Boolean Matrix Factorization Meets Consecutive Ones Property

Boolean matrix factorization is a natural and a popular technique for summarizing binary matrices. In this paper, we study a problem of Boolean matrix factorization where we additionally require that the factor matrices have consecutive ones property (OBMF). A major application of this optimization problem comes from graph visualization: standard techniques for visualizing graphs are circular or linear layout, where nodes are ordered in circle or on a line. A common problem with visualizing graphs is clutter due to too many edges. The standard approach to deal with this is to bundle edges together and represent them as ribbon. We also show that we can use OBMF for edge bundling combined with circular or linear layout techniques. We demonstrate that not only this problem is NP-hard but we cannot have a polynomial-time algorithm that yields a multiplicative approximation guarantee (unless P = NP). On the positive side, we develop a greedy algorithm where at each step we look for the best 1-rank factorization. Since even obtaining 1-rank factorization is NP-hard, we propose an iterative algorithm where we fix one side and and find the other, reverse the roles, and repeat. We show that this step can be done in linear time using pq-trees. We also extend the problem to cyclic ones property and symmetric factorizations. Our experiments show that our algorithms find high-quality factorizations and scale well

nZVI mobility and transport: laboratory test and numerical model

Zerovalent iron nanoparticles (nZVI) are becoming one of the most widely recommended nanomaterials for soil and groundwater remediation. However, when nZVI are injected in the groundwater flow, the behavior (mobility, dispersion, distribution) is practically unknown. This fact generally results in the use of enormous quantities of them at the field scale. The uncertainties are on the effective volumes reached from the plume of nZVI because their tendency to aggregate and their weight can cause their settling and deposition. So, the mobility of nanoparticles is a real issue, which can often lead to inefficient or expensive soil remediation. Furthermore, there is another aspect that must be considered: the fate of these nZVI in the groundwater and their possible impact on the subsoil environment. All these considerations have led us to propose an application of nZVI simulating the permeation technique through a laboratory experience, finalized to have a better, or even simpler description of their real behavior when injected in a flow in the subsoil. A two-dimensional laboratory-scale tank was used to study the dispersion and transport of nZVI. A nZVI solution, with a concentration equal to 4.54 g/L, was injected into glass beads, utilized as porous medium. The laboratory experiment included a digital camera to acquire the images. The images were then used for calibrating a numerical model. The results of the mass balance confirm the validity of the proposed numerical model, obtaining values of velocity (5.41 x 10(-3) m/s) and mass (1.9 g) of the nZVI of the same order of those from the experimental tests. Several information were inferred from both experimental and numerical tests. Both demonstrate that nZVI plume does not behave as a solute dissolved in water, but as a mass showing its own mobility ruled mainly from the buoyancy force. A simple simulation of a tracer input and a nZVI plume are compared to evidence the large differences between their evolution in time and space. This means that commercial numerical models, if not corrected, cannot furnish a real forecast of the volume of influence of the injected nZVI. Further deductions can be found from the images and confirmed by means the numerical model where the detachment effect is much smaller than the attachment one (ratio k(d)/k(a) = 0.001). From what is reported, it is worthwhile to pay attention on the localization of the contaminants source/plume to reach an effective treatment and it is important to go further in the improvement of solution for the limiting the nanoparticles aggregation phenomenon

Generating Realistic Synthetic Population Datasets

Modern studies of societal phenomena rely on the availability of large datasets capturing attributes and activities of synthetic, city-level, populations. For instance, in epidemiology, synthetic population datasets are necessary to study disease propagation and intervention measures before implementation. In social science, synthetic population datasets are needed to understand how policy decisions might affect preferences and behaviors of individuals. In public health, synthetic population datasets are necessary to capture diagnostic and procedural characteristics of patient records without violating confidentialities of individuals. To generate such datasets over a large set of categorical variables, we propose the use of the maximum entropy principle to formalize a generative model such that in a statistically well-founded way we can optimally utilize given prior information about the data, and are unbiased otherwise. An efficient inference algorithm is designed to estimate the maximum entropy model, and we demonstrate how our approach is adept at estimating underlying data distributions. We evaluate this approach against both simulated data and on US census datasets, and demonstrate its feasibility using an epidemic simulation application

Lymphatic endothelium stimulates melanoma metastasis and invasion via MMP14-dependent Notch3 and b1-integrin activation

Lymphatic invasion and lymph node metastasis correlate with poor clinical outcome in melanoma. However, the mechanisms of lymphatic dissemination in distant metastasis remain incompletely understood. We show here that exposure of expansively growing human WM852 melanoma cells, but not singly invasive Bowes cells, to lymphatic endothelial cells (LEC) in 3D co-culture facilitates melanoma distant organ metastasis in mice. To dissect the underlying molecular mechanisms, we established LEC co-cultures with different melanoma cells originating from primary tumors or metastases. Notably, the expansively growing metastatic melanoma cells adopted an invasively sprouting phenotype in 3D matrix that was dependent on MMP14, Notch3 and β1-integrin. Unexpectedly, MMP14 was necessary for LEC-induced Notch3 induction and coincident β1-integrin activation. Moreover, MMP14 and Notch3 were required for LEC-mediated metastasis of zebrafish xenografts. This study uncovers a unique mechanism whereby LEC contact promotes melanoma metastasis by inducing a reversible switch from 3D growth to invasively sprouting cell phenotype

The secretory senescence in otorhinolaryngology: Principles of treatment

Atrophy or hypofunction of the salivary gland because of aging, radiotherapy or disease causes hyposalivation and impairs the quality of life of patients by compromising mastication, swallowing and speech and by leading to a loss of taste. Moreover, hyposalivation exacerbates dental caries and induces periodontal disease, and oral candidiasis. Currently, no satisfactory therapies have been established to solve salivary hypofunction. Current treatment options for atrophy or hypofunction of the salivary glands in clinical practice are only symptomatic and include saliva substitutes and parasympathetic agonists, such as pilocarpine, to stimulate salivary flow. However, parasympathomimetics have systemic side effects, so different treatment options are necessary, and research has recently focused on this. The main strategies that have been proposed to restore salivary gland atrophy and hypofunction are gene therapy by gene activation/silencing during stem cell differentiation and by the use of viral vectors, such as adenoviruses; cell-based therapy with salivary gland cells, stem cells and non-salivary gland and/ or non-epithelial cells to regenerate damaged salivary gland cells; replacement with tissue bioengineering in which organoids from pluripotent stem cells are used in the development of organ replacement regenerative therapy. Remarkable progression in this research field has been made in the last decade, but a definitive therapy for salivary gland hypofunction has not been developed due to intrinsic challenges that come with each approach. However, with research efforts in the future, a range of precision medicine therapies may become available individualized to each patient

Human papillomavirus testing as an optional screening tool in low-resource settings of Latin America: experience from the Latin American Screening study

Hybrid capture II (HC II) test for oncogenic human papillomaviruses (HPV) was carried out in a cohort of 4284 women at their first clinical visit. Overall prevalence of HPV was 17.1%, decreasing with age from 33.9% among women below 20 years to only 11.0% among those older than 41 years. HPV prevalence was significantly higher among current smokers (odds ratio [OR] ¼ 1.31; 95% CI 1.1–1.6), in women with two or more lifetime sexual partners (OR ¼ 1.9; 95% CI 1.6–2.4), and those women with two or more sexual partners during the past 12 months prior to examination (OR ¼ 1.6; 95% CI 1.2–2.2). HPV detection increased in parallel with increasing cytologic abnormality, being highest in women with high-grade squamous intraepithelial lesion (P ¼ 0.001). Specificity of the HPV test in detecting histologically confirmed cervical disease was 85% (95% CI 83.9–86.1). Sensitivity of the HPV test in detecting histologic abnormalities increased in parallel with disease severity, ranging from 51.5% for cervical intraepithelial neoplasia (CIN) 1 to 96.5% for CIN 3 and 100.0% for cancer, with respective decline of positive predictive value. These data suggest that HPV testing with HC II assay might be a viable screening tool among this population with relatively high prevalence of cervical disease

Hormonal contraceptives and the length of their use are not independent risk factors for high-risk HPV infections or high-grade CIN

AIMS: To evaluate the role of hormonal contraceptives as a risk factor of high-risk human papillomavirus (HR-HPV), cervical intraepithelial lesions (CIN) and cervical cancer in our multi-center population-based LAMS (Latin American Screening) study. METHODS: A cohort study with >12,000 women from Brazil and Argentina using logistic regression to analyze the covariates of hormonal contraception (HOC - oral, injections, patches, implants, vaginal ring and progesterone intrauterine system) use followed by multivariate modeling for predictors of HR-HPV and CIN2+. RESULTS: HR-HPV infection was a consistent risk factor of high-grade CIN in all three groups of women. The length of HOC use was not significantly related to high-grade squamous intraepithelial lesions (HSIL)+ Pap (p = 0.069), LSIL+ Pap (p = 0.781) or ASCUS+ (p = 0.231). The same was true with the length of HOC use and histology CIN3+ (p = 0.115) and CIN2+ (p = 0.515). Frequently, HOC users have previously shown more HPV-related lesions, as well as lower HPV prevalence if they were current smokers. But HOC use and time of usage were not independent risk factors of either HR-HPV infection or high-grade CIN using multiple logistic regressions. CONCLUSIONS: No evidence was found for an association between the use of HOC with an increased risk for HR-HPV infection or high-grade CIN in this cohort.This study is a part of the ongoing LAMS (Latin American Screening) study, entitled: Improving Health Systems Towards Equality-Based Control of Cervical Cancer in Latin America, and is supported by the INCO-DEV Program of the European Commission (Project No. ICA4-CT-2001-10013). The generous contribution of Digene Corporation (USA) who donated the HCII tests at our disposal is gratefully acknowledged

Evaluation of visual inspection with acetic acid (VIA), Lugol’s iodine (VILI), cervical cytology and HPV testing as cervical screening tools in Latin America

Objectives: To assess the performance indicators of visual inspection with acetic acid (VIA) and visual inspection with Lugol’s iodine (VILI) in four Latin American centres participating in the ongoing Latin AMerican Screening (LAMS) study, in settings with moderate incidence of cervical disease and with poorly to moderately well-organized cervical cancer screening. Setting: Three Brazilian centres (São Paulo, Campinas and Porto Alegre) and one Argentine centre (Buenos Aires) recruited a total of 11,834 healthy women to undergo VIA, VILI, conventional Pap smear and Hybrid Capture II (HCII). Methods: Women who had a positive result from any of these tests were subjected to colposcopy and biopsies (if necessary), and women with high-grade cervical intraepithelial neoplasia (CIN) were properly treated. To control for verification bias, 5% of women with normal tests were referred for colposcopy, as were 20% of HCII-negative women. Results: Data on VIA (n = 11,834), VILI (n = 2994), conventional Pap smear (n = 10,138) and HCII (n = 4195) were available for test comparisons, calculating sensitivity, specificity, and positive and negative predictive values. Overall test positivity was 11.6% for VIA, 23.0% for VILI, 2.2% for Pap smear (LSIL threshold), 1.1% for Pap smear (HSIL threshold) and 17.1% for HCII. VIA was positive in 61.8% of the women with CIN 1, 57.0% of those with CIN 2, 35.0% of women with CIN 3 and in 21 of 28 (75%) of women with cancer. Approximately 10% of women with no detectable disease had an abnormal VIA. Regarding VILI, 83.3% of women diagnosed with CIN 1 and 62.5% of those with CIN 3 had an abnormal test. VILI failed to detect one of three cases of cancer. Both the sensitivity, specificity and positive predictive value of VIA and VILI in detecting CIN 2 or CIN 3 could be significantly improved depending on the combination with Pap smear or HCII (sensitivity up to 100.0% and specificity up to 99.8%). Conclusions: The LAMS study failed to reproduce the performance figures obtained with VIA and VILI (as stand-alone tests) in some other settings, where the prevalence of cervical disease was higher. However, a combined use of VIA or VILI with the Pap test or HCII allowed specific detection of cervical abnormalities.European Union (EU) - INCO-DEV Programme - Contract# ICA4-CT-2001-10013

Safety of screening with Human papillomavirus testing for cervical cancer at three-year intervals in a high-risk population: experience from the LAMS study

To assess whether human papillomavirus (HPV) testing is a safe enough approach to warrant extension of the screening intervals of baseline Papanicolaou (Pap)-/HPV- women in low-income settings.European Commission, INCO-DEV Programme (Contract # ICA4-CT-2001-10013). The generous contribution from DIGENE Inc. (USA) donating the HC 2 test

Lethal Factor Toxemia and Anti-Protective Antigen Antibody Activity in Naturally Acquired Cutaneous Anthrax

Cutaneous anthrax outbreaks occurred in Bangladesh from August to October 2009. As part of the epidemiological response and to confirm anthrax diagnoses, serum samples were collected from suspected case patients with observed cutaneous lesions. Anthrax lethal factor (LF), anti-protective antigen (anti-PA) immunoglobulin G (IgG), and anthrax lethal toxin neutralization activity (TNA) levels were determined in acute and convalescent serum of 26 case patients with suspected cutaneous anthrax from the first and largest of these outbreaks. LF (0.005–1.264 ng/mL) was detected in acute serum from 18 of 26 individuals. Anti-PA IgG and TNA were detected in sera from the same 18 individuals and ranged from 10.0 to 679.5 μg/mL and 27 to 593 units, respectively. Seroconversion to serum anti-PA and TNA was found only in case patients with measurable toxemia. This is the first report of quantitative analysis of serum LF in cutaneous anthrax and the first to associate acute stage toxemia with subsequent antitoxin antibody responses