Pan-squamous genomic profiling stratified by anatomic tumor site and viral association

Background: Squamous cell carcinomas (SCC) have diverse anatomic etiologies but may share common genomic biomarkers. We profiled 7,871 unique SCCs across nine anatomic sites to investigate commonality in genomic alterations (GA), tumor mutational burden (TMB), human papillomavirus (HPV) association, and mutational signatures. Methods: Tissue from over 8,100 unique SCC samples originating from nine anatomic sites (anogenital (anus, cervix, penis, vagina, vulva), esophagus, head and neck, lung, and skin) were sequenced by hybrid capture-based comprehensive genomic profiling to evaluate GA and TMB. About 3% of non-cutaneous SCC samples had UV signatures, indicative of potential primary site misdiagnoses, and were filtered from the analysis. Detection of HPV, including high-risk strains 16, 18, 31, 33, and 45, was implemented through de novo assembly of non-human sequencing reads and BLASTn comparison against all viral nucleotide sequences in the NCBI database. Results: The proportion of HPV+ patients by anatomic site varied, with the highest being anal (91%) and cervical (83%). The mutational landscape of each cohort was similar, regardless of anatomic origin, but clustered based on HPV status. The largest differences in GA frequency as stratified by HPV- vs. HPV+ were TP53 (87% vs. 12%), CDKN2A (45% vs. 6%), and PIK3CA (22% vs. 33%). The median TMB in cases originating from HPV-associated sites was similar, regardless of HPV status. Higher median TMB was observed in lung and skin cases, which exhibited significant enrichment of mutational signatures indicative of tobacco- and UV-induced DNA damage, respectively. Conclusions: HPV+ and HPV- SCC populations have distinct genomic profiles and, for the latter, anatomic site is correlated with TMB distribution, secondary to associated carcinogen exposure. As such, biomarkers such as TMB and UV signature can provide unexpected insight into site of origin misdiagnoses and may correlate with benefit from immune checkpoint inhibitors

Perioperative Care for Kidney Transplant Recipients

Transplantation carries significant mortality benefit compared to dialysis in end-stage kidney disease. Increased perioperative risk, however, results in a higher mortality in the first 3 months post-transplantation compared to remaining on haemodialysis. Consequently, optimal perioperative management is essential. Patients presenting for kidney transplantation require rapid assessment and preparation for theatre to minimise ischaemic times and improve mortality and graft outcomes. This task is often complicated by the presence of multiple medical comorbidities. Furthermore, early complications of hypotension, delayed graft function, renovascular and ureteric surgical complications and rejection render the perioperative phase of transplant challenging for the recipient and for the transplant team. In this chapter, we outline current practices in the assessment and management of kidney transplant recipients during the perioperative period, particularly focusing on their clinical application and the evidence underpinning them

Vector bundles on the projective line and finite domination of chain complexes

Finitely dominated chain complexes over a Laurent polynomial ring in one indeterminate are characterised by vanishing of their Novikov homology. We present an algebro-geometric approach to this result, based on extension of chain complexes to sheaves on the projective line. We also discuss the K-theoretical obstruction to extension.Comment: v1: 11 page

Palliative care needs in patients hospitalized with heart failure (PCHF) study: rationale and design

Abstract Aims The primary aim of this study is to provide data to inform the design of a randomized controlled clinical trial (RCT) of a palliative care (PC) intervention in heart failure (HF). We will identify an appropriate study population with a high prevalence of PC needs defined using quantifiable measures. We will also identify which components a specific and targeted PC intervention in HF should include and attempt to define the most relevant trial outcomes. Methods An unselected, prospective, near-consecutive, cohort of patients admitted to hospital with acute decompensated HF will be enrolled over a 2-year period. All potential participants will be screened using B-type natriuretic peptide and echocardiography, and all those enrolled will be extensively characterized in terms of their HF status, comorbidity, and PC needs. Quantitative assessment of PC needs will include evaluation of general and disease-specific quality of life, mood, symptom burden, caregiver burden, and end of life care. Inpatient assessments will be performed and after discharge outpatient assessments will be carried out every 4 months for up to 2.5 years. Participants will be followed up for a minimum of 1 year for hospital admissions, and place and cause of death. Methods for identifying patients with HF with PC needs will be evaluated, and estimates of healthcare utilisation performed. Conclusion By assessing the prevalence of these needs, describing how these needs change over time, and evaluating how best PC needs can be identified, we will provide the foundation for designing an RCT of a PC intervention in HF

Sea anemones may thrive in a high CO2 world

Increased seawater pCO 2, and in turn 'ocean acidification' (OA), is predicted to profoundly impact marine ecosystem diversity and function this century. Much research has already focussed on calcifying reef-forming corals (Class: Anthozoa) that appear particularly susceptible to OA via reduced net calcification. However, here we show that OA-like conditions can simultaneously enhance the ecological success of non-calcifying anthozoans, which not only play key ecological and biogeochemical roles in present day benthic ecosystems but also represent a model organism should calcifying anthozoans exist as less calcified (soft-bodied) forms in future oceans. Increased growth (abundance and size) of the sea anemone (Anemonia viridis) population was observed along a natural CO 2 gradient at Vulcano, Italy. Both gross photosynthesis (P G) and respiration (R) increased with pCO 2 indicating that the increased growth was, at least in part, fuelled by bottom up (CO 2 stimulation) of metabolism. The increase of P G outweighed that of R and the genetic identity of the symbiotic microalgae (Symbiodinium spp.) remained unchanged (type A19) suggesting proximity to the vent site relieved CO 2 limitation of the anemones' symbiotic microalgal population. Our observations of enhanced productivity with pCO 2, which are consistent with previous reports for some calcifying corals, convey an increase in fitness that may enable non-calcifying anthozoans to thrive in future environments, i.e. higher seawater pCO 2. Understanding how CO 2-enhanced productivity of non- (and less-) calcifying anthozoans applies more widely to tropical ecosystems is a priority where such organisms can dominate benthic ecosystems, in particular following localized anthropogenic stress. © 2012 Blackwell Publishing Ltd