Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental Sensing and Signal Transduction Pathways Regulating Morphopathogenic Determinants of Candida albicans

SUMMARY Candida albicans is an opportunistic fungal pathogen that is found in the normal gastrointestinal flora of most healthy humans. However, under certain environmental conditions, it can become a life-threatening pathogen. The shift from commensal organism to pathogen is often correlated with the capacity to undergo morphogenesis. Indeed, under certain conditions, including growth at ambient temperature, the presence of serum or N-acetylglucosamine, neutral pH, and nutrient starvation, C. albicans can undergo reversible transitions from the yeast form to the mycelial form. This morphological plasticity reflects the interplay of various signal transduction pathways, either stimulating or repressing hyphal formation. In this review, we provide an overview of the different sensing and signaling pathways involved in the morphogenesis and pathogenesis of C. albicans. Where appropriate, we compare the analogous pathways/genes in Saccharomyces cerevisiae in an attempt to highlight the evolution of the different components of the two organisms. The downstream components of these pathways, some of which may be interesting antifungal targets, are also discussed.
Information Technology Contests - Introduction to Computer Science in an Attractive Way

Computers, information and communication technology (ICT) are more and more involved in the education process. Students should learn to use information technologies (IT) in a suitable, effective way, and when learning any subject they should be capable to implement computer facilities and thus develop their learning methods. Competitions are an excellent tool to achieve these goals. Competitions play an important role as a source of inspiration and innovation - youngsters are attracted by competitions, they get easier involved in such an activity, more willingly discuss and become more active. IT contests may be a key to the potential of new knowledge and an attractive way of binding up technology and education. Interest in competitions essentially depends on problems. Really, choosing and developing interesting tasks (problems) is one of the most important issues bringing students into competitions. Attraction, invention, tricks, surprise should be desirable features of each problem presented to competitors. The problems have to be carefully selected, taking into account the different aspects of each problem. IT competitions should encourage students to think about computer science and to understand what it can be. Introduction to computers, learning by using ICT are the actions aimed at solution and analysis of particular problems. Before starting IT competitions, tasks must be planned very carefully and based on some theoretical analysis. The main attention is paid to develop some criteria for creating as well as selecting tasks. The history of the Lithuanian IT competition named ''Beaver'' started on October 21, 2004. Approximately 3500 students from about 150 comprehensive schools were involved in it. Afterwards, the workshop of participants from several foreign countries was held and building of a framework of the international ``Beaver'' competition was started. The paper deals with theoretical and practical issues of developing new kinds of competition in IT in Lithuania, called ``Beaver''.
Complete amino acid sequence of flavocytochrome b2 from baker's yeast.

Each subunit of baker's yeast flavocytochrome b2 can be selectively cleaved by proteases into two fragments, amino-terminal fragment alpha and carboxy-terminal fragment beta. The primary structure of the former has been reported before [Ghrir, B. , Becam, A. M. & Lederer, F. (1984) Eur. J. Biochem. 139, 59-74]. The amino acid sequence of the 197-residue fragment beta has now been established. The fragment was cleaved with cyanogen bromide; the three peptides thus obtained were submitted to digestions with Staphylococcus aureus V8 protease, chymotrypsin and trypsin, sometimes after succinylation. The complete fragment was also submitted to tryptic cleavage after citraconylation. Peptides were separated by thin-layer finger-printing or high-pressure liquid chromatography. They were mostly sequenced in a liquid-phase sequenator. The 511-residue amino acid sequence of the mature protein is thus completely established. Secondary structure predictions indicate an alternation of helical and extended structure, with a higher percentage of the former. Comparisons with other flavoproteins do not detect any significant sequence similarity.
Structural Recognition by Recombinant Human Heparanase That Plays Critical Roles in Tumor Metastasis

Human heparanase is an endo-β-d-glucuronidase that degrades heparan sulfate/heparin and has been implicated in a variety of biological processes, such as inflammation, tumor angiogenesis, and metastasis. Although the cloned enzyme has been demonstrated to have a critical role in tumor metastasis, the substrate specificity has been poorly understood. In the present study, the specificity of the purified recombinant human heparanase was investigated for the first time using a series of structurally defined oligosaccharides isolated from heparin/heparan sulfate. The best substrates were ΔHexUA(±2S)-GlcN(NS,6S)-GlcUA-GlcN(NS,6S)-GlcUA-GlcN(NS,6S) and ΔHexUA(2S)-GlcN(NS,6S)-GlcUA-GlcN(NS,6S) (where ΔHexUA, GlcN, GlcUA, NS, 2S, and 6S represent unsaturated hexuronic acid,d-glucosamine, d-glucuronic acid, 2-N-sulfate, 2-O-sulfate, and 6-O-disulfate, respectively). Based on the percentage conversion of the substrates to products under identical assay conditions, several aspects of the recognition structures were revealed. 1) The minimum recognition backbone is the trisaccharide GlcN-GlcUA-GlcN. 2) The target GlcUA residues are in the sulfated region. 3) The -GlcN(6S)-GlcUA-GlcN(NS)- sequence is essential but not sufficient as the cleavage site. 4) The IdoUA(2S) residue, located two saccharides away from the target GlcUA residue, claimed previously to be essential, is not indispensable. 5) The 3-O-sulfate group on the GlcN is dispensable and even has an inhibitory effect when located in a highly sulfated region. 6) Based on these and previous results, HexUA(2S)-GlcN(NS,6S)-IdoUA-GlcNAc(6S)-GlcUA-GlcN(NS,±6S)-IdoUA(2S)-GlcN(NS,6S) (where HexUA represents hexuronic acid) has been proposed as a probable physiological target octasaccharide sequence. These findings will aid establishing a quantitative assay method using the above tetrasaccharide and designing heparan sulfate-based specific inhibitors of the heparanase for new therapeutic strategies.
Association of HIV and Malaria With Mother-to-Child Transmission, Birth Outcomes, and Child Mortality

Objective:To assess the impact of HIV and malaria coinfection on mother-to-child HIV transmission (MTCT) and adverse birth outcomes. Methods:One hundred nine HIV-positive mother-infant pairs with a malaria diagnosis were identified in a community cohort and followed up postpartum. Maternal malaria was diagnosed by a rapid immunochromatographic test (ICT) on sera and histopathologic examination of placenta. Infant HIV was diagnosed within 6 weeks of birth using polymerase chain reaction (PCR) to capture in-utero and intrapartum HIV transmission. Log binomial models were used to assess the relative risk of MTCT, low birth weight, and preterm birth associated with malaria. Results:Approximately 17.4% of infants were HIV positive at or around birth, and the prevalence of serologic and placental malaria were 31% and 32%, respectively. HIV-positive mothers with serological ICT malaria were significantly more likely to have low-birth-weight infants, and low-birth-weight infants had significantly higher risk of MTCT compared with infants of normal birth weight. Although placental and serologic ICT malaria were significantly associated with MTCT, after adjusting for maternal HIV viral load, the risk of MTCT was significantly increased only for mothers coinfected with placental malaria (relative risk [RR] = 7.9, P = 0.025). Conclusions:Placental malaria increases the risk of MTCT after adjustment for viral load. Programs should focus on enhanced malaria prevention during pregnancy to decrease the risk of adverse birth outcomes and MTCT.
Microchannel wall coatings for protein separations by capillary and chip electrophoresis

The necessity for microchannel wall coatings in capillary and chip‐based electrophoretic analysis of biomolecules is well understood. The regulation or elimination of EOF and the prevention of analyte adsorption is essential for the rapid, efficient separation of proteins and DNA within microchannels. Microchannel wall coatings and other wall modifications are especially critical for protein separations, both in fused‐silica capillaries, and in glass or polymeric microfluidic devices. In this review, we present a discussion of recent advances in microchannel wall coatings of three major classes – covalently linked polymeric coatings, physically adsorbed polymeric coatings, and small molecule additives. We also briefly review modifications useful for polymeric microfluidic devices. Within each category of wall coatings, we discuss those used to eliminate EOF, to tune EOF, to prevent analyte adsorption, or to perform multiple functions. The knowledgeable application of the most promising recent developments in this area will allow for the separation of complex protein mixtures and for the development of novel microchannel wall modifications.
Cell migration : developmental methods and protocols

Part I. Introduction Cell Migration: An Overview Donna J. Webb, Huaye Zhang, and Alan F. Horwitz Part II. Basic Cell Migration and Related Assays Boyden Chamber Assay Hong-Chen Chen Wound-Healing Assay Luis G. Rodriguez, Xiaoyang Wu, and Jun-Lin Guan Analysis of Cell Migration Using the Dunn Chemotaxis Chamber and Time-Lapse Microscopy Claire M. Wells and Anne J. Ridley Cell-Adhesion Assays Dennis F. Kucik and Chuanyue Wu Cell-Spreading Assays Allison L. Berrier and Susan E. LaFlamme Cell-Scatter Assay Hong-Chen Chen Cell Migration Analyses Within Fibroblast-Derived 3-D Matrices Edna Cukierman Part III. Analysis of Cell Migration in Specialized Cell Systems Tumor Cell Invasion Assays Leslie M. Shaw Analysis of Endothelial Cell Migration Under Flow Song Li Angiogenesis Assays in the Chick CAM Chris Storgard, David Mikolon, and Dwayne G. Stupack Investigations of Neuronal Migration in the Central Nervous System Michael E. Ward and Yi Rao Part IV. Analysis of Cell Migration in Model Organisms Analysis of Cell Migration in Caenorhabditis elegans M. Afaq Shakir and Erik A. Lundquist Analysis of Cell Migration Using Drosophila as a Model System Jocelyn A. McDonald and Denise J. Montell Imaging Cell Movement During Dorsal Closure in Drosophila Embryos William Wood and Antonio Jacinto Analysis of Cell Movements in Zebrafish Embryos: Morphometrics and Measuring Movement of Labeled Cell Populations In Vivo Diane S. Sepich and Lilianna Solnica-Krezel The Xenopus Embryo as a Model System for Studies of Cell Migration Douglas W. DeSimone, Lance Davidson, Mungo Marsden, and Dominique Alfandari Neural Crest Migration Methods in the Chicken Embryo Maria Elena de Bellard and Marianne Bronner-Fraser In Vivo and In Vitro Models of Mammalian Angiogenesis Mien V. Hoang and Donald R. Senger Part V. Biochemical and Novel Approaches in Cell Migration Measurement of Protein Tyrosine Phosphorylation in Cell Adhesion Vidhya V. Iyer, Christoph Ballestrem, Joachim Kirchner, Benjamin Geiger, and Michael D. Schaller Cell-Adhesion Assays: Fabrication of an E-Cadherin Substratum and Isolation of Lateral and Basal Membrane Patches Frauke Drees, Amy Reilein, and W. James Nelson Application of Microscope-Based FRET to Study Molecular Interactions in Focal Adhesions of Live Cells Christoph Ballestrem and Benjamin Geiger Use of Multiphoton Imaging for Studying Cell Migration in the Mouse Andrea Flesken-Nikitin, Rebecca M. Williams, Warren R. Zipfel, Watt W. Webb, and Alexander Yu. Nikitin Using Microfluidic Channel Networks to Generate Gradients for Studying Cell Migration Daniel S. Rhoads, Sharvari M. Nadkarni, Loling Song, Camilla Voeltz, Eberhard Bodenschatz, and Jun-Lin Guan Index
The Relationship between the Time of Endoscopy and Morbidity and Mortality Rates in Patients with Upper Gastrointestinal Bleeding

Background: This study was done to evaluate the relationship between the time of endoscopy in patients with upper gastrointestinal bleeding with morbidity and mortality rates of patients at the Al Zahra Hospital emergency room. Materials and Methods: In a cohort study, 1152 patients at 2014 and 2015 have been hospitalized due to gastrointestinal bleeding in Al Zahra Hospital, were selected and demographic and clinical information and day and time of endoscopy and hospital mortality and fewer deaths than a month after discharge were studied, and prognosis was analyzed in terms of day and time of endoscopy. Results: Nine hundred and seventy-three cases (84.5%) of endoscopy were performed during the working days and 179 (15.5%) were performed on holidays. Moreover, 801 cases (69.5%) of endoscopy were done in the morning and 351 cases (30.5%) were performed in the evening and night shifts. The day and time of endoscopy had no significant effect on mortality in hospital and less than a month after but hospital death in whom underwent endoscopy by fellowship was significantly higher (P = 0.004). Conclusion: Endoscopy in nonholiday and holiday days and the time of endoscopy has no significant effect on hospital mortality 1 month after discharge. However, other factors such as endoscopy by attendant or fellowship, time between admission to endoscopy, age and sex of the patients, etc., were significantly effective on in-hospital mortality and death 1 months after discharge. Also faster and sooner endoscopy cannot reduce rate of blood transfusions or reduce the length of hospital stay but faster endoscopy of patients can reduce the risk of in-hospital death.
Towards changing the paradigm of software development in software industries: An emergence of agile software development

There has been drastic change and improvement in the software development after the publication of Agile manifesto[1] in, 2001. Agile Software Development (ASD) has changed the way of technology of manufacturing methods as it is easily applicable to the changes that consumer wanted to occur in its product Agile Software Development works on the practical purposes rather than documentation, as it is adapted by several successful industries for their manufacturing techniques. Besides the successful implementation of agile methods, there are still those large scale industries and organizations which are inadequate to apply the methods of Agile for their complex software projects. Hence, we have observed that Agile manifesto along with Agile Software Development bring out the faster change and more appropriate changes which is very much efficacious than the traditional models like waterfall model, Iterative model, etc. which have been created in previous time for the development purposes. In this paper, we have discussed the variations that have occurred and observed during its implementation. This paper is also providing software organizations deeper understanding about the factors that are important to ensure quality in Agile. This paper also review the recommendations for its implementation based on large complex projects and technologies which include the renovation of complex coding, testing, communication tools, etc. which will be the step towards success of Agile adaptation on large projects for the software development.
Representation and modeling of protein surface determinants

Surface characterization of peptides may provide useful information about functionality and potential interactions with other molecules. A description of a protein site through a surface that models the shape conferred by the exposed residues is an effective tool for the analysis and the modeling of proteins that may highlight similarities and relationships not detectable through comparisons at level of primary, secondary, and tertiary structure. This study concerns the development of a tool that extracts the residues that concur to the shape modeling of the surface of a protein or a portion of it. This task is accomplished without taking into account the order of the amino acids in the primary structure, but only according to the selection of a portion of the protein indicated through geometric parameters or an explicit list of amino acids belonging to the site of interest. Both in the case of an entire protein and in the case of a portion of it, the method provides the mesh that models the surface described by the exposed residues that constitute the external envelope. The developed tool which allows the extraction of the exposed residues, and thus of the potential function determinants, is applied to identify the amino acids that concur to the structural interaction in several protein complexes.
Trained Artificial Neural Network for Glaucoma Diagnosis Using Visual Field Data: A Comparison With Conventional Algorithms

PurposeTo evaluate and confirm the performance of an artificial neural network (ANN) trained to recognize glaucomatous visual field defects, and compare its diagnostic accuracy with that of other algorithms proposed for the detection of visual field loss. MethodsSITA Standard 30-2 visual fields, from 100 glaucoma patients and 116 healthy participants, formed the data set. Our ANN was a previously described fully trained network using scored pattern deviation probability maps as input data. Its diagnostic accuracy was compared to that of the Glaucoma Hemifield Test, the Pattern Standard Deviation index at the P<5% and <1%, and also to a technique based on the recognizing clusters of significantly depressed test points. ResultsThe included tests had early to moderate visual field loss (median MD=−6.16 dB). ANN achieved a sensitivity of 93% at a specificity level of 94% with an area under the receiver operating characteristic curve of 0.984. Glaucoma Hemifield Test attained a sensitivity of 92% at 91% specificity. Pattern Standard Deviation, with a cut off level at P<5% had a sensitivity of 89% with a specificity of 93%, whereas at P<1% the sensitivity and specificity was 72% and 97%, respectively. The cluster algorithm yielded a sensitivity of 95% and a specificity of 82%. ConclusionsThe high diagnostic performance of our ANN based on refined input visual field data was confirmed in this independent sample. Its diagnostic accuracy was slightly to considerably better than that of the compared algorithms. The results indicate the large potential for ANN as an important clinical glaucoma diagnostic tool.
Analyse systémique de la symbiose intracellulaire : évolution et organisation du réseau métabolique des endocytobiotes.

Les bacteries endocytobiotes vivent de maniere durable au sein meme des cellules des organismes qui les abritent. L'environnement particulier qu'est la cellule de l'hote, et le type de relations entre les deux partenaires (parasitisme ou mutualisme), ont naturellement des consequences sur l' evolution de leur metabolisme respectif. L'objectif global de cette these est de mieux comprendre l'inﬂuence du mode de vie sur l' evolution et le fonctionnement du metabolisme des endocytobiotes. Nous apprehendons le metabolisme d'une maniere globale, sous la forme de reseaux metaboliques. Le developpement de nouvelles methodes et d'outils d'exploration du reseau metabolique nous ont permis de realiser des analyses et des comparaisons de reseaux metaboliques complets avec un niveau de detail eleve. L'ensemble de ces analyses eclaire ainsi d'un jour nouveau le metabolisme des bacteries endocytobiotes par sa diversite, son evolution et la nature des interactions metaboliques entretenues avec l'hote.
Gene Family Analysis of the Arabidopsis Pollen Transcriptome Reveals Biological Implications for Cell Growth, Division Control, and Gene Expression Regulation1[w]

Upon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of one-third of the Arabidopsis (Arabidopsis thaliana) genome to define a first overview of the pollen transcriptome. We now extend that study to approximately 80% of the genome of Arabidopsis by using Affymetrix Arabidopsis ATH1 arrays and perform comparative analysis of gene family and gene ontology representation in the transcriptome of pollen and vegetative tissues. Pollen grains have a smaller and overall unique transcriptome (6,587 genes expressed) with greater proportions of selectively expressed (11%) and enriched (26%) genes than any vegetative tissue. Relative gene ontology category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome toward signaling, vesicle transport, and the cytoskeleton, suggestive of a commitment to germination and tube growth. Cell cycle analysis reveals an accumulation of G2/M-associated factors that may play a role in the first mitotic division of the zygote. Despite the relative underrepresentation of transcription-associated transcripts, nonclassical MADS box genes emerge as a class with putative unique roles in pollen. The singularity of gene expression control in mature pollen grains is further highlighted by the apparent absence of small RNA pathway components.
Design of wavelet based image fusion using A Trous algorithm

Image fusion presents a technique based on wavelet fusion for change detection in Synthetic Aperture Radar images. The image fusion technique is introduced to generate a difference image by using complementary information from a mean-ratio image and a log-ratio image. Our objective is to analyse the performance of the A Trous algorithm for Synthetic Aperture Radar Images. In our work, an improved additive-wavelet fusion method is presented using the A Trous algorithm and it is modified to suit the Grey scale Multispectral Images. This method is applied to the wavelet coefficients that are formulated by the mean ratio and log ratio difference images and produce the fused image. To analyse the performance of the fused image obtained above two methods information entropy, correlation coefficient and Root Mean Square Error are computed and quantitative analysis is done for two set of input source images.