Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms

Clustering non-Euclidean data is difficult, and one of the most used algorithms besides hierarchical clustering is the popular algorithm Partitioning Around Medoids (PAM), also simply referred to as k-medoids. In Euclidean geometry the mean-as used in k-means-is a good estimator for the cluster center, but this does not hold for arbitrary dissimilarities. PAM uses the medoid instead, the object with the smallest dissimilarity to all others in the cluster. This notion of centrality can be used with any (dis-)similarity, and thus is of high relevance to many domains such as biology that require the use of Jaccard, Gower, or more complex distances. A key issue with PAM is its high run time cost. We propose modifications to the PAM algorithm to achieve an O(k)-fold speedup in the second SWAP phase of the algorithm, but will still find the same results as the original PAM algorithm. If we slightly relax the choice of swaps performed (at comparable quality), we can further accelerate the algorithm by performing up to k swaps in each iteration. With the substantially faster SWAP, we can now also explore alternative strategies for choosing the initial medoids. We also show how the CLARA and CLARANS algorithms benefit from these modifications. It can easily be combined with earlier approaches to use PAM and CLARA on big data (some of which use PAM as a subroutine, hence can immediately benefit from these improvements), where the performance with high k becomes increasingly important. In experiments on real data with k=100, we observed a 200-fold speedup compared to the original PAM SWAP algorithm, making PAM applicable to larger data sets as long as we can afford to compute a distance matrix, and in particular to higher k (at k=2, the new SWAP was only 1.5 times faster, as the speedup is expected to increase with k)

Disseminated Well-Differentiated Gastro-Entero-Pancreatic Tumors Are Associated with Metabolic Syndrome

The association of well-differentiated gastro-entero-pancreatic neuroendocrine tumors (WD GEP-NETs) with metabolic syndrome (MetS), abdominal obesity, and fasting glucose abnormalities was recently described. The aim of this study was to evaluate whether the presence of MetS or any MetS individual component was also influenced by GEP-NET characteristics at diagnosis. A cohort of patients with WD GEP-NETs (n = 134), classified according to primary tumor location (gastrointestinal or pancreatic), pathological grading (G1 (Ki67 ≤ 2%) and G2 (>3 ≤ 20%) (WHO 2010), disease extension (localized, loco-regional, and metastatic), and presence of hormonal secretion syndrome (functioning/non-functioning), was evaluated for the presence of MetS criteria. After adjustment for age and gender, the odds of having MetS was significantly higher for patients with WD GEP-NET grade G1 (OR 4.35 95%CI 1.30–14.53) and disseminated disease (OR 4.52 95%CI 1.44–14.15). GEP-NET primary tumor location or secretory syndrome did not influence the risk for MetS. None of the tumor characteristics evaluated were associated with body mass index, fasting plasma glucose category, or any of the individual MetS components. Patients with GEP-NET and MetS depicted a higher risk of presenting a lower tumor grade and disseminated disease. The positive association between MetS and GEP-NET characteristics further highlights the potential link between the two conditions.This work did not receive any funding either from public, commercial, or nonprofit agencies

Network orchestration: new role of business incubators?

Purpose – The purpose of this paper is to analyze the performance of incubators in the stages of formationand development of incubated business networks, especially in bottom-up and top-down network models.Design/methodology/approach – The research is defined as qualitative and descriptive, with theapplication of multiple case studies, in which two networks of incubated businesses were investigated, onebeing top-down and the other bottom-up, which emerged within the incubation process of two businessincubators (CIETEC and INCIT). To make the study operational, 11 semi-structured interviews were carriedout and the thematic analysis of content was developed.Findings – The results pointed out that in the top-down network the incubator performs a new assignment,the network orchestration, which corresponds to the actions of formation, coordination and governance of thegroup. In the bottom-up network, it was found that the role of the incubator was to expand the value offersusually practiced.Research limitations/implications – As a limitation of the research, the very limitation of case studiesis pointed out that is they do not allow for generalizations.Practical implications – The research contributes to reflections on the effectiveness of the incubator andsheds light on the complementarity of networks in incubation processes, providing gains for incubators,incubated businesses and society.Originality/value – The originality of this document is the new role of the incubator, which isorchestration, and its categorization. The results allow us to understand the effects of providing networks andrelationships for incubated businesses. In addition, this study broadens the focus of traditional analyses of theincubator–incubated duo to consider the incubator–network–incubated trio

Non-AIDS-related comorbidities in people living with HIV-1 aged 50 years and older: The AGING POSITIVE study.

OBJECTIVE: To characterize the profile of non-AIDS-related comorbidities (NARC) in the older HIV-1-infected population and to explore the factors associated with multiple NARC. METHODS: This was a multicentre, cross-sectional study including HIV-1-infected patients aged ≥50 years, who were virologically suppressed and had been on a stable antiretroviral therapy (ART) regimen for at least 6 months. A multiple regression model explored the association between demographic and clinical variables and the number of NARC. RESULTS: Overall, 401 patients were enrolled. The mean age of the patients was 59.3 years and 72.6% were male. The mean duration of HIV-1 infection was 12.0 years and the median exposure to ART was 10.0 years. The mean number of NARC was 2.1, and 34.7% of patients had three or more NARC. Hypercholesterolemia was the most frequent NARC (60.8%), followed by arterial hypertension (39.7%) and chronic depression/anxiety (23.9%). Arterial hypertension and diabetes mellitus were the most frequently treated NARC (95.6% and 92.6% of cases, respectively). The linear regression analysis showed a positive relationship between age and NARC (B=0.032, 95% confidence interval 0.015-0.049; p=0.0003) and between the duration of HIV-1 infection and NARC (B=0.039, 95% confidence interval 0.017-0.059; p=0.0005). CONCLUSIONS: A high prevalence of NARC was found, the most common being metabolic, cardiovascular, and psychological conditions. NARC rates were similar to those reported for the general population, suggesting a larger societal problem beyond HIV infection. A multidisciplinary approach is essential to reduce the burden of complex multi-morbid conditions in the HIV-1-infected population.info:eu-repo/semantics/publishedVersio

An analytical solution for the settlement of stone columns beneath rigid footings

This paper presents a new approximate solution to study the settlement of rigid footings resting on a soft soil improved with groups of stone columns. The solution development is fully analytical, but finite element analyses are used to verify the validity of some assumptions, such as a simplified geometric model, load distribution with depth and boundary conditions. Groups of stone columns are converted to equivalent single columns with the same cross-sectional area. So, the problem becomes axially symmetric. Soft soil is assumed as linear elastic but plastic strains are considered in the column using the Mohr-Coulomb yield criterion and a non-associated flow rule, with a constant dilatancy angle. Soil profile is divided into independent horizontal slices and equilibrium of stresses and compatibility of deformations are imposed in the vertical and horizontal directions. The solution is presented in a closed form and may be easily implemented in a spreadsheet. Comparisons of the proposed solution with numerical analyses show a good agreement for the whole range of common values, which confirms the validity of the solution and its hypotheses. The solution also compares well with a small scale laboratory test available in literature

Immunophenotypic characterization of patients with American cutaneous leishmaniasis prior to and after treatment in Pernambuco, Brazil

Leishmania infections induce a specific activation of host immunological response, particularly characterized by T cell expansion. Studies indicate the importance of the balance between CD4+ and CD8+ T cells, in which the first ones would have their number reduced during the healing process. Meanwhile, CD25+ T cells have been associated with the suppression of the immune response. Since the immune response has an essential role in both healing and progression of diseases, this study aimed to identify the percentage of CD3+, CD4+, CD8+, CD16+ and CD25+ T cells in the peripheral blood of patients afflicted with American cutaneous leishmaniasis (ACL) - before and after treatment - and healthy controls. Peripheral blood was collected and transferred to cytometry tubes containing monoclonal antibodies specific for cell surface markers CD3, CD4, CD8, CD16 e CD25. The immunophenotypic and morphometric parameters of cells were determined by flow cytometry and the results demonstrated a significant increase in the number of T CD8+ cells after treatment, suggesting a cytotoxic T cell response. An increase in CD25+ T cells in patients with active ACL and after treatment was also observed, suggesting the participation of these cells in the modulation of the exacerbated effector response

Criticality in correlated quantum matter

At quantum critical points (QCP) \cite{Pfeuty:1971,Young:1975,Hertz:1976,Chakravarty:1989,Millis:1993,Chubukov:1 994,Coleman:2005} there are quantum fluctuations on all length scales, from microscopic to macroscopic lengths, which, remarkably, can be observed at finite temperatures, the regime to which all experiments are necessarily confined. A fundamental question is how high in temperature can the effects of quantum criticality persist? That is, can physical observables be described in terms of universal scaling functions originating from the QCPs? Here we answer these questions by examining exact solutions of models of correlated systems and find that the temperature can be surprisingly high. As a powerful illustration of quantum criticality, we predict that the zero temperature superfluid density, $\rho_{s}(0)$, and the transition temperature, $T_{c}$, of the cuprates are related by $T_{c}\propto\rho_{s}(0)^y$, where the exponent $y$ is different at the two edges of the superconducting dome, signifying the respective QCPs. This relationship can be tested in high quality crystals.Comment: Final accepted version not including minor stylistic correction

Mapeamento da fitomassa da caatinga do seridó pelos índices de área de planta e de vegetação da diferença normalizada

Phytomass is a critical information for economic and environmental activities like the establishment of policies for timber resources, forest management, studies of plant nutrient cycling, CO2 sink, among other. The phytomass of a Caatinga area was obtained by an empirical method using normalized difference vegetation index (NDVI) of Landsat images, the plant area index (PAI) and the phytomass inventory. At a first stage, linear, logarithmic and non-linear models were developed and tested. Bush and tree specimens were considered in the study, so that most of the individuals that contribute to the spectral answer detected by satellite images were included. At a second stage, the orbital parameter NDVI was used to map the PAI, which was used to map the phytomass, based on the relationship of this phytomass as a function of PAI. The residues between measurements and estimates based on NDVI varied from 0 to 84%, while the residues of total dry weight of phytomass per ha obtained by mapping and by dendrometrical equations varied from 5 to 104%, with a large trend of 166 and 448% in open Caatinga areas, due to the contribution of the herbaceous stratum to NDVI.A fitomassa, principalmente arbórea, é informação necessária em atividades econômicas e ambientais, como políticas de uso do recurso madeireiro, manejo florestal, estudos de ciclagem de nutrientes, absorção de CO2, entre outros. A finalidade deste estudo foi a verificação de um método empírico para o mapeamento da fitomassa da Caatinga do Seridó, integrando-se um inventário de fitomassa, o índice de área de planta (IAP) e o índice de vegetação da diferença normalizada (NDVI), por meio de imagens Landsat TM. Na primeira etapa foram desenvolvidos e testados modelos lineares, logarítmicos e não lineares. A abordagem de tamanho foi arbustiva e arbórea, incluindo-se a maior parte dos indivíduos que contribuem na resposta espectral mensurada por imagens de satélite. Em uma segunda etapa utilizamos o parâmetro orbital, NDVI, para o mapeamento do IAP, que por sua vez, foi utilizado para mapear a fitomassa. Os desvios entre mensurações de IAP e estimativas a partir do NDVI, variaram de 0 a 84%, enquanto que os desvios entre Peso Seco Total de Fitomassa por ha obtidos pelo mapeamento e por equações dendrométricas, variaram de 5 a 104%, com grandes tendências de 166 e 448% para áreas de caatinga aberta, provocada pela contribuição do estrato herbáceo no NDVI

The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas putida </it>KT2442 is a natural producer of polyhydroxyalkanoates (PHAs), which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made biopolymers. However, despite the substantial body of work on PHA production by <it>P. putida </it>strains, it is not yet clear how the bacterium re-arranges its whole metabolism when it senses the limitation of nitrogen and the excess of fatty acids as carbon source, to result in a large accumulation of PHAs within the cell. In the present study we investigated the metabolic response of KT2442 using a systems biology approach to highlight the differences between single- and multiple-nutrient-limited growth in chemostat cultures.</p> <p>Results</p> <p>We found that 26, 62, and 81% of the cell dry weight consist of PHA under conditions of carbon, dual, and nitrogen limitation, respectively. Under nitrogen limitation a specific PHA production rate of 0.43 (g·(g·h)^-1) was obtained. The residual biomass was not constant for dual- and strict nitrogen-limiting growth, showing a different feature in comparison to other <it>P. putida </it>strains. Dual limitation resulted in patterns of gene expression, protein level, and metabolite concentrations that substantially differ from those observed under exclusive carbon or nitrogen limitation. The most pronounced differences were found in the energy metabolism, fatty acid metabolism, as well as stress proteins and enzymes belonging to the transport system.</p> <p>Conclusion</p> <p>This is the first study where the interrelationship between nutrient limitations and PHA synthesis has been investigated under well-controlled conditions using a system level approach. The knowledge generated will be of great assistance for the development of bioprocesses and further metabolic engineering work in this versatile organism to both enhance and diversify the industrial production of PHAs.</p