Three-dimensional-based native alignment phenotype classification system: Description for use in planning for deformities during total knee arthroplasty.

Introduction: Total knee arthroplasty (TKA) is a complex surgical procedure that traditionally relies on two-dimensional radiographs for pre-operative planning. These radiographs may not capture the intricate details of individual knee anatomy, potentially limiting the precision of surgical interventions. With advancements in imaging technology, there is an opportunity to refine TKA outcomes. This study introduces the Native Alignment Phenotype classification system that is based on pre-operative 3-dimensional computed tomography (CT) scans, aiming to provide a more detailed understanding of knee deformities and their influence on characterizing knee osteoarthritis and planning for TKA procedures. Methods: There were 1406 pre-operative non-weight-bearing CT scans analyzed by a single surgeon experienced with robotically-assisted total knee arthroplasties. These scans were converted into three-dimensional models, focusing on the coronal and sagittal planes. Intraoperatively, the robotic system was used to capture native coronal and sagittal deformities for each patient. These values were captured with the patient's leg held in a non-stress, extension pose. A new classification system, 'The Native Alignment Phenotype', was developed to categorize the specific differences between individual knees. Results: There were four primary knee malalignments identified: varus deformity; valgus deformity; and two deformities in the sagittal plane. These malalignments were further categorized based on the degrees of deviation, creating groups with 5° coronal and sagittal ranges. A total of 77 phenotypic alignment patterns were found based on the analyzed cohort. In the coronal plane, varus HKA deformity between 6 and 10° was the most common, with 36.9% of the cases, followed by varus HKA alignment, which was between 0 and 5°, representing 34.3% of the cases. In the sagittal plane, neutral and flexion contracture deformities between 0 and 5° were the most common, with 32.6% of the cases, followed by a fixed flexion contracture alignment, which was between 6 and 10°, representing 28.7% of the cases. When combining coronal and sagittal planes, the most common alignment was the varus between 0 and 5° with a flexion contracture between 0 and 5° (12.5% of cases), closely followed by the varus between 6 and 10° with a flexion contracture between 6 and 10° (12.4% of cases). Conclusion: The Native Alignment Phenotype classification system offers a nuanced understanding of knee deformities based on three-dimensional (CT scan) assessments, potentially leading to improved surgical outcomes in TKA. By leveraging the detailed data from the CT scans, this system provides a more comprehensive view of the knee's anatomy, emphasizing the importance of individualized, data-driven approaches in knee surgery.

Hydrodynamics and phosphorus loading in an urbanized river channel influences response to future managed change: Insights from advection-dispersion modelling.

There is a need to understand what makes certain targeted measures for in-river phosphorus load reduction more effective than others. Therefore, this paper investigates multiple development scenarios in a small lowland polluted river draining an urban area (The Cut, Bracknell, UK), using an advection-dispersion model (ADModel-P). A comparative analysis is presented whereby changes in concentrations and fluxes of soluble reactive phosphorus (SRP) and organic phosphorus (OP) have been attributed to specific transformations (mineralization, sedimentation, resuspension, adsorption-desorption, and algal uptake) and correlated to controlling factors. Under present day conditions the river stretch is a net source of SRP (10.4 % increase in mean concentration) implying a release of previously accumulated material. Scenarios with the greatest impact are those based on managed reduction of phosphorus load in sources (e.g., 20 % increase in afforestation causes an in-river SRP and OP reduction of 1.3 % to 12.6 %) followed by scenarios involving changes in water temperature (e.g., 1 °C decrease leads to in-river SRP reduction around 3.1 %). Measures involving increased river residence time show the lowest effects (e.g., 16 % decrease in velocity results in under 0.02 % in-river SRP and OP reduction). For better understanding downstream persistence of phosphorus pollution and the effectiveness of mitigation measures the research demonstrates the importance of establishing when and where reaches are net adsorbers or desorbers, and whether sedimentation or resuspension is important.

Symptomatic and structural benefit of cathepsin K inhibition by MIV-711 in a subgroup with unilateral pain: post-hoc analysis of a randomised phase 2a clinical trial.

OBJECTIVES: Osteoarthritis (OA) development programmes face challenges due to discordance between structural changes and symptoms. A novel cathepsin-K inhibitor, MIV-711, recently reported structural benefits, but did not demonstrate a significant difference from placebo in symptoms. Previous work suggests that pain from non-target joints may confound OA pain outcomes. We therefore conducted an exploratory analysis in participants with predominantly unilateral knee pain from the MIV-711-201 trial. METHOSD: Participants scoring below median contralateral knee NRS pain at baseline from the MIV-711-201 phase 2a clinical trial (n=119) were analysed by treatment group for differences in change from baseline in WOMAC pain, quantitative magnetic resonance imaging bone area and cartilage thickness with a repeated-measures mixed model adjusting for relevant co-variates. RESULTS: In the subgroup with unilateral knee pain, treatment with MIV-711 100 mg led to greater reduction in WOMAC pain compared to placebo (-5.0, 95% CI: -8.69 to -1.3, p=0.008), while 200 mg did not (-2.5, 95% CI: -6.5 to 1.6, p=0.23). MIV-711 treatment was associated with a reduced change in bone area compared to placebo (200 mg; -19.6 mm2 , 95% CI: -36.2 to -3.0, p=0.02, and 100 mg; -12.5 mm2 , 95% CI: -27.8 to 2.8, p=0.11,). No observed differences between treatment groups in cartilage thickness were found in this subgroup. CONCLUSIONS: In a subgroup with predominantly unilateral knee pain, significant reduction in OA pain by MIV-711 100 mg treatment was found, with concurrent beneficial structural effects, highlighting the importance of appropriate pain inclusion criteria in OA trials.

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.

Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.

Meniscal tear outcome Study (METRO Study): a study protocol for a multicentre prospective cohort study exploring the factors which affect outcomes in patients with a meniscal tear.

INTRODUCTION: This study is designed to explore the baseline characteristics of patients under 55 years of age with a meniscal tear, and to describe the relationship between the baseline characteristics and patient-reported outcome measures (PROMs) over 12 months. Research has highlighted the need for a trial to investigate the effectiveness of arthroscopic meniscectomy in younger patients. Before this trial, we need to understand the patient population in greater detail. METHODS AND ANALYSIS: This is a multicentre prospective cohort study. Participants aged between 18 and 55 years with an MRI confirmed meniscal tear are eligible for inclusion. Baseline characteristics including age, body mass index, gender, PROMs duration of symptoms and MRI will be collected. The primary outcome measure is the Western Ontario Meniscal Evaluation Tool at 12 months. Secondary outcome measures will include PROMs such as EQ5D, Knee Injury and Osteoarthritis Outcome Score and patient global impression of change score at 3, 6 and 12 months. ETHICS AND DISSEMINATION: The study obtained approval from the National Research Ethics Committee West Midlands-Black Country research ethics committee (19/WM/0079) on 12 April 2019. The study is sponsored by the University of Warwick. The results will be disseminated via peer-reviewed publication. TRIAL REGISTRATION NUMBER: UHCW R&D Reference: IA428119. University of Warwick Sponsor ID: SC.08/18-19.

Use of acoustic emission to identify novel candidate biomarkers for knee osteoarthritis (OA).

Our objective was to determine the efficacy and feasibility of a new approach for identifying candidate biomarkers for knee osteoarthritis (OA), based on selecting promising candidates from a range of high-frequency acoustic emission (AE) measurements generated during weight-bearing knee movement. Candidate AE biomarkers identified by this approach could then be validated in larger studies for use in future clinical trials and stratified medicine applications for this common health condition. A population cohort of participants with knee pain and a Kellgren-Lawrence (KL) score between 1-4 were recruited from local NHS primary and secondary care sites. Focusing on participants' self-identified worse knee, and using our established movement protocol, sources of variation in AE measurement and associations of AE markers with other markers were explored. Using this approach we identified 4 initial candidate AE biomarkers, of which "number of hits" showed the best reproducibility, in terms of within-session, day to day, week to week, between-practitioner, and between-machine variation, at 2 different machine upper frequency settings. "Number of hits" was higher in knees with KL scores of 2 than in KL1, and also showed significant associations with pain in the contralateral knee, and with body weight. "Hits" occurred predominantly in 2 of 4 defined movement quadrants. The protocol was feasible and acceptable to all participants and professionals involved. This study demonstrates how AE measurement during simple sit-stand-sit movements can be used to generate novel candidate knee OA biomarkers. AE measurements probably reflect a composite of structural changes and joint loading factors. Refinement of the method and increasing understanding of factors contributing to AE will enable this approach to be used to generate further candidate biomarkers for validation and potential use in clinical trials.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples.

BACKGROUND: Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, 'ResPipe'. RESULTS: Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment. CONCLUSIONS: Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available ( https://gitlab.com/hsgweon/ResPipe ).

Evaluation of segmentation methods on head and neck CT: Auto-segmentation challenge 2015.

PURPOSE: Automated delineation of structures and organs is a key step in medical imaging. However, due to the large number and diversity of structures and the large variety of segmentation algorithms, a consensus is lacking as to which automated segmentation method works best for certain applications. Segmentation challenges are a good approach for unbiased evaluation and comparison of segmentation algorithms. METHODS: In this work, we describe and present the results of the Head and Neck Auto-Segmentation Challenge 2015, a satellite event at the Medical Image Computing and Computer Assisted Interventions (MICCAI) 2015 conference. Six teams participated in a challenge to segment nine structures in the head and neck region of CT images: brainstem, mandible, chiasm, bilateral optic nerves, bilateral parotid glands, and bilateral submandibular glands. RESULTS: This paper presents the quantitative results of this challenge using multiple established error metrics and a well-defined ranking system. The strengths and weaknesses of the different auto-segmentation approaches are analyzed and discussed. CONCLUSIONS: The Head and Neck Auto-Segmentation Challenge 2015 was a good opportunity to assess the current state-of-the-art in segmentation of organs at risk for radiotherapy treatment. Participating teams had the possibility to compare their approaches to other methods under unbiased and standardized circumstances. The results demonstrate a clear tendency toward more general purpose and fewer structure-specific segmentation algorithms.

Mains water leakage: Implications for phosphorus source apportionment and policy responses in catchments.

Effective strategies to reduce phosphorus (P)-enrichment of aquatic ecosystems require accurate quantification of the absolute and relative importance of individual sources of P. In this paper, we quantify the potential significance of a source of P that has been neglected to date. Phosphate dosing of raw water supplies to reduce lead and copper concentrations in drinking water is a common practice globally. However, mains water leakage (MWL) potentially leads to a direct input of P into the environment, bypassing wastewater treatment. We develop a new approach to estimate the spatial distribution and time-variant flux of MWL-P, demonstrating this approach for a 30-year period within the exemplar of the River Thames catchment in the UK. Our analyses suggest that MWL-P could be equivalent to up to c.24% of the P load entering the River Thames from sewage treatment works and up to c.16% of the riverine P load derived from agricultural non-point sources. We consider a range of policy responses that could reduce MWL-P loads to the environment, including incorporating the environmental damage costs associated with P in setting targets for MWL reduction, alongside inclusion of MWL-P within catchment-wide P permits.

The relationship between three-dimensional knee MRI bone shape and total knee replacement-a case control study: data from the Osteoarthritis Initiative.

OBJECTIVE: There is growing understanding of the importance of bone in OA. Our aim was to determine the relationship between 3D MRI bone shape and total knee replacement (TKR). METHODS: A nested case-control study within the Osteoarthritis Initiative cohort identified case knees with confirmed TKR for OA and controls that were matched using propensity scores. Active appearance modelling quantification of the bone shape of all knee bones identified vectors between knees having or not having OA. Vectors were scaled such that -1 and +1 represented the mean non-OA and mean OA shapes. RESULTS: Compared to controls (n = 310), TKR cases (n = 310) had a more positive mean baseline 3D bone shape vector, indicating more advanced structural OA, for the femur [mean 0.98 vs -0.11; difference (95% CI) 1.10 (0.88, 1.31)], tibia [mean 0.86 vs -0.07; difference (95% CI) 0.94 (0.72, 1.16)] and patella [mean 0.95 vs 0.03; difference (95% CI) 0.92 (0.65, 1.20)]. Odds ratios (95% CI) for TKR per normalized unit of 3D bone shape vector for the femur, tibia and patella were: 1.85 (1.59, 2.16), 1.64 (1.42, 1.89) and 1.36 (1.22, 1.50), respectively, all P < 0.001. After including Kellgren-Lawrence grade in a multivariable analysis, only the femur 3D shape vector remained significantly associated with TKR [odds ratio 1.24 (1.02, 1.51)]. CONCLUSION: 3D bone shape was associated with the endpoint of this study, TKR, with femoral shape being most associated. This study contributes to the validation of quantitative MRI bone biomarkers for OA structure-modification trials.

Longitudinal validation of periarticular bone area and 3D shape as biomarkers for knee OA progression? Data from the FNIH OA Biomarkers Consortium.

OBJECTIVE: To perform a longitudinal validation study of imaging bone biomarkers of knee osteoarthritis (OA) progression. METHODS: We undertook a nested case-control study within the Osteoarthritis Initiative in knees (one knee per subject) with a Kellgren and Lawrence grade of 1-3. Cases were defined as knees having the combination of medial tibiofemoral radiographic progression and pain progression at the 24-month, 36-month or 48-month follow-up compared with baseline. Controls (n=406) were eligible knees that did not meet both endpoint criteria and included 200 with neither radiographic nor pain progression, 103 with radiographic progression only and 103 with pain progression only. Bone surfaces in medial and lateral femur, tibia and patella compartments were segmented from MR images using active appearance models. Independent variables of primary interest included change from baseline to 24 months in (1) total area of bone and (2) position on three-dimensional (3D) bone shape vectors that discriminate OA versus non-OA shapes. We assessed the association of bone markers changes over 24 months with progression using logistic regression. RESULTS: 24-month changes in bone area and shape in all compartments were greater in cases than controls, with ORs of being a case per 1 SD increase in bone area ranging from 1.28 to 1.71 across compartments, and per 1 SD greater change in 3D shape vectors ranging from 1.22 to 1.64. Bone markers were associated most strongly with radiographic progression and only weakly with pain progression. CONCLUSIONS: In knees with mild-to-moderate radiographic OA, changes in bone area and shape over 24 months are associated with the combination of radiographic and pain progression over 48 months. This finding of association with longer term clinical outcome underscores their potential for being an efficacy of intervention biomarker in clinical trials.

A systematic review of the relationship between subchondral bone features, pain and structural pathology in peripheral joint osteoarthritis.

INTRODUCTION: Bone is an integral part of the osteoarthritis (OA) process. We conducted a systematic literature review in order to understand the relationship between non-conventional radiographic imaging of subchondral bone, pain, structural pathology and joint replacement in peripheral joint OA. METHODS: A search of the Medline, EMBASE and Cochrane library databases was performed for original articles reporting association between non-conventional radiographic imaging-assessed subchondral bone pathologies and joint replacement, pain or structural progression in knee, hip, hand, ankle and foot OA. Each association was qualitatively characterised by a synthesis of the data from each analysis based upon study design, adequacy of covariate adjustment and quality scoring. RESULTS: In total 2456 abstracts were screened and 139 papers were included (70 cross-sectional, 71 longitudinal analyses; 116 knee, 15 hip, six hand, two ankle and involved 113 MRI, eight DXA, four CT, eight scintigraphic and eight 2D shape analyses). BMLs, osteophytes and bone shape were independently associated with structural progression or joint replacement. BMLs and bone shape were independently associated with longitudinal change in pain and incident frequent knee pain respectively. CONCLUSION: Subchondral bone features have independent associations with structural progression, pain and joint replacement in peripheral OA in the hip and hand but especially in the knee. For peripheral OA sites other than the knee, there are fewer associations and independent associations of bone pathologies with these important OA outcomes which may reflect fewer studies; for example the foot and ankle were poorly studied. Subchondral OA bone appears to be a relevant therapeutic target. SYSTEMATIC REVIEW: PROSPERO registration number: CRD 42013005009.

Validated predictive modelling of the environmental resistome.

Multi-drug-resistant bacteria pose a significant threat to public health. The role of the environment in the overall rise in antibiotic-resistant infections and risk to humans is largely unknown. This study aimed to evaluate drivers of antibiotic-resistance levels across the River Thames catchment, model key biotic, spatial and chemical variables and produce predictive models for future risk assessment. Sediment samples from 13 sites across the River Thames basin were taken at four time points across 2011 and 2012. Samples were analysed for class 1 integron prevalence and enumeration of third-generation cephalosporin-resistant bacteria. Class 1 integron prevalence was validated as a molecular marker of antibiotic resistance; levels of resistance showed significant geospatial and temporal variation. The main explanatory variables of resistance levels at each sample site were the number, proximity, size and type of surrounding wastewater-treatment plants. Model 1 revealed treatment plants accounted for 49.5% of the variance in resistance levels. Other contributing factors were extent of different surrounding land cover types (for example, Neutral Grassland), temporal patterns and prior rainfall; when modelling all variables the resulting model (Model 2) could explain 82.9% of variations in resistance levels in the whole catchment. Chemical analyses correlated with key indicators of treatment plant effluent and a model (Model 3) was generated based on water quality parameters (contaminant and macro- and micro-nutrient levels). Model 2 was beta tested on independent sites and explained over 78% of the variation in integron prevalence showing a significant predictive ability. We believe all models in this study are highly useful tools for informing and prioritising mitigation strategies to reduce the environmental resistome.

Sewage effluent clean-up reduces phosphorus but not phytoplankton in lowland chalk stream (River Kennet, UK) impacted by water mixing from adjacent canal.

Information is provided on phosphorus in the River Kennet and the adjacent Kennet and Avon Canal in southern England to assess their interactions and the changes following phosphorus reductions in sewage treatment work (STW) effluent inputs. A step reduction in soluble reactive phosphorus (SRP) concentration within the effluent (5 to 13 fold) was observed from several STWs discharging to the river in the mid-2000s. This translated to over halving of SRP concentrations within the lower Kennet. Lower Kennet SRP concentrations change from being highest under base-flow to highest under storm-flow conditions. This represented a major shift from direct effluent inputs to a within-catchment source dominated system characteristic of the upper part to the catchment. Average SRP concentrations in the lower Kennet reduced over time towards the target for good water quality. Critically, there was no corresponding reduction in chlorophyll-a concentration, the waters remaining eutrophic when set against standards for lakes. Following the up gradient input of the main water and SRP source (Wilton Water), SRP concentrations in the canal reduced down gradient to below detection limits at times near its junction with the Kennet downstream. However, chlorophyll concentrations in the canal were in an order of magnitude higher than in the river. This probably resulted from long water residence times and higher temperatures promoting progressive algal and suspended sediment generations that consumed SRP. The canal acted as a point source for sediment, algae and total phosphorus to the river especially during the summer months when boat traffic disturbed the canal's bottom sediments and the locks were being regularly opened. The short-term dynamics of this transfer was complex. For the canal and the supply source at Wilton Water, conditions remained hypertrophic when set against standards for lakes even when SRP concentrations were extremely low.