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Abstract Background There is currently no method to precisely measure the errors that occur in the sequencing instrument/sequencer, which is critical for next-generation sequencing applications aimed at discovering the genetic makeup of heterogeneous cellular populations. Results We propose a novel computational method, SequencErr, to address this challenge by measuring the base correspondence between overlapping regions in forward and reverse reads. An analysis of 3777 public datasets from 75 research institutions in 18 countries revealed the sequencer error rate to be ~ 10 per million (pm) and 1.4% of sequencers and 2.7% of flow cells have error rates > 100 pm. At the flow cell level, error rates are elevated in the bottom surfaces and > 90% of HiSeq and NovaSeq flow cells have at least one outlier error-prone tile. By sequencing a common DNA library on different sequencers, we demonstrate that sequencers with high error rates have reduced overall sequencing accuracy, and removal of outlier error-prone tiles improves sequencing accuracy. We demonstrate that SequencErr can reveal novel insights relative to the popular quality control method FastQC and achieve a 10-fold lower error rate than popular error correction methods including Lighter and Musket. Conclusions Our study reveals novel insights into the nature of DNA sequencing errors incurred on DNA sequencers. Our method can be used to assess, calibrate, and monitor sequencer accuracy, and to computationally suppress sequencer errors in existing datasets.

Abstract Background The most commonly isolated organisms in a parapneumonic effusion include S. pneumoniae, H. influenzae, and S. aureus. If unusual organisms are isolated from the pleural space, further investigation is warranted to locate the primary source. We present a patient with an infected chronic renal cyst found to have an empyema secondary to Proteus mirabilis to highlight the importance of further diagnostic workup when encountering unusual organisms in the pleural space. Case presentation A 40-year-old African-American female, with a past medical history of asthma and sickle cell trait, presented with 5 weeks of upper respiratory tract symptoms and chest pain. A computed tomography angiogram (CTA) of the chest was negative for a pulmonary embolism but revealed a loculated left sided pleural effusion with associated left-lower lobe consolidation. She was started on empiric antibiotics, and a chest tube was inserted with drainage of frank pus. Fluid gram stain was positive for gram negative rods. Intrapleural fibrinolytics were administered for 72 h given the presence of loculations. With no improvement following fibrinolytics, she was taken to the operating room for large bore chest tube placement and left visceral pleura decortication. Pleural fluid cultures speciated to Proteus mirabilis, so further cross-sectional imaging of her abdomen/pelvis was pursued to evaluate for a primary source. A complex cystic lesion in the upper pole of the left kidney that communicated with the ipsilateral diaphragm was identified. Subsequent drainage and culture of the renal cyst was positive for Proteus mirabilis. Given clinical improvement following these interventions she was discharged with an extended course of antibiotics with plans for repeat imaging following completion of treatment. Conclusions While cases of Proteus mirabilis empyema have previously been reported as a consequence of conditions such as pyelonephritis, we present, to our knowledge, the first case of a Proteus mirabilis empyema as a consequence of an infected renal cyst communicating with the pleural space. This study highlights that further evaluation with cross-sectional imaging is warranted when unusual organisms are found in the pleural space. Anatomic abnormalities that become apparent on imaging may help elucidate the source of infection.

Genomic analysis of neuroblastoma has revealed important disease etiology. In this study, the authors assembled whole genome, exome and transcriptome data from over 700 neuroblastomas and identified molecular signatures correlated with age, and rare, potentially targetable variants overlooked in smaller cohorts.

Glycophosphatidylinositol-anchored proteins (GPI-APs) play essential roles in physiology, but their biogenesis and trafficking have not been systematically characterized. Here, we took advantage of the recently available haploid genetics approach to dissect GPI-AP pathways in human cells using prion protein (PrP) and CD59 as model molecules. Our screens recovered a large number of common and unexpectedly specialized factors in the GPI-AP pathways. PIGN, PGAP2, and PIGF, which encode GPI anchor-modifying enzymes, were selectively isolated in the CD59 screen, suggesting that GPI anchor composition significantly influences the biogenesis of GPI-APs in a substrate-dependent manner. SEC62 and SEC63, which encode components of the ER-targeting machinery, were selectively recovered in the PrP screen, indicating that they do not constitute a universal route for the biogenesis of mammalian GPI-APs. Together, these comparative haploid genetic screens demonstrate that, despite their similarity in overall architecture and subcellular localization, GPI-APs follow markedly distinct biosynthetic and trafficking pathways.

Neuropsychological symptoms associated with post-COVID-19 conditions may prevent patients from resuming normal activities at home or work. We report a retrospective, cross-sectional evaluation of neuropsychological and cardiopulmonary outcomes in 2 groups of patients: outpatients with mild enough infection to be spared from hospitalization and those who required inpatient admission. We hypothesized a dose-response model of post-COVID symptom severity in which persistent consequences would be more severe in those who experienced worse acute infections. In a dedicated COVID clinic, 321 patients were seen (33% outpatient, 67% inpatient). Outpatients skewed female, White, non-Hispanic, and younger. Outpatients had worse insomnia (measured with insomnia severity index) and were less able to resume their usual activities (EQ-5D-5L usual activities scale), despite inpatients experiencing worse cognition (Montreal Cognitive Assessment), having greater obesity (body mass index), decreased exercise tolerance (6-minute-walk distance), and more exertional oxygen desaturation. In both groups, insomnia worsened while cognition improved significantly with time from infection to testing while controlling for patient age; other variables did not. In logistic regression, female sex, higher MoCA score, EQ-5D-5L “usual activities” subscore, less oxygen desaturation with exertion, and longer time from infection remained as significant associations with outpatient status. Our study demonstrated that the functional sequelae of post-COVID-19 conditions in patients with mild acute disease have the potential to be as severe as that in patients who have recovered from severe illness.

The comprehensive understanding of cellular signaling pathways remains a challenge due to multiple layers of regulation that may become evident only when the pathway is probed at different levels or critical nodes are eliminated. To discover regulatory mechanisms in canonical WNT signaling, we conducted a systematic forward genetic analysis through reporter-based screens in haploid human cells. Comparison of screens for negative, attenuating and positive regulators of WNT signaling, mediators of R-spondin-dependent signaling and suppressors of constitutive signaling induced by loss of the tumor suppressor adenomatous polyposis coli or casein kinase 1α uncovered new regulatory features at most levels of the pathway. These include a requirement for the transcription factor AP-4, a role for the DAX domain of AXIN2 in controlling β-catenin transcriptional activity, a contribution of glycophosphatidylinositol anchor biosynthesis and glypicans to R-spondin-potentiated WNT signaling, and two different mechanisms that regulate signaling when distinct components of the β-catenin destruction complex are lost. The conceptual and methodological framework we describe should enable the comprehensive understanding of other signaling systems.

[This corrects the article DOI: 10.1371/journal.pone.0208540.].

The relationship between cardiovascular disease and abnormalities in sleep architecture is complex and bi-directional. Sleep disordered breathing (SDB) often confounds human studies examining sleep in the setting of heart failure, and the independent impact of isolated right or left heart failure on sleep is difficult to assess. We utilized an animal model of right heart failure using pulmonary artery banding (PAB) in mice to examine the causal effect of right heart failure on sleep architecture. Four weeks after PAB or sham (control) surgery, sleep was measured by polysomnography for 48 hours and right ventricular (RV) hypertrophy confirmed prior to sacrifice. PAB resulted in right ventricular hypertrophy based on a 30% increase in the Fulton Index (p < 0.01). After PAB, mice spent significantly more time in NREM sleep compared to the control group over a 24 hour period (53.5 ± 1.5% vs. 46.6 ± 1.4%; p < 0.01) and exhibited an inability to both cycle into REM sleep and decrease delta density across the light/sleep period. Our results support a phenotype of impaired sleep cycling and increased 'sleepiness' in a mouse model of RV dysfunction.