An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Partitioning into phosphatidylcholine-cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation

Membrane-water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field. The methodology is general and can also be used for other applications where coarse-grained simulations are appropriate. This article addresses the effect on membrane-water partitioning of adding cholesterol to POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Nine contrasting neutral, zwitterionic and charged solutes are tested. Agreement between experiment and simulation is generally good, with the most challenging cases being permanently charged solutes. For all solutes, partitioning is found to be insensitive to membrane cholesterol concentration up to 25% mole fraction. Hence, for assessment of bioaccumulation into a range of membranes (such as those found in fish), partitioning data measured in pure lipid membranes are still informative.

Modification to Mirels scoring system location component improves fracture prediction for metastatic disease of the proximal femur

BACKGROUND

Correctly identifying patients at risk of femoral fracture due to metastatic bone disease remains a clinical challenge. Mirels criteria remains the most widely referenced method with the advantage of being easily calculated but it suffers from poor specificity. The purpose of this study was to develop and evaluate a modified Mirels scoring system through scoring modification of the original Mirels location component within the proximal femur.

METHODS

Computational (finite element) experiments were performed to quantify strength reduction in the proximal femur caused by simulated lytic lesions at defined locations. Virtual spherical defects representing lytic lesions were placed at 32 defined locations based on axial (4 axial positions: neck, intertrochanteric, subtrochanteric or diaphyseal) and circumferential (8 circumferential: 45-degree intervals) positions. Finite element meshes were created, material property assignment was based on CT mineral density, and femoral head/greater trochanter loading consistent with stair ascent was applied. The strength of each femur with a simulated lesion divided by the strength of the intact femur was used to calculate the Location-Based Strength Fraction (LBSF). A modified Mirels location score was next defined for each of the 32 lesion locations with an assignment of 1 (LBSF > 75%), 2 (LBSF: 51-75%), and 3 (LBSF: 0-50%). To test the new scoring system, data from 48 patients with metastatic disease to the femur, previously enrolled in a Musculoskeletal Tumor Society (MSTS) cross-sectional study was used. The lesion location was identified for each case based on axial and circumferential location from the CT images and assigned an original (2 or 3) and modified (1,2, or 3) Mirels location score. The total score for each was then calculated. Eight patients had a fracture of the femur and 40 did not over a 4-month follow-up period. Logistic regression and decision curve analysis were used to explore relationships between clinical outcome (Fracture/No Fracture) and the two Mirels scoring methods.

RESULTS

The location-based strength fraction (LBSF) was lowest for lesions in the subtrochanteric and diaphyseal regions on the lateral side of the femur; lesions in these regions would be at greatest risk of fracture. Neck lesions located at the anterior and antero-medial positions were at the lowest risk of fracture. When grouped, neck lesions had the highest LBSF (83%), followed by intertrochanteric (72%), with subtrochanteric (50%) and diaphyseal lesions (49%) having the lowest LBSF. There was a significant difference (p < 0.0001) in LBSF between each axial location, except subtrochanteric and diaphyseal which were not different from each other (p = 0.96). The area under the receiver operator characteristic (ROC) curve using logistic regression was greatest for modified Mirels Score using site specific location of the lesion (Modified Mirels-ss, AUC = 0.950), followed by a modified Mirels Score using axial location of lesion (Modified Mirels-ax, AUC = 0.941). Both were an improvement over the original Mirels score (AUC = 0.853). Decision curve analysis was used to quantify the relative risks of identifying patients that would fracture (TP, true positives) and those erroneously predicted to fracture (FP, false positives) for the original and modified Mirels scoring systems. The net benefit of the scoring system weighed the benefits (TP) and harms (FP) on the same scale. At a threshold probability of fracture of 10%, use of the modified Mirels scoring reduced the number of false positives by 17-20% compared to Mirels scoring.

CONCLUSIONS

A modified Mirels scoring system, informed by detailed analysis of the influence of lesion location, improved the ability to predict impending pathological fractures of the proximal femur for patients with metastatic bone disease. Decision curve analysis is a useful tool to weigh costs and benefits concerning fracture risk and could be combined with other patient/clinical factors that contribute to clinical decision making.

Potential for supraphysiologic fluid shear stresses in a rat cemented knee replacement model

The mechano-biologic environment associated with aseptic loosening of cemented joint replacements is not fully understood. The goal of this study was to use a preclinical rat knee arthroplasty model to explore the changes in cement-bone morphology and micromotion that occur with in vivo service. Narrow gaps between cement and bone under the tibial tray were present at early time points, and with even small magnitude micromotion, resulted in large micromotion-to-gap width ratios. These data were then used to develop models of fluid flow in the cement-bone gaps to estimate potential for high fluid shear stress (FSS). Modeling results revealed supraphysiologic (>4 Pa) FSS were possible, particularly for cases in which eccentric loading applied to the implant and if the fluid in the gap consisted of marrow or synovial fluid. The early, high FSS environment, could cause fluid-induced periprosthetic osteolysis locally, resulting in progressive loss of cement-bone fixation.

Deep modeling of plasma and neutral fluctuations from gas puff turbulence imaging

The role of turbulence in setting boundary plasma conditions is presently a key uncertainty in projecting to fusion energy reactors. To robustly diagnose edge turbulence, we develop and demonstrate a technique to translate brightness measurements of HeI line radiation into local plasma fluctuations via a novel integrated deep learning framework that combines neutral transport physics and collisional radiative theory for the 3³D - 2³P transition in atomic helium with unbounded correlation constraints between the electron density and temperature. The tenets for experimental validity are reviewed, illustrating that this turbulence analysis for ionized gases is transferable to both magnetized and unmagnetized environments with arbitrary geometries. Based on fast camera data on the Alcator C-Mod tokamak, we present the first two-dimensional time-dependent experimental measurements of the turbulent electron density, electron temperature, and neutral density, revealing shadowing effects in a fusion plasma using a single spectral line.

Progressive loss of implant fixation in a preclinical rat model of cemented knee arthroplasty

Aseptic loosening of total knee arthroplasty continues to be a challenging clinical problem. The progression of the loosening process, from the initial well-fixed component, is not fully understood. In this study, loss of fixation of cemented hemiarthroplasty was explored using 9-month-old Sprague-Dawley rats with 0, 2, 6, 12, 26 week end points. Morphological and cellular changes of cement-bone fixation were determined for regions directly below the tibial tray (epiphysis) and distal to the tray (metaphysis). Loss of fixation, with a progressive increase in cement-bone gap volume was found in the epiphysis (0.162  mm³ /week), but did not progress appreciably in the metaphysis (0.007 mm³ /week). In the epiphysis, there was an early and sustained elevation of osteoclasts adjacent to the cement border and development of a fibrous tissue layer between the cement and bone. There was early formation of bone around the cement in the metaphysis, resulting in a condensed bone layer without osteoclastic bone resorption or development of a fibrous tissue layer. Implant positioning was also an important factor in the cement-bone gap formation, with greater gap formation for implants that were placed medially on the tibial articular surface. Loss of fixation in the rat model mimicked patterns found in human arthroplasty where cement-bone gaps initiate under the tibial tray, at the periphery of the implant. This preclinical model could be used to study early biological response to cemented fixation and associated contributions of mechanical instability, component alignment, and periprosthetic inflammation.

Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning

With a view to high-throughput simulations, we present an automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field. The method scales to larger molecules and a broader chemical space than existing schemes. The core of the mapping process is a graph-based analysis of the molecule's bonding network, which has the advantages of being fast, general, and preserving symmetry. The parameterization process pays special attention to coarse-grained beads in aromatic rings. It also includes a method for building efficient and stable frameworks of constraints for molecules with structural rigidity. The performance of the method is tested on a diverse set of 87 neutral organic molecules and the ability of the resulting models to capture octanol-water and membrane-water partition coefficients. In the latter case, we introduce an adaptive method for extracting partition coefficients from free-energy profiles to take into account the interfacial region of the membrane. We also use the models to probe the response of membrane-water partitioning to the cholesterol content of the membrane.

Differing susceptibility of C57BL/6J and DBA/2J mice-parents of the murine BXD family, to severe acute respiratory syndrome coronavirus infection

The ongoing coronavirus disease-2019 (COVID-19) pandemic, caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that is closely related to SARS-CoV, poses a grave threat to global health and has devastated societies worldwide. One puzzling aspect of COVID-19 is the impressive variation in disease manifestations among infected individuals, from a majority who are asymptomatic or exhibit mild symptoms to a smaller, largely age-dependent fraction who develop life-threatening conditions. Some of these differences are likely the consequence of host genetic factors. Systems genetics using diverse and replicable cohorts of isogenic mice represents a powerful way to dissect those host genetic differences that modulate microbial infections. Here we report that the two founders of the large BXD family of mice—C57BL/6J and DBA/2J, differ substantially in their susceptibility to a mouse-adapted SARS-CoV, MA15. Following intranasal viral challenge, DBA/2J develops a more severe disease than C57BL/6J as evidenced by more pronounced and sustained weight loss. Disease was accompanied by high levels of pulmonary viral replication in both strains early after infection but substantially delayed viral clearance in DBA/2J. Our data reveal that the parents of the BXD family are segregated by clear phenotypic differences during MA15 infection and support the feasibility of using this family to systemically dissect the complex virus-host interactions that modulate disease progression and outcome of infection with SARS-CoV, and provisionally also with SARS-CoV-2.

Standardization of assay representation in the Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

Nearest-neighbor connectedness theory: A general approach to continuum percolation

We introduce a method to estimate continuum percolation thresholds and illustrate its usefulness by investigating geometric percolation of noninteracting line segments and disks in two spatial dimensions. These examples serve as models for electrical percolation of elongated and flat nanofillers in thin film composites. While the standard contact volume argument and extensions thereof in connectedness percolation theory yield accurate predictions for slender nanofillers in three dimensions, they fail to do so in two dimensions, making our test a stringent one. In fact, neither a systematic order-by-order correction to the standard argument nor invoking the connectedness version of the Percus-Yevick approximation yield significant improvements for either type of particle. Making use of simple geometric considerations, our new method predicts a percolation threshold of ρ_{c}l^{2}≈5.83 for segments of length l, which is close to the ρ_{c}l^{2}≈5.64 found in Monte Carlo simulations. For disks of area a we find ρ_{c}a≈1.00, close to the Monte Carlo result of ρ_{c}a≈1.13. We discuss the shortcomings of the conventional approaches and explain how usage of the nearest-neighbor distribution in our method bypasses those complications.

The effects of air stress during storage and low packing density on the fermentation and aerobic stability of corn silage inoculated with Lactobacillus buchneri 40788

We determined if a microbial inoculant could improve the fermentation and aerobic stability of corn silage subjected to various challenges during storage that included an air stress challenge and low packing density. In Experiment 1, whole-plant corn was untreated (CTR) or treated (INO, Lactobacillus buchneri 40788 and Pediococcus pentosaceus 12455. Five individually replicated 7.5-L silos, at a density of 240 kg of dry matter (DM)/m³, for each treatment were kept sealed (NAS) for 19 wk, air stressed early (ES, 3 h/wk for wk 1-9), or air stressed late during storage (LS, 3 h/wk for wk 10-19). Inoculation increased the number of agar-culturable lactic acid bacteria regardless of air stress status, but it did not affect the relative abundance of Lactobacillus. Early, but not late air stress, resulted in silages with a higher relative abundance of Acetobacter when compared with NAS. Silages treated with INO had greater concentrations of acetic acid than CTR. Numbers of yeasts were lowest for INO regardless of air stress and CTR-LS had the most yeasts among all treatments. Silages that were not air stressed had a higher relative abundance of Candida tropicalis than air stressed silages. Monascus purpureus was detected in ES and LS but not in NAS, and its relative abundance was numerically higher in CTR-ES than in INO-ES and statistically higher in CTR-LS compared with INO-LS. Early air stress numerically reduced aerobic stability compared with NAS, and there was a statistical tendency for lower stability in LS compared with NAS. Inoculation improved aerobic stability regardless of when the air stress occurred. In Experiment 2, corn silage was prepared with the same primary treatments of CTR and INO but was packed at a low (LD; 180 kg of DM/m³) or a normal (ND; 240 kg of DM/m³) density and sealed (NAS) or air stressed (AS; 24 h on d 28, 42, and 89) for 92 d of storage. The concentration of acetic acid was greater in INO compared with CTR and in AS compared with NAS. Numbers of yeasts were lower in NAS compared with AS regardless of inoculation and they were lower in INO-AS compared with CTR-AS. Treatment with INO improved aerobic stability but the improvement was better in NAS versus AS and better in ND versus LD. Overall, our experiments corroborate past findings showing that INO markedly improves the aerobic stability of corn silage but they are the first to show that improvement can be sustained even when the silage was exposed to regular air stresses and when packed at a low density.

Evaluating the effects of Lactobacillus animalis and Propionibacterium freudenreichii on performance and rumen and fecal measures in lactating dairy cows

Two experiments evaluated the effect of supplementation with a bacterial direct-fed microbial on performance and apparent total-tract nutrient digestion of dairy cows. In experiment 1, 30 multiparous cows (75 ± 32 d in milk) were randomly assigned to 1 of 2 treatments fed for 10 wk. All cows were fed a diet containing 23.8% starch. Treatments were top dressed to rations twice daily and consisted of a combination of Lactobacillus animalis (1 × 10⁹ cfu/d) and Propionibacterium freudenreichii (2 × 10⁹ cfu/d; LAPF) or carrier alone (CON). In experiment 2, 6 ruminally cannulated cows (123 ± 129 d in milk) were randomly assigned to a crossover design with two 6-wk periods. Cows received the same CON or LAPF treatment as in experiment 1. Cows were fed the same 23.8% starch diet as experiment 1 during wk 1 through 5 of each period, and then cows were abruptly switched to a 31.1% starch diet for wk 6. For both experiments, intake and milk yield were measured daily, and milk samples were collected weekly. In experiment 1, fecal grab samples were collected every 6 h on d 7 of experimental wk 1, 2, 4, 6, 8, and 10. Fecal consistency was scored, and fecal starch was measured in daily composite samples. Fecal composites from a subset of 7 cows per treatment were used to measure apparent total-tract nutrient digestion. In experiment 2, rumen pH was continuously recorded during wk 5 and 6. On d 7 of wk 5 (the final day of feeding the 23.8% starch ration), d 1 of wk 6 (the day of diet transition), and d 7 of wk 6 (the final day of feeding the 31.1% starch ration), rumen in situ digestion was determined. Samples of rumen fluid and feces were collected every 6 h on those days for measurement of fecal starch (composited by cow within day), rumen volatile fatty acids, and fecal pH. Rumen and fecal samples were collected at one time point on those days for microbiota assessment. In experiment 1, treatment did not affect intake, milk yield, milk composition, or fecal score. The LAPF treatment decreased fecal starch percentage and tended to increase starch digestion compared with CON, but the differences were very small (0.59 vs. 0.78% and 98.74 vs. 98.46%, respectively). Digestion of other nutrients was unaffected. In experiment 2, LAPF increased rumen pH following the abrupt switch to the high-starch diet, but milk yield was lower for LAPF compared with CON (35.7 vs. 33.2 kg/d). Contrary to the decrease in fecal starch with LAPF observed in experiment 1, fecal starch tended to be increased by LAPF following the abrupt ration change in experiment 2 (2.97 vs. 2.15%). Few effects of treatment on rumen and fecal microbial populations were detectable. Under the conditions used in our experiments, addition of the bacterial direct-fed microbials did not have a marked effect on animal performance, ruminal measures, or total-tract nutrient digestion.

Control of Superselectivity by Crowding in Three-Dimensional Hosts

Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous three-dimensional structure. In contrast to similar superselective binding previously observed at surfaces, we have identified that a key effect in a three-dimensional environment is that the presence of inert crowding agents can significantly enhance or even introduce superselectivity. In essence, molecular crowding initially suppresses binding via an entropic penalty, but the clients can then more easily form many bonds simultaneously. We demonstrate the robustness of the superselective behavior with respect to client valency, linker length, and binding interactions in Monte Carlo simulations of an archetypal lattice polymer model.

Evaluation of immunologic parameters in canine glioma patients treated with an oncolytic herpes virus

AIM

To molecularly characterize the tumor microenvironment and evaluate immunologic parameters in canine glioma patients before and after treatment with oncolytic human IL-12-expressing herpes simplex virus (M032) and in treatment naïve canine gliomas.

METHODS

We assessed pet dogs with sporadically occurring gliomas enrolled in Stage 1 of a veterinary clinical trial that was designed to establish the safety of intratumoral oncoviral therapy with M032, a genetically modified oncolytic herpes simplex virus. Specimens from dogs in the trial and dogs not enrolled in the trial were evaluated with immunohistochemistry, NanoString, Luminex cytokine profiling, and multi-parameter flow cytometry.

RESULTS

Treatment-naive canine glioma microenvironment had enrichment of Iba1 positive macrophages and minimal numbers of T and B cells, consistent with previous studies identifying these tumors as immunologically "cold". NanoString mRNA profiling revealed enrichment for tumor intrinsic pathways consistent with suppression of tumor-specific immunity and support of tumor progression. Oncolytic viral treatment induced an intratumoral mRNA transcription signature of tumor-specific immune responses in 83% (5/6) of canine glioma patients. Changes included mRNA signatures corresponding with interferon signaling, lymphoid and myeloid cell activation, recruitment, and T and B cell immunity. Multiplexed protein analysis identified a subset of oligodendroglioma subjects with increased concentrations of IL-2, IL-7, IL-6, IL-10, IL-15, TNFα, GM-CSF between 14 and 28 days after treatment, with evidence of CD4⁺ T cell activation and modulation of IL-4 and IFNγ production in CD4⁺ and CD8⁺ T cells isolated from peripheral blood.

CONCLUSION

These findings indicate that M032 modulates the tumor-immune microenvironment in the canine glioma model.

Radiographic and Biomechanical Assessment of Three Implant Designs for Canine Cementless Total Hip Replacement

OBJECTIVE

 The aim of this study was to evaluate the relationship between radiographic fit/fill measurements and biomechanical performance of three canine cementless total hip implant designs using an in vitro biomechanical testing protocol that replicates compression and torsion.

STUDY DESIGN

 Eighteen (six/group) canine cadaveric femurs were implanted with one of three cementless total hip implant designs: (1) collarless, (2) collared or (3) lateral bolt stems. Femoral length, canal flare index (CFI), canal fill, stem fit, stem level and stem angle were measured as independent variables. Biomechanical performance was tested using physiological, non-destructive gait loading (loading protocols) and destructive testing (failure protocols).

RESULTS

 During loading protocols, compressive stiffness was influenced by stem level (p < 0.05) and torsional stiffness was influenced by stem level and CFI for collarless stems (p < 0.05). During failure protocols, peak load was influenced by mediolateral (ML) stem angle (p < 0.05) and CFI (p < 0.01) for collarless stems and CFI for lateral bolt stems (p < 0.05). Peak torque was influenced by ML stem angle, craniocaudal stem angle and CFI for collarless stems (p < 0.05) and average ML fill for collared stems (p < 0.05).

CONCLUSION

 Biomechanical performance of collarless stems in cementless hip arthroplasty is more impacted by radiographic fit/fill than lateral bolt and collared stems. As a result, collarless stems may be more dependent on preoperative fit and intraoperative precision.

Potential COVID-19 papain-like protease PLpro inhibitors: repurposing FDA-approved drugs

Using the crystal structure of SARS-CoV-2 papain-like protease (PLpro) as a template, we developed a pharmacophore model of functional centers of the PLpro inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PLpro. The conformations of these compounds underwent 3D fingerprint similarity clusterization, followed by docking of possible conformers to the binding pocket of PLpro. Docking of random compounds to the binding pocket of protease was also done for comparison. Free energies of the docking interaction for the selected compounds were lower than for random compounds. The drug list obtained includes inhibitors of HIV, hepatitis C, and cytomegalovirus (CMV), as well as a set of drugs that have demonstrated some activity in MERS, SARS-CoV, and SARS-CoV-2 therapy. We recommend testing of the selected compounds for treatment of COVID-19.

Phase transitions on non-uniformly curved surfaces: coupling between phase and location

For particles confined to two dimensions, any curvature of the surface affects the structural, kinetic and thermodynamic properties of the system. If the curvature is non-uniform, an even richer range of behaviours can emerge. Using a combination of bespoke Monte Carlo, molecular dynamics and basin-hopping methods, we show that the stable states of attractive colloids confined to non-uniformly curved surfaces are distinguished not only by the phase of matter but also by their location on the surface. Consequently, the transitions between these states involve cooperative migration of the entire colloidal assembly. We demonstrate these phenomena on toroidal and sinusoidal surfaces for model colloids with different ranges of interactions as described by the Morse potential. In all cases, the behaviour can be rationalised in terms of three universal considerations: cluster perimeter, stress, and the packing of next-nearest neighbours.

Similitude of cement-bone micromechanics in cemented rat and human knee replacement

A preclinical rat knee replacement model was recently developed to explore the biological and mechanobiological changes of trabecular resorption for cement-bone interdigitated regions. The goal here was to evaluate the relevance of this model compared with human knee replacement with regards to functional micromechanics. Eight nonsurvival, cemented knee replacement surgeries were performed, the interdigitated gap morphology was quantified, and interface micromotion between cement and bone was measured for 1 to 5 bodyweight loading. Computational fluid dynamics modeling of unit cell geometries with small gaps between trabeculae and cement was used to estimate fluid flow. Gap width (3.6 μm) was substantially smaller compared with cement-bone gaps reported in human knee replacement (11.8 μm). Micromotion at the cement-bone border was also decreased for the rat knee replacement (0.48 μm), compared with human (1.97 μm), for 1 bodyweight loading. However, the micromotion-to-gap width ratio (0.19 and 0.22 for, rat and human), and estimated fluid shear stress (6.47 and 7.13 Pa, for rat and human) were similar. Replicating the fluid dynamic characteristics of cement-bone interdigitated regions in human knee replacements using preclinical models may be important to recapitulate trabecular resorption mechanisms due to proposed supraphysiologic fluid shear stress. Statement of clinical significance: local cement-bone micromotion due to joint loading may contribute to the process of clinical loosening in total joint replacements. This work shows that while micromotion and gap morphology are diminished for the rat knee model compared to human, the motion-to-gap ratio, and corresponding fluid shear stress are of similar magnitudes.

Comparison of Clostridioides difficile Stool Toxin Concentrations in Adults With Symptomatic Infection and Asymptomatic Carriage Using an Ultrasensitive Quantitative Immunoassay

Background

We used an ultrasensitive, quantitative single molecule array (Simoa) immunoassay to test whether concentrations of Clostridioides (formerly Clostridium) difficile toxins A and/or B in the stool of adult inpatients with C. difficile infection (CDI) were higher than in asymptomatic carriers of toxinogenic C. difficile.

Methods

Patients enrolled as CDI-NAAT had clinically significant diarrhea and a positive nucleic acid amplification test (NAAT), per US guidelines, and received CDI treatment. Potential carriers had recently received antibiotics and did not have diarrhea; positive NAAT confirmed carriage. Baseline stool samples were tested by Simoa for toxin A and B.

Results

Stool toxin concentrations in both CDI-NAAT (n = 122) and carrier-NAAT (n = 44) cohorts spanned 5 logs (0 pg/mL to >100000 pg/mL). Seventy-nine of 122 (65%) CDI-NAAT and 34 of 44 (77%) carrier-NAAT had toxin A + B concentration ≥20 pg/mL (clinical cutoff). Median toxin A, toxin B, toxin A + B, and NAAT cycle threshold (Ct) values in CDI-NAAT and carrier-NAAT cohorts were similar (toxin A, 50.6 vs 60.0 pg/mL, P = .958; toxin B, 89.5 vs 42.3 pg/mL, P = .788; toxin A + B, 197.2 vs 137.3 pg/mL, P = .766; Ct, 28.1 vs 28.6, P = .354). However, when CDI/carrier cohorts were limited to those with detectable toxin, respective medians were significantly different (A: 874.0 vs 129.7, P = .021; B: 1317.0 vs 81.7, P = .003, A + B, 4180.7 vs 349.6, P = .004; Ct, 25.8 vs 27.7, P = .015).

Conclusions

Toxin concentration did not differentiate an individual with CDI from one with asymptomatic carriage. Median stool toxin concentrations in groups with CDI vs carriage differed, but only when groups were defined by detectable stool toxin (vs positive NAAT).

A novel tool for standardizing clinical data in a semantically rich model

Standardizing clinical information in a semantically rich data model is useful for promoting interoperability and facilitating high quality research. Semantic Web technologies such as Resource Description Framework can be utilized to their full potential when a model accurately reflects the semantics of the clinical situation it describes. To this end, ontologies that abide by sound organizational principles can be used as the building blocks of a semantically rich model for the storage of clinical data. However, it is a challenge to programmatically define such a model and load data from disparate sources. The PennTURBO Semantic Engine is a tool developed at the University of Pennsylvania that transforms concise RDF data into a source-independent, semantically rich model. This system sources classes from an application ontology and specifically defines how instances of those classes may relate to each other. Additionally, the system defines and executes RDF data transformations by launching dynamically generated SPARQL update statements. The Semantic Engine was designed as a generalizable data standardization tool, and is able to work with various data models and incoming data sources. Its human-readable configuration files can easily be shared between institutions, providing the basis for collaboration on a standard data model.

Understanding the impact of one-dimensional pore containing 10MR and 12MR and aluminium content on MTH reaction pathways: direct synthesis of heteroatom containing UZM-55

We directly synthesized one-dimensional zeolite UZM-55 as an aluminosilicate and catalyzed MTH to understand pore structure influence on catalytic properties.

Early Changes in Cement-Bone Fixation Using a Novel Rat Knee Replacement Model

Trabecular resorption from interdigitated regions between cement and bone has been found in postmortem-retrieved knee replacements, but the viability of interdigitated bone, and the mechanism responsible for this bone loss is not known. In this work, a Sprague-Dawley (age 12 weeks) rat knee replacement model with an interdigitated cement-bone interface was developed. Morphological and cellular changes in the interdigitated region of the knee replacement over time (0, 2, 6, or 12 weeks) were determined for ovariectomy (OVX) and Sham OVX treatment groups. Interdigitated bone volume fraction (BV/TV) increased with time for Sham OVX (0.022 BV/TV/wk) and OVX (0.015 BV/TV/wk) group, but the rate of increase was greater for the Sham OVX group (p = 0.0064). Tissue mineral density followed a similar increase with time in the interdigitated regions. Trabecular resorption, when it did occur, started at the cement border with medullary-adjacent bone in the presence of osteoclasts. There was substantial loss of viable bone (~80% empty osteocyte lacunae) in the interdigitated regions. Pre-surgical fluorochrome labels remained in the interdigitated regions, and did not diminish with time, indicating that the bone was not remodeling. There was also some evidence of continued surface mineralization in the interdigitated region after cementing of the knee, but this diminished over time. Statement of clinical significance: Interdigitated bone with cement provides mechanical stability for success of knee replacements. Improved understanding of the fate of the interdigitated bone over time could lead to a better understanding of the loosening process and interventions to prevent loss of fixation. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:2163-2171, 2019.

A Biomechanical Comparison of Four Hip Arthroplasty Designs in a Canine Model

OBJECTIVE

 The aim of this study was to develop an in vitro biomechanical protocol for canine cementless hip arthroplasty that represents physiological gait loading (compression and torsion) and to evaluate if three alternative implant designs improve fixation compared with the traditional collarless, tapered stem in the clinically challenging case of moderate canal flare index.

STUDY DESIGN

 Twenty-four (six/group) laboratory-prepared canine constructs were tested using a simulated gait and overload (failure) protocol. Construct stiffness, failure load/displacement and migration were measured as outcome variables.

RESULTS

 Simulated gait loading did not show any significant differences between implant types for peak displacement, peak rotation, torsional stiffness, subsidence or inducible displacement. The collared and collarless stem groups were stiffer in compression compared with the collarless with a lateral bolt and short-stem groups. Increasing the loading above simulated gait showed significant reductions in compressive and torsional stiffness for all implant constructs. Despite the reductions, the short-stem group showed significantly higher stiffness compared with the other three groups.

CONCLUSION

 Peak failure loads (compressive and torsional) in this study were approximately four to seven times the simulated gait loading (430 N, 1.6 Nm) regardless of implant type and highlight the importance of limiting activity level (trotting, jumping) following hip replacement in the postoperative period and during the osseointegration of the implant.

A Complex Zeolite Containing Multiple Ring Sizes in a Single Channel: One-Dimensional Zeolite UZM-55

Zeolites are porous aluminosilicate materials utilized in a variety of sorption, separation, and catalytic applications. The oil refining industry in particular has seen a number of significant advances due to the introduction of new technologies enabled by new zeolites. Of particular importance are zeolites with 10- or 12-membered ring pores, resulting in pore shapes and sizes appropriate for the interaction with small hydrocarbon molecules. Here, the synthesis of a new zeolite UZM-55 is reported and the idealized structure thereof is presented. The most complex structure solved to date, UZM-55 possesses a large triclinic unit cell containing 52 T-sites. The material uniquely contains both 10- and 12-membered ring pores in a single, undulating one-dimensional channel, the first example in a zeolitic material of multiple delimiting rings in a single channel. This discovery opens new opportunities in shape-selective adsorption and catalysis. Demonstrated here is the unique adsorption behavior of UZM-55, shown both experimentally and computationally to adsorb one nonane molecule per unit cell in a linear conformation.

Controlling Fragment Competition on Pathways to Addressable Self-Assembly

Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building blocks, each of which occupies a defined location in the target. The requirement that each type of building block appears exactly once in each copy of the target introduces severe restrictions on the combinations of particles and on the pathways that lead to successful self-assembly. These restrictions can limit the efficiency of self-assembly and the final yield of the product. In particular, partially formed fragments may compete with each other if their compositions overlap, since they cannot be combined. Here, we introduce a "completability" algorithm to quantify competition between self-assembling fragments and use it to deduce general principles for suppressing the effects of fragment incompatibility in the self-assembly of small addressable clusters. Competition originates from loops in the bonding network of the target structure, but loops may be needed to provide structural rigidity and thermodynamic stability. An optimal compromise can be achieved by careful choice of bonding networks and by promoting semihierarchical pathways that rule out competition between early fragments. These concepts are illustrated in simulations of self-assembly in two contrasting addressable targets of 20 unique components each.

Occupational and patient radiation doses in a modern cardiac electrophysiology laboratory

PURPOSE

Technological advancements have greatly expanded the field of cardiac electrophysiology, requiring greater demands on imaging systems and potentially delivering higher radiation doses to patients and operators. With little contemporary research on occupational and patient radiation risk in the electrophysiology laboratory, the aim of this study was to analyze radiation doses, including occupational fetal doses, over approximately the last decade. We benchmarked the occupational data to our patient radiation dose data to allow for comparison and to put into perspective the associated radiation risks.

METHODS

Occupational radiation dosimetry analyzed included data from an 11-year period for physicians, a 7-year period for nurses, and a 9-year period for fetal doses. Patient-related dose metrics over an 8-year period were also analyzed.

RESULTS

In the physician and nursing groups, there was a nearly 70% decrease in the average occupational radiation doses over the given periods. Within the electrophysiology department, the average fetal occupational doses were very low, close to 0 μSv. The average reference point air kerma per patient for all electrophysiology procedures decreased from nearly 600 mGy/procedure in 2010 to just over 100 mGy/procedure in 2017.

CONCLUSIONS

Patient and occupational radiation doses in our laboratories significantly decreased over the periods analyzed as a result of clinical and technical staff efforts as well as advances in imaging technology. The radiation-related risk to individuals working in our electrophysiology laboratories, including pregnant women, is very low. Data reported herein could be used by other institutions to evaluate their occupational and patient radiation safety practices.

Prevention and treatment of secretory diarrhea by the lysophosphatidic acid analog Rx100

IMPACT STATEMENT

A critical barrier in treating diarrheal disease is easy-to-use effective treatments. Rx100 is a first in class, novel small molecule that has shown efficacy after both subcutaneous and oral administration in a mouse cholera-toxin- and Citrobacter rodentium infection-induced diarrhea models. Our findings indicate that Rx100 a metabolically stable analog of the lipid mediator lysophosphatidic acid blocks activation of CFTR-mediated secretion responsible for fluid discharge in secretory diarrhea. Rx100 represents a new treatment modality which does not directly block CFTR but attenuates its activation by bacterial toxins. Our results provide proof-of-principle that Rx100 can be developed for use as an effective oral or injectable easy-to-use drug for secretory diarrhea which could significantly improve care by eliminating the need for severely ill patients to regularly consume large quantities of oral rehydration therapies and offering options for pediatric patients.

The Lupus Inhibitor: A Study of Its Heterogeneity

The plasmas of six patients with prolonged activated partial thromboplastin times were studied in detail. In five of the six, the Russell’s viper venom and prothrombin times were likewise prolonged. Five of the patients had documented systemic lupus erythematosus; one lacked the necessary criteria for this diagnosis. On quantitation, factor XI was decreased in all six; factors X and XII were diminished in five of the six. When tested for inhibitory activity, plasma from each of the patients prolonged the celite eluate inhibition test for factor XII and/or XI inhibition. In the formation of the Xa-V-phospholipid-Ca2+ complex (prothrombinase), factors X and Xa were inhibited to a greater degree than factor V or the phospholipid. Finally, each plasma was isofocused, the inhibitory fractions were identified and the clotting factor specificity of each inhibitory peak was determined.Fractions inhibitory against factors XI and XII isofocused with the IgG in each patient’s plasma. Based on the data presented from these six patients, the “lupus inhibitor” is in fact a heterogeneous collection of inhibitors directed against factors XII, XI and X rather than a homogeneous entity.

Continuum percolation of polydisperse rods in quadrupole fields: Theory and simulations

We investigate percolation in mixtures of nanorods in the presence of external fields that align or disalign the particles with the field axis. Such conditions are found in the formulation and processing of nanocomposites, where the field may be electric, magnetic, or due to elongational flow. Our focus is on the effect of length polydispersity, which-in the absence of a field-is known to produce a percolation threshold that scales with the inverse weight average of the particle length. Using a model of non-interacting spherocylinders in conjunction with connectedness percolation theory, we show that a quadrupolar field always increases the percolation threshold and that the universal scaling with the inverse weight average no longer holds if the field couples to the particle length. Instead, the percolation threshold becomes a function of higher moments of the length distribution, where the order of the relevant moments crucially depends on the strength and type of field applied. The theoretical predictions compare well with the results of our Monte Carlo simulations, which eliminate finite size effects by exploiting the fact that the universal scaling of the wrapping probability function holds even in anisotropic systems. Theory and simulation demonstrate that the percolation threshold of a polydisperse mixture can be lower than that of the individual components, confirming recent work based on a mapping onto a Bethe lattice as well as earlier computer simulations involving dipole fields. Our work shows how the formulation of nanocomposites may be used to compensate for the adverse effects of aligning fields that are inevitable under practical manufacturing conditions.

Antigen-specific interferon-gamma release is decreased following the single intradermal comparative cervical skin test in African buffaloes (Syncerus caffer)

Effective disease management of wildlife relies on the strategic application of ante-mortem diagnostic tests for early identification and removal of M. bovis-infected animals. To improve diagnostic performance, interferon-gamma release assays (IGRAs) are often used in conjunction with the tuberculin skin test (TST). Since buffaloes are major maintenance hosts of M. bovis, optimal application of bovine TB diagnostic tests are especially important. We aimed to determine whether the timing of blood collection relative to the TST has an influence on IFN-γ production and diagnostic outcome in African buffaloes. Release of IFN-γ in response to bovine purified protein derivative (PPD), avian PPD and PC-HP^® and PC-EC^® peptides was measured by Bovigam^® and an in-house IGRA in a group of Bovigam^®-positive and - negative buffaloes at the time the TST was performed and three days later. There was significantly lower IFN-γ release in response to these antigens post-TST in Bovigam^®-positive buffaloes, but no significant changes in Bovigam^®-negative buffaloes. Also, a significantly greater proportion of buffaloes were Bovigam^®-positive prior to the TST than three days later. We therefore recommend that blood samples for use in IGRAs be collected prior to or at the time the TST is performed to facilitate the correct identification of greater numbers of IGRA-positive buffaloes.

Seroprevalence of Mycobacterium bovis infection in warthogs (Phacochoerus africanus) in bovine tuberculosis-endemic regions of South Africa

Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), has been reported in many species including suids. Wild boar are important maintenance hosts of the infection with other suids, that is domestic and feral pigs, being important spillover hosts in the Eurasian ecosystem and in South Africa, warthogs (Phacochoerus africanus) may play a similar role in M. bovis-endemic areas. However, novel diagnostic tests for warthogs are required to investigate the epidemiology of bTB in this species. Recent studies have demonstrated that serological assays are capable of discriminating between M. bovis-infected and uninfected warthogs (Roos et al., ). In this study, an indirect ELISA utilizing M. bovis purified protein derivative (PPD) as a test antigen was used to measure the prevalence and investigate risk factors associated with infection in warthogs from uMhkuze Nature Reserve and the southern region of the Greater Kruger National Park (GKNP). There was a high overall seroprevalence of 38%, with adult warthogs having a higher risk of infection (46%). Seroprevalence also varied by geographic location with warthogs from Marloth Park in the GKNP having the greatest percentage of positive animals (63%). This study indicates that warthogs in M. bovis-endemic areas are at high risk of becoming infected with mycobacteria. Warthogs might present an under-recognized disease threat in multi-species systems. They might also serve as convenient sentinels for M. bovis in endemic areas. These findings highlight the importance of epidemiological studies in wildlife to understand the role each species plays in disease ecology.

Trabecular resorption patterns of cement-bone interlock regions in total knee replacements

With in vivo service, there is loss of mechanical interlock between trabeculae and PMMA cement in total knee replacements. The mechanisms responsible for the loss of interlock are not known, but loss of interlock results in weaker cement-bone interfaces. The goal of this study was to determine the pattern of resorption of interdigitated bone using a series of 20 postmortem retrieved knee replacements with a wide range of time in service (3-22 years). MicroCT scans were obtained of a segment of the cement-bone interface below the tibial tray for each implant. Image processing methods were used to determine interface morphology and to identify supporting, interdigitated, resorbed, and isolated bone as a function of axial position. Overall, the amount of remaining interdigitated bone decreased with time in service (p = 0.0114). The distance from the cement border (at the extent of cement penetration into the bone bed) to 50% of the interdigitated volume decreased with time in service (p = 0.039). Isolated bone, when present, was located deep in the cement layer. Overall, resorption appears to start at the cement border and progresses into the cement layer. Initiation of trabecular resorption near the cement border may be a consequence of proximity to osteoclastic cells in the adjacent marrow space.

CLINICAL SIGNIFICANCE

Aseptic loosening of joint replacements remains an important clinical problem. This work explores the process and pattern of trabecular bone resorption responsible for loss of interface fixation. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2773-2780, 2017.

Tuberculosis serosurveillance and management practices of captive African elephants (Loxodonta africana) in the Kavango-Zambezi Transfrontier Conservation Area

Transfrontier conservation areas represent an international effort to encourage conservation and sustainable development. Their success faces a number of challenges, including disease management in wildlife, livestock and humans. Tuberculosis (TB) affects humans and a multitude of non-human animal species and is of particular concern in sub-Saharan Africa. The Kavango-Zambezi Transfrontier Conservation Area encompasses five countries, including Zimbabwe, and is home to the largest contiguous population of free-ranging elephants in Africa. Elephants are known to be susceptible to TB; thus, understanding TB status, exposure and transmission risks to and from elephants in this area is of interest for both conservation and human health. To assess risk factors for TB seroprevalence, a questionnaire was used to collect data regarding elephant management at four ecotourism facilities offering elephant-back tourist rides in the Victoria Falls area of Zimbabwe. Thirty-five working African elephants were screened for Mycobacterium tuberculosis complex antibodies using the ElephantTB Stat-Pak and the DPP VetTB Assay for elephants. Six of 35 elephants (17.1%) were seropositive. The risk factor most important for seropositive status was time in captivity. This is the first study to assess TB seroprevalence and risk factors in working African elephants in their home range. Our findings will provide a foundation to develop guidelines to protect the health of captive and free-ranging elephants in the southern African context, as well as elephant handlers through simple interventions. Minimizing exposure through shared feed with other wildlife, routine TB testing of elephant handlers and regular serological screening of elephants are recommended as preventive measures.

Optimising minimal building blocks for addressable self-assembly

Addressable structures are characterised by the set of unique components from which they are built and by the specific location that each component occupies. For an addressable structure to self-assemble, its constituent building blocks must be encoded with sufficient information to define their positions with respect to each other and to enable them to navigate to those positions. DNA, with its vast scope for encoding specific interactions, has been successfully used to synthesise addressable systems of several hundred components. In this work we examine the complementary question of the minimal requirements for building blocks to undergo addressable self-assembly driven by a controlled temperature quench. Our testbed is an idealised model of cubic particles patterned with attractive interactions. We introduce a scheme for optimising the interactions using a variant of basin-hopping and a negative design principle. The designed building blocks are tested dynamically in simple target structures to establish how their complexity affects the limits of reliable self-assembly.

Urban Emissions of Water Vapor in Winter

Elevated water vapor (H2Ov) mole fractions were occassionally observed downwind of Indianapolis, IN, and the Washington, D.C.-Baltimore, MD, area during airborne mass balance experiments conducted during winter months between 2012 and 2015. On days when an urban H2Ov excess signal was observed, H2Ov emissions estimates range between 1.6 × 104 and 1.7 × 105 kg s-1, and account for up to 8.4% of the total (background + urban excess) advected flow of atmospheric boundary layer H2Ov from the urban study sites. Estimates of H2Ov emissions from combustion sources and electricity generation facility cooling towers are 1-2 orders of magnitude smaller than the urban H2Ov emission rates estimated from observations. Instances of urban H2Ov enhancement could be a result of differences in snowmelt and evaporation rates within the urban area, due in part to larger wintertime anthropogenic heat flux and land cover differences, relative to surrounding rural areas. More study is needed to understand why the urban H2Ov excess signal is observed on some days, and not others. Radiative transfer modeling indicates that the observed urban enhancements in H2Ov and other greenhouse gas mole fractions contribute only 0.1°C day-1 to the urban heat island at the surface. This integrated warming through the boundary layer is offset by longwave cooling by H2Ov at the top of the boundary layer. While the radiative impacts of urban H2Ov emissions do not meaningfully influence urban heat island intensity, urban H2Ov emissions may have the potential to alter downwind aerosol and cloud properties.

Peri-Implant Distribution of Polyethylene Debris in Postmortem-Retrieved Knee Arthroplasties: Can Polyethylene Debris Explain Loss of Cement-Bone Interlock in Successful Total Knee Arthroplasties?

BACKGROUND

Loss of mechanical interlock between cement and bone with in vivo service has been recently quantified for functioning, nonrevised, cemented total knee arthroplasties (TKAs). The cause of interlocking trabecular resorption is not known. The goal of this study is to quantify the distribution of PE debris at the cement-bone interface and determine if polyethylene (PE) debris is locally associated with loss of interlock.

METHODS

Fresh, nonrevised, postmortem-retrieved TKAs (n = 8) were obtained en bloc. Laboratory-prepared constructs (n = 2) served as negative controls. The intact cement-bone interface of each proximal tibia was embedded in Spurr's resin, sectioned, and imaged under polarized light to identify birefringent PE particles. PE wear particle number density was quantified at the cement-bone interface and distal to the interface, and then compared with local loss of cement-bone interlock.

RESULTS

The average PE particle number density for postmortem-retrieved TKAs ranged from 8.6 (1.3) to 24.9 (3.1) particles/mm2 (standard error) but was weakly correlated with years in service. The average particle number density was twice as high as distal (>5mm) to the interface compared to at the interface. The local loss of interlock at the interface was not related to the presence, absence, or particle density of PE.

CONCLUSION

PE debris can migrate extensively along the cement-bone interface of well-fixed tibial components. However, the amount of local bone loss at the cement-bone interface was not correlated with the amount of PE debris at the interface, suggesting that the observed loss of trabecular interlock in these well-fixed TKAs may be due to alternative factors.

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life

Motivation

High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades.

Results

In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree.

Availability and Implementation

T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources.

Contact

icarbon@ncsu.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

Severe mortality impact of the 1957 influenza pandemic in Chile

Introduction

Epidemiological studies of the 1957 influenza pandemic are scarce, particularly from lower‐income settings.

Methods

We analyzed the spatial–temporal mortality patterns of the 1957 influenza pandemic in Chile, including detailed age‐specific mortality data from a large city, and investigated risk factors for severe mortality impact across regions.

Results

Chile exhibited two waves of excess mortality in winter 1957 and 1959 with a cumulative excess mortality rate of 12 per 10 000, and a ~10‐fold mortality difference across provinces. High excess mortality rates were associated with high baseline mortality (R²=41.8%; P=.02), but not with latitude (P>.7). Excess mortality rates increased sharply with age. Transmissibility declined from R=1.4‐2.1 to R=1.2‐1.4 between the two pandemic waves.

Conclusions

The estimated A/H2N2 mortality burden in Chile is the highest on record for this pandemic—about three to five times as severe as that experienced in wealthier nations. The global impact of this pandemic may be substantially underestimated from previous studies based on high‐income countries.

A modelling approach demonstrating micromechanical changes in the tibial cemented interface due to in vivo service

Post-operative changes in trabecular bone morphology at the cement-bone interface can vary depending on time in service. This study aims to investigate how micromotion and bone strains change at the tibial bone-cement interface before and after cementation. This work discusses whether the morphology of the post-mortem interface can be explained by studying changes in these mechanical quantities. Three post-mortem cement-bone interface specimens showing varying levels of bone resorption (minimal, extensive and intermediate) were selected for this study Using image segmentation techniques, masks of the post-mortem bone were dilated to fill up the mould spaces in the cement to obtain the immediately post-operative situation. Finite element (FE) models of the post-mortem and post-operative situation were created from these segmentation masks. Subsequent removal of the cement layer resulted in the pre-operative situation. FE micromotion and bone strains were analyzed for the interdigitated trabecular bone. For all specimens micromotion increased from the post-operative to the post-mortem models (distally, in specimen 1: 0.1 to 0.5µm; specimen 2: 0.2 to 0.8µm; specimen 3: 0.27 to 1.62µm). Similarly bone strains were shown to increase from post-operative to post-mortem (distally, in specimen 1: -185 to -389µε; specimen 2: -170 to -824µε; specimen 3: -216 to -1024µε). Post-mortem interdigitated bone was found to be strain shielded in comparison with supporting bone indicating that failure of bone would occur distal to the interface. These results indicate that stress shielding of interdigitated trabeculae is a plausible explanation for resorption patterns observed in post-mortem specimens.

Vaccine coverage and adherence to EPI schedules in eight resource poor settings in the MAL-ED cohort study

BACKGROUND

Launched in 1974, the Expanded Program on Immunization (EPI) is estimated to prevent two-three million deaths annually from polio, diphtheria, tuberculosis, pertussis, measles, and tetanus. Additional lives could be saved through better understanding what influences adherence to the EPI schedule in specific settings.

METHODS

The Etiology, Risk Factors and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) study followed cohorts in eight sites in South Asia, Africa, and South America and monitored vaccine receipt over the first two years of life for the children enrolled in the study. Vaccination histories were obtained monthly from vaccination cards, local clinic records and/or caregiver reports. Vaccination histories were compared against the prescribed EPI schedules for each country, and coverage rates were examined in relation to the timing of vaccination. The influence of socioeconomic factors on vaccine timing and coverage was also considered.

RESULTS

Coverage rates for EPI vaccines varied between sites and by type of vaccine; overall, coverage was highest in the Nepal and Bangladesh sites and lowest in the Tanzania and Brazil sites. Bacillus Calmette-Guérin coverage was high across all sites, 87-100%, whereas measles vaccination rates ranged widely, 73-100%. Significant delays between the scheduled administration age and actual vaccination date were present in all sites, especially for measles vaccine where less than 40% were administered on schedule. A range of socioeconomic factors were significantly associated with vaccination status in study children but these results were largely site-specific.

CONCLUSIONS

Our findings highlight the need to improve measles vaccination rates and reduce delayed vaccination to achieve EPI targets related to the establishment of herd immunity and reduction in disease transmission.

Potential Role of Growth Factors and Extracellular Matrix in Wound Healing after Laryngotracheal Reconstruction

Laryngotracheal reconstruction (LTR) has been used for more than 20 years to treat infants and children with subglottic stenosis. Results after pediatric LTR have been satisfactory; however, approximately 10% of children have recurrent airway narrowing after LTR. The purpose of our study was to determine whether a correlation existed between specific growth factors and extracellular matrix in patients with adequate wound healing capability as compared with patients with poor wound healing capability. Histologic sections from 27 patients who underwent LTR were cut, and immunohistochemical staining was performed for transforming growth factor-β, platelet-derived growth factor, fibronectin, tenascin, transforming growth factor-α, and vascular endothelial growth factor. Results showed that patients with adequate wound healing capability had a positive correlation with vasculature fibronectin, vasculature tenascin, and stromal fibronectin. Patients with poor wound healing capability had a positive correlation with stromal vascular endothelial growth factor.