Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data.

MOTIVATION: Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing data, such as SCIΦ and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these methods are not scalable to the extensive genomic breadth of single-cell whole-genome (scWGS) and whole-exome sequencing (scWES) data. RESULTS: Here, we report on a new scalable method, Phylovar, which extends the phylogeny-guided variant calling approach to sequencing datasets containing millions of loci. Through benchmarking on simulated datasets under different settings, we show that, Phylovar outperforms SCIΦ in terms of running time while being more accurate than Monovar (which is not phylogeny-aware) in terms of SNV detection. Furthermore, we applied Phylovar to two real biological datasets: an scWES triple-negative breast cancer data consisting of 32 cells and 3375 loci as well as an scWGS data of neuron cells from a normal human brain containing 16 cells and approximately 2.5 million loci. For the cancer data, Phylovar detected somatic SNVs with high or moderate functional impact that were also supported by bulk sequencing dataset and for the neuron dataset, Phylovar identified 5745 SNVs with non-synonymous effects some of which were associated with neurodegenerative diseases. AVAILABILITY AND IMPLEMENTATION: Phylovar is implemented in Python and is publicly available at https://github.com/NakhlehLab/Phylovar.

The devil's in the dosing: severe drug-induced liver injury in a hydroxychloroquine-naive patient with subacute cutaneous lupus erythematosus and porphyria cutanea tarda.

A 29-year-old woman with a 1.5 year history of photosensitive skin lesions on her hands presented with a malar rash, bullous lesions on her hands, and was diagnosed with subacute lupus erythematosus after serologies revealed a positive antinuclear antibody test (1:2560), and antibodies to Ro/SSA and dsDNA. Hydroxychloroquine (400 mg/day) was prescribed and the patient developed severe drug-induced liver injury. Biopsy of her bullous skin lesions was consistent with porphyria cutanea tarda, as were her serological and urinary exams. She was successfully treated with therapeutic phlebotomy. This case identifies porphyria cutanea tarda as an important differential diagnosis for the rheumatologist to consider when evaluating patients with bullous skin lesions. Hydroxychloroquine in lower doses is an effective treatment for porphyria cutanea tarda; at doses used to treat systemic lupus erythematosus and subacute cutaneous lupus, there is a potentially life-threatening complication of hepatotoxicity.

Hierarchical patterning of hydrogels by replica molding of impregnated breath figures leads to superoleophobicity.

The surface chemistry and topography govern the spreading of liquids on a solid. When an oil drop makes a contact angle, θ > 90° on a solid surface, the solid is termed as oleophobic. Adding roughness to an inherently oleophobic surface enhances its oil dewetting and can lead to superoleophobicity when θ > 150°. In this study, we introduce the concept of a two-tier hierarchical roughness on the surface of soft materials such as hydrogels by forming the patterned inverse replica of breath figure polymer films impregnated with nanoparticles. The directed deposition of nanoparticles in the breath figure pores is accomplished by an aerosol assisted technique that exclusively leads to deposition within the pores and filling of the pores. The inverse replica of such impregnated films exhibits a close packed hexagonally structured second tier of surface roughness which directly leads to a superoleophobic surface. Since these structures have well defined geometries, it is possible to estimate the contact angle by assuming a partial wetting of the oil drop in a 'fakir' state on the rough surface. The estimation is in good agreement with the experimental contact angle value. While the work demonstrates a facile method to impart superoleophobicity to a hydrogel surface, it also demonstrates new methods to imbue breath figure pores with functional materials that can be easily transferred to the pores of the inverse replica.

Independent risk factors for the co-colonization of vancomycin-resistant Enterococcus faecalis and methicillin-resistant Staphylococcus aureus in the region most endemic for vancomycin-resistant Staphylococcus aureus isolation.

In the majority of cases of vancomycin-resistant Staphylococcus aureus (VRSA), vancomycin-resistant Enterococcus faecalis (VR E. faecalis) served as the vanA donor to S. aureus. Previous studies that evaluated the risk factors for co-colonization with VRE and MRSA did not differentiate between VR E. faecalis and VR E. faecium. This study aimed to identify variables associated with VR E. faecalis and MRSA co-colonization. A retrospective case-control study from January 2008 to December 2009 was conducted at the Detroit Medical Center. Data were extracted from charts and pharmacy records. Unique patients co-colonized with VR E. faecalis and MRSA (defined as isolation of MRSA within 7 days of VR E. faecalis isolation) were compared with patients with VR E. faecalis who were not co-colonized with MRSA. A total of 546 patients with VR E. faecalis isolation were identified. 85 (15.6 %) VR E. faecalis patients were co-colonized with MRSA and 461 (84.4 %) VR E. faecalis patients were not co-colonized with MRSA. The mean age of the study cohort was 65.9 ± 16.4 years, 424 (77.7 %) were African-American, and 270 (49.5 %) were residing in long-term care institutions. Independent predictors of co-colonization of VR E. faecalis and MRSA were male gender, impaired consciousness, ICU stay prior to VR E. faecalis isolation, indwelling devices, and isolation of VR E. faecalis from wounds. MRSA was frequently isolated from the same culture specimen as VR E. faecalis (n = 39, 45.9 %), most commonly from wounds. This large study of patients with VR E. faecalis identified the severity of illness, indwelling devices, and chronic wounds as independent predictors of co-colonization with VR E. faecalis and MRSA.

Enhanced antibactericidal function of W4+-doped titania-coated nickel ferrite composite nanoparticles: a biomaterial system.

The study demonstrates a distinct enhancement of antimicrobial activity of W4+-doped titania that is coated on nickel ferrite nanoparticles in comparison to undoped titania. The composite nanoparticles were synthesized by uniquely combining reverse micelle and chemical hydrolysis synthesis methods [Rana S, Rawat J, Misra RDK, Acta Biomater 2005;1:691]. The superior antimicrobial activity of W4+-doped titania is related to the inhibition of electron-hole recombination and decrease in the band gap energy of titania. The function of the ferrite is to facilitate the removal of nanoparticles from the sprayed surface using a small magnetic field. The coating of ferrite nanoparticles with titania retains superparamagnetic character and magnetic strength of composite nanoparticles signifying non-deterioration of magnetic properties and promoting their use as removable antimicrobial photocatalyst nanoparticles.