Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving gene quantification by adjustable spot-image restoration

MOTIVATION One of the major factors that complicate the task of microarray image analysis is that microarray images are distorted by various types of noise. In this study a robust framework is proposed, designed to take into account the effect of noise in microarray images in order to assist the demanding task of microarray image analysis. The proposed framework, incorporates in the microarray image processing pipeline a novel combination of spot adjustable image analysis and processing techniques and consists of the following stages: (1) gridding for facilitating spot identification, (2) clustering (unsupervised discrimination between spot and background pixels) applied to spot image for automatic local noise assessment, (3) modeling of local image restoration process for spot image conditioning (adjustable wiener restoration using an empirically determined degradation function), (4) automatic spot segmentation employing seeded-region-growing, (5) intensity extraction and (6) assessment of the reproducibility (real data) and the validity (simulated data) of the extracted gene expression levels. RESULTS Both simulated and real microarray images were employed in order to assess the performance of the proposed framework against well-established methods implemented in publicly available software packages (Scanalyze and SPOT). Regarding simulated images, the novel combination of techniques, introduced in the proposed framework, rendered the detection of spot areas and the extraction of spot intensities more accurate. Furthermore, on real images the proposed framework proved of better stability across replicates. Results indicate that the proposed framework improves spots' segmentation and, consequently, quantification of gene expression levels. AVAILABILITY All algorithms were implemented in Matlab (The Mathworks, Inc., Natick, MA, USA) environment. The codes that implement microarray gridding, adaptive spot restoration and segmentation/intensity extraction are available upon request. Supplementary results and the simulated microarray images used in this study are available for download from: ftp://users:bioinformatics@mipa.med.upatras.gr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The Evolving Genotypic Profile of HIV-1 Mutations Related to Antiretroviral Treatment in the North Region of Brazil

HIV related mutations can be associated with decreased susceptibility to antiretrovirals and treatment failures. There is scarce information about HIV mutations in persons failing HIV treatment in North of Brazil. Our aim was to evaluate evolution of HIV subtypes and mutations patterns related to antiretroviral therapy in this region. We investigated HIV resistance profile in adults failing antiretroviral regimen in Northern Brazil from January, 2004, through December, 2013. Genotype data was evaluated through Stanford University algorithm. There were 377 genotypes from different individuals to evaluate. Resistance mutations were similar to worldwide reports and related to antiretroviral exposure. Most prevalent mutations in the reverse transcriptase gene were M184V (80.1%) and K130N (40.6%). Thymidine associated mutations were more frequent in multiexperienced patients. Most common protease mutations were M46I, V82A, I54V, L90M, I84V, M46L, and L76V. Subtype B was the most prevalent (90.7%). There were differences between subtypes B and non-B mutations. We documented for the first time subtypes and patterns of HIV associated mutations in Northern Brazil. A1 subtype was identified for the first time in this area. Depending on drug regimen and how experienced the patient is, an empirical switch of a failing antiretroviral treatment could be a reasonable option.
Beat-to-Beat Tracking of Pulse Pressure and Its Respiratory Variation Using Heart Sound Signal in Patients Undergoing Liver Transplantation

Purpose: To investigate the possibility of esophageal phonocardiography as a monitor for invasively measured pulse pressure (PP) and its respiratory variation (PPV) in patients undergoing liver transplantation. Methods: In 24 liver transplantation recipients, all hemodynamic parameters, including PP and PPV, were measured during five predetermined surgical phases. Simultaneously, signals of esophageal heart sounds (S1, S2) were identified, and S1–S2 interval (phonocardiographic systolic time, PST) and its respiratory variation (PSV) within a 20-s window were calculated. Beat-to-beat correlation between PP and its corresponding PST was assessed during each time window, according to the surgical phases. To compare PPV and PSV along with 5 phases (a total of 120 data pairs), Pearson correlation was conducted. Results: Beat-to-beat PST values were closely correlated with their corresponding 3360 pairs of PP values (median r = 0.568 [IQR 0.246–0.803]). Compared with the initial phase of surgery, correlation coefficients were significantly lower during the reperfusion period (median r = 0.717 [IQR 0.532–0.886] vs. median r = 0.346 [IQR 0.037–0.677]; p = 0.002). The correlation between PSV and PPV showed similar variation according to the surgical phases (r = 0.576 to 0.689, p < 0.05, for pre-reperfusion; 0.290 to 0.429 for the post-reperfusion period). Conclusions: Continuous monitoring of intraoperative PST with an esophageal stethoscope has the potential to act as an indirect estimator of beat-to-beat arterial PP. Moreover, PSV appears to exhibit a trend similar to that of PPV with moderate accuracy. However, variation according to the surgical phase limits the merit of the current results, thereby necessitating cautious interpretation.
Investigating the reaction of BitTorrent content publishers to antipiracy actions

During recent years, a few countries have put in place online antipiracy laws and there has been some major enforcement actions against violators. This raises the question that to what extent antipiracy actions have been effective in deterring online piracy? This is a challenging issue to explore because of the difficulty to capture user behavior, and to identify the subtle effect of various underlying (and potentially opposing) causes. In this paper, we tackle this question by examining the impact of two major antipiracy actions, the closure of Megaupload and the implementation of the French antipiracy law, on publishers in the largest BitTorrent portal who are major providers of copyrighted content online. We capture snapshots of BitTorrent publishers at proper times relative to the targeted antipiracy event and use the trends in the number and the level of activity of these publishers to assess their reaction to these events. Our investigation illustrates the importance of examining the impact of antipiracy events on different groups of publishers and provides valuable insights on the effect of selected major antipiracy actions on publishers' behavior.
Specification of unique Pit-1 activity in the hGH locus control region

The human GH (hGH) gene cluster is regulated by a remote 5′ locus control region (LCR). HSI, an LCR component located 14.5 kb 5′ to the hGH-N promoter, constitutes the primary determinant of high-level hGH-N activation in pituitary somatotropes. HSI encompasses an array of three binding sites for the pituitary-specific POU homeodomain factor Pit-1. In the present report we demonstrate that all three Pit-1 sites in the HSI array contribute to LCR activity in vivo. Furthermore, these three sites as a unit are fully sufficient for position-independent and somatotrope-restricted hGH-N transgene activation. In contrast, the hGH-N transgene is not activated by Pit-1 sites native to either the hGH-N or rat (r)GH gene promoters. These findings suggest that the structures of the Pit-1 binding sites at HSI specify distinct chromatin-dependent activities essential for LCR-mediated activation of hGH in the developing pituitary.
Appraisal of Antihyperlipidemic Activities of Lentinus lepideus in Hypercholesterolemic Rats

Abstract The wild edible mushroom, Lentinus lepideus has recently been cultivated for commercial use in Korea. While the mushroom has been widely used for nutritional and medicinal purposes, the possible anti-hyperlipidemic action is unclear. The effects of dietary L. lepideus on plasma and feces biochemical and on the liver histological status were investigated in hypercholesterolemic rats. Six-wk-old female Sprague-Dawley albino rats were divided into three groups of 10 rats each. Bio-chemical and histological examinations were performed. A diet containing 5% L. lepideus fruiting bodies reduced plasma total cholesterol, triglyceride, low-density lipoprotein, total lipid, phospholipids, and the ratio of low-density to high-density lipoprotein. Body weight was reduced. The diet did not adversely affect plasma biochemical and enzyme profiles. L. lepideus reduced significantly plasma β- and pre-β-lipoprotein, while α-lipoprotein content was increased. A histological study of hepatic cells by conventional hematoxylin-eosin and oil red O staining revealed normal findings for mushroom-fed hyper-cholesterolemic rats. The present study suggests that a diet supplemented with L. lepideus can provide health benefits by acting on the atherogenic lipid profile in hypercholesterolemic rats.
ALMA and Sub-millimeter-wave Astronomy

The Atacama Large Millimeter/submillimeter Array (ALMA) will be the premier millimeter and submillimeter telescope in the world when completed in 2012. ALMA will be a transformational telescope that allows astronomers to image and study at unprecedented detail the origin of stars and planets, galaxies and biologically relevant chemistry, fundamental issues in our attempt to understand how the Universe developed. ALMA represents a qualitative step forward - it will be 10-100 times more sensitive and have 10-100 times better angular resolution than any current telescope working at these wavelengths. The combination of unprecedented sensitivity and excellent resolution of ALMA will transform the astrophysics of the birth of planets, stars and galaxies from the realm of largely theoretical modeling to the realm of directly viewing nature at work. The current status of ALMA will be described. Other submillimeter astronomical projects currently under construction or consideration will also be described.
Anytime characteristics of spatially coupled code

In this paper, we propose an efficient channel coding scheme for anytime communications. We design this anytime code based on spatially coupled LDPC codes and investigate the performance over binary erasure channels. Through density evolution analysis, we asymptotically show the desired anytime properties of the proposed code. We also numerically predict the finite-length performance of the anytime code. We develop an adaptive window decoding technique to ensure a low complexity anytime receiver. Through simulation, we compare the performance of our proposed code with existing anytime codes.
Birth Cohort Effects in Influenza Surveillance Data: Evidence that First Influenza Infection Affects Later Influenza-Associated Illness.

BACKGROUND The evolution of influenza A viruses results in birth cohorts that have different initial influenza virus exposures. Historically, A/H3 predominant seasons have been associated with more severe influenza-associated disease; however, since the 2009 pandemic there are suggestions that some birth cohorts experience more severe illness in A/H1 predominant seasons. METHODS U.S. influenza virologic, hospitalization and mortality surveillance data during 2000-2017 were analyzed for cohorts born between 1918 and 1989 that likely had different initial influenza virus exposures based on viruses circulating during early childhood. Relative risk/rate during H3 compared to H1 predominant seasons during pre-pandemic versus pandemic and later periods were calculated for each cohort. RESULTS During the pre-pandemic period, all cohorts had more influenza-associated disease during H3 predominant seasons than H1 predominant seasons. During the pandemic and later period, four cohorts had higher hospitalization and mortality rates during H1 predominant seasons than H3 predominant seasons. DISCUSSION Birth cohort differences in risk of influenza-associated disease by influenza A virus subtype can be seen in U.S. influenza surveillance data and differ between pre-pandemic and pandemic and later periods. As the population ages, the amount of influenza-associated disease may be greater in future H1 predominant seasons than H3 predominant seasons.
SOME SET THEORIES ARE MORE EQUAL

The proof of independence of the Continuum Hypothesis by Paul Cohen in 1963 and the avalanche of additional independence results was the trigger to a very intensive discourse about the future of Set Theory and its foundational role in Mathematics. It will be only fair to say that while the invention of forcing initiated the blooming of Set Theory as a technical mathematical discipline, it had a shocking effect on the perception of Set Theory as the framework in which all of Mathematics (or at least a major part of it) can be formalized.The prevailing tone of these reactions is that Set Theory (at least as formalized by the Zermelo-Fraenkel axioms, denoted by ZFC) lost its uniqueness.What made the shock even more dramatic was the fact the proof of the independence of the Continuum Hypothesis showed that ZFC gives us very little information about the size of the Continuum and as far as the axioms are concerned there is a huge range of possibilities like 2א0 = א1, 2א0 = א2 . 2א0 = א211086 . 2א0 = אω+1720 = אω1 . Here are two quotes from many: Such results show that axiomatic Set Theory is hopelessly incomplete. If there are a multitude of set theories then none of them can claim the central place in Mathematics. (Mostowski-1967 [29]) Beyond classical analysis there is an infinity of different mathematics and for the time being no definitive reason compels us to chose one rather than another. (Dieudonné-1976 [? ]) This shock is somewhat puzzling because the fact that ZFC is not complete and therefore contains some independent statements was well known in view of Gödel’s incompleteness theorems. Gödel himself in the early version of [15] is confident that CH is independent of ZFC.
Central aspects of systemic oestradiol negative‐ and positive‐feedback on the reproductive neuroendocrine system

The central nervous system regulates fertility via the release of gonadotrophin‐releasing hormone (GnRH). This control revolves around the hypothalamic‐pituitary‐gonadal axis, which operates under traditional homeostatic feedback by sex steroids from the gonads in males and most of the time in females. An exception is the late follicular phase in females, when homeostatic feedback is suspended and a positive‐feedback response to oestradiol initiates the preovulatory surges of GnRH and luteinising hormone. Here, we briefly review the history of how mechanisms underlying central control of ovulation by circulating steroids have been studied, discuss the relative merit of different model systems and integrate some of the more recent findings in this area into an overall picture of how this phenomenon occurs.
Serodiagnosis of infectious mononucleosis by using recombinant Epstein-Barr virus antigens and enzyme-linked immunosorbent assay technology

Four recombinant, diagnostically useful Epstein-Barr virus (EBV) proteins representative of the viral capsid antigen (p150), diffuse early antigen (p54), the major DNA-binding protein (p138), and the EBV nuclear antigen (p72) (W. Hinderer, H. Nebel-Schickel, H.H. Sonneborn, M. Motz, R. Kühbeck, and H. Wolf, J. Exp. Clin. Cancer Res. 7[Suppl.]:132, 1988) were used to set up individual enzyme-linked immunosorbent assays (ELISAs) for the qualitative and quantitative detection of immunoglobulin M (IgM) and IgG antibodies. In direct comparison with results obtained by standard immunofluorescence or immunoperoxidase assays, it was then shown that the recombinant EBV ELISAs provide the means for specific and sensitive serodiagnosis of infectious mononucleosis (IM) caused by EBV. The most useful markers in sera from such patients proved to be IgM antibodies against p54, p138, and p150. Additional positive markers for recent or ongoing IM apparently were IgG antibodies against p54 and p138. In contrast, anti-p72 IgG had a high preference for sera from healthy blood donors and, therefore, can be considered indicative of past exposure to the virus. Altogether, the individual ELISAs proved to be as specific and at least as sensitive for the diagnosis of IM as the currently available standard techniques are. Moreover, our findings suggest that, by combining individual test antigens, a workable ELISA system consisting of three assays (IgM against p54, p138, and p150; IgG against p54 and p138; and IgG against p72) can be established for the standardized rapid diagnosis of acute EBV infections.
Disruption of the actin cytoskeleton after microinjection of proteolytic fragments of alpha-actinin

Alpha-actinin can be proteolytically cleaved into major fragments of 27 and 53 kD using the enzyme thermolysin. The 27-kD fragment contains an actin-binding site and we have recently shown that the 53-kD fragment binds to the cytoplasmic domain of beta 1 integrin in vitro (Otey, C. A., F. M. Pavalko, and K. Burridge. 1990. J. Cell Biol. 111:721-729). We have explored the behavior of the isolated 27- and 53-kD fragments of alpha-actinin after their microinjection into living cells. Consistent with its containing a binding site for actin, the 27-kD fragment was detected along stress fibers within 10-20 min after injection into rat embryo fibroblasts (REF-52). The 53-kD fragment of alpha-actinin, however, concentrated in focal adhesions of REF-52 cells 10-20 min after injection. The association of this fragment with focal adhesions in vivo is consistent with its interaction in vitro with the cytoplasmic domain of the beta 1 subunit of integrin, which was also localized at these sites. When cells were injected with greater than 5 microM final concentration of either alpha-actinin fragment and cultured for 30-60 min, most stress fibers were disassembled. At this time, however, many of the focal adhesions, particularly those around the cell periphery, remained after most stress fibers had gone. By 2 h after injection only a few small focal adhesions persisted, yet the cells remained spread. Identical results were obtained with other cell types including primary chick fibroblasts, BSC-1, MDCK, and gerbil fibroma cells. Stress fibers and focal adhesions reformed if cells were allowed to recover for 18 h after injection. These data suggest that introduction of the monomeric 27-kD fragment of alpha-actinin into cells may disrupt the actin cytoskeleton by interfering with the function of endogenous, intact alpha-actinin molecules along stress fibers. The 53-kD fragment may interfere with endogenous alpha-actinin function at focal adhesions or by displacing some other component that binds to the rod domain of alpha-actinin and that is needed to maintain stress fiber organization.
Endogenous sex hormones and risk of venous thromboembolism in young women

The risk of venous thromboembolism (VTE) in young women can predominantly be attributed to exogenous hormone use. The influence of (abnormalities in) endogenous sex hormones, as in polycystic ovary syndrome (PCOS) or primary ovarian insufficiency (POI), on VTE risk is uncertain.
Testosterone deficiency reduces cardiac hypertrophy in a rat model of severe volume overload

The aim of the study was to characterize if the development of cardiac hypertrophy (CH) caused by severe left ventricle (LV) volume overload (VO) from chronic aortic valve regurgitation (AR) in male rats was influenced by androgens. We studied Wistar rats with/without orchiectomy (Ocx) either sham‐operated (S) or with severe AR for 26 weeks. Loss of testosterone induced by Ocx decreased general body growth. Cardiac hypertrophy resulting from AR was relatively more important in intact (non‐Ocx) animals than in Ocx ones compared to their respective S group (60% vs. 40%; P = 0.019). The intact AR group had more LV dilation, end‐diastolic LV diameter being increased by 37% over S group and by 17% in AROcx rats (P < 0.0001). Fractional shortening (an index of systolic function) decreased only by 15% in AROcx compared to 26% for intact AR animals (P = 0.029). Changes in LV gene expression resulting from CH were more marked in intact rats than in AROcx animals, especially for genes linked to extracellular matrix remodeling and energy metabolism. The ratio of hydroxyacyl‐Coenzyme A dehydrogenase activity over hexokinase activity, an index of the shift of myocardial substrate use toward glucose from the preferred fatty acids, was significantly decreased in the AR group but not in AROcx. Finally, pJnk2 LV protein content was more abundant in AR than in AROcx rats, indicating decreased activation of this stress pathway in the absence of androgens. In summary, testosterone deficiency in rats with severe LV VO resulted in less CH and a normalization of the LV gene expression profile.
Therapeutic strategies that act on the peripheral nervous system in primary headache disorders

ABSTRACT Introduction: Acute and preventive treatment of primary headache disorders is not completely resolved with regard to efficacy, safety, and tolerability. Hence, peripheral and central neuromodulation can provide therapeutic alternatives in drug-resistant cases. Peripheral targets of neuromodulation include invasive and non-invasive neurostimulation and electrical and chemical nerve and ganglion blockades. Areas covered: A PubMed search of papers published from January 2012 to October 2018 was conducted. The goal of this review was to analyze the efficacy and safety of invasive (implantable) peripheral neurostimulation methods (the occipital nerve, the cervical branch of vagal nerve, the sphenopalatine ganglion) and non-invasive (transcutaneous) peripheral neurostimulation methods (the occipital nerve, the supraorbital nerve, and the cervical and auricular branches of the vagal nerve), based on the results of published clinical trials and case series. Acting also on the peripheral nervous system, peripheral nerve (i.e. greater occipital nerve) and ganglion (i.e. sphenopalatine ganglion) blockades, botulinum neurotoxin type A-hemagglutinin complex therapies, and calcitonin gene-related peptide-related monoclonal antibody treatments in this patient population are also discussed. Expert opinion: This review summarizes the latest results on the therapeutic strategies acting on the periphery in primary headache disorders. These therapeutic options are minimally invasive or non-invasive, efficacious, safe, and well tolerated.
Synthesis and Characterization of Graphene Oxide/Chitosan Composite Aerogels with High Mechanical Performance

Chitosan, a semi-crystalline biomolecule, has attracted wide attention due to its high synthesis flexibility. In this study, to improve the mechanical properties of chitosan aerogels (CSAs), graphene oxide (GO) was extracted and introduced into chitosan aerogels as fillers. The porous CSAs/GO composite aerogels were fabricated by an environmentally friendly freeze-drying process with different GO contents (0, 0.5, 1.0, 1.5, wt.%). The characteristics of the CSAs/GO were investigated by scanning electron microscopy (SEM), mechanical measurements and mercury porosimeter. The crystallinity of samples was characterized by X-ray diffraction (XRD). The mechanism of the effect of graphene oxide on chitosan was studied by Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). The results show that the microstructure of the samples is developed in the network structure. The porosity of CSAs/GO aerogels is as high as 87.6%, and the tensile strength of the films increased from 6.60 MPa to 10.56 MPa with the recombination of graphene oxide. The crystallinity (CrI) of composite aerogels increased from 27% to 81%, which indicates that graphene oxide improves the mechanical properties of chitosan by chemical crosslinking.