TTK is Getting MPI-Ready

This system paper documents the technical foundations for the extension of the Topology ToolKit (TTK) to distributed-memory parallelism with the Message Passing Interface (MPI). While several recent papers introduced topology-based approaches for distributed-memory environments, these were reporting experiments obtained with tailored, mono-algorithm implementations. In contrast, we describe in this paper a versatile approach (supporting both triangulated domains and regular grids) for the support of topological analysis pipelines, i.e., a sequence of topological algorithms interacting together, possibly on distinct numbers of processes. While developing this extension, we faced several algorithmic and software engineering challenges, which we document in this paper. Specifically, we describe an MPI extension of TTK's data structure for triangulation representation and traversal, a central component to the global performance and generality of TTK's topological implementations. We also introduce an intermediate interface between TTK and MPI, both at the global pipeline level, and at the fine-grain algorithmic level. We provide a taxonomy for the distributed-memory topological algorithms supported by TTK, depending on their communication needs and provide examples of hybrid MPI+thread parallelizations. Detailed performance analyses show that parallel efficiencies range from 20% to 80% (depending on the algorithms), and that the MPI-specific preconditioning introduced by our framework induces a negligible computation time overhead. We illustrate the new distributed-memory capabilities of TTK with an example of advanced analysis pipeline, combining multiple algorithms, run on the largest publicly available dataset we have found (120 billion vertices) on a standard cluster with 64 nodes (for a total of 1536 cores). Finally, we provide a roadmap for the completion of TTK's MPI extension, along with generic recommendations for each algorithm communication category.

Does burnout affect clinical reasoning? An observational study among residents in general practice

BACKGROUND

Burnout results from excessive demands at work. Caregivers suffering from burnout show a state of emotional exhaustion, leading them to distance themselves from their patients and to become less efficient in their work. While some studies have shown a negative impact of burnout on physicians' clinical reasoning, others have failed to demonstrate any such impacts. To better understand the link between clinical reasoning and burnout, we carried out a study looking for an association between burnout and clinical reasoning in a population of general practice residents.

METHODS

We conducted a cross-sectional observational study among residents in general practice in 2017 and 2019. Clinical reasoning performance was assessed using a script concordance test (SCT). The Maslach Burnout Inventory for Human Services Survey (MBI-HSS) was used to determine burnout status in both original standards of Maslach's burnout inventory manual (conventional approach) and when individuals reported high emotional exhaustion in combination with high depersonalization or low personal accomplishment compared to a norm group ("emotional exhaustion +1" approach).

RESULTS

One hundred ninety-nine residents were included. The participants' mean SCT score was 76.44% (95% CI: 75.77-77.10). In the conventional approach, 126 residents (63.31%) had no burnout, 37 (18.59%) had mild burnout, 23 (11.56%) had moderate burnout, and 13 (6.53%) had severe burnout. In the "exhaustion + 1" approach, 38 residents had a burnout status (19.10%). We found no significant correlation between burnout status and SCT scores either for conventional or "exhaustion + 1" approaches.

CONCLUSIONS

Our data seem to indicate that burnout status has no significant impact on clinical reasoning. However, one speculation is that SCT mostly examines the clinical reasoning process's analytical dimension, whereas emotions are conventionally associated with the intuitive dimension. We think future research might aim to explore the impact of burnout on intuitive clinical reasoning processes.

Long-term follow-up of the Medical Research Council CLASICC trial of conventional versus laparoscopically assisted resection in colorectal cancer

BACKGROUND

Laparoscopic resection is used widely in the management of colorectal cancer; however, the data on long-term outcomes, particularly those related to rectal cancer, are limited. The results of long-term follow-up of the UK Medical Research Council trial of laparoscopically assisted versus open surgery for colorectal cancer are presented.

METHODS

A total of 794 patients from 27 UK centres were randomized to laparoscopic or open surgery in a 2:1 ratio between 1996 and 2002. Long-term follow-up data were analysed to determine differences in survival outcomes and recurrences for intention-to-treat and actual treatment groups.

RESULTS

Median follow-up of all patients was 62·9 (interquartile range 22·9 - 92·8) months. There were no statistically significant differences between open and laparoscopic groups in overall survival (78·3 (95 per cent confidence interval (c.i.) 65·8 to 106·6) versus 82·7 (69·1 to 94·8) months respectively; P = 0·780) and disease-free survival (DFS) (89·5 (67·1 to 121·7) versus 77·0 (63·3 to 94·0) months; P = 0·589). In colonic cancer intraoperative conversions to open surgery were associated with worse overall survival (hazard ratio (HR) 2·28, 95 per cent c.i. 1·47 to 3·53; P < 0·001) and DFS (HR 2·20, 1·31 to 3·67; P = 0·007). In terms of recurrence, no significant differences were observed by randomized procedure. However, at 10 years, right colonic cancers showed an increased propensity for local recurrence compared with left colonic cancers: 14·7 versus 5·2 per cent (difference 9·5 (95 per cent c.i. 2·3 to 16·6) per cent; P = 0·019).

CONCLUSION

Long-term results continue to support the use of laparoscopic surgery for both colonic and rectal cancer.

Expression of cyclin D2 is an independent predictor of the development of hepatic metastasis in colorectal cancer

INTRODUCTION

Cyclin D1 has been implicated in the progression of several cancers by virtue of its influence on progression of the G1/S phase of the cell cycle. However, little is known about the possible roles of cyclin D2 and D3 in colorectal cancers (CRCs).

METHOD

We investigated the expression levels of cyclin D2 and D3 in 84 CRC specimens. Antigen expression was determined by immunohistochemical analysis of cyclin D1, D2, D3, p16INK4A and Ki67 on tissue microarrays constructed using core samples from tumour centres and margins.

RESULTS

For the whole cohort, expression of cyclin D2 at the margin was associated with vascular invasion (P = 0.039), lymph node metastasis (P = 0.020) and liver metastasis (P < 0.001). In patients with stage I and II tumours (n = 84), elevated cyclin D2 and D3 were associated with vascular invasion (P = 0.014 and 0.028 respectively), liver metastasis (P = 0.001 and 0.007 respectively) and reduced disease specific survival (Cyclin D2, P < 0.022). No association was noted between the proliferative marker Ki-67 and the D-type cyclins.

CONCLUSION

These findings suggest that cyclin D2 expression at the invasive margin of CRCs is associated with liver metastasis and may serve as a useful prognostic marker and indicator of the need for adjuvant therapy.

Enhanced hot-electron localization and heating in high-contrast ultraintense laser irradiation of microcone targets

We report experiments demonstrating enhanced coupling efficiencies of high-contrast laser irradiation to nanofabricated conical targets. Peak temperatures near 200 eV are observed with modest laser energy (10 J), revealing similar hot-electron localization and material heating to reduced mass targets (RMTs), despite having a significantly larger mass. Collisional particle-in-cell simulations attribute the enhancement to self-generated resistive (approximately 10 MG) magnetic fields forming within the curvature of the cone wall, which confine energetic electrons to heat a reduced volume at the tip. This represents a different electron confinement mechanism (magnetic, as opposed to electrostatic sheath confinement in RMTs) controllable by target shape.

Randomized double-blind phase II survival study comparing immunization with the anti-idiotypic monoclonal antibody 105AD7 against placebo in advanced colorectal cancer

The cancer vaccine 105AD7 is an anti-idiotypic monoclonal antibody that mimics the tumour-associated antigen 791T/gp72 (CD55, Decay Accelerating Factor) on colorectal cancer cells. Phase I studies in patients with advanced disease confirmed that 105AD7 is non-toxic, and that T cell responses could be generated. A prospective, randomized, double-blind, placebo-controlled survival study in patients with advanced colorectal cancer was performed. 162 patients were enrolled between April 1994 and October 1996. Patients attended at trial entry, and at 6 and 12 weeks, where they received 105AD7 or placebo. Study groups were comparable in terms of patient demographics, and time from diagnosis of advanced colorectal cancer (277.1 v 278.6 days). Baseline disease was similar, with 50% of patients having malignancy in at least 2 anatomic sites. Compliance with treatment was poor, with only 50% of patients receiving 3 planned vaccinations. Median survival from randomization date was 124 and 184 days in 105AD7 and placebo arms respectively (P = 0.38), and 456 and 486 days from the date of diagnosis of advanced disease (P = 0.82). 105AD7 vaccination does not prolong survival in patients with advanced colorectal cancer. The reasons for lack of efficacy are unclear, but may reflect the high tumour burden in the patient population, and poor compliance with immunization. Further vaccine studies should concentrate on patients with minimal residual disease.

Management of "brittle" diabetes with a preprogrammable implanted insulin pump delivering intraperitoneal insulin

OBJECTIVE

Glycaemic control in a young woman with "brittle" diabetes.

DESIGN

Use of a preprogrammable fully implanted pump (Infusaid) to deliver insulin intraperitoneally at variable rates, giving a total dose of about 60 units/24 h.

SETTING

Endocrinology department in a teaching hospital.

PATIENT

Thirty year old woman with 15 years' history of "brittle" diabetes.

MAIN OUTCOME MEASURES

Glycated haemoglobin concentration; plasma glucose concentration.

RESULTS

After implantation of the pump there was an immediate and sustained improvement in diabetic control. The patient's glycated haemoglobin concentration decreased from 15.2% to 9.2% over seven months. Her daily glucose concentrations were in the range 3.5-12 mmol/l. She has not been admitted to hospital since implantation of the pump, which was eight months before the time of writing.

CONCLUSION

The implanted programmable intraperitoneal insulin pump may be of value in the management of patients with "brittle" diabetes in whom other attempts at glycaemic control have failed.

Retrospective study of histological features of acute rejection in renal allografts and comparison with circulating T cell populations

The histological severity of acute rejection in renal allografts was determined for 39 rejection episodes in 30 renal transplant recipients. Data were compared with the peripheral blood T cell subset ratios measured before and at the onset of the rejection episode. T cell subset ratios showed no correlation with the histological severity of rejection, nor with the reversibility of the rejection episode. The grade of histological rejection on biopsy was predictive of graft survival. We conclude that renal biopsy remains the best method for determining the severity and outcome of acute allograft rejection episodes.

The response of the lower oesophageal sphincter to a test-meal stimulus

The response of the lower oesophageal sphincter to test meals has been assessed using two manometric techniques. Tests in which the sphincteric pressures were continuously monitored proved to be the most satisfactory and test meals which were predominantly meat extract provided the greatest stimulus. Normal subjects increased the sphincteric pressure 86.7 per cent above the basal levels within 30 minutes of the introduction of the test meal, whereas patients with symptomatic hiatus hernia had diminished responses with pressure increases of only 30 per cent above basal levels. Patients with peptic ulceration or stricture of the oesophagus failed to respond to any form of test meal.