ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data

We present ViPRA-Haplo, a de novo strain-specific assembly workflow for reconstructing viral haplotypes in a viral population from paired-end next generation sequencing (NGS) data. The proposed Viral Path Reconstruction Algorithm (ViPRA) generates a subset of paths from a De Bruijn graph of reads using the pairing information of reads. The paths generated by ViPRA are an over-estimation of the true contigs. We propose two refinement methods to obtain an optimal set of contigs representing viral haplotypes. The first method clusters paths reconstructed by ViPRA using VSEARCH [1] based on sequence similarity, while the second method, MLEHaplo, generates a maximum likelihood estimate of viral populations. We evaluated our pipeline on both simulated and real viral quasispecies data from HIV (and real data from SARS-COV-2). Experimental results show that ViPRA-Haplo, although still an overestimation in the number of true contigs, outperforms the existing tool, PEHaplo, providing up to 9% better genome coverage on HIV real data. In addition, ViPRA-Haplo also retains higher diversity of the viral population as demonstrated by the presence of a higher percentage of contigs less than 1000 base pairs (bps), which also contain k-mers with counts less than 100 (representing rarer sequences), which are absent in PEHaplo. For SARS-CoV-2 sequencing data, ViPRA-Haplo reconstructs contigs that cover more than 90% of the reference genome and were able to validate known SARS-CoV-2 strains in the sequencing data.

Individual perceptions of community efficacy for non-communicable disease management in twelve communities in China: cross-sectional and longitudinal analyses

OBJECTIVES

This objective of this study was to use empirical data to assess cross-sectional variation singular and changes over time in community efficacy for non-communicable diseases (NCDs) management (COEN) and to examine individual factors associated with changes in COEN.

STUDY DESIGN

This was a longitudinal observational study.

METHODS

Participants with hypertension and diabetes were randomly selected from 12 communities from three cities in eastern China, and a baseline survey and a 1-year follow-up were conducted. The COEN scale has five dimensions: community physical environment (CPE), behavioral risk factors (BRF), mental health and social relationships (MHSR), community health management (CHM), and community organisations and activities (COA). Mixed-effects models were used to investigate the change in COEN over time and the association between individual factors and changes in COEN.

RESULTS

COEN scores showed significant variation singular among the 12 communities (P < 0.001) at the baseline. In the mixed-effects model, CPE (β coefficient: 1.62, P < 0.001), BRF (0.90, P < 0.001), MHSR (0.86, P < 0.001), CHM (0.46, P < 0.001), and total scores (β = 3.57, P < 0.001) increased significantly over time. The changes in COEN were associated with individual characteristics (e.g., older, men, more educated).

CONCLUSIONS

Cross-sectional variations and changes over time in COEN demonstrated the utility of a sensitive instrument. Factors such as age, gender, marriage, education level, and employment may affect the financial and social resources assignment for NCD management. Our findings suggest that further high-quality studies are needed to better evaluate the effect of community empowerment on the prevention and control of NCDs.

Onboarding of siponimod in secondary progressive multiple sclerosis patients in Australia: Novel, real-world evidence from the MSGo digital support programme

Background

Siponimod is approved for use in people with secondary progressive multiple sclerosis (pwSPMS). An integrated digital platform, MSGo, was developed for pwSPMS and clinicians to help navigate the multiple steps of the pre-siponimod work-up.

Objective

To explore real-world onboarding experiences of siponimod amongst pwSPMS in Australia.

Methods

Retrospective, non-interventional, longitudinal, secondary analysis of data extracted from MSGo (20 April 2022). The primary endpoint was the average time for siponimod onboarding; secondary endpoints were adherence and sub-group analyses of variables influencing onboarding.

Results

Mixed-cure modelling estimated that 58% of participants (N = 368, females 71%, median age of 59 years) registered in MSGo would ever initiate siponimod. The median time to initiation was 56 days (95% CI [47-59] days). Half of the participants cited 'waiting for vaccination' as the reason for initiation delay. Cox regression analyses found participants with a nominated care partner had faster onboarding (HR 2.1, 95% CI [1.5-3.0]) and were more likely to continue self-reporting daily siponimod dosing than were those without a care partner (HR 2.2, 95% CI [1.3-3.7]).

Conclusions

Despite the limitations of self-reported data and the challenges of the COVID-19 pandemic, this study provides insights into siponimod onboarding in Australia and demonstrates the positive impact of care partner support.

Designing Calcium Silicate Cements with On-Demand Properties for Precision Endodontics

Calcium silicate (C3S) cements are available in kits that do not account for patients' specific needs or clinicians' preferences regarding setting time, radiopacity, mechanical, and handling properties. Moreover, slight variations in powder components and liquid content affect cement's properties and bioactivity. Unfortunately, it is virtually impossible to optimize several cement properties simultaneously via the traditional "one variable at a time" strategy, as inputs often induce trade-offs in properties (e.g., a higher water-to-powder ratio [W/P] increases flowability but decreases mechanical properties). Herein, we used Taguchi's methods and genetic algorithms (GAs) to simultaneously analyze the effect of multiple inputs (e.g., powder composition, radiopacifier concentration, and W/P) on setting time, pH, flowability, diametral tensile strength, and radiopacity, as well as prescribe recipes to produce cements with predicted properties. The properties of cements designed with GAs were experimentally tested, and the results matched the predictions. Finally, we show that the cements increased the genetic expression of odonto/osteogenic genes, alkaline phosphatase activity, and mineralization potential of dental pulp stem cells. Hence, GAs can produce cements with tailor-made properties and differentiation potential for personalized endodontic treatment.

Material risk: vitreoretinal surgery, evisceration, enucleation and sympathetic ophthalmia-where are we currently?

Sympathetic ophthalmia (SO) is known to occur after severe penetrating eye injury, evisceration and even enucleation surgery. Recent evidence suggests that a greater risk lies after multiple vitreoretinal procedures. The risk of SO following evisceration is only minimally greater than that following enucleation surgery. This review evaluates literature on SO to date and provides figures for the risk of developing SO for the purposes of the consent process. The issue of SO and Material Risk following vitreoretinal surgery is reviewed and figures for the purposes of consent are outlined. This is of particular relevance for patients in whom the contralateral eye is and will likely remain the better seeing eye. Sympathetic ophthalmitis is known to occur after severe penetrating eye injury, after evisceration and enucleation. More recently, sympathetic ophthalmitis has been recognised to occur after vitreoretinal surgery. This article reviews the evidence on material risk when consenting patients for elective and emergency eye procedures after ocular trauma or surgery. When a globe needs to be removed because of irreparable ocular injury, previous publications dictated the procedure to be an enucleation because of the fear of an increased risk of SO after an evisceration. Perhaps the issue of material risk of sympathetic ophthalmia (SO) remains over-emphasised by ophthalmic plastic surgeons and under-recognised by vitreoretinal surgeons during the consent process for evisceration, enucleation and vitreoretinal surgery. Antecedent trauma and number of previous surgeries may actually be a more significant risk factor than the type of eye removal. Recent medicolegal cases also help us understand the importance of the discussion of this risk. We present our current understanding of the risk of SO after different procedures and suggest how this information may be included in a patient consent.

Sustainable multi-trait selection index based on production, reproduction, and health traits for genetic improvement of Murrah buffaloes

Selection of Murrah buffaloes based on production, reproduction, and health traits play an important role in sustainable genetic improvement. With the aim to construct an index comprising of production, reproduction and health traits of Murrah buffaloes, the production and reproduction data during a 50-year span (1971-2020) and for health traits data of 27 years (1994-2020) were analyzed. Various three, four, five, and six trait combinations of production, reproduction, and health traits were explored for construction of performance indices. The income and expenditure method was used to calculate relative economic values (REV) for traits under consideration. A total of 37 performance indices were constructed using a multi-trait combination of production, reproduction, and health traits. Out of 37 indices, the (ADMY-PY-DO-AFC-FF) based index was identified as the best, with 78%, 2%, and 20% weightage given to production, reproduction, and female fertility, respectively. Furthermore, when REVs of traits were increased by 25% and 50%, there was no change observed in the relative importance of traits in the best index, indicating that the index was robust to substantial increases in economic values. Therefore, it is recommended that the above constructed composite selection index can be employed in selection of female buffaloes to achieve sustainable genetic gain.

Effect of Tooth Loss on Cognitive Function among Older Adults in Singapore

Evidence suggests a longitudinal association between tooth loss and cognitive function. However, the temporality of this association is not well understood. We investigated the effect of several emulated tooth loss prevention scenarios on cognitive function. We used data from 3 waves (baseline: 2009, second wave: 2011-2012, and third wave: 2015) of the Panel on Health and Ageing of Singaporean Elderly (PHASE). PHASE targeted older adults, aged ≥60 y, in Singapore. Number of teeth was used as a time-varying exposure (baseline, second wave). Cognitive function (Short Portable Mental Status Questionnaire score) in the third wave was assessed as the outcome. Multiple time-invariant (baseline) and time-varying (baseline and second wave) covariates were included. The "longitudinal modified treatment policy approach" combined with targeted minimum loss-based estimation was used to define and estimate additive effects of emulated tooth loss prevention scenarios. Emulated scenarios were the following: what if edentate people retained 1 to 4 teeth (scenario 1), what if those with <5 teeth retained 5 to 9 teeth (scenario 2), what if those with <10 teeth retained 10 to 19 teeth (scenario 3), and what if everyone retained ≥20 teeth (scenario 4)? A total of 1,516 participants, excluding those with severe cognitive impairment, were included (male: 41.6%). The mean age at baseline was 70.6 y (SD = 7.1). The mean SPMSQ score at baseline was 2.06 (SD = 0.02) for edentulous, 1.55 (SD = 0.04) for 1 to 4 teeth, 1.61 (SD = 0.03) for 5 to 9 teeth, 1.73 (SD = 0.02) for 10 to 19 teeth, and 1.71 (SD = 0.02) for ≥20 teeth. Additive effect of hypothetical intervention gradually increased with intensity of prevention from scenario 1 to scenario 4 (scenario 1: -0.02 [95% CI, -0.08 to 0.04], scenario 2: -0.05 [95% CI, -0.11 to -0.00], scenario 3: -0.07 [95% CI, -0.14 to -0.00], scenario 4: -0.15 [95% CI, -0.23 to -0.06]). Emulated tooth loss prevention interventions were associated with better cognitive function score. Therefore, preventing tooth loss could potentially benefit maintenance of cognitive function among older adults.

Intensive Blood Pressure Management Preserves Functional Connectivity in Patients with Hypertension from the Systolic Blood Pressure Intervention Randomized Trial

BACKGROUND AND PURPOSE

The Systolic Blood Pressure Intervention (SPRINT) randomized trial demonstrated that intensive blood pressure management resulted in slower progression of cerebral white matter hyperintensities, compared with standard therapy. We assessed longitudinal changes in brain functional connectivity to determine whether intensive treatment results in less decline in functional connectivity and how changes in brain functional connectivity relate to changes in brain structure.

MATERIALS AND METHODS

Five hundred forty-eight participants completed longitudinal brain MR imaging, including resting-state fMRI, during a median follow-up of 3.84 years. Functional brain networks were identified using independent component analysis, and a mean connectivity score was calculated for each network. Longitudinal changes in mean connectivity score were compared between treatment groups using a 2-sample t test, followed by a voxelwise t test. In the full cohort, adjusted linear regression analysis was performed between changes in the mean connectivity score and changes in structural MR imaging metrics.

RESULTS

Four hundred six participants had longitudinal imaging that passed quality control. The auditory-salience-language network demonstrated a significantly larger decline in the mean connectivity score in the standard treatment group relative to the intensive treatment group (P = .014), with regions of significant difference between treatment groups in the cingulate and right temporal/insular regions. There was no treatment group difference in other networks. Longitudinal changes in mean connectivity score of the default mode network but not the auditory-salience-language network demonstrated a significant correlation with longitudinal changes in white matter hyperintensities (P = .013).

CONCLUSIONS

Intensive treatment was associated with preservation of functional connectivity of the auditory-salience-language network, while mean network connectivity in other networks was not significantly different between intensive and standard therapy. A longitudinal increase in the white matter hyperintensity burden is associated with a decline in mean connectivity of the default mode network.

Modern cemented Furlong hemiarthroplasty: Are dislocations rates better?

BACKGROUND

Dislocation following hip hemiarthroplasty is a major complication with increased mortality and morbidity. Data looking at dislocation following contemporary bipolar stems are lacking in literature.

METHODS

Retrospective review of our prospective national hip fracture database over a two-year period. Group 1 comprised of consecutive patients receiving bipolar Furlong prosthesis (N222) while Group 2 was made up of a historical cohort (uncemented; N254). Clinical and radiological records were reviewed to determine dislocation rates, causes and associative factors of dislocations. Data were analysed using SPSS.

RESULTS

Following 476 hemiarthroplasties performed during the study period, 12 (2.5%) dislocations were reported (eight in Group 1; four in Group 2). There was no significant difference in dislocation rates (3.6% vs 1.6%) between groups (p = 0.159). Subgroup analysis of Group 1 demonstrated a significant difference in dislocations with Furlong cemented (6%) as compared with Furlong uncemented (0%) hemiarthroplasties (p = 0.024). Following dislocation, death rates increased to 8.3% from 1.7% in both groups.

CONCLUSION

There is a statistically significant increase in dislocation rate following use of cemented Furlong prosthesis when compared to similar uncemented prosthesis at the same treatment period. However, when compared to traditional uncemented prosthesis, there is no difference in dislocation rates.

Magnetocardiography as a noninvasive diagnostic strategy for suspected coronary microvascular dysfunction

Background

Coronary microvascular dysfunction (CMD) is increasingly recognized as an independent predictor of mortality with a 4-fold higher risk. However current diagnostic modalities are limited by the need for an invasive procedure, access, cost, and exposure of ionizing radiation.

Purpose

To investigate the ability of magnetocardiography (MCG) to identify CMD in patients with suspected ischemia and no obstructive coronary artery disease (INOCA).

Methods

This is an observational, prospective pilot study of patients scheduled for coronary functional angiography (CFA), gold standard for evaluation for CMD (defined as coronary flow reserve (CFR) ≤2). 13 patients underwent both CFA and a noninvasive 36-channel MCG scan. A machine learning model was developed to characterize the presence of CMD in these patients against age matched controls (AMCs). The model consists of a logistic regression classifier which takes features representing the relative strengths of the “characteristic dipoles” of the MCG scan as input. The characteristic dipoles are parameterizations of the three strongest magnetic field map components resulting from a singular value decomposition of the MCG signal. A total of 37 patients were included in this analysis including 13 patients who completed CFA (7 had CMD and 6 had CFR &gt;2 and included in the AMCs group). An additional 24 asymptomatic, healthy patients that did not undergo CFR were also included in the AMC group.

Results

The mean age for AMCs was 57 years (70% women) and mean age for CMD patients was 54 years (100% women). The performance of the model was evaluated using repeated stratified cross-validation with 5 folds and 3 repeats, resulting in 15 different 80%/20% train/test splits. Figure 1 shows the distribution of samples belonging to the CMD and AMC groups in a 2-dimensional representation of the feature space. The clear separation of the two groups and the clustering of the AMCs demonstrates the ability of the model to identify patients with CMD. We found that MCG had a mean accuracy of 94.8% (±6.4%), sensitivity of 100% (±0.0%) and specificity of 93.3% (±8.2%) for the detection of CMD using gold standard CFR ≤2 as reference.

Conclusion(s)

First study to show that MCG can be used with 94.8% accuracy to identify CMD among patients suspicious for INOCA with no exposure to ionization, 90 seconds of scan time and minimal cost. The use of this noninvasive modality to identify CMD warrants further investigation.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Genetesis

Outcomes in Nonagenarians with Hip Fractures Treated Conservatively and Surgically

Introduction

We aimed to assess the clinical outcomes in nonagenarians following a hip fracture. We also further investigated the factors that influence these outcomes, such as method of treatment (operative versus conservative), co-morbidities, and pre-morbid function.

Materials and methods

We studied 65 nonagenarians that were identifiable from our hospital hip fracture database. We reviewed various parameters of these patients admitted after sustaining a hip fracture (neck of femur or intertrochanteric) and investigated how these parameters affected patient outcomes. The main outcomes studied were: inpatient morbidity, and mortality at one year.

Results

Inpatient morbidity was more likely in patients with an ASA grade of 3 to 5. Urinary tract infection was the most common medical complication. The 1-year mortality was 15.4% and was significantly influenced by advancing age. Surgically managed patients had a 1-year mortality rate (14.3%) slightly less than non-operative patients (17.4%). Post injury mobility was significantly better in those who received operative treatment with 63% of surgical cases regaining ambulatory status versus 7% of conservatively managed patients.

Conclusions

We presented the outcomes of hip fractures in an extreme age group in the population. In nonagenarians with hip fractures surgery was associated with a 1-year mortality rate of 14.3% which is comparable to the general hip fracture population and less than the mortality rate of conservatively managed patients (17.4%). The primary advantage of surgery would be that two-thirds of patients return to ambulatory status. This information is useful to counsel patients and their families especially since the elderly are often more fearful of surgical intervention.

Recombination marks the evolutionary dynamics of a recently endogenized retrovirus

All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term coevolution of ERV and host because germline infections are rare and expansion is slow, and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. We previously established the locus-specific distribution of cervid ERV (CrERV) in populations of mule deer. In this study, we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short- and long-insert mate pair reads and CrERV sequence generated at each locus. We report that CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting interlineage recombinants then endogenize and subsequently expand. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.

Graphene Nanocoating: High Quality and Stability upon Several Stressors

Titanium implants present 2 major drawbacks-namely, the long time needed for osseointegration and the lack of inherent antimicrobial properties. Surface modifications and coatings to improve biomaterials can lose their integrity and biological potential when exposed to stressful microenvironments. Graphene nanocoating (GN) can be deposited onto actual-size dental and orthopedic implants. It has antiadhesive properties and can enhance bone formation in vivo. However, its ability to maintain structural integrity and quality when challenged by biologically relevant stresses remains largely unknown. GN was produced by chemical vapor deposition and transferred to titanium via a polymer-assisted transfer technique. GN has high inertness and did not increase expression of inflammatory markers by macrophages, even in the presence of lipopolysaccharides. It kept high coverage at the top tercile of tapered dental implant collars after installation and removal from bone substitute and pig maxilla. It also resisted microbiologically influenced corrosion, and it maintained very high coverage area and quality after prolonged exposure to biofilms and their removal by different techniques. Our findings show that GN is unresponsive to harsh and inflammatory environments and that it maintains a promising level of structural integrity on the top tercile of dental implant collars, which is the area highly affected by biofilms during the onset of implant diseases. Our findings open the avenues for the clinical studies required for the use of GN in the development of implants that have higher osteogenic potential and are less prone to implant diseases.

Clinico-radiological findings of neuroendocrine tumour metastases to the orbit

Purpose: We present the clinico-radiological findings of neuroendocrine tumour metastases to the orbit.Methods: This was a multicentre, retrospective study of patients with neuroendocrine tumour metastases to the orbit. Data was collected from medical records across five different sites within Australia and the United Kingdom.Results: Nine patients (eleven lesions) were identified. The most common presenting complaint was diplopia (5/9, 56%). Disease occurred bilaterally in two patients. Seven patients (78%) had extraocular muscle involvement. The lateral recti (4/9, 44%) and superior recti (2/9, 22%) were the most commonly affected. Ocular presentation preceded primary tumour diagnosis in three patients (33%). On orbital imaging, metastases were most commonly reported as well circumscribed, ovoid or round, heterogeneous, contrast-enhancing masses. Features of intralesional haemorrhage and bony invasion are uncommonly reported.Conclusions: Neuroendocrine tumour metastasis to the orbit is uncommon. Metastases have a propensity for the extraocular muscles, commonly presenting as heterogeneous, well circumscribed, contrast-enhancing lesions on neuroimaging. New ocular symptoms, a history of neuroendocrine tumours, and these radiological findings, should lead to high clinical suspicion of metastatic disease. Atypical findings warrant biopsy to exclude other causes of orbital lesions.

A unique case of light chain (AL) amyloidosis masquerading as hypophosphatemic osteomalacia

Light chain (AL) amyloidosis is the result of a clonal plasma cell disorder which causes organ damage by deposition of misfolded light chains. Kidney is a common site of amyloid deposition. Proteinuria, usually in nephrotic range and unexplained renal insufficiency are the main manifestations of renal injury. We report a unique case of renal involvement by AL amyloidosis masquerading as metabolic bone disease. 38 year old male patient presented with progressively increasing diffuse bony pains, low backache and proximal weakness of both lower limbs since two years. On investigation, he was detected to have hypophosphatemic osteomalacia due to renal phosphate loss which was fibroblast growth factor 23 (FGF23)- independent. He also had nephrotic range low molecular weight proteinuria. Renal biopsy to ascertain the aetiology revealed deposition of amyloid fibrils in the glomerular mesangium on electron microscopy. Its characterization by immunofluorescence (IF) was consistent with immunoglobulin light chain (AL) amyloidosis. In the absence of a demonstrable plasma cell clone on bone marrow biopsy, we made a diagnosis of monoclonal gammopathy of renal significance (MGRS). He was treated with chemotherapy following which there was symptomatic improvement and reduction in phosphaturia. This case describes a unique presentation of renal injury due to AL amyloidosis masquerading as hypophosphatemic osteomalacia. The aim of this report is to highlight that hypophosphatemia in adults is usually acquired and treatment of underlying etiology results in cure, unlike in children where genetic counseling and phosphate replacement is the mainstay of treatment.

Predictors for rapid progression of coronary calcification: an optical coherence tomography (OCT) study

Background

The natural progression of coronary calcification has not been systematically studied. In vivo coronary calcium can be evaluated by OCT.

Purpose

To identify the incidence and predictors for rapid progression of coronary calcification.

Methods

Patients with serial OCT imaging at baseline and at 6 months were selected from our database. Changes in calcium index during 6-month follow-up and predictors for progression of calcification were studied. Calcium index was defined as the product of the mean calcium arc and calcium length. Rapid progression of calcification was defined as an increase in calcium index above the median value.

Results

Among 187 patients who had serial OCT imaging, 235 calcified plaques were identified in 108 patients (57.8%) at baseline with median calcium index of 132.0 (Interquartile range 58.5–281.2). After 6 months, the calcium index increased in 95.3% of calcified plaques from 132.0 to 178.2 (p&lt;0.001). In multivariable analysis, diabetes mellitus (DM), chronic kidney disease (CKD), lipid-rich plaque, and macrophages were found to be independent predictors for rapid progression of coronary calcification (table). Interestingly, rapid progression of calcification was associated with a significant reduction of inflammatory features (thin-cap fibroatheroma [TCFA]; baseline 21.2% vs. follow-up 11.9%, p=0.003, macrophages; baseline 74.6% vs. follow-up 61.0%, p=0.001).

Conclusions

This study demonstrated that DM, CKD, lipid-rich plaque, and macrophages were independent predictors for rapid progression of coronary calcification. High level of vascular inflammation may stimulate rapid progression of calcification.

Funding Acknowledgement

Type of funding source: None

Peri-orbital surgical emphysema following endoscopic dacryocystorhinostomy

BACKGROUND

Peri-orbital surgical emphysema is a rare complication that can occur after lacrimal surgery. It has only been described in isolated cases, following external dacryocystorhinostomy (n = 2) and Lester Jones tube insertion (n = 1).

METHOD

A retrospective, non-comparative case series was conducted of patients who developed surgical emphysema following endoscopic dacryocystorhinostomy.

RESULTS

A total of 356 endoscopic dacryocystorhinostomy cases (primary, n = 316; revision, n = 40) were performed over a six-year period. Seven cases of post-operative surgical emphysema were identified, all of which were preceded by uncontrolled sneezing, nose-blowing or coughing within the first week of surgery. The occurrence of surgical emphysema post-endoscopic dacryocystorhinostomy in our centre was 7 in 356, or 2 per cent, over six years.

CONCLUSION

This is the first study to report the occurrence of surgical emphysema post-endoscopic dacryocystorhinostomy. Clinicians may wish to suggest patients stifle the aforementioned triggers within the first week to reduce the potential for surgical emphysema.

QuagmiR: a cloud-based application for isomiR big data analytics

SUMMARY

MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role in cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiRs, it permits extensive customization of the query process and reference databases to meet the user 's diverse research needs.

AVAILABILITY AND IMPLEMENTATION

QuagmiR is written in Python and can be obtained freely from GitHub (https://github.com/Gu-Lab-RBL-NCI/QuagmiR). QuagmiR can be run from the command line on local machines, as well as on high-performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud (https://cancergenomicscloud.org).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Search for L5 Earth Trojans with DECam

Most of the major planets in the Solar System support populations of co-orbiting bodies, known as Trojans, at their L4 and L5 Lagrange points. In contrast, Earth has only one known co-orbiting companion. This paper presents the results from a search for Earth Trojans using the DECam instrument on the Blanco Telescope at CTIO. This search found no additional Trojans in spite of greater coverage compared to previous surveys of the L5 point. Therefore, the main result of this work is to place the most stringent constraints to date on the population of Earth Trojans. These constraints depend on assumptions regarding the underlying population properties, especially the slope of the magnitude distribution (which in turn depends on the size and albedo distributions of the objects). For standard assumptions, we calculate upper limits to a 90% confidence limit on the L5 population of N ET < 1 for magnitude H < 15.5, N ET =60-85 for H < 19.7, and N ET = 97 for H=20.4. This latter magnitude limit corresponds to Trojans ∼300 m in size for albedo 0.15. At H=19.7, these upper limits are consistent with previous L4 Earth Trojan constraints and significantly improve L5 constraints.

Inhibiting Corrosion of Biomedical-Grade Ti-6Al-4V Alloys with Graphene Nanocoating

The identification of metal ions and particles in the vicinity of failed implants has raised the concern that biomedical titanium alloys undergo corrosion in healthy and infected tissues. Various surface modifications and coatings have been investigated to prevent the deterioration and biocorrosion of titanium alloys but so far with limited success. Graphene is a cytocompatible atom-thick film made of carbon atoms. It has a very high surface area and can be deposited onto metal objects with complex shapes. As the carbon lattice has a very small pore size, graphene has promising impermeability capacity. Here, we show that graphene coating can effectively protect Ti-6Al-4V from corrosion. Graphene nanocoatings were produced on Ti-6Al-4V grade 5 and 23 discs and subjected to corrosive challenge (0.5M NaCl supplemented with 2-ppm fluoride, pH of 2.0) up to 30 d. The linear polarization resistance curves and electrochemical impedance spectroscopy analysis showed that the graphene-coated samples presented higher corrosion resistance and electrochemical stability at all time points. Moreover, the corrosion rate of the graphene-coated samples was very low and stable (~0.001 mm/y), whereas that of the uncoated controls increased up to 16 and 5 times for grade 5 and 23 (~0.091 mm/y) at the end point, respectively. The surface oxidation, degradation (e.g., crevice defects), and leaching of Ti, Al, and V ions observed in the uncoated controls were prevented by the graphene nanocoating. The Raman mappings confirmed that the graphene nanocoating presented high structural stability and resistance to mechanical stresses and chemical degradation, keeping >99% of coverage after corrosion challenge. Our findings open the avenues for the use of graphene as anticorrosion coatings for metal biomedical alloys and implantable devices.

Hand function outcome in closed small bone fractures treated by open reduction and internal fixation by mini plate or closed crossed pinning: a randomized controlled trail

PURPOSE

No study in literature clearly gives advantage of one method of surgical fixation of fracture over the other in metacarpal and phalangeal bones of hand comparing wider outcome measures.

MATERIALS AND METHODS

A randomized controlled trial between closed reduction and percutaneous Kirschner wire fixation or open reduction and internal fixation with mini fragment plates was conducted. A total of 32 patients with 16 in each group were taken in tertiary-level teaching hospital from 2014 to 2016. Four patients lost to follow-up apart from 32 studied. Inclusion criteria were age group 16-60 years, fresh (3 days) closed shaft fractures of metacarpal and phalanges. Outcome evaluated were time to union of fracture, degree of strength achieved measured with dynamometer, DASH scoring, range of motion of hand and each digit.

RESULTS

Both groups were comparable in terms of return to full hand function, union and total range of motion. K wire fixation results were slightly better than plating group in terms of early DASH score and grip strength after fixation.

CONCLUSION

No modality was found to be superior for fixation of small bone fractures of hand. But K wire being cheaper and without inherent complication of plating like scar and tendon irritation, K wire fixation is preferred over plating in shaft fractures of metacarpal and phalanges.

LEVEL OF EVIDENCE

Level I Therapeutic study.

A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations

Human Endogenous Retrovirus type K (HERV-K) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at a specific genomic location. It is possible that HERV-Ks contribute to human disease because people differ in both number and genomic location of these retroviruses. Indeed viral transcripts, proteins, and antibody against HERV-K are detected in cancers, auto-immune, and neurodegenerative diseases. However, attempts to link a polymorphic HERV-K with any disease have been frustrated in part because population prevalence of HERV-K provirus at each polymorphic site is lacking and it is challenging to identify closely related elements such as HERV-K from short read sequence data. We present an integrated and computationally robust approach that uses whole genome short read data to determine the occupation status at all sites reported to contain a HERV-K provirus. Our method estimates the proportion of fixed length genomic sequence (k-mers) from whole genome sequence data matching a reference set of k-mers unique to each HERV-K locus and applies mixture model-based clustering of these values to account for low depth sequence data. Our analysis of 1000 Genomes Project Data (KGP) reveals numerous differences among the five KGP super-populations in the prevalence of individual and co-occurring HERV-K proviruses; we provide a visualization tool to easily depict the proportion of the KGP populations with any combination of polymorphic HERV-K provirus. Further, because HERV-K is insertionally polymorphic, the genome burden of known polymorphic HERV-K is variable in humans; this burden is lowest in East Asian (EAS) individuals. Our study identifies population-specific sequence variation for HERV-K proviruses at several loci. We expect these resources will advance research on HERV-K contributions to human diseases.

Human Endogenous Retrovirus type K (HERV-K) is the youngest of retrovirus families in the human genome and is the only group of endogenous retroviruses that has polymorphic members; a locus containing a HERV-K can be occupied in one individual but empty in others. HERV-Ks could contribute to disease risk or pathogenesis but linking one of the known polymorphic HERV-K to a specific disease has been difficult. We develop an easy to use method that reveals the considerable variation existing among global populations in the prevalence of individual and co-occurring polymorphic HERV-K, and in the number of HERV-K that any individual has in their genome. Our study provides a reference of diversity for the currently known polymorphic HERV-K in global populations and tools needed to determine the profile of all known polymorphic HERV-K in the genome of any patient population.

The Long-Term Impact of Functional Disability on Hospitalization Spending in Singapore

Singapore is one of the fastest-aging populations due to increased life expectancy and lowered fertility. Lifestyle changes increase the burden of chronic diseases and disability. These have important implications for social protection systems. The goal of this paper is to model future functional disability and healthcare expenditures based on current trends. To project the health, disability and hospitalization spending of future elders, we adapted the Future Elderly Model (FEM) to Singapore. The FEM is a dynamic Markov microsimulation model developed in the US. Our main source of population data was the Singapore Chinese Health Study (SCHS) consisting of 63,000 respondents followed up over three waves from 1993 to 2010. The FEM model enables us to investigate the effects of disability compounded over the lifecycle and hospitalization spending, while adjusting for competing risk of multi-comorbidities. Results indicate that by 2050, 1 in 6 elders in Singapore will have at least one ADL disability and 1 in 3 elders will have at least one IADL disability, an increase from 1 in 12 elders and 1 in 5 elders respectively in 2014. The highest prevalence of functional disability will be in those aged 85 years and above. Lifetime hospitalization spending of elders aged 55 and above is US$24,400 (30.2%) higher among people with functional disability compared to those without disability. Policies that successfully tackle diabetes and promote healthy living may reduce or delay the onset of disability, leading to potential saving. In addition, further technological improvements may reduce the financial burden of disability.

Management of congenital ichthyoses: European guidelines of care, part one

These guidelines for the management of congenital ichthyoses have been developed by a multidisciplinary group of European experts following a systematic review of the current literature, an expert conference held in Toulouse in 2016 and a consensus on the discussions. They summarize evidence and expert-based recommendations and are intended to help clinicians with the management of these rare and often complex diseases. These guidelines comprise two sections. This is part one, covering topical therapies, systemic therapies, psychosocial management, communicating the diagnosis and genetic counselling.

Management of congenital ichthyoses: European guidelines of care, part two

These guidelines for the management of congenital ichthyoses have been developed by a multidisciplinary group of European experts following a systematic review of the current literature, an expert conference held in Toulouse in 2016, and a consensus on the discussions. These guidelines summarize evidence and expert-based recommendations and intend to help clinicians with the management of these rare and often complex diseases. These guidelines comprise two sections. This is part two, covering the management of complications and the particularities of some forms of congenital ichthyosis.

Feasibility and Results of Cancer Registry and Noncommunicable Disease Cohort Data Linkages in India

Background: Cancer registries worldwide are vital to determine cancer burden, plan cancer control measures, and facilitate research. Population-based cancer registries are a priority for LMICs by the UICC; the National Cancer Registry Program (NCRP) of India oversees 28 such registries. A primary function of registries is to combine data for the same individual from multiple sources. For other disease cohorts where cancer is an outcome of interest, registries can potentially connect information by linking datasets together. Barriers to successful registration and linkages include systems in which cancer is not a notifiable disease, no universal unique individual identifier exists, and lack of trained personnel. This study utilizes technology and infrastructure to develop better linkages, surveillance, and outcomes. Aim: To assess the feasibility of linking large cohorts designed for cardio-metabolic disease research with cancer registries in New Delhi and Chennai; determine additional steps required for linkage accuracy and completeness; and develop detailed protocols for future applications. Methods: A pilot protocol for linkage between a large diabetes cohort and cancer registries in Delhi and Chennai was developed using MatchPro, a probabilistic record linkage program developed for cancer registries. Probabilistic software links datasets together in the presence of uncertainty (eg misspelled or abbreviated names) to identify record pairs with high probability of representing the same individual. For this study, algorithms were developed to address unique aspects of names and demographics in India. The software and algorithms focused on: detecting duplicates in cancer registries; and linking registries with external files from diabetes cohorts. In Delhi, 3 1-year datasets covering 3 years (2010, 2011, 2012) were linked with the diabetes cohort; in Chennai, the linkage included 3 5-year datasets covering 15 years (2000-04, '05-'09, '10-'14). The unique ID (Aadhaar) is not collected or linked systematically between different systems at this point in time. Results: Linkage attempts yielded potential matches ranked according to probabilistic scores; highest scores were reviewed to determine true matches. In Chennai, this process yielded: (2010-2014) 21% self-reported (SR) cases matching perfectly, 36% requiring follow-up, 13 nonreported (NR) cases found; 2005-2009: 33% SR cases matched perfectly, 1 NR case found; 2000-2004: 1 NR case. Also, 2 training workshops on data linkages and software were held. Conclusion: Linkages between cancer registries and other data sources are feasible in LMICs using probabilistic record linkage software augmented by manual matching. Future efforts to use existing epidemiologic resources (cohorts) and cancer research infrastructure (registries and clinical centers) can enhance research including understanding shared risk factors and pathophysiologic mechanisms e.g., between cancer and other NCD.

Results of trabecular metal augments in Paprosky IIIA and IIIB defects

Aims

The advent of trabecular metal (TM) augments has revolutionized the management of severe bone defects during acetabular reconstruction. The purpose of this study was to evaluate patients undergoing revision total hip arthroplasty (THA) with the use of TM augments for reconstruction of Paprosky IIIA and IIIB defects.

Patients and Methods

A retrospective study was conducted at four centres between August 2008 and January 2015. Patients treated with TM augments and TM shell for a Paprosky grade IIIA or IIIB defect, in the absence of pelvic discontinuity, and who underwent revision hip arthroplasty with the use of TM augments were included in the study. A total of 41 patients with minimum follow-up of two years were included and evaluated using intention-to-treat analysis.

Results

There were 36 (87.8%) patients with a Paprosky IIIA defect and five (12.2%) patients with a Paprosky IIIB defect. The mean age was 56.7 years (28 to 94). There were 21 (51.2%) women and 20 (48.8%) men. The mean follow-up was 39.4 months (12 to 96). One (2%) patient died after eight years. No failures were noted in the series. The mean survivorship was 100% at the time of latest follow-up.

Conclusion

The results of this multicentre study showed encouraging short- and mid-term results for the use of TM augments in the management of Paprosky grade IIIA and IIIB defects. Cite this article: Bone Joint J 2018;100-B:903–8.

Abstract 2348: Low-cost and accurate human leukocyte antigen (HLA) class I typing of The Cancer Genome Atlas on the Seven Bridges Cancer Genomics Cloud

The Cancer Genome Atlas (TCGA)network has generated more than2.5petabytes of genomic dataover the last decade, with

petabyte-scale additions of dataexpected inthe coming years. Access and analysis of this informationonalocal compute

environment is challenging due tothe volume of dataand lack of sufficient computing resources at many research organizations.

The Cancer Genomics Cloud Pilot project from the National Cancer Institute (NCI)has helped indemocratizing access toTCGA

by co-localizing datawith computational resources onthe cloud. Funded as part of this project, the SevenBridges Cancer

Genomics Cloud (CGC)hosts nearly 5petabytes of public datafrom TCGA, the Simons Genome Diversity Project, the

Therapeutically Applicable Research toGenerate Effective Treatments (TARGET)initiative, The Cancer Imaging Archive (TCIA),

and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). The CGCprovides academic researchers with asecure,

scalable, cloud-based cancer research platform that includes collaborative tools for accessing, uploading, analyzing, and

visualizing data. The platform uses resource descriptionframeworks, dataharmonization, and metadatacurationtofacilitate

effective querying, and bioinformatics tools are implemented onthe CGCusing the CommonWorkflow Language (CWL), an

emerging standard for describing computational workflows, tosupport computational reproducibility. Since its launch in2016, the

CGChas enabled researchers from around the world tounderstand humangenetics and cancer biology through the analysis of

large public datasets and private datainacloud computing environment. Inthis poster, we present anexample of analysis of

TCGAdataonthe CGC. The OptiType tool for HumanLeukocyte Antigenclass I typing was used toprofile 8,872RNA-Seq

samples present inthe TCGAdataset. All samples were accurately processed within2days using arobust, fault-tolerant, and

cost-efficient CWL descriptionof OptiType that enabled analysis for less than50cents per sample onaverage. This case study

demonstrates how cloud computing resources canfacilitate the successful analysis of large cohorts of datausing custom

pipelines in a robust, scalable, and reproducible manner.

Citation Format: Raunaq Malhotra, Alexandar Krasnitz, Anurag Sethi, Erik Lehnert, Elizabeth H. Williams, Davis-Dusenbery N. Brandi. Low-cost and accurate human leukocyte antigen (HLA) class I typing of The Cancer Genome Atlas on the Seven Bridges Cancer Genomics Cloud [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2348.

The Immune Landscape of Cancer

We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.

Outcomes of lower eyelid retractor recession and lateral horn lysis in lower eyelid elevation for facial nerve palsy

PurposeTo report outcomes and complications of lower eyelid retractor recession and lateral horn lysis (RR) for lower eyelid elevation in patients with facial nerve palsy (FNP).Patients and methodsRetrospective review. Patients with FNP undergoing RR alone (group 1) or with adjunctive procedures (canthal suspension-group 2, tarsorrhaphy-group 3, and full-thickness skin graft-group 4) during a 5-year period were included. Patient demographics, lagophthalmos, occurrence of eyelid malpositions, recurrent retraction, and repeat procedures were noted from medical records. Measures of lower eyelid height (LEH) and lid lag on downgaze were obtained from standard photographs.ResultsForty-two patients (23 females, mean age was 59 years) were included. Mean follow-up was 24 months (range 6-77). Median improvement in LEH following surgery was significant in Group 1 (0.90 mm, IQR: 0.37-0.91, P=0.20) and in Group 2 (0.51 mm, IQR: 0.30-1.37, P<0.001), respectively. Median improvement in blink lagophthalmos was 3.00 mm (IQR: 3.00-3.50, P=0.02) in Group 1 and 3.50 mm (IQR: 1.75-5.00, P<0.001) in Group 2. Median improvement in lagophthalmos on gentle eye closure was 2.00 mm (IQR: 1.50-3.00, P=0.02) in Group 1 and 1.00 mm (IQR: 0-2.13, P=0.006) in Group 2. No new cases of ectropion were noted. 23.5% of patients required a repeat RR at a mean interval of 20 (range 1-70) months and a further 9.8% required a third procedure at a mean interval of 21 (range 18-29) months.ConclusionRR improves lower eyelid retraction and lagophthalmos in FNP either alone or when combined as an adjunctive procedure. It does not aggravate paralytic ectropion although repeated retractor recessions may be required to improve retraction.

Using the Seven Bridges Cancer Genomics Cloud to Access and Analyze Petabytes of Cancer Data

Next-generation sequencing has produced petabytes of data, but accessing and analyzing these data remain challenging. Traditionally, researchers investigating public datasets like The Cancer Genome Atlas (TCGA) would download the data to a high-performance cluster, which could take several weeks even with a highly optimized network connection. The National Cancer Institute (NCI) initiated the Cancer Genomics Cloud Pilots program to provide researchers with the resources to process data with cloud computational resources. We present protocols using one of these Cloud Pilots, the Seven Bridges Cancer Genomics Cloud (CGC), to find and query public datasets, bring your own data to the CGC, analyze data using standard or custom workflows, and benchmark tools for accuracy with interactive analysis features. These protocols demonstrate that the CGC is a data-analysis ecosystem that fully empowers researchers with a variety of areas of expertise and interests to collaborate in the analysis of petabytes of data. © 2017 by John Wiley & Sons, Inc.

The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research

The Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org) enables researchers to rapidly access and collaborate on massive public cancer genomic datasets, including The Cancer Genome Atlas. It provides secure on-demand access to data, analysis tools, and computing resources. Researchers from diverse backgrounds can easily visualize, query, and explore cancer genomic datasets visually or programmatically. Data of interest can be immediately analyzed in the cloud using more than 200 preinstalled, curated bioinformatics tools and workflows. Researchers can also extend the functionality of the platform by adding their own data and tools via an intuitive software development kit. By colocalizing these resources in the cloud, the CGC enables scalable, reproducible analyses. Researchers worldwide can use the CGC to investigate key questions in cancer genomics. Cancer Res; 77(21); e3-6. ©2017 AACR.

Outcomes for severe aponeurotic ptosis using posterior approach white-line advancement ptosis surgery

PurposeThe purpose of the study was to report the outcome of posterior approach white-line advancement surgery for severe involutional aponeurotic ptosis.Patients and methodsThis was a retrospective review of an interventional case series of all patients undergoing surgery for severe involutional aponeurotic ptosis during a 42-month period at a single center. The inclusion criteria were severe involutional ptosis (upper eyelid margin reflex distance (MRD) ≤1 mm) undergoing posterior approach surgery. There was minimum 3-month follow-up. The main outcome measures were type of ptosis (primary or recurrent), preoperative margin reflex distance, levator function and eyelid skin crease height, presence of visible iris sign (VIS), documented unusual intraoperative findings, postoperative complications, and follow-up time.ResultsOf the 836 procedures for ptosis, 122 procedures (76 patients) met the inclusion criteria for this study. Mean postoperative follow-up was 28 (median 18, range 12-98) weeks. Success rates were 80.3% (98/122) overall, 81.5% (66/81) in the non-VIS group, and 78% (32/41) in the VIS group. There was no significant difference between the two groups (P=0.411). Failures were due to undercorrection, with <2 mm MRD in 75% (18/24), overcorrection with >4.5 mm MRD in 16.7% (4/24), and inter-eyelid height asymmetry of >1 mm in 8.3% (2/122).ConclusionsOutcomes of ptosis surgery for severe aponeurotic ptosis using a posterior approach white-line advancement are comparable to, and possibly better than, anterior approach in eyelids with VIS.