Optimal individualized decision rules from a multi-arm trial: A comparison of methods and an application to tailoring inter-donation intervals among blood donors in the UK.

There is a growing interest in precision medicine where individual heterogeneity is incorporated into decision-making and treatments are tailored to individuals to provide better healthcare. One important aspect of precision medicine is the estimation of the optimal individualized treatment rule (ITR) that optimizes the expected outcome. Most methods developed for this purpose are restricted to the setting with two treatments, while clinical studies with more than two treatments are common in practice. In this work, we summarize methods to estimate the optimal ITR in the multi-arm setting and compare their performance in large-scale clinical trials via simulation studies. We then illustrate their utilities with a case study using the data from the INTERVAL trial, which randomly assigned over 20,000 male blood donors from England to one of the three inter-donation intervals (12-week, 10-week, and eight-week) over two years. We estimate the optimal individualized donation strategies under three different objectives. Our findings are fairly consistent across five different approaches that are applied: when we target the maximization of the total units of blood collected, almost all donors are assigned to the eight-week inter-donation interval, whereas if we aim at minimizing the low hemoglobin deferral rates, almost all donors are assigned to donate every 12 weeks. However, when the goal is to maximize the utility score that "discounts" the total units of blood collected by the incidences of low hemoglobin deferrals, we observe some heterogeneity in the optimal inter-donation interval across donors and the optimal donor assignment strategy is highly dependent on the trade-off parameter in the utility function.Medical Research Council programme MC_UU_00002/

Assessing regional patterns of juvenile salmon growth in the Salish Sea

Early marine juvenile growth in Pacific salmon is generally positively correlated with overall survival to reproductive age. In this study, regional patterns of juvenile salmon growth are being analyzed over a two-year period (2012-2013) in the Salish Sea and surrounding waters to better assess juvenile productivity, via growth, in the Salish Sea and surrounding waters to provide us insight into possible mechanisms regulating survival. Insulin-like growth factor-1 (IGF-1), a hormone used to assess instantaneous growth in fishes, including juvenile salmon, was measured in late June and early July of 2012 and 2013 in the Strait of Georgia, Johnstone Strait, Queen Charlotte Strait, and Puget Sound. Juvenile sockeye (Oncorhynchus nerka) and pink salmon (O. gorbuscha) were collected in 2012, whereas juvenile coho (O. kisutch), Chinook (O. tshawytscha), and chum salmon (O. keta) where obtained in both years. In 2012 IGF-1 levels were highest in pink salmon from the Gulf Islands and Puget Sound; this was a unique pattern among the 5 species of juvenile salmon sampled. Coho salmon IGF-1 levels were highest in samples from the Northern Strait of Georgia. Chinook salmon IGF-1 levels were significantly higher in the Strait of Georgia than Puget Sound. The only regions where IGF-1 values were consistently low for three of the four species were Queen Charlotte Strait and Johnstone Strait. Analyses of 2013 IGF-1 levels (juvenile coho, Chinook, chum and a low number of sockeye) are underway and scheduled plans to obtain samples in late June to early July of 2014 are in place

Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease

The cause of Crohn's disease (CD) remains poorly understood. Counterintuitively, these patients possess an impaired acute inflammatory response, which could result in delayed clearance of bacteria penetrating the lining of the bowel and predispose to granuloma formation and chronicity. We tested this hypothesis in human subjects by monitoring responses to killed Escherichia coli injected subcutaneously into the forearm. Accumulation of 111In-labeled neutrophils at these sites and clearance of 32P-labeled bacteria from them were markedly impaired in CD. Locally increased blood flow and bacterial clearance were dependent on the numbers of bacteria injected. Secretion of proinflammatory cytokines by CD macrophages was grossly impaired in response to E. coli or specific Toll-like receptor agonists. Despite normal levels and stability of cytokine messenger RNA, intracellular levels of tumor necrosis factor (TNF) were abnormally low in CD macrophages. Coupled with reduced secretion, these findings indicate accelerated intracellular breakdown. Differential transcription profiles identified disease-specific genes, notably including those encoding proteins involved in vesicle trafficking. Intracellular destruction of TNF was decreased by inhibitors of lysosomal function. Together, our findings suggest that in CD macrophages, an abnormal proportion of cytokines are routed to lysosomes and degraded rather than being released through the normal secretory pathway

Intraoperative electron radiation therapy as an important treatment modality in retroperitoneal sarcoma

Local recurrence (LR) rates in patients with retroperitoneal sarcoma (RPS) are high, ranging from 40% to 80%, with no definitive studies describing the best way to administer radiation. Intraoperative electron beam radiation therapy (IOERT) provides a theoretical advantage for access to the tumor bed with reduced toxicity to surrounding structures. The goal of this study was to evaluate the role of IOERT in high-risk patients

Recent Salmon Declines: A Result of Lost Feeding Opportunities Due to Bad Timing?

As the timing of spring productivity blooms in near-shore areas advances due to warming trends in global climate, the selection pressures on out-migrating salmon smolts are shifting. Species and stocks that leave natal streams earlier may be favoured over later-migrating fish. The low post-release survival of hatchery fish during recent years may be in part due to static release times that do not take the timing of plankton blooms into account. This study examined the effects of release time on the migratory behaviour and survival of wild and hatchery-reared coho salmon (Oncorhynchus kisutch) using acoustic and coded-wire telemetry. Plankton monitoring and near-shore seining were also conducted to determine which habitat and food sources were favoured. Acoustic tags (n = 140) and coded-wire tags (n = 266,692) were implanted into coho salmon smolts at the Seymour and Quinsam Rivers, in British Columbia, Canada. Differences between wild and hatchery fish, and early and late releases were examined during the entire lifecycle. Physiological sampling was also carried out on 30 fish from each release group. The smolt-to-adult survival of coho salmon released during periods of high marine productivity was 1.5- to 3-fold greater than those released both before and after, and the fish's degree of smoltification affected their downstream migration time and duration of stay in the estuary. Therefore, hatchery managers should consider having smolts fully developed and ready for release during the peak of the near-shore plankton blooms. Monitoring chlorophyll a levels and water temperature early in the spring could provide a forecast of the timing of these blooms, giving hatcheries time to adjust their release schedule

COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records

BACKGROUND: Updatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework. METHODS: In this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status. FINDINGS: Among 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1. INTERPRETATION: Our analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources. FUNDING: British Heart Foundation Data Science Centre, led by Health Data Research UK

Aspects of the glaciation and superficial deposits of Pembrokeshire

"Since the publication of the work of Jehu and Charlesworth the distribution and significance of the glacial deposits of the Irish Sea have remained in a somewhat confused condition." So said Professor w.D. Evans in 1964. This thesis represents an attempt to remove the confusion from one small corner of the Irish Sea basin; it is concentrated largely in North Pembrokeshire, and aims to resolve some of the stratigraphic and chronological problems concerned with the Pleistocene deposits of the region. There is a long history of research into the glaciation of North Pembrokeshire. Most of the early work was undertaken in Dewisland (the St. David's Peninsula), but in the major contributions of Jehu (1904) ond Charlesworth (1929) something was revealed of the Pleistocene history of North Pembrokeshire as a whole. Subsequent work has been greatly influenced by these two authors, and there has been no detailed field study of the area since Charlesworth. As a result, many controversies have arisen in recent years; these range from the purely stratigraphic problems of the classic tripartite drift succession and the nature of the Upper Boulder-clay to the absolute age of the Pembrokeshire drifts. Again, there is doubt concerning the number of glaciations represented in North Pembrokeshire; about the existence of the South Wales End-moraine, the pro-glacial lakes, and the so-called overflow channels of Charlesworth; and about the age and origins of the coastal features of the county. These are among the problems that this thesis attempts to answer. [Please see pdf. for full abstract