3,769 research outputs found
A Spectral Algorithm with Additive Clustering for the Recovery of Overlapping Communities in Networks
This paper presents a novel spectral algorithm with additive clustering
designed to identify overlapping communities in networks. The algorithm is
based on geometric properties of the spectrum of the expected adjacency matrix
in a random graph model that we call stochastic blockmodel with overlap (SBMO).
An adaptive version of the algorithm, that does not require the knowledge of
the number of hidden communities, is proved to be consistent under the SBMO
when the degrees in the graph are (slightly more than) logarithmic. The
algorithm is shown to perform well on simulated data and on real-world graphs
with known overlapping communities.Comment: Journal of Theoretical Computer Science (TCS), Elsevier, A Para\^itr
Punica granatum (Pomegranate) juice provides an HIV-1 entry inhibitor and candidate topical microbicide
BACKGROUND: For â 24 years the AIDS pandemic has claimed â 30 million lives, causing â 14,000 new HIV-1 infections daily worldwide in 2003. About 80% of infections occur by heterosexual transmission. In the absence of vaccines, topical microbicides, expected to block virus transmission, offer hope for controlling the pandemic. Antiretroviral chemotherapeutics have decreased AIDS mortality in industrialized countries, but only minimally in developing countries. To prevent an analogous dichotomy, microbicides should be: acceptable; accessible; affordable; and accelerative in transition from development to marketing. Already marketed pharmaceutical excipients or foods, with established safety records and adequate anti-HIV-1 activity, may provide this option. METHODS: Fruit juices were screened for inhibitory activity against HIV-1 IIIB using CD4 and CXCR4 as cell receptors. The best juice was tested for inhibition of: (1) infection by HIV-1 BaL, utilizing CCR5 as the cellular coreceptor; and (2) binding of gp120 IIIB and gp120 BaL, respectively, to CXCR4 and CCR5. To remove most colored juice components, the adsorption of the effective ingredient(s) to dispersible excipients and other foods was investigated. A selected complex was assayed for inhibition of infection by primary HIV-1 isolates. RESULTS: HIV-1 entry inhibitors from pomegranate juice adsorb onto corn starch. The resulting complex blocks virus binding to CD4 and CXCR4/CCR5 and inhibits infection by primary virus clades A to G and group O. CONCLUSION: These results suggest the possibility of producing an anti-HIV-1 microbicide from inexpensive, widely available sources, whose safety has been established throughout centuries, provided that its quality is adequately standardized and monitored
COVID-19 therapy target discovery with context-aware literature mining
The abundance of literature related to the widespread COVID-19 pandemic is
beyond manual inspection of a single expert. Development of systems, capable of
automatically processing tens of thousands of scientific publications with the
aim to enrich existing empirical evidence with literature-based associations is
challenging and relevant. We propose a system for contextualization of
empirical expression data by approximating relations between entities, for
which representations were learned from one of the largest COVID-19-related
literature corpora. In order to exploit a larger scientific context by transfer
learning, we propose a novel embedding generation technique that leverages
SciBERT language model pretrained on a large multi-domain corpus of scientific
publications and fine-tuned for domain adaptation on the CORD-19 dataset. The
conducted manual evaluation by the medical expert and the quantitative
evaluation based on therapy targets identified in the related work suggest that
the proposed method can be successfully employed for COVID-19 therapy target
discovery and that it outperforms the baseline FastText method by a large
margin.Comment: Accepted to the 23rd International Conference on Discovery Science
(DS 2020
Routine pattern discovery and anomaly detection in individual travel behavior
Discovering patterns and detecting anomalies in individual travel behavior is
a crucial problem in both research and practice. In this paper, we address this
problem by building a probabilistic framework to model individual
spatiotemporal travel behavior data (e.g., trip records and trajectory data).
We develop a two-dimensional latent Dirichlet allocation (LDA) model to
characterize the generative mechanism of spatiotemporal trip records of each
traveler. This model introduces two separate factor matrices for the spatial
dimension and the temporal dimension, respectively, and use a two-dimensional
core structure at the individual level to effectively model the joint
interactions and complex dependencies. This model can efficiently summarize
travel behavior patterns on both spatial and temporal dimensions from very
sparse trip sequences in an unsupervised way. In this way, complex travel
behavior can be modeled as a mixture of representative and interpretable
spatiotemporal patterns. By applying the trained model on future/unseen
spatiotemporal records of a traveler, we can detect her behavior anomalies by
scoring those observations using perplexity. We demonstrate the effectiveness
of the proposed modeling framework on a real-world license plate recognition
(LPR) data set. The results confirm the advantage of statistical learning
methods in modeling sparse individual travel behavior data. This type of
pattern discovery and anomaly detection applications can provide useful
insights for traffic monitoring, law enforcement, and individual travel
behavior profiling
Electrochemical determination of hydroquinone using hydrophobic ionic liquid-type carbon paste electrodes
Three types of carbon paste electrodes (CPEs) with different liquid binders were fabricated, and their electrochemical behavior was characterized via a potassium hexacyanoferrate(II) probe. 1-Octyl-3-methylimidazolium hexafluorophosphate ionic liquid (IL) as a hydrophobic conductive pasting binder showed better electrochemical performance compared with the commonly employed binder. The IL-contained CPEs demonstrated excellent electroactivity for oxidation of hydroquinone. A diffusion control mechanism was confirmed and the diffusion coefficient (D) of 5.05 Ă 10-4 cm2 s-1 was obtained. The hydrophobic IL-CPE is promising for the determination of hydroquinone in terms of high sensitivity, easy operation, and good durability
Neurospora from natural populations: Population genomics insights into the Life history of a model microbial Eukaryote
The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research
Remote Manipulation of Droplets on a Flexible Magnetically Responsive Film
The manipulation of droplets is used in a wide range of applications, from lab-on-a-chip devices to bioinspired functional surfaces. Although a variety of droplet manipulation techniques have been proposed, active, fast and reversible manipulation of pure discrete droplets remains elusive due to the technical limitations of previous techniques. Here, we describe a novel technique that enables active, fast, precise and reversible control over the position and motion of a pure discrete droplet with only a permanent magnet by utilizing a magnetically responsive flexible film possessing actuating hierarchical pillars on the surface. This magnetically responsive surface shows reliable actuating capabilities with immediate field responses and maximum tilting angles of ???90??. Furthermore, the magnetic responsive film exhibits superhydrophobicity regardless of tilting angles of the actuating pillars. Using this magnetically responsive film, we demonstrate active and reversible manipulation of droplets with a remote magnetic force.open0
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Bioavailability in soils
The consumption of locally-produced vegetables by humans may be an important exposure pathway for soil contaminants in many urban settings and for agricultural land use. Hence, prediction of metal and metalloid uptake by vegetables from contaminated soils is an important part of the Human Health Risk Assessment procedure. The behaviour of metals (cadmium, chromium, cobalt, copper, mercury, molybdenum, nickel, lead and zinc) and metalloids (arsenic, boron and selenium) in contaminated soils depends to a large extent on the intrinsic charge, valence and speciation of the contaminant ion, and soil properties such as pH, redox status and contents of clay and/or organic matter. However, chemistry and behaviour of the contaminant in soil alone cannot predict soil-to-plant transfer. Root uptake, root selectivity, ion interactions, rhizosphere processes, leaf uptake from the atmosphere, and plant partitioning are important processes that ultimately govern the accumulation ofmetals and metalloids in edible vegetable tissues. Mechanistic models to accurately describe all these processes have not yet been developed, let alone validated under field conditions. Hence, to estimate risks by vegetable consumption, empirical models have been used to correlate concentrations of metals and metalloids in contaminated soils, soil physico-chemical characteristics, and concentrations of elements in vegetable tissues. These models should only be used within the bounds of their calibration, and often need to be re-calibrated or validated using local soil and environmental conditions on a regional or site-specific basis.Mike J. McLaughlin, Erik Smolders, Fien Degryse, and Rene Rietr
Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes
Non-healing chronic ulcers are a serious complication of diabetes and are a major healthcare problem. While a host of treatments have been explored to heal or prevent these ulcers from forming, these treatments have not been found to be consistently effective in clinical trials. An understanding of the changes in gene expression in the skin of diabetic patients may provide insight into the processes and mechanisms that precede the formation of non-healing ulcers. In this study, we investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic). This information may be useful in identifying the causal factors and potential therapeutic targets for the prevention and treatment of diabetic related diseases
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