Subband domain coding of binary textual images for document archiving

Cataloged from PDF version of article.In this work, a subband domain textual image compression method is developed. The document image is first decomposed into subimages using binary subband decompositions. Next, the character locations in the subbands and the symbol library consisting of the character images are encoded. The method is suitable for keyword search in the compressed data. It is observed that very high compression ratios are obtained with this method. Simulation studies are presented

Identification of Novel Reference Genes Based on MeSH Categories

Cataloged from PDF version of article.Transcriptome experiments are performed to assess protein abundance through mRNA expression analysis. Expression levels of genes vary depending on the experimental conditions and the cell response. Transcriptome data must be diverse and yet comparable in reference to stably expressed genes, even if they are generated from different experiments on the same biological context from various laboratories. In this study, expression patterns of 9090 microarray samples grouped into 381 NCBI-GEO datasets were investigated to identify novel candidate reference genes using randomizations and Receiver Operating Characteristic (ROC) curves. The analysis demonstrated that cell type specific reference gene sets display less variability than a united set for all tissues. Therefore, constitutively and stably expressed, origin specific novel reference gene sets were identified based on their coefficient of variation and percentage of occurrence in all GEO datasets, which were classified using Medical Subject Headings (MeSH). A large number of MeSH grouped reference gene lists are presented as novel tissue specific reference gene lists. The most commonly observed 17 genes in these sets were compared for their expression in 8 hepatocellular, 5 breast and 3 colon carcinoma cells by RT-qPCR to verify tissue specificity. Indeed, commonly used housekeeping genes GAPDH, Actin and EEF2 had tissue specific variations, whereas several ribosomal genes were among the most stably expressed genes in vitro. Our results confirm that two or more reference genes should be used in combination for differential expression analysis of large-scale data obtained from microarray or next generation sequencing studies. Therefore context dependent reference gene sets, as presented in this study, are required for normalization of expression data from diverse technological backgrounds. © 2014 Ersahin et al

Implicit motif distribution based hybrid computational kernel for sequence classification

Motivation: We designed a general computational kernel for classification problems that require specific motif extraction and search from sequences. Instead of searching for explicit motifs, our approach finds the distribution of implicit motifs and uses as a feature for classification. Implicit motif distribution approach may be used as modus operandi for bioinformatics problems that require specific motif extraction and search, which is otherwise computationally prohibitive. Results: A system named P2SL that infer protein subcellular targeting was developed through this computational kernel. Targeting-signal was modeled by the distribution of subsequence occurrences (implicit motifs) using self-organizing maps. The boundaries among the classes were then determined with a set of support vector machines. P2SL hybrid computational system achieved ∼81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes. P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol. © The Author 2004. Published by Oxford University Press. All rights reserved

Search for axions in streaming dark matter

A new search strategy for the detection of the elusive dark matter (DM) axion is proposed. The idea is based on streaming DM axions, whose flux might get temporally enormously enhanced due to gravitational lensing. This can happen if the Sun or some planet (including the Moon) is found along the direction of a DM stream propagating towards the Earth location. The experimental requirements to the axion haloscope are a wide-band performance combined with a fast axion rest mass scanning mode, which are feasible. Once both conditions have been implemented in a haloscope, the axion search can continue parasitically almost as before. Interestingly, some new DM axion detectors are operating wide-band by default. In order not to miss the actually unpredictable timing of a potential short duration signal, a network of co-ordinated axion antennae is required, preferentially distributed world-wide. The reasoning presented here for the axions applies to some degree also to any other DM candidates like the WIMPs.Comment: 5 page

Effects of highly active antiretroviral therapy on semen parameters of a cohort of 770 HIV-1 infected men

Background HIV-1 infected patients show impaired semen parameters. Currently, it is not clear whether HIV-1 infection itself or antiretroviral therapy have an effect on semen parameters. We aim evaluate semen quality in a large cohort of fertile HIV-1 infected men under stable highly active antiretroviral therapy (HAART) and to assess the effect of HAART type and duration on semen parameters. Materials and methods Between January 2010 and June 2014, we enrolled in a retrospective case-control study 770 HIV-1 patients under stable HAART asking a reproductive counselling with their HIV negative partner. Co-infections with HBV or HCV, genital tract infections and known causes of infertility represented exclusion criteria. Semen samples were analysed and compared with the WHO reference values. A multivariate analysis including HAART type and duration, age, viral load and CD4 count, was performed on 600 patients out of 770. Results The median values of all semen parameters were significantly lower among HIV-1 infected patients compared to the WHO reference group, with a significant proportion of patients having values below the 5th percentile of the WHO reference value. In a multivariate analysis, only age and viral load negatively impacted progressive motility (\u3b2 -0.3 (95% CI: -0.5; -0.0) %, p<0.05) and semen morphology (\u3b2 -0.00 (95% CI: -0.00; -0.00) %, p0.01), while no associations were detected as regards HAART type and duration. Conclusions HIV-1 infected patients showed a significant impairment of semen parameters compared to the reference values. HAART type and duration showed no associations with semen quality. Further research is needed to investigate implications for clinical care of HIV infected men desiring a child

Infertility as a cancer risk factor \u2013 a review

Ovarian, endometrial and breast cancers are associated with several risk factors, such as low parity,infertility, early age at menarche, and late age at menopause. Frequently most of these risk factors coexist in infertile patients and some studies suggested that the different infertility causes can be involved in cancer risk development. In particular case\u2013control and cohort studies investigated the possible role of ovulatory disorders, endometriosis and unexplained infertility in increasing the risk of this disease. Most studies have shown no overall increased risk in invasive ovarian cancer in subfertile patients, although nulliparity has been consistently associated with increased rates of ovarian tumor, in particular with borderline and endometrioid cancers in patients with a history of endometriosis. Different studies reported that infertile women are not at risk for breast cancer. However, women affected by infertility may be more at risk for endometrial cancer, particularly if affected by ovulatory disorders. Moreover, infertility is now often treated with medical devices that could by themselves modify the hormonal environment and be cofactors in the cellular changes towards cancer development. However, although early studies suggested that infertility medications were associated to increased risk in ovarian cancer, subsequent studies have been mainly reassuring, although suggesting that type and duration of medical treatment can increase the malignancy risk. An increased risk of endometrial cancer in patients undergoing infertility treatment has been reported, as expected by the similar structure shared by clomiphene and tamoxiphene. Since breast cancer is widely recognized as having a hormonal etiology, a possible role of fertility medications to promote cancer has been hypothesized. However, many large studies were not able to find an associated risk of breast cancer. In conclusion, nowadays, firm answers about the precise effects of infertility and its treatment on cancer risk are not available but findings are generally reassuring. Further studies about fertility drug treatments on larger populations may offer in the future longer follow-up and more precise data with better adjustments for confounding factors

Filtered Variation method for denoising and sparse signal processing

We propose a new framework, called Filtered Variation (FV), for denoising and sparse signal processing applications. These problems are inherently ill-posed. Hence, we provide regularization to overcome this challenge by using discrete time filters that are widely used in signal processing. We mathematically define the FV problem, and solve it using alternating projections in space and transform domains. We provide a globally convergent algorithm based on the projections onto convex sets approach. We apply to our algorithm to real denoising problems and compare it with the total variation recovery. © 2012 IEEE

Soil salinity related to physical soil characteristics and irrigation management in four Mediterranean irrigation districts

25 Pag., 6 Tabl., 1 Fig. The definitive version is available at: http://www.sciencedirect.com/science/journal/03783774Irrigated agriculture is threatened by soil salinity in numerous arid and semiarid areas of the Mediterranean basin. The objective of this work was to quantify soil salinity through electromagnetic induction (EMI) techniques and relate it to the physical characteristics and irrigation management of four Mediterranean irrigation districts located in Morocco, Spain, Tunisia and Turkey. The volume and salinity of the main water inputs (irrigation and precipitation) and outputs (crop evapotranspiration and drainage) were measured or estimated in each district. Soil salinity (ECe) maps were obtained through electromagnetic induction surveys (ECa readings) and district-specific ECa–ECe calibrations. Gravimetric soil water content (WC) and soil saturation percentage (SP) were also measured in the soil calibration samples. The ECa–ECe calibration equations were highly significant (P 0.1) with WC, and was only significantly correlated (P Morocco (2.2 dS m−1) > Spain (1.4 dS m−1) > Turkey (0.45 dS m−1). Soil salinity was mainly affected by irrigation water salinity and irrigation efficiency. Drainage water salinity at the exit of each district was mostly affected by soil salinity and irrigation efficiency, with values very high in Tunisia (9.0 dS m−1), high in Spain (4.6 dS m−1), moderate in Morocco (estimated at 2.6 dS m−1), and low in Turkey (1.4 dS m−1). Salt loads in drainage waters, calculated from their salinity (ECdw) and volume (Q), were highest in Tunisia (very high Q and very high ECdw), intermediate in Turkey (extremely high Q and low ECdw) and lowest in Spain (very low Q and high ECdw) (there were no Q data for Morocco). Reduction of these high drainage volumes through sound irrigation management would be the most efficient way to control the off-site salt-pollution caused by these Mediterranean irrigation districts.This study was supported by the European Commission research project INCO-CT-2005-015031.Peer reviewe

Uterine artery Doppler pulsatility index at 11-38 weeks in ICSI pregnancies with egg donation

BACKGROUND: Uterine artery Doppler pulsatility index (UtA-PI) may be different in pregnancies with egg donation (ICSI-ED) as compared to conceptions with autologous intra-cytoplasmatic sperm injection (autologous ICSI) and to spontaneous conceptions (SC). METHODS: One hundred and ninety-four pregnant women with different modes of conception (MC) were prospectively evaluated: 53 ICSI-ED, 36 autologous ICSI and 105 SC. To evaluate the effects of different MC on PI, multivariable linear regression (MLR) models predicting UtA-PI were fitted after adjustment for maternal age, body mass index, race, parity, smoking status and gestational age. RESULTS: In the first trimester, at MLR, autologous ICSI was not associated with a significantly different UtA-PI [estimate (EST) 0.01; 95% confidence interval (CI) -0.19, 0.2; P=0.9] when compared to SC. Conversely, MC by ICSI-ED was associated with lower first trimester UtA-PI (EST -0.32; CI -0.55, -0.08; P=0.01) when compared to SC. At MLR, MC by autologous ICSI and by ICSI-ED were not associated with significant differences in the second and third trimester UtA-PI when compared to SC. CONCLUSION: ICSI-ED conception presented lower UtA-PI when compared to SC at 11+0-13+6 weeks but not at later assessments. Correction of UtA-PI measurement specifying the origin of oocyte may be useful in first trimester screening