Lift & Project Systems Performing on the Partial-Vertex-Cover Polytope

We study integrality gap (IG) lower bounds on strong LP and SDP relaxations derived by the Sherali-Adams (SA), Lovasz-Schrijver-SDP (LS+), and Sherali-Adams-SDP (SA+) lift-and-project (L&P) systems for the t-Partial-Vertex-Cover (t-PVC) problem, a variation of the classic Vertex-Cover problem in which only t edges need to be covered. t-PVC admits a 2-approximation using various algorithmic techniques, all relying on a natural LP relaxation. Starting from this LP relaxation, our main results assert that for every epsilon > 0, level-Theta(n) LPs or SDPs derived by all known L&P systems that have been used for positive algorithmic results (but the Lasserre hierarchy) have IGs at least (1-epsilon)n/t, where n is the number of vertices of the input graph. Our lower bounds are nearly tight. Our results show that restricted yet powerful models of computation derived by many L&P systems fail to witness c-approximate solutions to t-PVC for any constant c, and for t = O(n). This is one of the very few known examples of an intractable combinatorial optimization problem for which LP-based algorithms induce a constant approximation ratio, still lift-and-project LP and SDP tightenings of the same LP have unbounded IGs. We also show that the SDP that has given the best algorithm known for t-PVC has integrality gap n/t on instances that can be solved by the level-1 LP relaxation derived by the LS system. This constitutes another rare phenomenon where (even in specific instances) a static LP outperforms an SDP that has been used for the best approximation guarantee for the problem at hand. Finally, one of our main contributions is that we make explicit of a new and simple methodology of constructing solutions to LP relaxations that almost trivially satisfy constraints derived by all SDP L&P systems known to be useful for algorithmic positive results (except the La system).Comment: 26 page

The presence of psychological trauma symptoms in resuscitation providers and an exploration of debriefing practices

Introduction Witnessing traumatic experiences can cause post-traumatic stress disorder (PTSD). The true impact on healthcare staff of attending in-hospital cardiac arrests (IHCAs) has not been studied. This cross-sectional study examined cardiac arrest debriefing practices and the burden of attending IHCAs on nursing and medical staff. Methods A 33-item questionnaire-survey was sent to 517 doctors (of all grades), nurses and health-care assistants (HCAs) working in the emergency department, the acute medical unit and the intensive care unit of a district general hospital between April and August 2018. There were three sections: demographics; cardiac arrest and debriefing practices; trauma-screening questionnaire (TSQ). Results The response rate was 414/517 (80.1%); 312/414 (75.4%) were involved with IHCAs. Out of 1463 arrests, 258 (17.6%) were debriefed. Twenty-nine of 302 (9.6%) staff screened positively for PTSD. Healthcare assistants and Foundation Year 1 doctors had higher TSQ scores than nurses or more senior doctors (p = 0.02, p = 0.02, respectively). Debriefing was not associated with PTSD risk (p = 0.98). Only 8/67 (11.9%) of resuscitation leaders had prior debriefing training. Conclusions Nearly 10% of acute care staff screened positively for PTSD as a result of attending an IHCA, with junior staff being most at risk of developing trauma symptoms. Very few debriefs occurred, possibly because of a lack of debrief training amongst cardiac arrest team leaders. More support is required for acute care nursing and medical staff following an IHCA

Correction: Peak plasma interleukin-6 and other peripheral markers of inflammation in the first week of ischaemic stroke correlate with brain infarct volume, stroke severity and long-term outcome

In table 3, the correlation coefficient between peak plasma cortisol and mRS at 3 months (column 4, row 5), should read 0.48, not 0 [1]

Clinical outcome following acute ischaemic stroke relates to both activation and autoregulatory inhibition of cytokine production

BACKGROUND: As critical mediators of local and systemic inflammatory responses, cytokines are produced in the brain following ischaemic stroke. Some have been detected in the circulation of stroke patients, but their role and source is unclear. Focusing primarily on interleukin(IL)-1-related mechanisms, we serially measured plasma inflammatory markers, and the production of cytokines by whole blood, from 36 patients recruited within 12 h and followed up to 1 year after acute ischaemic stroke (AIS). RESULTS: Admission plasma IL-1 receptor antagonist (IL-1ra) concentration was elevated, relative to age-, sex-, and atherosclerosis-matched controls. IL-1β, soluble IL-1 receptor type II, tumour necrosis factor (TNF)-α, TNF-RII, IL-10 and leptin concentrations did not significantly differ from controls, but peak soluble TNF receptor type I (sTNF-RI) in the first week correlated strongly with computed tomography infarct volume at 5–7 days, mRS and BI at 3 and 12 months. Neopterin was raised in patients at 5–7 d, relative to controls, and in subjects with significant atherosclerosis. Spontaneous IL-1β, TNF-α and IL-6 gene and protein expression by blood cells was minimal, and induction of these cytokines by lipopolysaccharide (LPS) was significantly lower in patients than in controls during the first week. Minimum LPS-induced cytokine production correlated strongly with mRS and BI, and also with plasma cortisol. CONCLUSION: Absence of spontaneous whole blood gene activation or cytokine production suggests that peripheral blood cells are not the source of cytokines measured in plasma after AIS. Increased plasma IL-1ra within 12 h of AIS onset, the relationship between sTNF-RI and stroke severity, and suppressed cytokine induction suggests early activation of endogenous immunosuppressive mechanisms after AIS

Peak plasma interleukin-6 and other peripheral markers of inflammation in the first week of ischaemic stroke correlate with brain infarct volume, stroke severity and long-term outcome

BACKGROUND: Cerebral ischaemia initiates an inflammatory response in the brain and periphery. We assessed the relationship between peak values of plasma interleukin-6 (IL-6) in the first week after ischaemic stroke, with measures of stroke severity and outcome. METHODS: Thirty-seven patients with ischaemic stroke were prospectively recruited. Plasma IL-6, and other markers of peripheral inflammation, were measured at pre-determined timepoints in the first week after stroke onset. Primary analyses were the association between peak plasma IL-6 concentration with both modified Rankin score (mRS) at 3 months and computed tomography (CT) brain infarct volume. RESULTS: Peak plasma IL-6 concentration correlated significantly (p < 0.001) with CT brain infarct volume (r = 0.75) and mRS at 3 months (r = 0.72). It correlated similarly with clinical outcome at 12 months or stroke severity. Strong associations were also noted between either peak plasma C-reactive protein (CRP) concentration or white blood cell (WBC) count, and all outcome measures. CONCLUSIONS: These data provide evidence that the magnitude of the peripheral inflammatory response is related to the severity of acute ischaemic stroke, and clinical outcome

Simulating carbon accumulation and loss in the central Congo peatlands

Peatlands of the central Congo Basin have accumulated carbon over millennia. They currently store some 29 billion tonnes of carbon in peat. However, our understanding of the controls on peat carbon accumulation and loss and the vulnerability of this stored carbon to climate change is in its infancy. Here we present a new model of tropical peatland development, DigiBog_Congo, that we use to simulate peat carbon accumulation and loss in a rain-fed interfluvial peatland that began forming ~20,000 calendar years Before Present (cal. yr BP, where ‘present’ is 1950 CE). Overall, the simulated age-depth curve is in good agreement with palaeoenvironmental reconstructions derived from a peat core at the same location as our model simulation. We find two key controls on long-term peat accumulation: water at the peat surface (surface wetness) and the very slow anoxic decay of recalcitrant material. Our main simulation shows that between the Late Glacial and early Holocene there were several multidecadal periods where net peat and carbon gain alternated with net loss. Later, a climatic dry phase beginning ~5200 cal. yr BP caused the peatland to become a long-term carbon source from ~3975 to 900 cal. yr BP. Peat as old as ~7000 cal. yr BP was decomposed before the peatland's surface became wetter again, suggesting that changes in rainfall alone were sufficient to cause a catastrophic loss of peat carbon lasting thousands of years. During this time, 6.4 m of the column of peat was lost, resulting in 57% of the simulated carbon stock being released. Our study provides an approach to understanding the future impact of climate change and potential land-use change on this vulnerable store of carbon

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

Immune evasion is a hallmark of cancer. Losing the ability to present neoantigens through human leukocyte antigen (HLA) loss may facilitate immune evasion. However, the polymorphic nature of the locus has precluded accurate HLA copy-number analysis. Here, we present loss of heterozygosity in human leukocyte antigen (LOHHLA), a computational tool to determine HLA allele-specific copy number from sequencing data. Using LOHHLA, we find that HLA LOH occurs in 40% of non-small-cell lung cancers (NSCLCs) and is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity. The focal nature of HLA LOH alterations, their subclonal frequencies, enrichment in metastatic sites, and occurrence as parallel events suggests that HLA LOH is an immune escape mechanism that is subject to strong microenvironmental selection pressures later in tumor evolution. Characterizing HLA LOH with LOHHLA refines neoantigen prediction and may have implications for our understanding of resistance mechanisms and immunotherapeutic approaches targeting neoantigens. Video Abstract [Figure presented] Development of the bioinformatics tool LOHHLA allows precise measurement of allele-specific HLA copy number, improves the accuracy in neoantigen prediction, and uncovers insights into how immune escape contributes to tumor evolution in non-small-cell lung cancer

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Variability of the systemic acute phase response after ischemic stroke

Despite apparent relationships between ischemic stroke and the acute phase response (APR), considerable variation in the APR exists between individuals. We therefore performed post-hoc analysis of individual APR profiles in 31 patients with ischemic stroke in relation to volume of brain infarction. Patients with ischemic stroke had serial blood samples taken within 12 h, and up to 12 months of symptom onset, for analysis of plasma C-reactive protein (CRP) and interleukin-6 (IL-6). Computed tomography (CT) brain infarct volume was measured at 5 to 7 days (median 23.9 cm3). An increase in plasma CRP after the admission sample was evident in 94% of patients by day 5 to 7 (median increase 558% of admission value). CRP response, assessed as area under the curve between admission and day 5 to 7, correlated strongly (r = 0.62, p &lt;0.001) with CT infarct volume. Those with greater infarct volumes had more evidence of infection, either prior to or during the first week after stroke. The pattern of response was similar for IL-6, although only 77% showed an increase in plasma IL-6 after the admission sample (median increase 148% of admission value). These data suggest that, although infection and other factors may contribute to systemic inflammation, the extent of acute brain injury after ischemic stroke is a major factor influencing the magnitude and variability of the APR. © 2006 Elsevier B.V. All rights reserved