Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis.

Non-actionable Results, Accuracy, and Effect of First- and Second-line Line Probe Assays for Diagnosing Drug-Resistant Tuberculosis, Including on Smear-Negative Specimens, in a High-Volume Laboratory.

Background: Rapid tuberculosis (TB) drug susceptibility testing (DST) is crucial. Genotype MTBDRsl is a widely deployed World Health Organization (WHO)-endorsed assay. Programmatic performance data, including non-actionable results from smear-negative sputum, are scarce.

Spatial heterogeneity of extensively drug resistant-tuberculosis in Western Cape Province, South Africa.

Tuberculosis (TB) remains a leading infectious disease killer globally. Treatment outcomes are especially poor among people with extensively drug-resistant (XDR) TB, until recently defined as rifampicin-resistant (RR) TB with resistance to an aminoglycoside (amikacin) and a fluoroquinolone (ofloxacin). We used laboratory TB test results from Western Cape province, South Africa between 2012 and 2015 to identify XDR-TB and pre-XDR-TB (RR-TB with resistance to one second-line drug) spatial hotspots.

Diagnosing Tuberculosis: What Do New Technologies Allow Us to (Not) Do?

New tuberculosis (TB) diagnostics are at a crossroads: their development, evaluation, and implementation is severely damaged by resource diversion due to COVID-19. Yet several technologies, especially those with potential for non-invasive non-sputum-based testing, hold promise for efficiently triaging and rapidly confirming TB near point-of-care. Such tests are, however, progressing through the pipeline slowly and will take years to reach patients and health workers.

Variants in Bedaquiline-Candidate-Resistance Genes: Prevalence in Bedaquiline-Naive Patients, Effect on MIC, and Association with Mycobacterium tuberculosis Lineage.

Studies have shown that variants in bedaquiline-resistance genes can occur in isolates from bedaquiline-naive patients. We assessed the prevalence of variants in all bedaquiline-candidate-resistance genes in bedaquiline-naive patients, investigated the association between these variants and lineage, and the effect on phenotype. We used whole-genome sequencing to identify variants in bedaquiline-resistance genes in isolates from 509 bedaquiline treatment naive South African tuberculosis patients.

Effectiveness of the Novel Anti-TB Bedaquiline against Drug-Resistant TB in Africa: A Systematic Review of the Literature.

Background: In 2018, an estimated 10.0 million people contracted tuberculosis (TB), and 1.5 million died from it, including 1.

RResolver: efficient short-read repeat resolution within ABySS.

Background: De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes. De novo short-read assemblers commonly use de Bruijn graphs, where nodes are sequences of equal length k, also known as k-mers.

Diffuse optical spectroscopic method for tissue and body composition assessment.

Significance: Growing levels of obesity and metabolic syndrome have driven demand for more advanced forms of body composition assessment. While various techniques exist to measure body composition, devices are typically expensive and not portable, involve radiation [in the case of dual-energy x-ray absorptiometry (DXA)], and are limited to analysis of adiposity while metabolic information from blood supply and oxygenation are not considered.

Aim: We evaluate whether diffuse optical spectroscopic imaging (DOSI) can be used to predict site-specific adiposity and percent fat (whole body) while simultaneously providing information about local tissue hemoglobin levels and oxygenation.

Subgroup Analyses by European Country-Specific Reimbursement Requirements Confirm Efficacy for Ixekizumab in Psoriasis.

Background: Biologic drugs are generally recommended for treating moderate-to-severe psoriasis. While eligibility criteria are primarily defined by clinical treatment guidelines, access to these therapies varies between European countries and is regulated by country-specific reimbursement criteria. This post-hoc subgroup analysis of integrated data from two phase III trials (UNCOVER-2 and -3) reports the efficacy of ixekizumab relative to that of etanercept in patients with moderate-to-severe plaque psoriasis selected into groups defined by original reimbursement criteria from eight European countries.

High mortality among patients hospitalized for drug-resistant tuberculosis with acquired second-line drug resistance and high HIV prevalence.

Objectives: We compared mortality between HIV-positive and HIV-negative South African adults with drug-resistant tuberculosis (DR-TB) and high incidence of acquired second-line drug resistance.

Methods: We performed a retrospective review of DR-TB patients with serial second-line TB drug susceptibility tests (2008-2015) who were hospitalized at a specialized TB hospital. We used Kaplan-Meier analysis and Cox models to examine associations with mortality.

Biomechanical analysis of anterior stability after 15% glenoid bone loss: comparison of Bankart repair, dynamic anterior stabilization, dynamic anterior stabilization with Bankart repair, and Latarjet.

Background: Dynamic anterior shoulder stabilization (DAS) with Bankart repair is a recently described stabilization technique thought to be more robust than an isolated Bankart repair while avoiding many coracoid transfer-related complications and technical demands. DAS involves transfer of the long head biceps through a subscapularis split to the anterior glenoid to create a sling effect. We hypothesize that DAS with Bankart repair will restore anterior stability in a human-cadaveric model with subcritical (15%) glenoid bone loss.

Localization of EccA at the growing pole in Mycobacterium smegmatis.

Background: Bacteria require specialized secretion systems for the export of molecules into the extracellular space to modify their environment and scavenge for nutrients. The ESX-3 secretion system is required by mycobacteria for iron homeostasis. The ESX-3 operon encodes for one cytoplasmic component (EccA) and five membrane components (EccB3 - EccE3 and MycP).

Tribocorrosion is common but mild in modular humeral components in shoulder arthroplasty: an implant retrieval analysis.

Background: Wear and corrosion at the junctions of modular implants are increasingly recognized issues in the design of hip and knee arthroplasty prostheses, yet less is known about their significance in shoulder arthroplasty.

Methods: A query of paired total shoulder implant specimens (eg, humeral head and stem components from the same patient) was performed using an institutional implant retrieval registry. Implants were examined under a stereomicroscope and evaluated for evidence of fretting and corrosion using the modified Goldberg scoring system.

Single-cell analysis implicates T17-to-T2 cell plasticity in the pathogenesis of palmoplantar pustulosis.

Background: Palmoplantar pustulosis (PPP) is a severe inflammatory skin disorder characterized by eruptions of painful, neutrophil-filled pustules on the palms and soles. Although PPP has a profound effect on quality of life, it remains poorly understood and notoriously difficult to treat.

Objective: We sought to investigate the immune pathways that underlie the pathogenesis of PPP.

ntEdit+Sealer: Efficient Targeted Error Resolution and Automated Finishing of Long-Read Genome Assemblies.

High-quality genome assemblies are crucial to many biological studies, and utilizing long sequencing reads can help achieve higher assembly contiguity. While long reads can resolve complex and repetitive regions of a genome, their relatively high associated error rates are still a major limitation. Long reads generally produce draft genome assemblies with lower base quality, which must be corrected with a genome polishing step.

Comparative Genetic Analysis of Psoriatic Arthritis and Psoriasis for the Discovery of Genetic Risk Factors and Risk Prediction Modeling.

Objectives: Psoriatic arthritis (PsA) has a strong genetic component, and the identification of genetic risk factors could help identify the ~30% of psoriasis patients at high risk of developing PsA. Our objectives were to identify genetic risk factors and pathways that differentiate PsA from cutaneous-only psoriasis (PsC) and to evaluate the performance of PsA risk prediction models.

Methods: Genome-wide meta-analyses were conducted separately for 5,065 patients with PsA and 21,286 healthy controls and separately for 4,340 patients with PsA and 6,431 patients with PsC.

Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa.

Extensively drug-resistant tuberculosis (XDR-TB), defined as resistance to at least isoniazid (INH), rifampicin (RIF), a fluoroquinolone (FQ) and a second-line injectable drug (SLID), is difficult to treat and poses a major threat to TB control. The transmission dynamics and distribution of XDR () strains have not been thoroughly investigated. Using whole genome sequencing data on 461 XDR- strains, we aimed to investigate the geographical distribution of XDR- strains in the Western Cape Province of South Africa over a 10 year period (2006-2017) and assess the association between sub-lineage, age, gender, geographical patient location and membership or size of XDR-TB clusters.

Upper Blepharoplasty and Brow Rejuvenation in Men.

The upper lid-brow junction is a complex anatomic zone that undergoes many interconnected age-related changes. Although considerable effort has gone into defining the ideal female eye and brow, no such work has been done for the male. Typically, men develop forehead and glabellar lines in conjunction with either upper lid hooding, brow ptosis, or blepharoptosis, whereas some men develop hollowing of the upper lid sulcus.

International eDelphi Study to Reach Consensus on the Methotrexate Dosing Regimen in Patients With Psoriasis.

Importance: A clear dosing regimen for methotrexate in psoriasis is lacking, and this might lead to a suboptimal treatment. Because methotrexate is affordable and globally available, a uniform dosing regimen could potentially optimize the treatment of patients with psoriasis worldwide.

Objective: To reach international consensus among psoriasis experts on a uniform dosing regimen for treatment with methotrexate in adult and pediatric patients with psoriasis and identify potential future research topics.