A framework for reconstructing transmission networks in infectious diseases.

In this paper, we propose a general framework for the reconstruction of the underlying cross-regional transmission network contributing to the spread of an infectious disease. We employ an autoregressive model that allows to decompose the mean number of infections into three components that describe: intra-locality infections, inter-locality infections, and infections from other sources such as travelers arriving to a country from abroad. This model is commonly used in the identification of spatiotemporal patterns in seasonal infectious diseases and thus in forecasting infection counts. However, our contribution lies in identifying the inter-locality term as a time-evolving network, and rather than using the model for forecasting, we focus on the network properties without any assumption on seasonality or recurrence of the disease. The topology of the network is then studied to get insight into the disease dynamics. Building on this, and particularly on the centrality of the nodes of the identified network, a strategy for intervention and disease control is devised.

An Orthogonally Equivariant Estimator of the Covariance Matrix in High Dimensions and for Small Sample Sizes.

We introduce an estimation method of covariance matrices in a high-dimensional setting, i.e., when the dimension of the matrix, p, is larger than the sample size n. Specifically, we propose an orthogonally equivariant estimator. The eigenvectors of such estimator are the same as those of the sample covariance matrix. The eigenvalue estimates are obtained from an adjusted profile likelihood function derived by approximating the integral of the density function of the sample covariance matrix over its eigenvectors, which is a challenging problem in its own right. Exact solutions to the approximate likelihood equations are obtained and employed to construct estimates that involve a tuning parameter. Bootstrap and cross-validation based algorithms are proposed to choose this tuning parameter under various loss functions. Finally, comparisons with two well-known orthogonally equivariant estimators are given, which are based on Monte-Carlo risk estimates for simulated data and misclassification errors in real data analyses.

A treelet transform analysis to relate nutrient patterns to the risk of hormonal receptor-defined breast cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC).

OBJECTIVE: Pattern analysis has emerged as a tool to depict the role of multiple nutrients/foods in relation to health outcomes. The present study aimed at extracting nutrient patterns with respect to breast cancer (BC) aetiology. DESIGN: Nutrient patterns were derived with treelet transform (TT) and related to BC risk. TT was applied to twenty-three log-transformed nutrient densities from dietary questionnaires. Hazard ratios (HR) and 95 % confidence intervals computed using Cox proportional hazards models quantified the association between quintiles of nutrient pattern scores and risk of overall BC, and by hormonal receptor and menopausal status. Principal component analysis was applied for comparison. SETTING: The European Prospective Investigation into Cancer and Nutrition (EPIC). SUBJECTS: Women (n 334 850) from the EPIC study. RESULTS: The first TT component (TC1) highlighted a pattern rich in nutrients found in animal foods loading on cholesterol, protein, retinol, vitamins B12 and D, while the second TT component (TC2) reflected a diet rich in ß-carotene, riboflavin, thiamin, vitamins C and B6, fibre, Fe, Ca, K, Mg, P and folate. While TC1 was not associated with BC risk, TC2 was inversely associated with BC risk overall (HRQ5 v. Q1=0·89, 95 % CI 0·83, 0·95, P trend<0·01) and showed a significantly lower risk in oestrogen receptor-positive (HRQ5 v. Q1=0·89, 95 % CI 0·81, 0·98, P trend=0·02) and progesterone receptor-positive tumours (HRQ5 v. Q1=0·87, 95 % CI 0·77, 0·98, P trend<0·01). CONCLUSIONS: TT produces readily interpretable sparse components explaining similar amounts of variation as principal component analysis. Our results suggest that participants with a nutrient pattern high in micronutrients found in vegetables, fruits and cereals had a lower risk of BC.

Primary preventive potential for stroke by avoidance of major lifestyle risk factors: the European Prospective Investigation into Cancer and Nutrition-Heidelberg cohort.

BACKGROUND AND PURPOSE: Because primary prevention of stroke is a priority, our aim was to assess the primary preventive potential of major lifestyle risk factors for stroke in middle-aged women and men. METHODS: Among 23,927 persons, 551 (195 women and 356 men) had a first diagnosis of stroke during an average follow-up of 12.7 years. Using Cox proportional hazards models, we estimated the associations of adiposity, smoking, physical activity, alcohol consumption, and diet with risk of developing stroke. A competing risk model built from cause-specific proportional hazards models accounting for concurrent risk of death was used to calculate relative and absolute reductions in stroke occurrences that could have been achieved by maintaining a healthy lifestyle pattern. RESULTS: Obesity, smoking, alcohol consumption, diet, and physical inactivity were each identified as modifiable lifestyle risk factors for stroke. About 38% of stroke cases were estimated as preventable through adherence to a healthy lifestyle profile (never smoking, maintaining optimal body mass index and waist circumference, performing physical exercise, consuming a moderate quantity of alcohol, and following a healthy dietary pattern). Age-specific estimates of 5-year incidence rates for stroke in the actual cohort and in a hypothetical, comparable cohort of individuals following a healthy lifestyle would be reduced from 153 to 94 per 100,000 women and from 261 to 161 per 100,000 men for the age group 60 to 65 years. CONCLUSIONS: Our analysis confirms the strong primary prevention potential for stroke based on avoidance of excess body weight, smoking, heavy alcohol consumption, unhealthy diet, and physical inactivity.

Primary preventive potential of major lifestyle risk factors for acute myocardial infarction in men: an analysis of the EPIC-Heidelberg cohort.

The aim of this study was to assess the preventive potential of major lifestyle risk factors for acute myocardial infarction (AMI) in middle-aged men. Among 10,981 men in the Heidelberg cohort of the European Prospective Investigation into Cancer and Nutrition, aged 40.2-65.8 years when recruited, 378 developed first-ever AMI during a median follow-up period of 11.4 years. Current smoking, excess body weight, being physically inactive, but not high alcohol consumption, were identified as the major lifestyle risk factors for AMI using Cox regression analysis. A competing AMI risk model built from cause-specific Cox regression models and considering the risk of death predicted 353 AMI cases, 182 (51.6%) of which were estimated as preventable through adherence to a healthy lifestyle profile (never smoking, normal body weight, physically active, and moderate alcohol consumption). The calculated age-specific 5-year incidence rates for AMI in the actual cohort and in a hypothetical, comparable cohort with all men following the healthy lifestyle profile were 128 and 39, respectively, per 100,000 person-years for the age group 40-44, increasing to 468 and 307 per 100,000 person-years for the age group 65-69. The estimated AMI incidence rates for men with the healthy lifestyle profile are still somewhat higher than the average rates reported for documented low-incidence regions, such as parts of Japan. Our analysis confirms the strong primary preventive potential for AMI based on avoidance of smoking and excess body weight, and on regular physical activity.

Management of single malignant lung nodules in elderly patients (70 years or older) who are not candidates for lobectomy.

PURPOSE: The aim of this study was to evaluate and compare sublobar resection plus intraoperative seed implant (IOS) versus stereotactic body radiation therapy (SBRT) in patients with single malignant lung nodules in patients 70 years of age or older. MATERIALS AND METHODS: A retrospective chart review was performed and 47 patients with adequate information were selected for analysis. Thirty patients with single malignant lung nodules received SBRT. Seventeen patients received limited surgical resection plus radioactive seed implantation for solitary malignant lung nodules. Univariate statistical analysis showed a significant difference only for the age in the 2 groups: the mean age in the radioactive seed group, 78.8 years versus 76.1 years in the SBRT group (2-sided, P=0.05). RESULTS: There was high local control and minimal toxicity with either treatment modality and no significant difference among the 2 groups in terms of local control, survival, and toxicity. However, the distant failure was higher but not statistically significant in the SBRT group (9 of 30 patients in SBRT vs. 0 of 17 in IOS, P=0.1). CONCLUSIONS: Our study has shown excellent outcomes and limited toxicity in both IOS and SBRT for treatment of single malignant lung nodules in patients who are not candidates for lobectomy. However, a randomized trial is needed in this group of elderly patients to determine the most appropriate treatment.

A high proliferative index of recurrent melanoma is associated with worse survival.

OBJECTIVE: Previous melanoma studies evaluating prognostic factors of survival at recurrence have focused on primary tumor characteristics and clinical variables at first recurrence. We examined the prognostic relevance of recurrent tumor proliferation. METHODS: 114 melanoma patients with available recurrent tissues who were prospectively enrolled at New York University Medical Center were studied. Standard of care prognostic variables (e.g. stage at initial diagnosis and lactate dehydrogenase level) and recurrent tissue expression of proliferative marker Ki-67 were evaluated for their association with overall survival. RESULTS: High Ki-67 expression was observed in 57 (50%) of the 114 recurrent melanomas. On univariate analysis, the median overall survival of patients whose recurrent tumors overexpressed Ki-67 was significantly shorter than that of patients whose recurrent tumors had low Ki-67 expression (3.6 vs. 9.5 years, p = 0.03). On multivariate analysis, a high proliferative index of the recurrent melanoma remained an independent predictor of worse overall survival, controlling for stage at initial diagnosis, disease-free survival, and stage at first recurrence [HR = 2.09 (95% CI 1.24-3.54), p = 0.006]. CONCLUSIONS: Our results demonstrate the prognostic relevance of tumor proliferation in recurrent melanoma patients. Data also support restratification of risk assessment upon recurrence that considers tumor biology in addition to clinical variables evaluated as part of the standard of care.

Clinical relevance of SKP2 alterations in metastatic melanoma.

In this study, we investigated the mechanism(s) of altered expression of protooncogene SKP2 in metastatic melanoma and its clinical relevance in patients with metastatic melanoma. The genomic status of SKP2 was assessed in cell lines by sequencing, single nucleotide polymorphism array, and genomic PCR. Copy number status was then evaluated for concordance with SKP2 mRNA and protein expression. SKP2 protein was further evaluated by immunohistochemistry in 93 human metastatic tissues. No mutations were identified in SKP2. Increased copy number at the SKP2 locus was observed in 6/14 (43%) metastatic cell lines and in 9/22 (41%) human metastatic tissues which was associated with overexpression of SKP2 protein. Overexpression of SKP2 protein in human tissues was associated with worse survival in a multivariate model controlling for the site of metastasis. Copy number gain is a major contributing mechanism of SKP2 overexpression in metastatic melanoma. Results may have implications for the development of therapeutics that target SKP2.

Limited resection followed by intraoperative seed implantation is comparable to stereotactic body radiotherapy for solitary lung cancer.

BACKGROUND: The objective of this study was to compare the outcomes of patients who underwent wedge resection plus intraoperative brachytherapy versus patients who received stereotactic body radiotherapy (SBRT) for single malignant lung nodules. METHODS: A retrospective chart review included 55 patients who were treated for single lung nodules, and 47 of those patients who had adequate information were chosen for the current analysis. Twenty-five patients with single malignant lung nodules received SBRT. Twenty-two patients underwent limited surgical resection plus radioactive seed implantation for solitary malignant lung nodules. RESULTS: Univariate statistical analysis demonstrated a significance difference only for age in the 2 groups: The mean age in the radioactive seed group (66.6 years) was statistically significantly different from the mean of the age in the SBRT group (75.9 years; 2-sided P=.04). No significant differences were observed between the 2 groups in terms of local control, distant metastasis, survival, or toxicity. CONCLUSIONS: The current results demonstrated comparable efficacy in outcome and toxicity between surgical resection with radioactive seed implantation and SBRT for the treatment of single malignant lung nodules in patients who were not candidates for lobectomy/pneumonectomy.

Accurately assessing her-2/neu status in needle core biopsies of breast cancer patients in the era of neoadjuvant therapy: emerging questions and considerations addressed.

BACKGROUND: Emerging data show that patients with operable, HER-2/neu overexpressed/amplified breast carcinomas have significantly better responses (more frequently obtaining pathologic complete response and greater percent disease-free survival) when treated with trastuzumab (Herceptin) simultaneously with neoadjuvant chemotherapy than with chemotherapy alone. With the increasing use of neoadjuvant therapies, clinicians require information on biomarkers including HER-2/neu status at the time of needle core biopsy. Concordance rates between fluorescence in situ hybridization (FISH)-determined HER-2/neu status on needle core biopsies and on subsequent excisional biopsies of the same tumor have not been well studied. Moreover, the practice of automatically performing ("reflexing") 2+ immunohistochemical (IHC) staining needle core biopsies for FISH analysis on the same sample needs to be validated. In this study, we set out to (1) determine the accuracy of HER-2/neu status as determined by FISH on needle core biopsy material compared with FISH on the subsequent excisional biopsy of the same tumor with special consideration of IHC 2+staining cases and (2) determine the constancy of HER-2/neu status in pre-neoadjuvant and post-neoadjuvant chemotherapy-treated tumor in the form of needle core biopsy and excisional biopsy samples, respectively. DESIGN: 100 patients whose needle core biopsies and subsequent excisional biopsy samples were pathologically evaluated at our institution were studied. For each patient, unstained sections from both specimens were prepared and used for IHC or FISH. IHC was carried out using the HercepTest kit (DAKO, Carpinteria, CA). Parallel unstained slides were used to carry out FISH (dual probe, Vysis). Statistical analyses were carried out on the resulting data generated after interpretation. RESULTS: The concordance rate between FISH results determined on the needle core biopsy and subsequent excisional biopsy of the same tumor was 86% (kappa=0.56, P=2x10). If equivocal FISH cases (> or =1.8 to < or =2.2 amplification ratio) in a needle core biopsy or excisional biopsy specimen or both, were excluded, the concordance rate increased to 95% (kappa coefficient=0.86, P=2x10). Fourteen of 100 (14%) cases showed 2+ IHC staining in the needle core biopsy specimen with good concordance of FISH-determined HER-2/neu status between the needle core biopsy and excisional biopsy specimens (79% agreement and kappa=0.512, P=0.05). Nine, 3, and 2 cases of the 14 cases were amplified, equivocal, and negative on the excisional biopsy specimens, respectively. Of the 15 patients who received neoadjuvant chemotherapy, 93% and 87% had no change in HER-2/neu status as determined by IHC or FISH, respectively, in the excisional biopsy specimen when compared with that determined on the prior core biopsy sample. CONCLUSIONS: Excellent overall concordance was achieved between FISH-determined HER-2/neu status on the needle core biopsy and that determined on the subsequent excisional biopsy of the same tumor. These results suggest that intratumoral heterogeneity of HER-2/neu assessed by FISH is not a significant confounding factor when analyzing smaller sized samples. Furthermore, 79% of 2+IHC staining needle core biopsy cases showed concordant FISH results in the needle core biopsy and subsequent excisional biopsy specimens. Our results show good concordance, however, larger cohorts need to be studied to verify this finding. HER-2/neu status remains unchanged in the majority of cases when comparing pre-neoadjuvant and post-neoadjuvant chemotherapy-treated specimens.

Chromosome 6p22 locus associated with clinically aggressive neuroblastoma.

BACKGROUND: Neuroblastoma is a malignant condition of the developing sympathetic nervous system that most commonly affects young children and is often lethal. Its cause is not known. METHODS: We performed a genomewide association study by first genotyping blood DNA samples from 1032 patients with neuroblastoma and 2043 control subjects of European descent using the Illumina HumanHap550 BeadChip. Samples from three independent groups of patients with neuroblastoma (a total of 720 patients) and 2128 control subjects were then genotyped to replicate significant associations. RESULTS: We observed a significant association between neuroblastoma and the common minor alleles of three consecutive single-nucleotide polymorphisms (SNPs) at chromosome band 6p22 and containing the predicted genes FLJ22536 and FLJ44180 (P=1.71x10(-9) to 7.01x10(-10); allelic odds ratio, 1.39 to 1.40). Homozygosity for the at-risk G allele of the most significantly associated SNP, rs6939340, resulted in an increased likelihood of the development of neuroblastoma (odds ratio, 1.97; 95% confidence interval, 1.58 to 2.45). Subsequent genotyping of the three 6p22 SNPs in three independent case series confirmed our observation of an association (P=9.33x10(-15) at rs6939340 for joint analysis). Patients with neuroblastoma who were homozygous for the risk alleles at 6p22 were more likely to have metastatic (stage 4) disease (P=0.02), amplification of the MYCN oncogene in the tumor cells (P=0.006), and disease relapse (P=0.01). CONCLUSIONS: A common genetic variation at chromosome band 6p22 is associated with susceptibility to neuroblastoma.