Pangenome graph construction from genome alignments with Minigraph-Cactus

Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.

Occupational Nerve Injuries due to Metallic Foreign Bodies: A Case Series of Eighteen Patients

Introduction

Peripheral nerve injuries (PNIs) remain an important health problem. PNIs mostly affect young men as this age group is mostly involved in road traffic accidents and other injuries at workplace. PNI can occur from foreign bodies like metal chips while working in industries using lathe machines. Among PNI's, injuries to the ulnar nerve, the brachial plexus and the median nerve are the most frequent lesions encountered.

Materials and methods

This presentation is on a series of 18 cases of nerve injuries among industrial workers located from finger level up to the arm excluding the brachial plexus due to metallic foreign bodies entering while operating lathe machines over a period of two years with patients being followed-up over a one year period.

Results

Mean age in this series was 31.3 years with age range 16-40 years and all were males. Two patients had more than one nerve involvement and one patient had associated vascular injury. All the patients showed functional improvement. Most common nerve injured was median nerve. Most common site for nerve injury was forearm. Combined lesions most commonly involved the ulnar and median nerves.

Conclusion

Social cost of traumatic peripheral nerve injuries is significant since it has a higher incidence in young, previously healthy, and economically active people.

Diagnostic performance of saliva RT-PCR test as a diagnostic tool and its utility in the detection of SARS-CoV-2 shedding with different patient characteristics: Prospective observational study

BACKGROUND

Salivary shedding of SARS-CoV-2 is a known entity and its role has been established in transmission of the disease. The present study was performed to evaluate the duration of viral shedding in saliva in COVID-19 patients and its variation among symptomatic and asymptomatic patients with or without co-morbidities.

METHODS

The present prospective observational study was conducted at the COVID-19 care hospital associated with primary to tertiary care in New Delhi, India. A total of 124 COVID-19 confirmed cases enrolled in two phases (January-March 2021; April-June 2021) who consented for 48hrly saliva and nasopharyngeal swab (NPS) specimens till discharge from the hospital for SARS-CoV-2 detection were included. The specimens obtained were tested for SARS-CoV-2 by Real-Time PCR.

RESULTS

The sensitivity and the specificity of RT-PCR on saliva were 81.7 ​% and 85.0 ​%, respectively. The sensitivity of saliva-based PCR was comparable in symptomatic and asymptomatic patients (81.6 ​% vs 82.1 ​%). The sensitivity of saliva-based PCR markedly increased in the second phase of enrollment as compared to the first phase (92.6 ​% vs 78.5 ​%) indicating higher level of salivary shedding by the delta variant of SARS-CoV-2. The sensitivity of PCR on saliva was the highest up to day seven of illness. The median duration of RNA shedding in saliva was comparable among the symptomatic and asymptomatic patients. The severity of the disease was not associated with the duration of SARS-CoV-2 shedding in saliva.

CONCLUSIONS

SARS-CoV-2 shedding in saliva continued till seven days in large number of patients including asymptomatic patients. Saliva is non-inferior to NPS specimen in the diagnosis of SARS-CoV-2. Saliva specimen is recommended as a good alternate to NPS for SARS-CoV-2 testing.

Generation of map on natural environmental background absorbed dose rate in India

A systematic mapping of natural absorbed dose rate was carried out to assess the existing exposure situation in India. The mammoth nationwide survey covered the entire terrestrial region of the country comprising of 45127 sampling grids (grid size 36 km²) with more than 100,000 data points. The data was processed using Geographic Information System. This study is based on established national and international approaches to provide linkage with conventional geochemical mapping of soil. Majority (93%) of the absorbed dose rate data was collected using handheld radiation survey meters and remaining were measured using environmental Thermo Luminescent Dosimeters. The mean absorbed dose rate of the entire country including several mineralized regions, was found to be 96 ± 21 nGy/h. The median, Geometric Mean and Geometric Standard Deviation values of absorbed dose rate were 94, 94 and 1.2 nGy/h, respectively. Among the High Background Radiation Areas of the country, absorbed dose rate varied from 700 to 9562 nGy/h in Karunagappally area of Kollam district, Kerala. The absorbed dose rate in the present nationwide study is comparable with the global database.

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Cohort profile: the ESC EURObservational Research Programme Non-ST-segment elevation myocardial infraction (NSTEMI) Registry

AIMS

The European Society of Cardiology (ESC) EURObservational Research Programme (EORP) Non-ST-segment elevation myocardial infarction (NSTEMI) Registry aims to identify international patterns in NSTEMI management in clinical practice and outcomes against the 2015 ESC Guidelines for the management of acute coronary syndromes in patients presenting without ST-segment-elevation.

METHODS AND RESULTS

Consecutively hospitalised adult NSTEMI patients (n = 3620) were enrolled between 11 March 2019 and 6 March 2021, and individual patient data prospectively collected at 287 centres in 59 participating countries during a two-week enrolment period per centre. The registry collected data relating to baseline characteristics, major outcomes (in-hospital death, acute heart failure, cardiogenic shock, bleeding, stroke/transient ischaemic attack, and 30-day mortality) and guideline-recommended NSTEMI care interventions: electrocardiogram pre- or in-hospital, pre-hospitalization receipt of aspirin, echocardiography, coronary angiography, referral to cardiac rehabilitation, smoking cessation advice, dietary advice, and prescription on discharge of aspirin, P2Y12 inhibition, angiotensin converting enzyme inhibitor (ACEi)/angiotensin receptor blocker (ARB), beta-blocker, and statin.

CONCLUSION

The EORP NSTEMI Registry is an international, prospective registry of care and outcomes of patients treated for NSTEMI, which will provide unique insights into the contemporary management of hospitalised NSTEMI patients, compliance with ESC 2015 NSTEMI Guidelines, and identify potential barriers to optimal management of this common clinical presentation associated with significant morbidity and mortality.

Semi-automated assembly of high-quality diploid human reference genomes

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Impact of bifurcation lesion on 10-year mortality in the SYNTAX trial

Background

Percutaneous coronary intervention (PCI) of bifurcation lesions is associated with higher rates of adverse events, and currently it is unclear whether PCI or coronary artery bypass grafting (CABG) is the safer treatment for these patients at very long-term follow up.

Objectives

To investigate the impact of bifurcation lesions on observed all-cause 10-year mortality in the SYNTAX trial.

Methods

In the SYNTAX Extended Survival study, 10-year observed mortality was compared among four groups: (a) presence of ≥1 bifurcation lesion and treatment with PCI (n=649), (b) no bifurcation lesion and treatment with PCI (n=248), (c) presence of ≥1 bifurcation lesion and treatment with CABG (n=651), and (d) no bifurcation lesion and treatment with CABG (n=239).

Results

Compared to patients without bifurcations, those with bifurcation lesion(s) treated with PCI had a significantly higher risk of all-cause death (19.8% vs 30.1%; HR: 1.55, 95% CI: 1.12 to 2.14; p=0.007), whereas following CABG, mortality was similar in patients with or without bifurcation lesion(s) (23.3% vs 23.0%; HR: 0.81, 95% CI: 0.59 to 1.12; p=0.207). (Figure1) There was a significant interaction between bifurcation lesion(s) and treatment arm (p for interaction=0.006).

In PCI patients, at 5-years there was no significant difference in mortality between 1- vs 2-stent techniques, whereas at 10-years, a 2-stent technique was associated with higher mortality (33.3% vs 25.9%; HR: 1.51, 95% CI: 1.06 to 2.14; p=0.021, Figure2).

Conclusions

Bifurcation lesion(s) require special attention from the heart team discussion, considering the higher 10-year all-cause mortality associated with PCI. Careful evaluation of bifurcation lesion complexity may be helpful in decision-making.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): The SYNTAX Extended Survival study was supported by the German Foundation of Heart Research (Frankfurt am Main, Germany). The SYNTAX trial, during 0-5 years follow-up, was funded by Boston Scientific Corporation (Marlborough, MA, USA). Both sponsors had no role in the study design, data collection, data analyses, and interpretation of the study data, nor were involved in the decision to publish the final manuscript. The principal investigators and authors had complete scientific freedom.

Ten years survival benefit of CABG or PCI based on individual prediction

Background

To compare the observed and individual predicted mortalities according to the SYNTAX score II 2020 (SSII-2020) in the all-comers SYNTAX population, and retrospectively assess the appropriateness of revascularization with percutaneous coronary intervention (PCI) and coronary artery bypass grafting (CABG) in patients with three vessel disease (3VD) and/or left main disease (LMCAD).

Methods

Internal and external validation of the SSII-2020 to predict 10-year all-cause death was performed in the respective randomized and registry SYNTAX populations. Differences in individual predicted mortalities following CABG or PCI were ranked and displayed with the observed mortalities. The proportions of screened patients deriving a survival benefit from CABG or PCI were determined retrospectively.

Results

A total of 2602 participants (as-treated population) were included in the randomized and registry cohorts. In the randomized cohort, all-cause mortality at 10 years, as an average treatment effect, was 23.8% (199/865) with CABG and 28.6% (249/901) with PCI, with a differential survival benefit of 4.6% (95% CI: 0.58% to 8.7%, log-rank p value=0.023). In the CABG and PCI registries, mortalities were 27.8% (167/644) and 55.4% (99/192), respectively. Calibration and discrimination of the SSII-2020 was helpful in CABG and PCI patients in the randomized and registry cohorts. In the PCI registry, the SSII-2020 underestimated mortality since specific comorbidities that entail high mortality are not included in the formula (C-index: 0.72, intercept: 0.38, slope: 0.66), whilst in the CABG registry, it predicted mortality with a helpful calibration and discrimination (C-index: 0.70, intercept: 0.00, slope: 0.76). The proportions of patients with a predicted survival benefit following CABG and PCI were respectively 78.3% (1383/1766) and 21.7% (383/1766) in the randomized cohort, and 82.4% (2143/2602) and 17.7% (459/2602) in the whole SYNTAX trial population.

Conclusion

In the randomized and registry cohort of this all-comers population with 3VD and/or LMCAD, there was reasonable agreement between the individual predicted and observed mortalities after CABG or PCI, such that the predicted 10-year survival benefit might be helpful in determining the appropriateness of each modality of revascularization.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): The SYNTAX Extended Survival study was supported by the German Foundation of Heart Research (Frankfurt am Main, Germany). The SYNTAX trial, during 0-5 years follow-up, was funded by Boston Scientific Corporation (Marlborough, MA, USA). Both sponsors had no role in the study design, data collection, data analyses, and interpretation of the study data, nor were involved in the decision to publish the final manuscript. The principal investigators and authors had complete scientific freedom.

Quantitative angiographic assessment of aortic regurgitation post 11 different types of TAVI devices a multicentre pooled analysis of 2665 valves

Background

Regurgitation following TAVR impacts all-cause mortality. So far, no quantitative comparison of regurgitation by the same core lab has been performed among the various commercially available transcatheter heart valves (THV) We aimed to compare quantitative angiographic aortic regurgitation (AR) of 11 different types of THVs.

Method

This is a multicentre retrospective corelab pooled analysis of aortograms from 2704 consecutive patients treated with 11 different THV devices. Analysis was done by quantitative videodensitometric aortography (LVOT-AR), which is an objective, accurate, and reproducible tool for assessment of AR following TAVR. This method relies on time density changes in contrast medium after injection in the ascending aorta and its regurgitation (and subsequent density increase) in the LVOT. The ratio between the areas under the two-time density curves of these regions quantifies the AR in absolute percentage. The valves evaluated include ACURATE neo2 (n=120), Lotus (n=546), Myval (n=108), VitaFlow (n=105), Evolut PRO (n=95), SAPIEN 3 (n=397), Evolut R (n=295), SAPIEN XT (n=239), ACURATE neo (n=120), Venus-A (n=113) and CoreValve (n=532). Stratification of continuous variable regurgitation into categorical variables was performed according to the following pre-determined threshold criteria: 1) none/trace regurgitation (LVOT-AR<6%); 2) mild (6%≤ LVOT-AR ≤17%); and 3) moderate or severe (LVOT-AR >17%).

Results

The addition of anti PVR sealing features to the new generations ACURATE neo2 THV proved to be effective in reduction the incidence of significant PVR In comparison with the first generation ACURATE neo.

Myval, VitaFlow and Venus-A THVs are showing promising results.

Although the incidence of moderate/severe AR has regressed over time with new generations of THVs, the incidence of mild AR is still prominent with all THVs still exhibiting mild AR with an incidence ranging between 30% and 50% with the exception of the Lotus valve that had an 19% incidence of mild AR

Conclusion

ACURATE neo2 had the lowest severe/moderate percentage of AR showing significant improvements in comparison to ACURATE neo. Myval, VitaFlow and Venus-A are promising options in the THV armamentarium. These results should be confirmed in prospective randomized, head-to-head comparisons between THVs.

Funding Acknowledgement

Type of funding sources: None.

Abstract P1117: Transcriptional Changes In Failing Hearts In A South Asian Cohort Capture Molecular Pathophysiology Underlying Maladaptive Remodelling And Reflect A Consistent Disease Gene Signature

Heart failure (HF) is a leading cause of death worldwide and research focused on human cardiac tissue provides insights into underlying disease mechanisms. In this study, we performed transcriptome analyses on cardiac tissue from 21 South Asian (SA) HF patients and compared them with 21 controls without HF. The aim was to i) probe dysregulated genes and pathways in HF and ii) identify a core HF gene signature conserved across etiologies and ethnicities. Gene set enrichment analyses on dysregulated genes (DGs) showed positive enrichment of Gene Ontology terms for ECM remodelling, immune signalling and negative enrichment of terms like cardiac conduction, muscle contraction reflecting altered molecular signalling and cellular cross-talk in failing hearts. The immune cell signatures among the DGs suggest changes in immune milieu which correlates with altered immune signalling pathways. Although poor concordance in DGs across studies on HF transcriptome is well documented, evidence on stratification potential of select DGs is still preliminary. Using an independent component analysis and a machine learning based workflow, we identified gene signatures from two cohorts (SA, GSE116250) independently. We refined these into a core signature after cross validating their stratification potential and by removing the genes with low potential. The core signature effectively separated HF from control samples in SA, GSE116250 and other cohorts potentially reflecting central elements underlying end stage HF. In summary, the transcriptome analyses from SA HF cohort highlights the pathways reflecting HF pathophysiology and reiterates conserved themes across public HF cohorts.

Epidemiology and impact of frailty in patients with atrial fibrillation in Europe

BACKGROUND

Frailty is a medical syndrome characterised by reduced physiological reserve and increased vulnerability to stressors. Data regarding the relationship between frailty and atrial fibrillation (AF) are still inconsistent.

OBJECTIVES

We aim to perform a comprehensive evaluation of frailty in a large European cohort of AF patients.

METHODS

A 40-item frailty index (FI) was built according to the accumulation of deficits model in the AF patients enrolled in the ESC-EHRA EORP-AF General Long-Term Registry. Association of baseline characteristics, clinical management, quality of life, healthcare resources use and risk of outcomes with frailty was examined.

RESULTS

Among 10,177 patients [mean age (standard deviation) 69.0 (11.4) years, 4,103 (40.3%) females], 6,066 (59.6%) were pre-frail and 2,172 (21.3%) were frail, whereas only 1,939 (19.1%) were considered robust. Baseline thromboembolic and bleeding risks were independently associated with increasing FI. Frail patients with AF were less likely to be treated with oral anticoagulants (OACs) (odds ratio 0.70, 95% confidence interval 0.55-0.89), especially with non-vitamin K antagonist OACs and managed with a rhythm control strategy, compared with robust patients. Increasing frailty was associated with a higher risk for all outcomes examined, with a non-linear exponential relationship. The use of OAC was associated with a lower risk of outcomes, except in patients with very/extremely high frailty.

CONCLUSIONS

In this large cohort of AF patients, there was a high burden of frailty, influencing clinical management and risk of adverse outcomes. The clinical benefit of OAC is maintained in patients with high frailty, but not in very high/extremely frail ones.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Residual ctDNA after treatment predicts early relapse in patients with early-stage non-small cell lung cancer

BACKGROUND

Identification of residual disease in patients with localized non-small cell lung cancer (NSCLC) following treatment with curative intent holds promise to identify patients at risk of relapse. New methods can detect circulating tumour DNA (ctDNA) in plasma to fractional concentrations as low as a few parts per million, and clinical evidence is required to inform their use.

PATIENTS AND METHODS

We analyzed 363 serial plasma samples from 88 patients with early-stage NSCLC (48.9%/28.4%/22.7% at stage I/II/III), predominantly adenocarcinomas (62.5%), treated with curative intent by surgery (n = 61), surgery and adjuvant chemotherapy/radiotherapy (n = 8), or chemoradiotherapy (n = 19). Tumour exome sequencing identified somatic mutations and plasma was analyzed using patient-specific RaDaR™ assays with up to 48 amplicons targeting tumour-specific variants unique to each patient.

RESULTS

ctDNA was detected before treatment in 24%, 77% and 87% of patients with stage I, II and III disease, respectively, and in 26% of all longitudinal samples. The median tumour fraction detected was 0.042%, with 63% of samples <0.1% and 36% of samples <0.01%. ctDNA detection had clinical specificity >98.5% and preceded clinical detection of recurrence of the primary tumour by a median of 212.5 days. ctDNA was detected after treatment in 18/28 (64.3%) of patients who had clinical recurrence of their primary tumour. Detection within the landmark timepoint 2 weeks to 4 months after treatment end occurred in 17% of patients, and was associated with shorter recurrence-free survival [hazard ratio (HR): 14.8, P <0.00001] and overall survival (HR: 5.48, P <0.0003). ctDNA was detected 1-3 days after surgery in 25% of patients yet was not associated with disease recurrence. Detection before treatment was associated with shorter overall survival and recurrence-free survival (HR: 2.97 and 3.14, P values 0.01 and 0.003, respectively).

CONCLUSIONS

ctDNA detection after initial treatment of patients with early-stage NSCLC using sensitive patient-specific assays has potential to identify patients who may benefit from further therapeutic intervention.

First Direct Detection Constraints on Planck-Scale Mass Dark Matter with Multiple-Scatter Signatures Using the DEAP-3600 Detector

Dark matter with Planck-scale mass (≃10^{19}  GeV/c^{2}) arises in well-motivated theories and could be produced by several cosmological mechanisms. A search for multiscatter signals from supermassive dark matter was performed with a blind analysis of data collected over a 813 d live time with DEAP-3600, a 3.3 t single-phase liquid argon-based detector at SNOLAB. No candidate signals were observed, leading to the first direct detection constraints on Planck-scale mass dark matter. Leading limits constrain dark matter masses between 8.3×10^{6} and 1.2×10^{19}  GeV/c^{2}, and ^{40}Ar-scattering cross sections between 1.0×10^{-23} and 2.4×10^{-18}  cm^{2}. These results are interpreted as constraints on composite dark matter models with two different nucleon-to-nuclear cross section scalings.

Correlation of Nuclear Morphometry with Clinicopathologic Parameters in Malignant Breast Aspirates

Background Nuclear size, shape, chromatin pattern, and nucleolar size and number have all been reported to change in breast cancer.

Aim The aim of the study was to quantify nuclear changes on malignant breast aspirates using morphometry and to correlate the morphometric parameters with clinicopathologic features such as cytologic grade, tumor size, lymph node status, mitotic index, and histopathologic grade.

Materials and Methods Forty-five cases of carcinoma breast diagnosed on cytology were included in this study. Cytologic grading was performed as per the Robinson’s cytologic grading system. Nuclear morphometry was done on Papanicolaou stained smears. One hundred nonoverlapping cells per case were evaluated. Both geometrical and textural parameters were evaluated.

Results Comparison of cytologic grades with most morphometric features (nuclear area, perimeter, shape, long axis, short axis, intensity, total run length, and TI homogeneity) was highly significant on statistical analysis. Correlation with tumor size yielded significant results for nuclear area, perimeter, long and short axes, and intensity with p < 0.05. The study of lymph node status and morphometry showed a highly significant statistical association with all the parameters. Mitotic count was significantly associated with all the geometric parameters and one textural parameter (total run length). On correlation of ductal carcinoma in situ and histopathological Grades 1 to 3 with morphometry, it was found that all the parameters except long–run emphasis were highly significant with p < 0.001.

Conclusion Morphometry as a technique holds immense promise in prognostication in breast carcinoma.

Long-term prediction of mortality and comparative treatment benefit following percutaneous or surgical revascularization

Background

The SYNTAX score II 2020 (SSII-2020), which was derived and externally validated from randomized trials, was designed to predict death following percutaneous coronary intervention (PCI) and coronary artery bypass grafting (CABG) in patients with three-vessel disease and/or left main disease. We aimed to investigate its value in identifying the safest modality of revascularization in a non-randomized setting.

Methods

Five-year mortality was assessed in 7362 patients with three-vessel disease and/or left main disease enrolled in a Japanese PCI/CABG registry. New-generation drug eluting stents and imaging guidance became the default PCI strategy during enrolment of the last cohort. The discriminative ability of the SSII-2020 for 5-year mortality was assessed using Harrell's C statistic (C-index). Agreement between observed and predicted rates of all-cause mortality following either PCI or CABG and treatment benefit (absolute risk difference) for this outcome were assessed by calibration plots.

Results

The SSII-2020 had helpful discrimination (C-index = 0.72) and good calibration (intercept = −0.11, slope = 0.92) for 5-year mortality. The absolute risk difference in mortality between CABG and PCI (treatment benefit) was well calibrated when the whole population was grouped into quarters according to the predicted absolute risk difference of 5-year mortality. The observed differences in survival in favor of CABG were 4.2% (0.1 to 8.2%, log-rank p=0.05) and 8.5% (3.8 to 13.2%, log-rank p&lt;0.01) in the respective third and fourth quarters. In contrast, the observed differences in survival were not significantly different in either the first (3.0% [−0.8 to 6.8%, log-rank p=0.12]) or the second quarter (1.3% [−2.4 to 5.1%, log-rank p=0.39]).

Conclusions

The SSII-2020 is well able to predict death at 5 years – and the mortality difference between PCI and CABG, and therefore has the potential to support decision making on revascularization in patients with three-vessel disease and/or left main coronary artery disease.

Funding Acknowledgement

Type of funding sources: None.

Correlation of Nuclear Morphometry with Clinicopathologic Parameters in Malignant Breast Aspirates

Objectives The primary objective of this study was to correlate nuclear morphometric parameters with clinicopathologic features such as cytologic grade, tumor size, lymph node status, mitotic index, and histopathologic grade. Secondary objective was to quantify nuclear changes on malignant breast aspirates using morphometry. Material and Methods Forty-five cases of carcinoma breast diagnosed on cytology were included in this study. These were graded into cytologic grades 1, 2, and 3 as per Robinson's cytologic grading system. Nuclear morphometry was done in all cases on smears stained with Papanicolaou stain. Clinicopathologic parameters including cytological grade, tumor size, lymph node status, mitotic count, and histological grade were correlated with nuclear morphometric parameters, namely, area, perimeter, shape, long axis, short axis, intensity, long-run emphasis, total run length, and T1 homogeneity. Results There were 9 cases in cytologic grade 1, 26 in grade 2, and 10 cases in cytologic grade 3. Histopathology showed 42 cases of infiltrating duct carcinoma, not otherwise specified (IDC, NOS) and 3 cases (6.7%) of ductal carcinoma in situ (DCIS). IDC (NOS) included 6, 27, and 9 cases in grades 1, 2, and 3, respectively. Majority of our cases had a tumor size less than 5 cm ( n = 38, 84.4%) and had positive nodes ( n = 30, 66.7%). Correlation of cytologic and histopathologic grades (including DCIS) with all morphometric features except long-run emphasis was statistically significant. Correlation of morphometry with tumor size yielded significant results for nuclear area, perimeter, long and short axes, and intensity with p < 0.05. Study of lymph node status (positive/negative) versus morphometry showed a highly significant statistical association with all the geometric as well as textural parameters. Mitotic count was significantly associated with all the geometric parameters and one textural parameter (total run length). Statistics Continuous variables were presented as mean ± standard deviation and compared using the two-tailed, independent sample t -test and one-way analysis of variance test. Tests were performed at significance level of 0.05. Conclusion Morphometry is an objective technique which holds immense promise in prognostication in breast carcinoma.

Pulse-shape discrimination against low-energy Ar-39 beta decays in liquid argon with 4.5 tonne-years of DEAP-3600 data

The DEAP-3600 detector searches for the scintillation signal from dark matter particles scattering on a 3.3 tonne liquid argon target. The largest background comes from 39 Ar beta decays and is suppressed using pulse-shape discrimination (PSD). We use two types of PSD estimator: the prompt-fraction, which considers the fraction of the scintillation signal in a narrow and a wide time window around the event peak, and the log-likelihood-ratio, which compares the observed photon arrival times to a signal and a background model. We furthermore use two algorithms to determine the number of photons detected at a given time: (1) simply dividing the charge of each PMT pulse by the mean single-photoelectron charge, and (2) a likelihood analysis that considers the probability to detect a certain number of photons at a given time, based on a model for the scintillation pulse shape and for afterpulsing in the light detectors. The prompt-fraction performs approximately as well as the log-likelihood-ratio PSD algorithm if the photon detection times are not biased by detector effects. We explain this result using a model for the information carried by scintillation photons as a function of the time when they are detected.

C-reactive protein (CRP) and Erythrocyte Sedimentation Rate (ESR) Trends following Total Hip and Knee Arthroplasties in an Indian Population - A Prospective Study

INTRODUCTION

To evaluate the trends of C-reactive protein (CRP) and Erythrocyte sedimentation rate (ESR) in the first three weeks after uncomplicated total hip (THR) and total knee (TKR) arthroplasty/replacement in the Indian population and to compare it with available literature.

MATERIALS AND METHODS

A total of 90 patients were enrolled for this prospective study, of which 30 were unilateral THR, 30 were unilateral TKR (U/L TKR) and 30 were simultaneous bilateral TKR (B/L TKR). Serum CRP and ESR were measured on the day before surgery and post-operatively on day 1st, 2nd, 3rd, 7th, 12th, and at the end of 3rd week.

RESULTS

CRP showed a peak at day 2nd with normalisation to pre-operative value by the end of 3rd week. While ESR showed a peak on day 3rd and continued to remain elevated even at end of 3rd week post-operatively. Both mean CRP and ESR values were higher in THR patients followed by in B/L TKR and then in U/L TKR patients.

CONCLUSION

CRP persists to be the best acute phase reactant in the early post-operative phase with a relatively typical pattern as compared to ESR. CRP values peak at post-operative day 2nd and then show a gradual decline. However, its normalisation to pre-operative baseline values may vary among different groups of population.

Computational methods for chromosome-scale haplotype reconstruction

High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.

Chromosome-scale, haplotype-resolved assembly of human genomes

Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for phased assembly either do not generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method named diploid assembly (DipAsm) that uses long, accurate reads and long-range conformation data for single individuals to generate a chromosome-scale phased assembly within 1 day. Applied to four public human genomes, PGP1, HG002, NA12878 and HG00733, DipAsm produced haplotype-resolved assemblies with minimum contig length needed to cover 50% of the known genome (NG50) up to 25 Mb and phased ~99.5% of heterozygous sites at 98–99% accuracy, outperforming other approaches in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies for the discovery of structural variants (SVs), including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as the human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) regions. DipAsm will facilitate high-quality precision medicine and studies of individual haplotype variation and population diversity.

Assembly of phased human genomes is achieved by combining long reads and long-range conformational data.

A haplotype-aware de novo assembly of related individuals using pedigree sequence graph

MOTIVATION

Reconstructing high-quality haplotype-resolved assemblies for related individuals has important applications in Mendelian diseases and population genomics. Through major genomics sequencing efforts such as the Personal Genome Project, the Vertebrate Genome Project (VGP) and the Genome in a Bottle project (GIAB), a variety of sequencing datasets from trios of diploid genomes are becoming available. Current trio assembly approaches are not designed to incorporate long- and short-read data from mother-father-child trios, and therefore require relatively high coverages of costly long-read data to produce high-quality assemblies. Thus, building a trio-aware assembler capable of producing accurate and chromosomal-scale diploid genomes of all individuals in a pedigree, while being cost-effective in terms of sequencing costs, is a pressing need of the genomics community.

RESULTS

We present a novel pedigree sequence graph based approach to diploid assembly using accurate Illumina data and long-read Pacific Biosciences (PacBio) data from all related individuals, thereby generalizing our previous work on single individuals. We demonstrate the effectiveness of our pedigree approach on a simulated trio of pseudo-diploid yeast genomes with different heterozygosity rates, and real data from human chromosome. We show that we require as little as 30× coverage Illumina data and 15× PacBio data from each individual in a trio to generate chromosomal-scale phased assemblies. Additionally, we show that we can detect and phase variants from generated phased assemblies.

AVAILABILITY AND IMPLEMENTATION

https://github.com/shilpagarg/WHdenovo.

A diploid assembly-based benchmark for variants in the major histocompatibility complex

Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - the Major Histocompatibility Complex (MHC). Here, we develop a human genome benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle sample HG002. We assemble a single contig for each haplotype, align them to the reference, call phased small and structural variants, and define a small variant benchmark for the MHC, covering 94% of the MHC and 22368 variants smaller than 50 bp, 49% more variants than a mapping-based benchmark. This benchmark reliably identifies errors in mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks.

Enabling large-scale genome editing at repetitive elements by reducing DNA nicking

To extend the frontier of genome editing and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks and single-strand breaks. We used a set of gRNAs targeting repetitive elements-ranging in target copy number from about 32 to 161 000 per cell. dBEs enabled survival after large-scale base editing, allowing targeted mutations at up to ∼13 200 and ∼12 200 loci in 293T and human induced pluripotent stem cells (hiPSCs), respectively, three orders of magnitude greater than previously recorded. These dBEs can overcome current on-target mutation and toxicity barriers that prevent cell survival after large-scale genome engineering.

Systems approach for assessment of maternal deaths in Rajasthan: A feasibility study

Background

High maternal mortality in the state like Rajasthan, which is at second rank in terms of high Maternal Mortality Ratio (MMR) in India, require concentrated efforts in this direction The objectives of this study were to assess the magnitude and trend of maternal death and underlying factors contributing to maternal deaths in Rajasthan and to identify barriers and challenges in reporting maternal deaths in Rajasthan.

Methods

Data related to maternal deaths, cause of deaths and live births were retrieved from official Government sources and MMR was calculated. To find out the underlying factors contributing to maternal deaths, Verbal Autopsies were conducted through household surveys. In-depth interviews of health care staff were conducted to carry out the 'SWOT' analysis in order to identify the barriers in reporting maternal deaths. Data was analysed using SPSS version 23.

Results

A total of 7185 maternal deaths were reported from Rajasthan in last five years. The mean age of mothers was 25.18±4.98 years. Haemorrhage were reported as most common cause of maternal death (17%) followed by Severe hypertension or fits (8%) and obstructed labour (2%). The median duration of hospital stay was 23 hours (IQR=7.5-70). Maximum deaths were reported during post-partum period (61%), while around one fourth of the deaths happened during delivery.

Conclusions

The discrepancies were observed in the reporting of number and causes of maternal deaths. The trend and forecasted figures were quite different from the published National and State level reports in this regard.

Key messages

need to streamline and strengthen the Maternal Deaths Surveillance and Response to track the number of deaths and get the exact information about the underlying factors contributing to them. Effective strategies can be developed to reduce the Maternal Deaths in the State.

Linking language features to clinical symptoms and multimodal imaging in individuals at clinical high risk for psychosis

BACKGROUND

Abnormalities in the semantic and syntactic organization of speech have been reported in individuals at clinical high-risk (CHR) for psychosis. The current study seeks to examine whether such abnormalities are associated with changes in brain structure and functional connectivity in CHR individuals.

METHODS

Automated natural language processing analysis was applied to speech samples obtained from 46 CHR and 22 healthy individuals. Brain structural and resting-state functional imaging data were also acquired from all participants. Sparse canonical correlation analysis (sCCA) was used to ascertain patterns of covariation between linguistic features, clinical symptoms, and measures of brain morphometry and functional connectivity related to the language network.

RESULTS

In CHR individuals, we found a significant mode of covariation between linguistic and clinical features (r = 0.73; p = 0.003), with negative symptoms and bizarre thinking covarying mostly with measures of syntactic complexity. In the entire sample, separate sCCAs identified a single mode of covariation linking linguistic features with brain morphometry (r = 0.65; p = 0.05) and resting-state network connectivity (r = 0.63; p = 0.01). In both models, semantic and syntactic features covaried with brain structural and functional connectivity measures of the language network. However, the contribution of diagnosis to both models was negligible.

CONCLUSIONS

Syntactic complexity appeared sensitive to prodromal symptoms in CHR individuals while the patterns of brain-language covariation seemed preserved. Further studies in larger samples are required to establish the reproducibility of these findings.

SAT0645-HPR MYTHS AND MISCONCEPTION ABOUT THE ILLNESS AND CONVENTIONAL SYNTHETIC DMARDS (CSDMARDS) IN PATIENTS WITH SYSTEMIC IMMUNO-INFLAMMATORY RHEUMATIC DISEASES (SIRDS): A STUDY BY RHEUMATOLOGY NURSE COUNSELOR

Background:

Myths and misconceptions about illness and conventional disease modifying anti-rheumatic drugs directly influence adherence to the prescribed treatment. It is estimated that 30–50% of patients do not adhere to their prescribed treatment due to various reasons where the beliefs of the patients play a crucial role. At our centre we the specialist rheumatology nurse counsel the patients at every visit and try to remove their myths and negative beliefs about the disease as well as the medications.

Objectives:

•To explore the common myths and misconceptions of regarding their disease and regarding the csDMARDs.

•To assess the efficacy of counseling in allaying their unfounded fear.

Methods:

A total of 450 patients with SIRDs at least 3 times attended the rheumatology out-patient clinic on csDMARDs were enrolled to complete a questionnaire that, besides demographic information, socio-economic status, and co- morbidities, had the following questions:

1.Self reported adherence to medication

2.Misbelieves regarding food items

3.What kind of health-provider was consulted at the onset of the symptoms

4.Their belief/knowledge regarding:

A. The need for physiotherapy.

B. Life style modification requirement

C. About osteoarthritis

D. Medication requirement during remission

E. Pregnancy and DMARDs

F. The need of vaccination

G. Health hazards of smoking and alcohol use

H. Harms of discontinuing treatment when they felt well

Results:

A total of 450 patients included spondyloarthropathy 150(34%), rheumatoid arthritis 200(45.7%), psoriatic arthritis 45(10%), and others 25(5.5%).The following observations was made:

1.Self-reported adherence to medication was in 250 (55%) patients; 200(45%) patient were non-adherent to treatment

2.382/450 (85%) patients had misbelieves regarding different food items.

3.225/450(50)% of the patients were not doing regular physiotherapy they were totally dependent on medications for symptoms relief.

4.387/450 (86%) patients confused the symptoms of osteoarthritis with that of RA.

5.315/450 (70 %) patients did not feel the requirement of continuing drugs during remission.

6.135/450 (30%) patients believed that while on DMARDs they cannot contemplate pregnancy.

7.351/450(78%) patients accept the need for vaccination when staring DMARDs

8.360/450 (80%) patients aware about side effect of smoking in disease but only 40 % were able to quit.

9.273/450 (60%) patients felt that more expensive medicines e.g.bDMARDs have more effects.

10.360/450 (80%) patients believed that DMARDs were ‘steroids’ and they increased weight. On analysis one patient have more than two myths simultaneously.

Conclusion:

Increased awareness of the patient’s beliefs about medicines is needed among health care providers. We should encourage patients to express their views about medicines as well as disease in order to optimize and personalize the information process. This can stimulate concordance and adherence to medication and follow up.These myths are deeply rooted in our society, single sitting counseling is not enough, and reinforcement is needed.

References:

[1]Tom Greenhalgh. Facts about rheumatoid arthritis: 7 myths you may encounter. Rheumatology Advisor. March 28, 2019.

Acknowledgments:

no

Disclosure of Interests:

None declared

SAT0644-HPR COMPLIANCE OF BIOLOGIC DISEASES MODIFYING ANTI-RHEUMATIC DRUGS (BDMARDS) WITH SYSTEMIC IMMUNO-INFLAMMATORY RHEUMATIC DISEASES (SIRDS). AN ASSESSMENT OF PATIENTS’ ADHERENCE AND NON- ADHERENCE CONCERNS

Background:

Patients with systemic immunoinflammatory rheumatic diseases (SIRDs) are often treated with bDMARDs when the response to conventional disease-modifying antirheumatic drugs (csDMARDs) is inadequate.There are, however, concerns about non-adherence to bDMARDs among patient. The non-adherence to bDMARDs may be caused by the various factors.

Objectives:

1.The main objective of present study was to find out the cause of discontinuation of bDMARDs

2.To find out the adherence and non-adherence rate for bDMARDs.

3.To identify the factors that are modifiable.

Methods:

800patients with SIRDs prescribed bDMARDs were interviewed to find out the demographic information, their socioeconomic status,and the disease duration.Additional information gathered included the comorbidities, the time for starting bDMARDs, the route of administration of bDMARDs, beliefs and perceptions about treatment efficacy and side effects if any.This was followed by looking at the adherence of bDMARDs; if they had discontinued then efforts was made to find out the reasons for the same.

Based on these findings the patients were classified into adherent and non-adherent categories. The data were analyzed further for

1.Factors that associated with persistence of bDMARDs.

2.Factors that were associated with discontinuation of bDMARDs.

Results:

A total of 800 patients were interviewed that included patients with ankylosing spondylitis 430(52.4%), rheumatoid arthritis 300(37.7%), psoriatic arthritis 45(5.2%), and others 25 (0.7%).On analysis 610(76%) patient were compliant but 190(24%) patient had discontinued the bDMARDs on their own. On comparison of both groups

Factors that were significantly related to self-discontinuation were:

•Negative beliefs about biologics (37%)

•Cost (33%)

•Reading side-effect profile on Google search (25%)

•Other co-morbidities (6%)

Factors that were significantly related to persistence of biologic treatment were:

•Good counseling by rheumatologist and rheumatology nurse (60%)

•Faith in the treating rheumatologist (25%)

•Fear of deformities and pain(15%)

On analysis it was found that a good counseling and clarifying the doubts of the patients regarding bDMARDs before starting the treatment encourages the patient to continue the biologic treatment, especially it allays their doubts about the drug adverse effects.

Conclusion:

Despite negative beliefs and misconceptions about bDMARDs, patient non-adherence at our center is not alarming.A positive reinforcement counseling appears to be the most significant factor to overcome the negative belief of patients.The affordability of the biologic treatment however remains a limiting factor in our centre as in other parts of India.

References:

[1]Tamas Koncz,MD,Marta,Pentek,Valentin,Brodszky,Katalin Ersek,MSc,Ewaorlewska&Laszlo Gulasi Volume10,2010 –Issue9 Adherence to biologic DMARD therapies in rheumatoid arthritis

Acknowledgments:

no

Disclosure of Interests:

None declared

FRI0601-HPR IMPACT OF LIFE STYLE MODIFICATION TECHNIQUE IN SYSTEMIC SCLEROSIS (SSC) PATIENTS: A STUDY BY RHEUMATOLOGY NURSES COUNSELOR

Background:

Systemic sclerosis (SSc) is an autoimmune the disease of the connective tissue that is clinically characterized by the involvement of skin (fibrosis, contractures of the finger joints), microvascular abnormalities (Raynaud’s phenomenon and complications), gastrointestinal involvement (gastroesophageal reflux disease - GERD, the lower GI tract involvement), musculoskeletal involvement (polyarthralgia, muscle disease), and involvement of internal organs (especially lungs, heart, and kidneys). Lifestyle modification techniques could have significant impact on various aspects of the disease including early disease control, increased drug adherence, positive attitude towards life, decreased financial burden of treatment, maintaining mobility and joints range of motion, minimizing or delaying joint contractures and decreased dependency with regular physical therapy. Counselling explaining the benefits of lifestyle modification related to these aspects of daily living may make a major difference in the quality of life of the patients with SSc.

Objectives:

To assess the benefits of lifestyle modification technique in improving the quality of life in patients with SSc.

Methods:

Patients with SSc attending the Rheumatology clinic of this institution, willing to participate in the survey, were enrolled in this study. All the information including the follow-up details were recorded in a pre-designed form. Their demographic information (age, gender) and disease characteristics (diagnosis, duration, treatment) were recorded, All the patients were explained the lifestyle modifications and their benefits, reinforced at each follow-up visit using posters (visual), written lifestyle modification techniques (using printed material) to raise their awareness of how to improve several of the above manifestations of SSc.

Results:

One hundred fifty (n=150) consecutive SSc patients were included in the study. It was observed that with repeated counselling 125 (83.3 %) patients adopted the lifestyle modification technique according to the advice imparted and felt a positive benefit in their daily life. However, 25 (16.6%) could not or did not follow the imparted lifestyle change advice on a regular basis. Those who were able to modify the life-style as counselled showed the following results:

Conclusion:

The lifestyle modification techniques are important to control disease and its complications. Thus, after intense and regular counselling by the specialist rheumatology nurses on the lifestyle modification technique (83.3%) adapted the advised lifestyle modifications. The study showed the important role specialist rheumatology nurses can play in educating patients and helping them improving their quality of life.

References:

[1] Hudson M, Thombs BD, Steele R. at ell. Canadian Scleroderma Research G. QOL in patients with systemic sclerosis compared to the general population and patients with other chronic conditions. J Rheumatol. 2009;36(4):768–72.

Disclosure of Interests:

None declared

An observational study to determine whether alignment of endotracheal tube indicator line with the vocal cords results in appropriate depth of intubation

Background: Inappropriate endotracheal tube placement depth may be associated with complications. Objective: To determine whether the accurate alignment of the indicator ring on the endotracheal tube at the level of the vocal cords, results in its appropriate placement. Design: Prospective observational study. Patients: 98 adult patients scheduled for general anesthesia with orotracheal intubation. Interventions: The indicator band mark on the endotracheal tube was accurately placed at the vocal cords level under video-laryngoscope view. The tube length at the right upper incisor and the distance between its tip and the carina was measured using fibreoptic bronchoscope. Data to validate methods to predict insertion depth was collected and evaluated. Main Outcome: To determine the distance between the tip of the endotracheal tube and the carina. Results: The endotracheal tube tip depth was inap- propriate in 46.94% cases and was <3 cm above the carina in 41.64% cases. This difference in this distance was similar (p = 0.246) in the two genders. A correlation was noted between topographic length and insertion depth in females only (r2 = 0.201 and p = 0.001). The mean tracheal length was 12.66 + 1.35 cm in males and 12.04 + 1.26 cm in females. Conclusion: We found a high incidence of endo- tracheal tube tip malposition despite the accurate placement of the indicator band at the vocal cords level. We suggest that international endotracheal tube design standards be defined and endotracheal tube manufacturers modify the standard intratracheal length.

Pangenome Graphs

Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes. These approaches often use graphical models of the pangenome to support algorithms for sequence alignment, visualization, functional genomics, and association studies. The additional information provided to these methods by the pangenome allows them to achieve superior performance on a variety of bioinformatic tasks, including read alignment, variant calling, and genotyping. Pangenome graphs stand to become a ubiquitous tool in genomics. Although it is unclear whether they will replace linearreference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.

Azathioprine induced pancreatitis, polyarthritis and panniculitis (PPP) syndrome in a patient with Crohn's disease

Azathioprine and 6-mercaptopurine have been widely used for maintenance of remission in patients with inflammatory bowel disease. The use of thiopurines is associated with multiple adverse effects including dose dependent cytopenias or idiosyncratic reaction. We report about a case of azathioprine related pancreatitis associated with polyarthralgia and panniculitis. Pancreatitis, polyarthritis and panniculitis (PPP) syndrome is an uncommon phenomenon which may accompany a number of pancreatic diseases including acute or chronic pancreatitis or pancreatic malignancy. To the best of our knowledge, this is the first report of Azathioprine related PPP syndrome.

Estimated Burden of Community-Onset Respiratory Syncytial Virus-Associated Hospitalizations Among Children Aged <2 Years in the United States, 2014-15

BACKGROUND

Respiratory syncytial virus (RSV) is a major cause of hospitalizations in young children. We estimated the burden of community-onset RSV-associated hospitalizations among US children aged <2 years by extrapolating rates of RSV-confirmed hospitalizations in 4 surveillance states and using probabilistic multipliers to adjust for ascertainment biases.

METHODS

From October 2014 through April 2015, clinician-ordered RSV tests identified laboratory-confirmed RSV hospitalizations among children aged <2 years at 4 influenza hospitalization surveillance network sites. Surveillance populations were used to estimate age-specific rates of RSV-associated hospitalization, after adjusting for detection probabilities. We extrapolated these rates using US census data.

RESULTS

We identified 1554 RSV-associated hospitalizations in children aged <2 years. Of these, 27% were admitted to an intensive care unit, 6% needed mechanical ventilation, and 5 died. Most cases (1047/1554; 67%) had no underlying condition. Adjusted age-specific RSV hospitalization rates per 100 000 population were 1970 (95% confidence interval [CI],1787 to 2177), 897 (95% CI, 761 to 1073), 531 (95% CI, 459 to 624), and 358 (95% CI, 317 to 405) for ages 0-2, 3-5, 6-11, and 12-23 months, respectively. Extrapolating to the US population, an estimated 49 509-59 867 community-onset RSV-associated hospitalizations among children aged <2 years occurred during the 2014-2015 season.

CONCLUSIONS

Our findings highlight the importance of RSV as a cause of hospitalization, especially among children aged <2 months. Our approach to estimating RSV-related hospitalizations could be used to provide a US baseline for assessing the impact of future interventions.