A hybrid Shewhart chart for visualizing and learning from epidemic data.

OBJECTIVE: As the globe endures the coronavirus disease 2019 (COVID-19) pandemic, we developed a hybrid Shewhart chart to visualize and learn from day-to-day variation in a variety of epidemic measures over time. CONTEXT: Countries and localities have reported daily data representing the progression of COVID-19 conditions and measures, with trajectories mapping along the classic epidemiological curve. Settings have experienced different patterns over time within the epidemic: pre-exponential growth, exponential growth, plateau or descent and/ or low counts after descent. Decision-makers need a reliable method for rapidly detecting transitions in epidemic measures, informing curtailment strategies and learning from actions taken. METHODS: We designed a hybrid Shewhart chart describing four 'epochs' ((i) pre-exponential growth, (ii) exponential growth, (iii) plateau or descent and (iv) stability after descent) of the COVID-19 epidemic that emerged by incorporating a C-chart and I-chart with a log-regression slope. We developed and tested the hybrid chart using international data at the country, regional and local levels with measures including cases, hospitalizations and deaths with guidance from local subject-matter experts. RESULTS: The hybrid chart effectively and rapidly signaled the occurrence of each of the four epochs. In the UK, a signal that COVID-19 deaths moved into exponential growth occurred on 17 September, 44 days prior to the announcement of a large-scale lockdown. In California, USA, signals detecting increases in COVID-19 cases at the county level were detected in December 2020 prior to statewide stay-at-home orders, with declines detected in the weeks following. In Ireland, in December 2020, the hybrid chart detected increases in COVID-19 cases, followed by hospitalizations, intensive care unit admissions and deaths. Following national restrictions in late December, a similar sequence of reductions in the measures was detected in January and February 2021. CONCLUSIONS: The Shewhart hybrid chart is a valuable tool for rapidly generating learning from data in close to real time. When used by subject-matter experts, the chart can guide actionable policy and local decision-making earlier than when action is likely to be taken without it.

Understanding variation in reported covid-19 deaths with a novel Shewhart chart application.

OBJECTIVE: Motivated by the coronavirus disease 2019 (covid-19) pandemic, we developed a novel Shewhart chart to visualize and learn from variation in reported deaths in an epidemic. CONTEXT: Without a method to understand if a day-to-day variation in outcomes may be attributed to meaningful signals of change-rather than variability we would expect-care providers, improvement leaders, policy-makers, and the public will struggle to recognize if epidemic conditions are improving. METHODS: We developed a novel hybrid C-chart and I-chart to detect within a geographic area the start and end of exponential growth in reported deaths. Reported deaths were the unit of analysis owing to erratic reporting of cases from variability in local testing strategies. We used simulation and case studies to assess chart performance and define technical parameters. This approach also applies to other critical measures related to a pandemic when high-quality data are available. CONCLUSIONS: The hybrid chart detected the start of exponential growth and identified early signals that the growth phase was ending. During a pandemic, timely reliable signals that an epidemic is waxing or waning may have mortal implications. This novel chart offers a practical tool, accessible to system leaders and frontline teams, to visualize and learn from daily reported deaths during an epidemic. Without Shewhart charts and, more broadly, a theory of variation in our epidemiological arsenal, we lack a scientific method for a real-time assessment of local conditions. Shewhart charts should become a standard method for learning from data in the context of a pandemic or epidemic.

A phase 1 trial of Vorinostat in combination with concurrent chemoradiation therapy in the treatment of advanced staged head and neck squamous cell carcinoma.

Purpose Vorinostat is a potent HDAC inhibitor that sensitizes head and neck squamous cell carcinoma (HNSCC) to cytotoxic therapy while sparing normal epithelium. The primary objective of this Phase I study was to determine the maximally tolerated dose (MTD) and safety of Vorinostat in combination with standard chemoradiation therapy treatment in HNSCC. Patients and Methods Eligible patients had pathologically confirmed Stage III, IVa, IVb HNSCC, that was unresectable or borderline resectable involving the larynx, hypopharynx, nasopharynx, and oropharynx. Vorinostat was administered at the assigned dosage level (100-400 mg, three times weekly) in a standard 3 + 3 dose escalation design. Vorinostat therapy began 1 week prior to initiation of standard, concurrent chemoradiation therapy and continued during the entire course of therapy. Results Twenty six patients met eligibility criteria and completed the entire protocol. The primary tumor sites included tonsil (12), base of tongue (9), posterior pharyngeal wall (1), larynx (4) and hypopharynx (3). Of the 26 patients, 17 were HPV-positive and 9 were HPV-negative. The MTD of Vorinostat was 300 mg administered every other day. Anemia (n = 23/26) and leukopenia (n = 20/26) were the most commonly identified toxicities. The most common Grade3/4 events included leukopenia (n = 11) and lymphopenia (n = 17). No patient had Grade IV mucositis, dermatitis or xerostomia. The median follow time was 33.8 months (range 1.6-82.9 months). Twenty four of 26 (96.2%) patients had a complete response to therapy. Conclusion Vorinostat in combination with concurrent chemoradiation therapy is a safe and highly effective treatment regimen in HNSCC. There was a high rate of complete response to therapy with toxicity rates comparable, if not favorable to existing therapies. Further investigation in Phase II and III trials is strongly recommended.

The Clinical Dilemma of Anticoagulation Use in Patients with Cerebral Amyloid Angiopathy and Atrial Fibrillation.

PURPOSE OF REVIEW: This review highlights current management of patients with concomitant cerebral amyloid angiopathy (CAA) and atrial fibrillation (AF). We review quantifying risk of ischemic and hemorrhagic stroke as well as treatments to minimize future risk. RECENT FINDINGS: Ischemic stroke risk in AF can be quantified by CHA2DS2-VASc and assessing left atrial echocardiographic characteristics. Patients deemed not low risk by CHA2DS2-VASC should be anticoagulated. CAA increases intracranial hemorrhage risk. CAA biomarkers include cortical microbleeds (CMBs), cortical superficial siderosis (cSS), convexal subarachnoid hemorrhage (cSAH), and lobar intracerebral hemorrhage (ICH). CAA with prior lobar ICH has an annual recurrence rate of 8.9%. CAA with cSAH carries an even higher annual lobar ICH risk of 19%. CMBs are associated with a dose-dependent risk of ICH, which rises with OACs. In patients with AF, antithrombotics should be avoided in CAA with predominant ICH, cSS, or cSAH features. Those with ≥ 2 CMB require in-depth risk-benefit analysis using a multidisciplinary approach.

Impact of serum HER2, TIMP-1, and CAIX on outcome for HER2+ metastatic breast cancer patients: CCTG MA.31 (lapatinib vs. trastuzumab).

BACKGROUND: The lapatinib-taxane combination led to shorter PFS than trastuzumab-taxane in HER2+ metastatic breast cancer. We investigated the prognostic and predictive effects of pretreatment serum HER2, CAIX, and TIMP-1. METHODS: MA.31 accrued 652 patients; 537 (82%) were centrally confirmed HER2+. Biomarkers were categorized for univariate and multivariable predictive investigations with a median cut-point, ULN cut-points (15 ng/ml for HER2; 506 pg/ml for CAIX; 454 pg/ml for TIMP-1), and custom cut-points (30 and 100 ng/ml for HER2). Stratified step-wise forward Cox multivariable analysis examined continuous and categorical effects of biomarkers on PFS in the ITT and central HER2+ populations; central HER2+ biomarker results are shown. RESULTS: Serum was banked for 472 (72%) of 652 patients. Higher serum HER2 (>median; >15; >30; or >100 ng/ml; p = 0.05-0.002); higher CAIX (>median; >506 pg/ml; p = 0.02; p = 0.001); and higher TIMP-1 (> median; > 454 pg/ml; p = 0.001; p = 0.02) had shorter univariate PFS. In multivariable analysis, higher continuous TIMP-1 was associated with significantly shorter PFS: HR = 1.001 (95% CI = 1.00-01.002; p = 0.004). Continuous serum HER2 and CAIX were not significantly associated with PFS. HER2 of 15 ng/ml or higher had shorter PFS (p = 0.02); higher categorical CAIX had shorter PFS (p = 0.01-0.08). Interaction terms of HER2, CAIX, and TIMP-1 with treatment were not significant; the predictive test power was low. CONCLUSIONS: Higher levels of serum TIMP-1, CAIX, and HER2 were significant prognostic biomarkers of shorter PFS. We found no significant interaction between serum biomarkers and response to lapatinib versus trastuzumab. Evaluation of TIMP-1 and CAIX-targeted therapy in addition to HER2-targeted therapy appears warranted in patients with elevated serum levels of these biomarkers.

Progression-free survival by local investigator versus independent central review: comparative analysis of the AGO-OVAR16 Trial.

BACKGROUND: Analysis of progression-free survival (PFS) as the primary endpoint in advanced epithelial ovarian, fallopian tube, and primary peritoneal cancer (AEOC) trials may be confounded by the difficulty of radiologic evaluation of disease progression and the potential for discrepancy between investigator and blinded independent central assessments. PFS as assessed by local investigator (INV) was the primary endpoint of AGO-OVAR16, a randomized, double-blind trial of pazopanib maintenance therapy in AEOC. To confirm the robustness of the primary analysis, PFS was also evaluated by blinded independent central review (BICR). METHODS: Patients with histologically confirmed AEOC (N = 940) were randomized 1:1 to receive pazopanib 800 mg/day or placebo for up to 24 months. Tumor response in the intent-to-treat population was evaluated by CT/MRI every 6 months and analyzed per RECIST 1.0. RESULTS: Pazopanib prolonged PFS versus placebo by INV (median 17.9 vs 12.3 months; hazard ratio [HR] = 0.766, 95% confidence interval [CI]: 0.643-0.911; P = 0.0021). Results for PFS by BICR were similar (median 15.4 vs 11.8 months; HR = 0.802, 95% CI: 0.678-0.949; P = 0.0084). Progression events were recorded later by INV in 23% of pazopanib-treated patients and 17% of placebo-treated patients. The overall concordance between INV and BICR assessments was 84% and 86% in the pazopanib and placebo arms, respectively. CONCLUSIONS: By INV and BICR assessments, maintenance therapy with pazopanib in AEOC provided a significantly longer PFS than placebo. The good overall concordance between INV and BICR assessments, as well as HR and P value consistency, supports the reliability of investigator-assessed PFS as the primary endpoint in AGO-OVAR16.

Heterogeneity of TERT promoter mutations status in squamous cell carcinomas of different anatomical sites.

Squamous cell carcinoma (SCC) can arise from different anatomical sites including the skin, head and neck, lung, esophagus, genital area, and so on. Despite the same histopathologic features and immunohistochemistry profile, the SCCs of different body sites can show tremendous differences in their presenting symptoms, risk factor associations, natural history, prognosis, and response to treatment. This may reflect the fact that SCCs are heterogenous and likely have unique molecular characteristics at different anatomical sites. Recurrent somatic mutations in the TERT promoter region were first reported in human melanomas. Subsequently, other tumors including cutaneous SCC were found to demonstrate high frequencies of the same mutations. However, the incidences of TERT promoter mutation in noncutaneous SCCs have not been systemically studied. We investigated the TERT promoter mutation status among SCCs from different sites. We collected 84 cases of SCC from the skin (27), head and neck (12), lung (25), and cervix (10), as well as 10 cases of urothelial carcinoma with squamous differentiation (UC-SqD). We found that the frequencies of TERT promoter mutation among SCC of different sits are quite heterogenous: ~70% in skin SCC and UC-SqD, 16.67% in head and neck SCC, and 0% in lung and cervix SCC. These results may support the hypothesis of different carcinogenesis mechanisms of SCC in different sites. It also indicates that TERT promoter mutation could be a biomarker for distinguishing skin SCC or UC-SqD vs pulmonary SCC.

Mycobacterium avium serovars 2 and 8 infections elicit unique activation of the host macrophage immune responses.

Mycobacterium avium is an opportunistic pathogen whose pathogenesis is attributed to its serovar-specific glycopeptidolipid (ssGPL), which varies among its 31 serovars. To determine if the presence and type of ssGPLs contribute to M. avium pathogenesis, we infected murine macrophages (mφs) with two M. avium wild type (wt) serovars (2 and 8) and their serovar-null strains. We examined the influence of ssGPL (presence and type) on cytokine production in non-activated (-IFN-γ) and activated (+IFN-γ) mφs, and the bacterial intra-mφ survival over a 6-day infection process. Serovar-2 infections activated TNF-α production that increased over the 6 day period and was capable of controlling the intra-mφ serovar-2 null strain. In contrast, the serovar-8 infection stimulated a strong pro-inflammatory response, but was incapable of removing the invading pathogen, maybe through IL-10 production. It was clear that the intracellular growth of serovar-null in contrast to the wt M. avium strains was easily controlled. Based on our findings and the undisputed fact that M. avium ssGPL is key to its pathogenesis, we conclude that it is not appropriate to dissect the pathogenesis of one M. avium serovar and apply those findings to other serovars.

IFN regulatory factor 5 is required for disease development in the FcgammaRIIB-/-Yaa and FcgammaRIIB-/- mouse models of systemic lupus erythematosus.

Polymorphisms in the transcription factor IFN regulatory factor 5 (IRF5) are strongly associated in human genetic studies with an increased risk of developing the autoimmune disease systemic lupus erythematosus. However, the biological role of IRF5 in lupus pathogenesis has not previously been tested in an animal model. In this study, we show that IRF5 is absolutely required for disease development in the FcgammaRIIB(-/-)Yaa and FcgammaRIIB(-/-) lupus models. In contrast to IRF5-sufficient FcgammaRIIB(-/-)Yaa mice, IRF5-deficient FcgammaRIIB(-/-)Yaa mice do not develop lupus manifestations and have a phenotype comparable to wild-type mice. Strikingly, full expression of IRF5 is required for the development of autoimmunity, as IRF5 heterozygotes had dramatically reduced disease. One effect of IRF5 is to induce the production of the type I IFN, IFN-alpha, a cytokine implicated in lupus pathogenesis. To address the mechanism by which IRF5 promotes disease, we evaluated FcgammaRIIB(-/-)Yaa mice lacking the type I IFN receptor subunit 1. Unlike the IRF5-deficient and IRF5-heterozygous FcgammaRIIB(-/-)Yaa mice, type I IFN receptor subunit 1-deficient FcgammaRIIB(-/-)Yaa mice maintained a substantial level of residual disease. Furthermore, in FcgammaRIIB(-/-) mice lacking Yaa, IRF5-deficiency also markedly reduced disease manifestations, indicating that the beneficial effects of IRF5 deficiency in FcgammaRIIB(-/-)Yaa mice are not due only to inhibition of the enhanced TLR7 signaling associated with the Yaa mutation. Overall, we demonstrate that IRF5 plays an essential role in lupus pathogenesis in murine models and that this is mediated through pathways beyond that of type I IFN production.

Requirement for DNA CpG content in TLR9-dependent dendritic cell activation induced by DNA-containing immune complexes.

Although TLR9 was originally thought to specifically recognize microbial DNA, it is now evident that mammalian DNA can be an effective TLR9 ligand. However, the DNA sequence required for TLR9 activation is controversial, as studies have shown conflicting results depending on the nature of the DNA backbone, the route of DNA uptake, and the cell type being studied. In systemic lupus erythematosus, a major route whereby DNA gains access to intracellular TLR9, and thereby activates dendritic cells (DCs), is through uptake as a DNA-containing immune complex. In this report, we used defined dsDNA fragments with a natural (phosphodiester) backbone and show that unmethylated CpG dinucleotides within dsDNA are required for murine DC TLR9 activation induced by a DNA-containing immune complex. The strongest activation is seen with dsDNA fragments containing optimal CpG motifs (purine-purine-CpG-pyrimidine-pyrimidine) that are common in microbial DNA but rare in mammalian DNA. Importantly, however, activation can also be induced by CpG-rich DNA fragments that lack these optimal CpG motifs and that we show are plentiful in CpG islands within mammalian DNA. No activation is induced by DNA fragments lacking CpG dinucleotides, although this CpG-free DNA can induce DC activation if internalized by liposomal transfection instead of as an immune complex. Overall, the data suggest that the release of CpG-rich DNA from mammalian DNA may contribute to the pathogenesis of autoimmune diseases such as systemic lupus erythematosus and psoriasis in which activation of TLR9 in DCs by self DNA has been implicated in disease pathogenesis.

Synesthesia, hallucination, and autism.

Synesthesia literally means a "union of the senses" whereby two or more of the five senses that are normally experienced separately are involuntarily and automatically joined together in experience (1, 2, 3). For example, some synesthetes experience a color when they hear a sound, although many instances of synesthesia also occur entirely within the visual sense. In this paper, I first mainly engage critically with Sollberger's view that there is reason to think that at least some synesthetic experiences can be viewed as truly veridical perceptions, and not as illusions or hallucinations (4). Among other things, I explore the possibility that many forms of synesthesia can be understood as experiencing what I will call "second-order secondary properties," that is, experiences of properties of objects induced by the secondary qualities of those objects. In doing so, I shed some light on why synesthesia is typically one-directional and its relation to some psychopathologies such as autism.

Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics.

In the current omics-age of research, major developments have been made in technologies that attempt to survey the entire repertoire of genes, transcripts, proteins, and metabolites present within a cell. While genomics has led to a dramatic increase in our understanding of such things as disease morphology and how organisms respond to medications, it is critical to obtain information at the proteome level since proteins carry out most of the functions within the cell. The primary tool for obtaining proteome-wide information on proteins within the cell is mass spectrometry (MS). While it has historically been associated with the protein identification, developments over the past couple of decades have made MS a robust technology for protein quantitation as well. Identifying quantitative changes in proteomes is complicated by its dynamic nature and the inability of any technique to guarantee complete coverage of every protein within a proteome sample. Fortunately, the combined development of sample preparation and MS methods have made it capable of quantitatively comparing many thousands of proteins obtained from cells and organisms.

Efficacy and safety following bosutinib dose reduction in patients with Philadelphia chromosome‒positive leukemias.

The recommended starting dose of bosutinib is 500 mg/day for chronic-phase (CP) or accelerated-/blast-phase Philadelphia chromosome-positive (Ph+) chronic myeloid leukemia (CML) resistant/intolerant to prior therapy. However, some patients may require dose reductions to manage the occurrences of adverse events (AEs). Bosutinib efficacy and safety were evaluated following dose reductions in a phase I/II study of Ph+ patients with CP CML resistant/intolerant to imatinib or imatinib plus dasatinib and/or nilotinib, and those with accelerated-/blast-phase CML or acute lymphoblastic leukemia after at least imatinib treatment. In all, 570 patients with ≥4 years' follow-up were included in this analysis. Among 144 patients who dose-reduced to bosutinib 400 mg/day (without reduction to 300 mg/day), 22 (15 %) had complete cytogenetic response (CCyR) before and after reduction, 40 (28 %) initially achieved CCyR after reduction, and 4 (3 %) only had CCyR before reduction. Among 95 patients who dose-reduced to bosutinib 300 mg/day, 23 (24 %) had CCyR before and after reduction, 13 (14 %) initially achieved CCyR after reduction, and 3 (3 %) only had CCyR before reduction. Results were similar to matched controls who remained on 500 mg/day, indicating dose reductions had not substantially affected efficacy. The incidence of treatment-emergent AEs was lower after dose reductions, particularly for gastrointestinal events. The incidence of hematologic toxicities generally was similar before and after dose reduction. The management of AEs with bosutinib through dose reduction can lead to improved/maintained efficacy and better tolerability; still, approximately half of patients on treatment at year 4 maintained a dose of ≥500 mg/day. ClinicalTrials.gov: NCT00261846.

A healthy bottom line: healthy life expectancy as an outcome measure for health improvement efforts.

CONTEXT: Good health is the most important outcome of health care, and healthy life expectancy (HLE), an intuitive and meaningful summary measure combining the length and quality of life, has become a standard in the world for measuring population health. METHODS: This article critically reviews the literature and practices around the world for measuring and improving HLE and synthesizes that information as a basis for recommendations for the adoption and adaptation of HLE as an outcome measure in the United States. FINDINGS: This article makes the case for adoption of HLE as an outcome measure at the national, state, community, and health care system levels in the United States to compare the effectiveness of alternative practices, evaluate disparities, and guide resource allocation. CONCLUSIONS: HLE is a clear, consistent, and important population health outcome measure that can enable informed judgments about value for investments in health care.

Outbreak of 2009 pandemic influenza A(H1N1), Los Lagos, Chile, April-June 2009.

On 17 May 2009, the first two cases of 2009 pandemic influenza A(H1N1) were confirmed in the Metropolitan region (Santiago, Chile). On 6 June 2009, Chile reported 500 confirmed cases, seven severe and two fatal. Because six of the severe cases and the two deaths occurred in the region of Los Lagos in southern Chile, a retrospective study was conducted using data on emergency room visits as well as laboratory viral surveillance, during the period from 1 April to 31 May, in order to establish the date of the beginning of the outbreak. From 1 to 27 June, data were collected in real time, to establish the real magnitude of the outbreak, describe its transmission, clinical severity and secondary attack rates. Confirmed cases, their household contacts and healthcare workers were interviewed. This analysis showed that the outbreak in Los Lagos started on 28 April. By 27 June, a total of 14.559 clinical cases were identified, affecting mostly 5-19 year-olds. The effective reproduction number during the initial phase (20 days) was 1.8 (1.6-2.0). Of the 190 confirmed cases with severe acute respiratory infection, 71 (37.4%) presented a risk condition or underlying illness.

A predictive survival model for patients with head and neck squamous cell carcinoma treated with immune check point inhibitors.

BACKGROUND: ICIs have expanded treatment options for HNSCC. A minority of the patients respond to these expensive treatments. PATIENTS AND METHODS: This is a single institutional retrospective review on 121 unresectable or metastatic HNSCC patients treated with ICIs. We predicted that inflammatory markers available through routine blood work, in addition to clinical characteristics may divide patients into groups more or less likely to respond to these agents. Here we develop and internally validate our nomogram to predict survival in patients treated with ICIs.

Learning networks for sustainable, large-scale improvement.

Large-scale improvement efforts known as improvement networks offer structured opportunities for exchange of information and insights into the adaptation of clinical protocols to a variety of settings.