OUP accepted manuscript

MOTIVATION

Nanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.

RESULTS

Here, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background.

AVAILABILITY AND IMPLEMENTATION

The C++ source code is available at https://gitlab.com/dacs-hpi/readbouncer.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Tracheomalacia after thyroidectomy for retrosternal goitres requiring sternotomy- a myth or reality?

INTRODUCTION

Tracheomalacia after thyroidectomy is not well understood. Reports on tracheomalacia are conflicting, with some suggesting a high rate and other large cohorts in which no tracheomalacia is reported. The aim of our study was to assess the incidence and factors associated with tracheomalacia after thyroidectomy in patients with retrosternal goitres requiring sternotomy at a high-volume tertiary care referral centre.

METHODS

A longitudinal cohort study was conducted from January 2011 to December 2019. All adult patients who underwent thyroidectomy with sternotomy were included. Tracheomalacia was considered when tracheal rings were soft compared with other parts (proximal or distal) of the trachea and required either tracheostomy or resection with anastomosis. The decision to perform a tracheostomy or to administer continuous or bilevel positive airway pressure postoperatively was made depending on the degree of tracheomalacia. Logistic regression analysis was used to assess factors associated with tracheomalacia.

RESULTS

We evaluated 40 patients who underwent thyroidectomy with sternotomy. The mean age of our cohort was 48.7 ± 11.3 years and the population was predominantly female (67.5%). One patient required tracheal resection with anastomosis, and two patients required tracheostomy. Multivariable logistic regression analysis did not reveal any patient- or thyroid-related factor significantly associated with the development of tracheomalacia in our cohort.

CONCLUSIONS

The incidence of tracheomalacia after thyroidectomy with sternotomy appears to be very low. However, the occurrence of tracheomalacia after thyroidectomy in cases of large goitre is possible and hence worrisome.

Association between mean platelet volume levels and inflammation in SLE patients presented with arthritis

BACKGROUND

Systemic lupus erythematosus (SLE) may be characterized by periods of remissions and chronic or acute relapses. The complexity of clinical presentation of the SLE patients leads to incorrect evaluation of disease activity. Mean platelet volume (MPV) has been studied as a simple inflammatory marker in several diseases. There is no study in the literature about MPV levels in adult SLE patients with arthritis.

OBJECTIVES

We aimed to investigate the MPV levels in the SLE population with arthritis during and between activations.

METHODS

The study consisted of 44 SLE patients with arthritis in activation period (Group 1), the same 44 SLE patients with arthritis in remission period (Group 2) and 44 healthy controls (Group 3). Erythrocyte sedimentation rate (ESR), creactive protein (CRP), white blood cell count, platelet count, and mean platelet volume (MPV) levels were retrospectively recorded from patient files.

RESULTS

The mean ages of the SLE subjects were 42 ± 16 years, while the mean ages of controls was 41 ± 17 years. MPV was significantly lower in Group 1(7.66±0.89fL) than in Group 2 (8.61±1.06 fL) and Group 3(8.62±1.11fL) (p<0.0001). The differences between groups reached statistical significance.

CONCLUSIONS

We suggest that MPV levels decrease in patients with arthritis of SLE activation when compared to the same patients in remission and healthy controls.

Ultrasound screening for interstitial lung disease in rheumatoid arthritis

OBJECTIVES

As interstitial lung disease (ILD) in rheumatoid arthritis (RA) patients is associated with increased mortality due to loss of diffusion capacity and pulmonary hypertension, regular screening for structural abnormalities of the lung is advised. In addition to standard radiological examination with computed x-ray tomography, ultrasound of the lung could allow non-invasive and radiation-free structural monitoring of the lung. The objective of this study was to test the frequency of abnormalities in lung sonography in patients with RA who did not have clinical signs or symptoms of lung disease.

METHODS

In a prospective study of 64 consecutive patients with rheumatoid arthritis and 40 healthy volunteers, we screened the pleura and the pulmonary parenchyma for sonographic abnormalities. All RA patients underwent high resolution computer tomography of the lung.

RESULTS

28% of RA patients showed pleural nodules or B-line phenomena. In these patients, CT scans showed signs of incipient interstitial lung disease. Lung sonography showed sporadic abnormalities in 7% of the healthy controls.

CONCLUSIONS

Transthoracic ultrasound of the lung is an inexpensive and safe tool to screen patients with RA for incipient pulmonary structural changes.

[Congenital esophageal duplication cysts: progressive dysphagia in adulthood]

Esophageal duplications are congenital abnormalities of the foregut. We present the case of a 33-year-old woman suffering from progressive dysphagia who had surgery for esophageal duplication. The following three criteria define the cystic lesion: an intimate attachment to the esophageal wall, the presence of a smooth muscle coat and a mucosal lining consisting of squamous and/or ciliated respiratory epithelium. Diverticula, bronchogenic cysts and cystic neoplasms have to be considered in the differential diagnosis. Congenital cystic esophageal duplication is a rare cause of dysphagia in adulthood.

Cytokeratin expression patterns as an indicator of tumour progression in oesophageal squamous cell carcinoma

Recent studies point out that cytokeratins (CKs) are involved in dynamic cell remodeling during cancer progression and particularly, CK expression patterns have been associated with invasion and metastasis. In oesophageal squamous cell cancer (ESCC), lymph node (LNN) metastasis is an important step in disease progression, invariably associated with an ominous prognosis. To assess whether specific CK expression patterns could represent reliable markers of tumor progression, a series of 111 ESCCs (59 lymph node-positive, 52-negative) derived from the high- incidence area of Linxian (Northern China), were subjected to immunohistochemical (IHC) analysis with an extensive panel of CK antibodies. Statistically significant differences were observed for CK18 (p=0.01), CK19 (p=0.04) and PKK1 (p=0.02) expression between the LNN-negative and LNN-positive ESCCs. Furthermore, significant correlation between specific CK distribution pattern and progressive disease (i.e., LNN metastasis) was evidenced. The results suggest that CK8, CK18 and CK19 expression and distribution pattern could be of predictive value as a marker of disease progression as defined by the appearance of lymph node metastases in oesophageal squamous cell cancer.