Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

Small-angle X-ray scattering has established itself as a common technique in structural biology research. Here, two novel Java applications to aid modelling of three-dimensional macromolecular structures based on small-angle scattering data are described. MolScat is an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data. SAFIR is a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version of MolScat is used to enable quick evaluation of the fit between the model and experimental scattering data. SAFIR also provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte Carlo approach

Charge density analysis of two polymorphs of antimony(III) oxide

High-resolution X-ray diffraction data have been collected on the cubic polymorph of antimony(III) oxide (senarmontite) to determine the charge distribution in the crystal. The results are in quantitative agreement with crystal Hartree–Fock calculations for this polymorph, and have been compared with theoretical calculations on the orthorhombic polymorph (valentinite). Information about the nature of bonding and relative bond strengths in the two polymorphs has been extracted in a straightforward manner via topological analysis of the electron density. All the close contacts in both polymorphs are found to be similar in nature based on the value of the Laplacian, the magnitude of the electron density and the local energy density at the bond critical points, and these characterise the observed interactions as substantially polar covalent, similar to molecular calculation results on Si–O and Ge–O. Electrostatic potential isosurfaces reveal the octopolar nature of this function for senarmontite, and shed light on the observed packing arrangement of Sb4O6 molecules in the crystal

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami

Investigation of the siliceous hydrogel phase formation in glass-ionomer cement paste

The microstructure evolution of a complex glass-ionomer cement (GIC) paste over the first 72 h of the cement setting reaction was investigated by small-angle neutron scattering (SANS) and infrared spectroscopy. GIC is a biocompatible material which is clinically used for dental fillings. In this study, GIC pastes were prepared, following the ISO9917-1:2007 cement preparation method, from medical grade poly(acrylic acid), SiO₂–Al₂O₃–P₂O₅–CaO–CaF₂ -based fluoroaluminosilicate glass and H₂O/D₂O solvent. During the setting reaction, polyacrylic acid attacks the fluoroaluminosilicate glass particles to form a siliceous hydrogel phase, glass core and hydrated polyacrylate matrix. The formation of the siliceous hydrogel structure and cross-linking of polyacrylate chains play important roles to harden the GIC. Infrared spectroscopy was used to identify the formation of the hydrogel phase and cross-linkage in GIC paste. In addition this paper reports SANS measurements for GIC pastes at different contrast conditions (H₂O:D₂O ratio) from the Bilby instrument at the Australian Centre for Neutron Scattering, ANSTO, Australia. The SANS data provide microstructure information for the hydrogel phase in GIC paste over the length scale of 10–5000 Å

Long-term Survey and Assessment of Large-River Fishes in Illinois, 2017

This report presents a summary of those data collected during segment 29 (2017-18) of the Long-term Survey and Assessment of Large-River Fishes in Illinois (LTEF), an annual survey by members of the Illinois Natural History Survey,with funds administered by the U.S. Fish and Wildlife Service and the Illinois Department of Natural Resources. Sampling for the LTEF program was conducted on: six reaches of the Illinois River Waterway, four segments or pools of the Mississippi River, and navigable portions of the Iroquois and Kankakee Rivers. In all segments of the LTEF program, all fish species collected were accurately identified, tallied, measured, and weighed. The catch rates of sportfish species were calculated as the number of individuals collected per hour (CPUEN± standard error). Structural indices [Proportional Size Distribution (PSD) and Relative Weight (Wr)] were also calculated for several species of interest to regional managers. Catch rates and species varied among all sampling locations and sampling periods. Gizzard Shad and Emerald Shiners comprised the majority of the individuals caught, and Silver Carp and Common Carp accounted for the greatest proportion of the biomass collected in most sampling areas of the survey. Future analysis of CPUEN and PSD trends in sportfish populations sampled by the program may indicate inter-annual recruitment patterns or/andlong-term trends in Illinois sportfish populations.Federal Aid in Sport Fish Restoration project F-101-Runpublishednot peer reviewe

Small angle neutron scattering study of a gehlenite-based ceramic fabricated from industrial waste

This paper presents a small angle neutron scattering (SANS) study of a novel porous gehlenite-based ceramic, synthesised from a homogeneous powder mixture of soda-lime-silicate (SLS) glass, α-alumina, calcite and calcium fluoride via solid-state sintering at 1200 °C. The products of sintering at single temperatures from 600 to 1200 °C are examined by X-ray diffraction (XRD). Sintering of the mixture below 1200 °C forms two intermediate phases (Na₂ CaSi₃ O₈ and Ca₄ Si₂ O₇ F₂ ). Nepheline and α-alumina are minor phases in the gehlenite-based ceramic fabricated through sintering at 1200 °C. The microstructure of the gehlenite-based ceramic is investigated using field-emission scanning electron microscopy (FESEM) and SANS at the Australian Centre for Neutron Scattering. This study also evaluated the specific surface area of the gehlenite-based ceramic (~3.0 m² cm⁻ ³) from quantitative analysis of SANS data

Long-term Survey and Assessment of Large-River Fishes in Illinois, 2016

3EXECUTIVE SUMMARYThis report presents a summary of those data collected during segment 28(2016-17) of the Long-term Survey and Assessment of Large-River Fishes in Illinois(LTEF), an annual survey by members of the Illinois Natural History Survey,with funds administered by the U.S. Fish and Wildlife Service and the Illinois Department of Natural Resources. Sampling for the LTEF program was conducted on: six reaches of the Illinois River Waterway, foursegments or pools of the Mississippi River, and navigable portions of the Iroquois and Kankakee Rivers. In all segments of the LTEF program, all fish species collected were accurately identified, tallied, measured, and weighed. The catchrates of sportfishspecies were calculated as the number of individuals collected per hour (CPUEN± standard error).Structural indices [Proportional Size Distribution (PSD) and Relative Weight (Wr)] were also calculated for several species of interest to regional managers. Catch rates and species varied among all sampling locationsand sampling periods. Emerald Shiners and Gizzard Shad comprised the majority of the individuals caught, andSilverCarpand Common Carp accounted for the greatest proportion of the biomass collected in most sampling areasof the survey. Futureanalysis of CPUENand PSD trends in sportfish populations sampled by the program may indicate inter-annual recruitment patterns or/andlong-term trends in Illinois sportfish populations.Federal Aid in Sport Fish Restoration F-101-R, Segment 28Illinois Department of Natural Resources, Division of Fisheriesunpublishednot peer reviewe

Key mechanisms by which post-ICU activities can improve in-ICU care: results of the international THRIVE collaboratives

Objective: To identify the key mechanisms that clinicians perceive improve care in the intensive care unit (ICU), as a result of their involvement in post-ICU programs. Methods: Qualitative inquiry via focus groups and interviews with members of the Society of Critical Care Medicine’s THRIVE collaborative sites (follow-up clinics and peer support). Framework analysis was used to synthesize and interpret the data. Results: Five key mechanisms were identified as drivers of improvement back into the ICU: (1) identifying otherwise unseen targets for ICU quality improvement or education programs—new ideas for quality improvement were generated and greater attention paid to detail in clinical care. (2) Creating a new role for survivors in the ICU—former patients and family members adopted an advocacy or peer volunteer role. (3) Inviting critical care providers to the post-ICU program to educate, sensitize, and motivate them—clinician peers and trainees were invited to attend as a helpful learning strategy to gain insights into post-ICU care requirements. (4) Changing clinician’s own understanding of patient experience—there appeared to be a direct individual benefit from working in post-ICU programs. (5) Improving morale and meaningfulness of ICU work—this was achieved by closing the feedback loop to ICU clinicians regarding patient and family outcomes. Conclusions: The follow-up of patients and families in post-ICU care settings is perceived to improve care within the ICU via five key mechanisms. Further research is required in this novel area

Enablers and Barriers to Implementing ICU Follow-Up Clinics and Peer Support Groups Following Critical Illness: The Thrive Collaboratives

OBJECTIVES: Data are lacking regarding implementation of novel strategies such as follow-up clinics and peer support groups, to reduce the burden of postintensive care syndrome. We sought to discover enablers that helped hospital-based clinicians establish post-ICU clinics and peer support programs, and identify barriers that challenged them. DESIGN: Qualitative inquiry. The Consolidated Framework for Implementation Research was used to organize and analyze data. SETTING: Two learning collaboratives (ICU follow-up clinics and peer support groups), representing 21 sites, across three continents. SUBJECTS: Clinicians from 21 sites. MEASUREMENT AND MAIN RESULTS: Ten enablers and nine barriers to implementation of "ICU follow-up clinics" were described. A key enabler to generate support for clinics was providing insight into the human experience of survivorship, to obtain interest from hospital administrators. Significant barriers included patient and family lack of access to clinics and clinic funding. Nine enablers and five barriers to the implementation of "peer support groups" were identified. Key enablers included developing infrastructure to support successful operationalization of this complex intervention, flexibility about when peer support should be offered, belonging to the international learning collaborative. Significant barriers related to limited attendance by patients and families due to challenges in creating awareness, and uncertainty about who might be appropriate to attend and target in advertising. CONCLUSIONS: Several enablers and barriers to implementing ICU follow-up clinics and peer support groups should be taken into account and leveraged to improve ICU recovery. Among the most important enablers are motivated clinician leaders who persist to find a path forward despite obstacles

Why Don't We Ask? A Complementary Method for Assessing the Status of Great Apes

Species conservation is difficult. Threats to species are typically high and immediate. Effective solutions for counteracting these threats, however, require synthesis of high quality evidence, appropriately targeted activities, typically costly implementation, and rapid re-evaluation and adaptation. Conservation management can be ineffective if there is insufficient understanding of the complex ecological, political, socio-cultural, and economic factors that underlie conservation threats. When information about these factors is incomplete, conservation managers may be unaware of the most urgent threats or unable to envision all consequences of potential management strategies. Conservation research aims to address the gap between what is known and what knowledge is needed for effective conservation. Such research, however, generally addresses a subset of the factors that underlie conservation threats, producing a limited, simplistic, and often biased view of complex, real world situations. A combination of approaches is required to provide the complete picture necessary to engage in effective conservation. Orangutan conservation (Pongo spp.) offers an example: standard conservation assessments employ survey methods that focus on ecological variables, but do not usually address the socio-cultural factors that underlie threats. Here, we evaluate a complementary survey method based on interviews of nearly 7,000 people in 687 villages in Kalimantan, Indonesia. We address areas of potential methodological weakness in such surveys, including sampling and questionnaire design, respondent biases, statistical analyses, and sensitivity of resultant inferences. We show that interview-based surveys can provide cost-effective and statistically robust methods to better understand poorly known populations of species that are relatively easily identified by local people. Such surveys provide reasonably reliable estimates of relative presence and relative encounter rates of such species, as well as quantifying the main factors that threaten them. We recommend more extensive use of carefully designed and implemented interview surveys, in conjunction with more traditional field methods