Quantification by droplet digital PCR and species identification by metabarcoding of environmental (e)DNA from Blainville's beaked whales, with assisted localization from an acoustic array.

Detection and identification of species, subspecies or stocks of whales, dolphins and porpoises at sea remain challenging, particularly for cryptic or elusive species like beaked whales (Family: Ziphiidae). Here we investigated the potential for using an acoustically assisted sampling design to collect environmental (e)DNA from beaked whales on the U.S.

Runs of homozygosity in killer whale genomes provide a global record of demographic histories.

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage.

Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence.

As bacteria transition from exponential to stationary phase, they change substantially in size, morphology, growth and expression profiles. These responses also vary between individual cells, but it has proved difficult to track cell lineages along the growth curve to determine the progression of events or correlations between how individual cells enter and exit dormancy. Here, we developed a platform for tracking more than 10 parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track batch populations.

Long-term outcomes of pediatric laparoscopic needled-assisted inguinal hernia repair: A 10-year experience.

Purpose: Laparoscopic inguinal hernia repair (LIHR) has gained wide acceptance over the past decade, although studies with longer term follow-up are lacking. We present one of the largest cohorts of children undergoing laparoscopic needle-assisted repair (LNAR) with long-term follow-up.

Methods: A clinical quality database was maintained for children ≤14 years of age who underwent laparoscopic needle-assisted repair between 2009 and 2017 with review of follow-up through 2019.

Killer whale genomes reveal a complex history of recurrent admixture and vicariance.

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools.

Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses.

Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates and cultural hitchhiking (linkage of genetic variation to culturally-transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal.

Single-cell microscopy of suspension cultures using a microfluidics-assisted cell screening platform.

Studies that rely on fluorescence imaging of nonadherent cells that are cultured in suspension, such as Escherichia coli, are often hampered by trade-offs that must be made between data throughput and imaging resolution. We developed a platform for microfluidics-assisted cell screening (MACS) that overcomes this trade-off by temporarily immobilizing suspension cells within a microfluidics chip. This enables high-throughput and automated single-cell microscopy for a wide range of cell types and sizes.

Web-Based Tool to Facilitate Shared Decision Making With Regard to Neoadjuvant Chemotherapy Use in Muscle-Invasive Bladder Cancer.

Purpose: Level 1 evidence supports the use of neoadjuvant chemotherapy (NAC) for the treatment of muscle-invasive bladder cancer (MIBC), but observational data demonstrate that this approach is underused. A barrier to shared decision making is difficulty in predicting and communicating survival estimates after cystectomy with or without NAC.

Methods: We included patients with MIBC from the National Cancer Database treated with cystectomy.

Telemedicine-Enabled Clinical Trial of Metformin in Patients With Prostate Cancer.

Purpose: Clinical trials are critical to informing cancer care but often are hampered by slow accrual and lack of generalizability because of poor geographic accessibility. We tested the feasibility of replacing onsite study visits with telemedicine visits in a prospective clinical trial.

Methods: Castration-naïve patients with prostate cancer and a rising serum prostate-specific antigen after definitive local therapy were eligible.

A microvascular compartment model validated using C-methylglucose liver PET in pigs.

The standard compartment model (CM) is widely used to analyse dynamic PET data. The CM is fitted to time-activity curves to estimate rate constants that describe the transport of a tracer between well-mixed compartments. The aim of this study was to develop and validate a more realistic microvascular compartment model (MCM) that includes capillary tracer concentration gradients, backflux from cells into the perfused capillaries and multiple re-uptakes during the passage through a capillary.

Management of Atypical Renal Cell Carcinomas.

Non-clear cell renal cell carcinoma (RCC) encompasses a diverse group of diseases, with research yielding different histologic findings and genetic profiles with each distinct subgroup. Simply mirroring the management techniques of clear cell RCC and borrowing from its growing armamentarium of therapeutic agents, while somewhat productive at first, but will ultimately be limiting. Further investigation into the molecular pathogenesis of disease, similarities and differences between specific subtypes, and mechanisms of resistance to therapeutics will help identify new targets, stimulate development of novel agents, and improve clinical trial offerings for non-clear cell RCC (nccRCC).

Federated optimisation of kinetic analysis problems.

Positron Emission Tomography (PET) data is intrinsically dynamic, and kinetic analysis of dynamic PET data can substantially augment the information provided by static PET reconstructions. Yet despite the insights into disease that kinetic analysis offers, it is not used clinically and seldom used in research beyond the preclinical stage. The utility of PET kinetic analysis is hampered by several factors including spatial inconsistency within regions of homogeneous tissue and relative computational expense when fitting complex models to individual voxels.

Preoperative warfarin reversal for early hip fracture surgery.

Purpose: To evaluate our hospital protocol of low-dose vitamin K titration for preoperative warfarin reversal for early hip fracture surgery.

Methods: Records of 16 men and 33 women aged 63 to 93 (mean, 81) years who were taking warfarin for atrial fibrillation (n=40), venous thromboembolism (n=9), cerebrovascular accident (n=3), and prosthetic heart valve (n=3) and underwent surgery for hip fractures were reviewed. The 3 patients with a prosthetic heart valve were deemed high risk for thromboembolism and the remainder low-risk.

Mass spec studio for integrative structural biology.

The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS(2)) data with protein modeling activities (Mass Spec Studio).

Intervention in childbirth: should we allow women to choose?

The issue of whether women should be able to choose to give birth by caesarean section in the absence of pregnancy complications remains a controversial topic. To explore the issues and allow the public the opportunity to voice their views, academics at Bournemouth University organised a public debate on the pros and cons of allowing women free choice with regard to intervention. Two teams, each with a well-known user representative, an experienced practitioner and an academic, debated the motion: "This house believes that women should be able to choose caesarean section on demand.

Point charges optimally placed to represent the multipole expansion of charge distributions.

We propose an approach for approximating electrostatic charge distributions with a small number of point charges to optimally represent the original charge distribution. By construction, the proposed optimal point charge approximation (OPCA) retains many of the useful properties of point multipole expansion, including the same far-field asymptotic behavior of the approximate potential. A general framework for numerically computing OPCA, for any given number of approximating charges, is described.

Platform dependencies in bottom-up hydrogen/deuterium exchange mass spectrometry.

Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS) platforms that consisted of a FT-MS and a high-resolution QTOF mass spectrometer, each with matched front-end fluidic systems.

Stochastic modeling of regulation of gene expression by multiple small RNAs.

A wealth of new research has highlighted the critical roles of small noncoding RNAs (sRNAs) in diverse processes, such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif composed of a master regulator protein whose expression is controlled by multiple sRNAs. However, the stochastic gene expression of a single target gene regulated by multiple sRNAs is currently not well understood.

Parent and emergency physician comfort with a system of on-line emergency-focused medical summaries for infants with significant cardiac disease.

Surveys were developed and administered to assess parental comfort with emergency care for children with special health care needs (CSHCN) with cardiac disease and the impact of a web-based database of emergency-focused clinical summaries (emergency information forms-EIF) called Midwest Emergency Medical Services for Children Information System (MEMSCIS) on parental attitudes regarding emergency care of their CSHCN. We hypothesized that MEMSCIS would improve the parent and provider outlook regarding emergencies of young children with heart disease in a randomized controlled trial. Children under age 2 were enrolled in MEMSCIS by study nurses associated with pediatric cardiac centers in a metropolitan area.