High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.

Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative.

Intrarenal pressure and flow rate profile using LithoVue™ elite: impact of different irrigation systems and working channel instruments.

Purpose: To report real-time IRP and FR while performing flexible ureteroscopy in porcine kidney model utilizing LithoVue™ Elite (Boston Scientific®) with different irrigation systems, including automated pumps.

Methods: Using an ex-vivo model of porcine kidney, IRPs were measured with LithoVue Elite. Ureteroscopic settings (US) were tested with all permutations of irrigation methods (IM), working channel occupant (WCO), and ureteral access sheaths (UAS).

Holmium:yttrium-aluminium-garnet laser with MOSES technology is more efficient than thulium fibre laser in supine mini-percutaneous nephrolithotomy.

Objectives: To address the paucity of literature comparing outcomes achieved with utilisation of the high-power holmium:yttrium-aluminium-garnet (Ho:YAG) laser with MOSES technology vs those achieved with the thulium fibre laser (TFL) in mini-percutaneous nephrolithotomy (PCNL).

Methods: A retrospective review was performed of patients undergoing supine mini-PCNL between August 2021 and May 2023. Exclusion criteria were urinary diversion, simultaneous utilisation of >1 laser platform, use of any other form of fragmentation, and ureteric stones.

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data.

The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete.

Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees.

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible.

Impact of Renal Access Angle and Speed of Nephroscope Retrieval Movements on the Vortex Effect.

Objective: To analyze the influence of different renal access angles (AAs) and nephroscope retrieval speeds on the efficacy of the vortex effect (VE) in mini-percutaneous nephrolithotomy (mini-PCNL). This study aimed to understand the poorly understood physical components of the VE.

Materials And Methods: A Pexiglas™ (KUS®) model was built based on the dimensions of a 15/16 F mini-PCNL set (Karl Storz).

The Vortex Effect in Minimally Invasive Percutaneous Nephrolithotomy.

Objective: To describe the physical principles of the vortex effect to better understand its applicability in minimally invasive percutaneous nephrolithotomy (MIP) procedures.

Methods: Two acrylic phantom models were built based on the cross-sectional area (CSA) ratio of a MIP nephroscope and access sheaths (15/16F and 21/22F MIP-M, Karl Storz). The nephroscope phantom was 10 mm in diameter.

A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea.

The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference.

Optimizing stone harvesting in miniaturized-PCNL: a critical examination of renal access angles, technology, and the role they play in operative efficiency.

Purpose: Stone retrieval can be a laborious aspect of percutaneous nephrolithotomy (PCNL). A unique phenomenon of mini-PCNL is the vortex-effect (VE), a hydrodynamic form of stone retrieval. Additionally, the vacuum-assisted sheath (VAS) was recently developed as a new tool for stone extraction.

Recanalize ureteral stents with focused ultrasound.

Background: Maintaining ureteral patency is imperative to preventing renal injury and systemic infection. Ureteral stents are small conduits connecting the kidney and the bladder. They have been widely used to treat ureteral obstructions and ureteral leaks.

Cost Implications of Routine Preoperative Blood Typing and Crossmatching Prior to Robot-Assisted Laparoscopic Partial Nephrectomy.

Introduction: The surgical treatment of small renal masses has shifted from open to minimally invasive approaches. Preoperative blood typing and product orders often mirror the practices of the open era. We aim to define the rate of transfusion after robot-assisted partial laparoscopic nephrectomy (RAPN) at an academic medical center and the costs associated with current practice.

Preoperative Optimization of Promotility in Robotic Prostatectomy and Minimally Invasive Kidney Surgery.

Introduction: Patients are routinely discharged postoperative day 1 following minimally invasive surgery (MIS) for prostate cancer and kidney cancer. Delays in discharge are often related to gastrointestinal symptoms such as nausea, abdominal pain and vomiting; however, the role of baseline constipation in these symptoms and resultant delays in discharge is unclear. We conducted a prospective observational study to describe the incidence of baseline constipation among patients undergoing MIS prostate and kidney surgery, and its relationship to length of stay (LOS).

On the rocks: can urologists identify stone composition based on endoscopic images alone? A worldwide survey of urologists.

Purpose: As part of the management of nephrolithiasis, determination of chemical composition of stones is important. Our objective in this study is to assess urologists' accuracy in making visual, intraoperative determinations of stone composition.

Materials And Methods: We conducted a REDCap survey asking urologists to predict stone composition based on intraoperative images of 10 different pure-composition kidney stones of 7 different types: calcium oxalate monohydrate (COM), calcium oxalate dihydrate (COD), calcium phosphate (CP) apatite, CP brushite, uric acid (UA), struvite (ST) and cystine (CY).

Breakage Costs in Flexible Ureteroscopy: Digital vs. Fiberoptic Modalities.

Objective: To compare the maintenance costs of digital flexible ureteroscopes (DFU) versus fiberoptic flexible ureteroscopes (FFU) to understand the long-term financial impact associated with breakage in a flexible ureteroscopy (f-URS) program.

Methods: Data for breakage of FFU and DFU at an academic institution from 2019 to 2021 were obtained from our vendor (Karl Storz) and analyzed by month. Correlation test was used to evaluate significant differences in number of procedures, number of breakage events, breakage rates, and repair cost per month.

Bird lineages colonizing urban habitats have diversified at high rates across deep time.

Aim: Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood.

Genomic insights into the evolutionary relationships and demographic history of kiwi.

Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses.

Image Distortion During Flexible Ureteroscopy: A Laboratory Model Comparing Super Pulsed Thulium Fiber Laser High-Power Ho:YAG Laser.

Digital ureteroscopes employ "chip-on-the-tip" technology that allows for significant improvement in image resolution. However, image distortion often occurs during laser lithotripsy owing to acoustic wave production. We sought to compare image distortion using different laser power settings and distances from the laser fiber tip to the scope for the Super Pulsed Thulium Fiber (SPTF) laser and high-power Holmium:YAG (Ho:YAG) laser.

Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation.

Background: Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation).

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina).