gas Emission Evaluation of the GTL Pathway.

Gas to liquids (GTL) products have the potential to replace petroleum-derived products, but the efficacy with which any sustainability goals can be achieved is dependent on the lifecycle impacts of the GTL pathway. Life cycle assessment (LCA) is an internationally established tool (with GHG emissions as a subset) to estimate these impacts. Although the International Standard Organization's ISO 14040 standard advocates the system boundary expansion method (also known as the "displacement method" or the "substitution method") for life-cycle analyses, application of this method for the GTL pathway has been limited until now because of the difficulty in quantifying potential products to be displaced by GTL coproducts. In this paper, we use LCA methodology to establish the most comprehensive GHG emissions evaluation to date of the GTL pathway. The influence of coproduct credit methods on the GTL GHG emissions results using substitution methodology is estimated to afford the Well-to-Wheels (WTW) greenhouse gas (GHG) intensity of GTL Diesel. These results are compared to results using energy-based allocation methods of reference GTL diesel and petroleum-diesel pathways. When substitution methodology is used, the resulting WTW GHG emissions of the GTL pathway are lower than petroleum diesel references. In terms of net GHGs, an interesting way to further reduce GHG emissions is to blend GTL diesel in refineries with heavy crudes that require severe hydrotreating, such as Venezuelan heavy crude oil or bitumen derived from Canadian oil sands and in jurisdictions with tight aromatic specifications for diesel, such as California. These results highlight the limitation of using the energy allocation approach for situations where coproduct GHG emissions reductions are downstream from the production phase.

Underwater application of quantitative PCR on an ocean mooring.

The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.

Cleft lip and palate: association with other congenital malformations.

UNLABELLED: Orofacial clefts are frequently associated with other congenital malformations. Studies vary in incidence and types of anomalies. OBJECTIVE: To evaluate associated malformations in orofacial cleft patients at a major research hospital. STUDY DESIGN: Medical records of 1127 patients, in the Cleft Palate/Craniofacial Clinic, Boys Town National Research Hospital, from January 1980 through February 2000 were reviewed. Patients were divided into two categories: 1) cleft palate only (CP), and 2) cleft lip, with or without cleft palate (CL +/- P). Further categorization included location and type, if any, of other congenital malformations. RESULTS: 47.2% of patients had CP and 52.8% had CL +/- P. 32.2% of all cleft patients had associated congenital malformations. The orofacial region was the most common site, followed by cardiovascular central nervous, and skeletal systems. Congenital malformations were more common in CP (38.7%), than CL +/- P (26.4%). Of malformations diagnosed, 63.1% were chromosomal/syndromic anomalies while 36.9% were non-chromosomal/syndromic. CONCLUSIONS: Recognition of the spectrum of congenital malformations, associated with orofacial clefting, is essential for further diagnostic testing and in some cases genetic counseling.

College students' attitudes toward their ADHD peers.

OBJECTIVE: The attitudes of college students with and without ADHD toward peers with ADHD were examined. METHOD: A total of 196 college students (30 diagnosed with ADHD) anonymously completed four attitude measures. General analyses of attitudes toward peers with ADHD as well as comparisons between those with and without ADHD are made. RESULTS: For all participants, but especially for those with ADHD, more frequent contact with peers with ADHD was associated with more positive attitudes toward individuals with ADHD. Only half of individuals with ADHD report receiving adequate accommodations, and only half of those report actually using the available accommodations. Overall, more negative than positive adjectives were endorsed as describing individuals with ADHD, and this was especially true for individuals with ADHD in comparison to those without ADHD. CONCLUSION: Contact with other individuals with ADHD may be especially important for college students with ADHD.

Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes.

A sandwich hybridization assay (SHA) was developed to detect 16S rRNAs indicative of phylogenetically distinct groups of marine bacterioplankton in a 96-well plate format as well as low-density arrays printed on a membrane support. The arrays were used in a field-deployable instrument, the Environmental Sample Processor (ESP). The SHA employs a chaotropic buffer for both cell homogenization and hybridization, thus target sequences are captured directly from crude homogenates. Capture probes for seven of nine different bacterioplankton clades examined reacted specifically when challenged with target and non-target 16S rRNAs derived from in vitro transcribed 16S rRNA genes cloned from natural samples. Detection limits were between 0.10-1.98 and 4.43- 12.54 fmole ml(-1) homogenate for the 96-well plate and array SHA respectively. Arrays printed with five of the bacterioplankton-specific capture probes were deployed on the ESP in Monterey Bay, CA, twice in 2006 for a total of 25 days and also utilized in a laboratory time series study. Groups detected included marine alphaproteobacteria, SAR11, marine cyanobacteria, marine group I crenarchaea, and marine group II euryarchaea. To our knowledge this represents the first report of remote in situ DNA probe-based detection of marine bacterioplankton.