2,598 research outputs found
Visualizing dimensionality reduction of systems biology data
One of the challenges in analyzing high-dimensional expression data is the
detection of important biological signals. A common approach is to apply a
dimension reduction method, such as principal component analysis. Typically,
after application of such a method the data is projected and visualized in the
new coordinate system, using scatter plots or profile plots. These methods
provide good results if the data have certain properties which become visible
in the new coordinate system and which were hard to detect in the original
coordinate system. Often however, the application of only one method does not
suffice to capture all important signals. Therefore several methods addressing
different aspects of the data need to be applied. We have developed a framework
for linear and non-linear dimension reduction methods within our visual
analytics pipeline SpRay. This includes measures that assist the interpretation
of the factorization result. Different visualizations of these measures can be
combined with functional annotations that support the interpretation of the
results. We show an application to high-resolution time series microarray data
in the antibiotic-producing organism Streptomyces coelicolor as well as to
microarray data measuring expression of cells with normal karyotype and cells
with trisomies of human chromosomes 13 and 21
A dynamic network approach for the study of human phenotypes
The use of networks to integrate different genetic, proteomic, and metabolic
datasets has been proposed as a viable path toward elucidating the origins of
specific diseases. Here we introduce a new phenotypic database summarizing
correlations obtained from the disease history of more than 30 million patients
in a Phenotypic Disease Network (PDN). We present evidence that the structure
of the PDN is relevant to the understanding of illness progression by showing
that (1) patients develop diseases close in the network to those they already
have; (2) the progression of disease along the links of the network is
different for patients of different genders and ethnicities; (3) patients
diagnosed with diseases which are more highly connected in the PDN tend to die
sooner than those affected by less connected diseases; and (4) diseases that
tend to be preceded by others in the PDN tend to be more connected than
diseases that precede other illnesses, and are associated with higher degrees
of mortality. Our findings show that disease progression can be represented and
studied using network methods, offering the potential to enhance our
understanding of the origin and evolution of human diseases. The dataset
introduced here, released concurrently with this publication, represents the
largest relational phenotypic resource publicly available to the research
community.Comment: 28 pages (double space), 6 figure
Community-acquired MRSA and pig-farming
BACKGROUND: Sporadic cases of CA-MRSA in persons without risk-factors for MRSA carriage are increasing. CASE PRESENTATION: We report a MRSA cluster among family members of a pig-farmer, his co-workers and his pigs. Initially a young mother was seen with mastitis due to MRSA. Six months later her baby daughter was admitted to the hospital with pneumococcal otitis. After staying five days in hospital, the baby was found to be MRSA positive. At that point it was decided to look for a possible source, such as other family members and house-hold animals, including pigs on the farm, since those were reported as a possible source of MRSA earlier. Swabs were taken from the throat and nares of family members and co-workers. A veterinarian obtained swabs from the nares, throat and perineum of 10 pigs. Swabs were cultured following a national protocol to detect MRSA that included the use of an enrichment broth. Animal and human strains were characterized by PFGE, spa-typing, MLST analysis, SSCmec, AGR typing, and the detection for PVL, LukM, and TSST toxin genes. Three family members, three co-workers, and 8 of the 10 pigs were MRSA positive. With the exception of the initial case (the mother) all persons were solely colonized, with no signs of clinical infections. After digestion with SmaI, none of the strains showed any bands using PFGE. All isolates belonged to spa type t108 and ST398. CONCLUSION: 1. This report clearly shows clonal spread and transmission between humans and pigs in the Netherlands. 2. MLST sequence type 398 might be of international importance as pig-MRSA, since this type was shown earlier to be present in epidemiologically unrelated French pigs and pig-farmers. 3. Research is needed to evaluate whether this is a local problem or a new source of MRSA, that puts the until now successful Search and Destroy policy of the Netherlands at risk
Comparing the performance of FA, DFA and DMA using different synthetic long-range correlated time series
Notwithstanding the significant efforts to develop estimators of long-range
correlations (LRC) and to compare their performance, no clear consensus exists
on what is the best method and under which conditions. In addition, synthetic
tests suggest that the performance of LRC estimators varies when using
different generators of LRC time series. Here, we compare the performances of
four estimators [Fluctuation Analysis (FA), Detrended Fluctuation Analysis
(DFA), Backward Detrending Moving Average (BDMA), and centred Detrending Moving
Average (CDMA)]. We use three different generators [Fractional Gaussian Noises,
and two ways of generating Fractional Brownian Motions]. We find that CDMA has
the best performance and DFA is only slightly worse in some situations, while
FA performs the worst. In addition, CDMA and DFA are less sensitive to the
scaling range than FA. Hence, CDMA and DFA remain "The Methods of Choice" in
determining the Hurst index of time series.Comment: 6 pages (including 3 figures) + 3 supplementary figure
A viscoelastic deadly fluid in carnivorous pitcher plants
Background : The carnivorous plants of the genus Nepenthes, widely
distributed in the Asian tropics, rely mostly on nutrients derived from
arthropods trapped in their pitcher-shaped leaves and digested by their
enzymatic fluid. The genus exhibits a great diversity of prey and pitcher forms
and its mechanism of trapping has long intrigued scientists. The slippery inner
surfaces of the pitchers, which can be waxy or highly wettable, have so far
been considered as the key trapping devices. However, the occurrence of species
lacking such epidermal specializations but still effective at trapping insects
suggests the possible implication of other mechanisms. Methodology/Principal
Findings : Using a combination of insect bioassays, high-speed video and
rheological measurements, we show that the digestive fluid of Nepenthes
rafflesiana is highly viscoelastic and that this physical property is crucial
for the retention of insects in its traps. Trapping efficiency is shown to
remain strong even when the fluid is highly diluted by water, as long as the
elastic relaxation time of the fluid is higher than the typical time scale of
insect movements. Conclusions/Significance : This finding challenges the common
classification of Nepenthes pitchers as simple passive traps and is of great
adaptive significance for these tropical plants, which are often submitted to
high rainfalls and variations in fluid concentration. The viscoelastic trap
constitutes a cryptic but potentially widespread adaptation of Nepenthes
species and could be a homologous trait shared through common ancestry with the
sundew (Drosera) flypaper plants. Such large production of a highly
viscoelastic biopolymer fluid in permanent pools is nevertheless unique in the
plant kingdom and suggests novel applications for pest control
The International-Trade Network: Gravity Equations and Topological Properties
This paper begins to explore the determinants of the topological properties
of the international - trade network (ITN). We fit bilateral-trade flows using
a standard gravity equation to build a "residual" ITN where trade-link weights
are depurated from geographical distance, size, border effects, trade
agreements, and so on. We then compare the topological properties of the
original and residual ITNs. We find that the residual ITN displays, unlike the
original one, marked signatures of a complex system, and is characterized by a
very different topological architecture. Whereas the original ITN is
geographically clustered and organized around a few large-sized hubs, the
residual ITN displays many small-sized but trade-oriented countries that,
independently of their geographical position, either play the role of local
hubs or attract large and rich countries in relatively complex
trade-interaction patterns
Susceptibility to Vibrio cholerae Infection in a Cohort of Household Contacts of Patients with Cholera in Bangladesh
Vibrio cholerae is the bacterium that causes cholera, a severe form of diarrhea that leads to rapid and potentially fatal dehydration when the infection is not treated promptly. Cholera remains an important cause of diarrhea globally, and V. cholerae continues to cause major epidemics in the most vulnerable populations. Although there have been recent discoveries about how the bacterium adapts to the human intestine and causes diarrhea, there is little understanding of why some people are protected from infection with V. cholerae. This article describes several factors that are associated with the risk of developing V. cholerae infection among people living in the same household with a patient with severe cholera who are at high risk of contracting the infection. One of the findings is that IgA antibodies, a type of antibody associated with immunity at mucosal surfaces such as the intestine, that target several components of the bacteria are associated with immunity to V. cholerae infection. This article also describes genetic and nutritional factors that additionally influence susceptibility to V. cholerae infection
Alcohol dehydrogenase 1B (ADH1B) genotype, alcohol consumption and breast cancer risk by age 50 years in a German case–control study
In a population-based study of 613 cases and 1082 controls, alcohol dehydrogenase 1B (ADH1B) genotype was not an independent risk factor for breast cancer, athough the possibility was raised that it modifies risk associated with high levels of alcohol consumption (OR 1.1, 95% confidence interval (CI) 0.8–1.6 for ADH1B*1/*1 genotype vs 0.2, 95% CI 0.1–1.0 for ADH1B*2 carriers)
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