Miracle-dz/UniFAR-FTUs huggingface dataset:
The Tup1 Corepressor Directs Htz1 Deposition at a Specific Promoter Nucleosome Marking the GAL1 Gene for Rapid Activation

ABSTRACT The SWR1 complex (SWR1-C)-dependent deposition of the histone variant Htz1 on promoter nucleosomes is typical of Saccharomyces cerevisiae genes whose expression is frequently reprogrammed. Although this epigenetic marking is of significant physiological importance, the determinants of Htz1 deposition, the conditions that set off SWR1-C occupancy, and the implications of Htz1 in transcriptional initiation are issues that remain unresolved. In this report, we addressed these questions by investigating the GAL1 promoter. We show that Htz1 is required for efficient Mediator recruitment and transcription only when the GAL1 promoter is under the influence of the Tup1 corepressor. In fact, we show that it is Tup1 that specifies Htz1 deposition for the promoter nucleosome covering the transcription start site. This deposition occurs rapidly following transcriptional repression, and it correlates with a Tup1-independent transient recruitment of the SWR1 complex. We propose that Tup1 cooperates with SWR1-C and specifies Htz1 deposition at GAL1, thereby marking the promoter for rapid neutralization from its repressive effects.
Relations of Clay Fraction Mineralogy, Structure and Water Retention in Oxidic Latosols (Oxisols) from the Brazilian Cerrado Biome

© 2012 Carducci et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Relations of Clay Fraction Mineralogy, Structure and Water Retention in Oxidic Latosols (Oxisols) from the Brazilian Cerrado Biome
Exaiination ofLeandlele Genotypes ofGlycine max(L.) Merr. forMembrane-Bound andBuffer-Soluble Soybean Lectin'

Membrane fractions fromseedlings offour soybean JGlcine max(L.) Merr.1 lines wereexamined byradioimmunoassay andhemagglutination assay forthe120,000 dalton soybean lectin. Twoofthelines (Sooty andT102)aregenotypicafly kleandlackbuffer-soluble soybean lectin; the remaining twolines (Beeson andHarosoy 63)areLeandproduce seeds thatcontain thelectin (Suetal.1980Biochim. Biophys. Acta629: 292304). BothTriton X-100 (0.5% v/v) andnonidet P-40(0.05% v/v) solubilized soybean lectin frommembrane fractions ofLecotyledons. Triton X-100 interfered substantially withtheassay ofprotein andhemagglutinating activity andwasunacceptable foruseinquantitative measurements. The nonidet P40-solubilized soybean lectin fromLecotyledons wasconsistently present bothinwashed 13,000g and82,500g membrane fractions, but itaccounted forless than1.5%ofthetotal (buffer-soluble plus membranebound) soybean lectin. Themembrane lectin waspurified bytheaffinity chromatography procedure devised forsoluble soybean lectin, anditwas immunologically indistinguishable fromauthentic soybean lectin. Membranefractions fromLecotyledons contained insignifcant amountsof radioisotope-labeled soybean lectin thathadbeenaddedduring homogenization, andpurified membrane fractions didnotbindthelectin inthe presence ofthehapten, D-galactose. These controls makeitunlikely that themembrane soybean lectin wasofcytoplasmic origin. Soybean lectin andother hemagglutinins werenotpresent inbuffer-soluble ormembrane fractions fromkkcotyledons orfromroots andhypocotyls ofanyofthe lines.
Immunolocalization of 5alpha-reductase isozymes in acne lesions and normal skin.

BACKGROUND Dihydrotestosterone mediates androgen-dependent diseases, such as acne, hirsutism, and androgenetic alopecia. This hormone is produced from testosterone by the 5alpha-reductase enzyme. There are 2 isozymes of 5alpha-reductase (types 1 and 2) that differ in their localization within the body and even within the skin. Activity of the type 1 isozyme predominates in sebaceous glands, where it may be involved in regulation of sebum production. Since specific inhibition of 5alpha-reductase type 1 may represent a novel therapeutic approach to acne, it is important to define the localization of these isozymes in normal sebaceous follicles and acne lesions. OBSERVATIONS Skin biopsy specimens were obtained from the backs of 11 subjects: 8 with acne and 3 without acne. Sections of normal follicles, open comedones, closed comedones, and inflammatory lesions were incubated with antibodies to types 1 and 2 5alpha-reductase. In all samples, the type 1 antibody localized specifically to sebaceous glands, and the type 2 antibody localized to the companion layer of the hair follicle (the innermost layer of the outer root sheath) and granular layer of the epidermis. Localization of the type 2 isozyme was also noted within the walls of open and closed comedones and in endothelial cells from sections of inflammatory lesions. CONCLUSIONS The immunolocalization of 5alpha-reductase isozymes in normal sebaceous follicles and acne follicles is similar to the pattern described in terminal hair follicles and corresponds with the findings of biochemical studies that have demonstrated predominance of type 1 activity in sebaceous glands. The function of type 2 5alpha-reductase in comedones or endothelial cells in inflammatory lesions is unknown.
Quantum Model of Decision-Making in Economics

The paper designs a quantum model of decision-making (QMDM) that utilizes neuroscientific evidence. The new model provides both normative and positive implications to economics. First, it enhances the study of decision-making which is an extension of the expected utility theory (EUT) in mathematical economics. Second, we demonstrate how the quantum model mitigates drawbacks of the expected utility theory of today.
Immunoproteomic Identification and Serological Responses to Novel Chlamydia pneumoniae Antigens That Are Associated with Persistent C. pneumoniae Infections1

The controversial discussion about the role of Chlamydia pneumoniae in atherosclerosis cannot be solved without a reliable diagnosis that allows discrimination between past and persistent infections. Using a proteomic approach and immunoblotting with human sera, we identified 31 major C. pneumoniae Ags originating from 27 different C. pneumoniae proteins. More than half of the proteins represent Chlamydia Ags not described previously. Using a comparative analysis of spot reactivity Pmp6, OMP2, GroEL, DnaK, RpoA, EF-Tu, as well as CpB0704 and CpB0837, were found to be immunodominant. The comparison of Ab-response patterns of sera from subjects with and without evidence for persisting C. pneumoniae, determined by multiple PCR analysis of PBMC and vasculatory samples, resulted in differential reactivity for 12 proteins, which is not reflected by reactivity of the sera in the microimmunofluorescence test, the current gold standard for serodiagnosis. Although reactivity of sera from PCR-positive donors was increased toward RpoA, MOMP, YscC, Pmp10, PorB, Pmp21, GroEL, and Cpaf, the reactivity toward YscL, Rho, LCrE, and CpB0837 was decreased, reflecting the altered protein expression of persisting C. pneumoniae in vitro. Our data provide the first evidence of a unique Ab-response pattern associated with persistent C. pneumoniae infections, which is a prerequisite for the serological determination of persistently infected patients.
An optimum microstrip via through a ground plane hole

This paper studies the optimum via through a ground plane hole connecting microstriplines on both sides. The via and hole are a discontinuity along the microstrip lines, therefore an optimum via is one that causes the least amount of reflection. Through the use of quasi-static theory on the fringe fields, the optimum radii of the via and the hole are found. These radii give an √L/C ratio of the discontinuity that is slightly more than Zo of the microstripline.
Congestion control optimization of M2M in LTE networks

This paper introduces optimization methods of M2M communication based on 3GPP standard. The optimization techniques are specified on M2M bearer within the mobile communication network. Its presentation intends to present an insight and approach to develop high quality communication frameworks for IoT data test-bed, based on Long Term Evolution (LTE) communications systems. The test-bed framework is achieved by featuring an emulation of Evolve Packet Core (EPC) construction using NetFPGA and OpenFlow platforms. The testbed model will be expected to offer the sensitiveness control over IoT communication data type. In addition the emulation scheme provided by this test-bed will allow an extensive achievement toward M2M over LTE compliance for IoT integrated architecture in the near future.
p38 Mitogen-activated protein kinase-induced glucocorticoid receptor phosphorylation reduces its activity: role in steroid-insensitive asthma.

BACKGROUND Although glucocorticoids are the most effective treatment for chronic inflammatory diseases, such as asthma, some patients show a poor response. IL-2 combined with IL-4 can alter glucocorticoid receptor (GR) ligand-binding affinity and modulate glucocorticoid function. OBJECTIVE We sought to confirm the altered ligand-binding affinity in a distinct group of steroid-dependent asthmatic subjects and examine the mechanism by which IL-2 and IL-4 modify the ligand-binding affinity of the GR. METHODS We examined PBMCs from healthy subjects, subjects with mild asthma, and steroid-dependent subjects with severe asthma using dexamethasone-binding assays and Western blot analysis of GR and phosphorylated activated transcription factor 2 expression. GR phosphorylation was measured after orthophosphate labeling and immunoprecipitation and cytokine production by means of ELISA. RESULTS GR ligand-binding affinity was reduced in the nucleus but not in the cytoplasm of steroid-dependent asthmatic subjects compared with that seen in healthy subjects (dissociation constant, 39.8 +/- 4.6 vs. 6.79 +/- 0.8 nmol/L). This difference in ligand-binding affinity could be mimicked by IL-2 and IL-4 cotreatment and was blocked by the p38 mitogen-activated kinase (MAPK) inhibitor SB203580. Activation of p38 MAPK by IL-2 and IL-4, as shown by means of phosphorylation of activated transcription factor 2, resulted in GR phosphorylation and reduced dexamethasone repression of LPS-stimulated GM-CSF release. p38 MAPK phosphorylation of CD2(+) T cells occurred on serine residues. The ability of dexamethasone to modulate IL-10 release was also inhibited by IL-2 and IL-4 cotreatment. These effects were also inhibited by SB203580. CONCLUSION These data show that p38 MAPK inhibitors may have potential in reversing glucocorticoid insensitivity and reestablishing the beneficial effects of glucocorticoids in patients with severe asthma.
De la conception physique aux outils d'administration et de tuning des entrepôts de données

Nous visons a travers cette these a proposer un ensemble d'approches permettant d'optimiser les entrepots de donnees et d'aider l'AED a bien mener cette optimisation. Nos approches d'optimisation reposent sur l'utilisation de trois techniques d'optimisation : la fragmentation horizontale primaire, derivee et les index de jointure binaires (IJB). Nous commencons par proposer une approche de fragmentation qui prend en consideration a la fois la performance (reduction du cout d'execution) et la manageabilite (controle du nombre de fragments generes). Nous proposons ensuite une approche gloutonne de selection d'IJB. L'utilisation separee de la fragmentation horizontale (FH) et des IJB ne permet pas d'exploiter les similarites existantes entre ces deux techniques. Nous proposons une approche de selection conjointe de la FH et des IJB. Cette approche peut etre utilisee pour le tuning de l'entrepot. Nous avons mene plusieurs experiences pour valider nos differentes approches. Nous proposons par la suite un outil permettant d'aider l'AED dans ses tâches de conception physique et de tuning. Mots cles : Conception physique, Tuning, Techniques d'optimisation, Fragmentation Horizontale, Index de Jointure Binaires.
The Island-Gate Varactor—A High-Q MOS Varactor for Millimeter-Wave Applications

A new accumulation MOS varactor with island-shaped poly gate layout is proposed to improve the quality factor ( Q-factor) at high frequency, which can be readily employed for CMOS-based millimeter-wave applications. Measured results up to 67 GHz show significant improvements in the Q-factor and the series resistance Rs over the conventional multi-finger MOS varactors with the same ground rule and gate area. The proposed island-gate MOS varactor is expected to improve the overall Q-factor of the LC tank of millimeter-wave oscillators.
A double-loop learning system for knowledge transfer and reuse in groups: application of a roadmapping approach

This paper studies the problems of knowledge transfer and operational reuse in distributed organisations. These issues can be summarised by the inherent contradiction between "detecting and boosting local innovation" (so that group learns from its entities) and "coding, standardising and transferring good practices and organisational capabilities" (so as group teaches its entities). This paper enlists theoretical mechanisms to solve this 'learner/teacher' duality. Then, an IT framework is proposed to manage and assess locally and globally this organisational learning, illustrated by its use in an automotive supplier group. Finally, new developments are made to make the learning system more sustainable.
Calf muscle mitochondrial and glycogenolytic ATP synthesis in patients with claudication due to peripheral vascular disease analysed using 31P magnetic resonance spectroscopy.

1. We set out to define abnormalities of oxidative ATP synthesis, cellular proton efflux and the efficiency of ATP usage in gastrocnemius muscle of patients with claudication due to peripheral vascular disease, using data obtained by 31P magnetic resonance spectroscopy during aerobic exercise and recovery. 2. Eleven patients with moderate claudication were studied and results were compared with 25 age-matched control subjects. Changes in pH and phosphocreatine concentration during recovery were used to calculate the maximum rate of oxidative ATP synthesis (Qmax.) and the capacity of net proton efflux. Changes in pH and phosphocreatine concentration were used to estimate rates of non-oxidative and (indirectly) oxidative ATP synthesis throughout exercise, taking account of abnormalities in proton efflux during exercise. 3. In patients with claudication, slow post-exercise phosphocreatine recovery showed a 42 +/- 9% decrease in Qmax. , and the slow ADP recovery was consistent with this. pH recovery was slow, showing a 77 +/- 9% decrease in the capacity for proton efflux. Both abnormalities are compatible with a substantial reduction in muscle blood flow. 4. During exercise, increased phosphocreatine depletion and intracellular acidification were a consequence of impaired oxidative ATP synthesis and the consequent increase in non-oxidative ATP synthesis, compounded by reduced proton efflux. The acidification prevented an increase in ADP concentration which could otherwise partially compensate for the oxidative defect. All these abnormalities are compatible with a reduced muscle blood flow. 5. In addition, initial-exercise changes in pH and phosphocreatine concentration implied a 44 +/- 5% reduction in 'effective muscle mass', necessitating an ATP turnover (per litre of muscle water) twice as high for given power output as in control muscle. Some of this is probably due to a localized loss of muscle fibres, but the rest appears to reflect reduced metabolic efficiency of the muscle. This is not a direct consequence of reduced blood flow, and may be related to change in muscle fibre type.
Outage probability of selection relaying networks with distributed switch and stay combining over Rayleigh fading channels

We propose and analyze a distributed switch and stay combining network with selection relaying with an aim to reduce the complexity at the destination as well as to make efficient use of the degrees of freedom of the channels by exploiting a limited feedback signal from the destination. In particular, whenever the currently connected link (either from the source or from the best relay) to the destination is not favorable to decoding, the destination will switch to the alternative link as per the rule of switch and stay combining. The performance of the proposed system is derived in terms of outage probability and achievable spectral efficiency. The analytic results show that the proposed system assisted by the selection relaying exhibits a higher spectral efficiency than incremental relaying with selection relaying at low SNR regime. Monte-Carlo simulations are performed to verify the analysis.
Super-resolution optical microscopy study of telomere structure

Abstract. Chromosome ends are shielded from exonucleolytic attack and inappropriate end-joining by terminal structures called telomeres; these structures are potential targets for anticancer drugs. Telomeres are composed of a simple DNA sequence (5′-TTAGGG-3′ in humans) repeated more than a thousand times, a short 3′ single-stranded overhang, and numerous proteins. Electron microscopy has shown that the 3′ overhang pairs with the complementary strand at an internal site creating a small displacement loop and a large double-stranded “t-loop. ” Our goal is to determine whether all telomeres adopt the t-loop configuration, or whether there are two or more distinct configurations. Progress in optimizing super-resolution (SR) microscopy for this ongoing investigation is reported here. Results suggest that under certain conditions sample preparation procedures may disrupt chromatin by causing loss of nucleosomes. This finding may limit the use of SR microscopy in telomere studies.
Strategic Patenting

Every day high-tech companies receive offers for "strategic patenting" and "patent mapping" services and "comprehensive patent analysis platforms. " What exactly are these things? The idea is simple. Instead of handling patent problems ad hoc, you devise a strategic plan-that is, one that establishes priorities so that you can jettison patents and filings not worth pursuing and defend yourself against the patents of others. You consider all the associated profits and losses comprehensively, as you would with finance or real estate.
Directed integration of viral DNA mediated by fusion proteins consisting of human immunodeficiency virus type 1 integrase and Escherichia coli LexA protein

We tested whether the selection of target sites can be manipulated by fusing retroviral integrase with a sequence-specific DNA-binding protein. A hybrid protein that has the Escherichia coli LexA protein fused to the C terminus of the human immunodeficiency virus type 1 integrase was constructed. The fusion protein, IN1-288/LA, retained the catalytic activities in vitro of the wild-type human immunodeficiency virus type 1 integrase (WT IN). Using an in vitro integration assay that included multiple DNA fragment as the target DNA, we found that IN1-288/LA preferentially integrated viral DNA into the fragment containing a DNA sequence specifically bound by LexA protein. No bias was observed when the LexA-binding sequence was absent, when the fusion protein was replaced by WT IN, or when LexA protein was added in the reaction containing IN1-288/LA. A majority of the integration events mediated by IN1-288/LA occurred within 30 bp of DNA flanking the LexA-binding sequence. The specificity toward the LexA-binding sequence and the distribution and frequency of target site usage were unchanged when the integrase component of the fusion protein was replaced with a variant containing a truncation at the N or C terminus or both, suggesting that the domain involved in target site selection resides in the central core region of integrase. The integration bias observed with the integrase-LexA hybrid shows that one effective means of altering the selection of DNA sites for integration is by fusing integrase to a sequence-specific DNA-binding protein.
High-pressure x-ray diffraction of SiO2 glass.

We have measured the x-ray structure factor S(Q) for SiO 2 glass to 42 GPa in the diamond-anvil cell using new experimental techniques for studying amorphous materials at high pressures. Large changes in the first sharp diffraction peak of S(Q) with increasing pressure provide evidence for changes in the medium-range order of the glass (length scales of ∼4-10 A). Average pair correlation functions at high pressure reveal significant changes in the nearest-neighbor geometry of the glass with compression. Between 8 and 28 GPa the coordination of Si increases, and at 42 GPa the value is close to six
A universal method for robust stabilization of nonlinear systems: unification and extension of smooth and non-smooth approaches

The current literature on the stabilization of nonlinear systems, particularly those whose linearization about the origin may contain uncontrollable modes, essentially contains two distinct methods: a smooth controller scheme (only under strict assumptions) and a non-smooth one. This paper introduces a more general setting under which: 1) unification of the two aforementioned schemes is achieved and 2) it is possible to find a continuously differentiable control law for some systems previously only stabilizable by a continuous controller. This new method is implicitly based on the ideas of homogeneous systems theory and the adding a power integrator technique
A new approach to tracking with active contours

This paper addresses the application of active contours or snakes for robust tracking of contours. Conventional snake approaches to tracking initialize the current frame snake with the snake obtained in the previous frame and then optimize this result considering only the current frame information. In our approach motion estimation is embedded in the energy minimization process of the snake. This is possible using a dynamic programming approach for this minimization and introducing a new term into the energy of the snake. In this way, larger displacements of the contour are allowed, and the tracking is more robust. This technique is applied for tracking facial features such as the contour of the face, the mouth, the nostrils and the eyebrows.
Cold Storage of Human Milk: Effect on Its Bacterial Composition

Objectives:In the last few years, it has been proved that human milk contains bacteria that constitute an important factor in the initiation and development of the neonatal gut microbiota. In this context, the objective of this study was to evaluate the effect of cold storage on the natural bacterial composition of breast milk. Materials and Methods:Breast milk samples provided by 34 healthy women and collected either by manual expression (n = 27) or breast pump (n = 7), were plated onto several culture media immediately after arrival at the laboratory (day 0) and after storage at −20°C for 6 weeks. A high number of isolates from 8 of the women were identified at the species level. Results:No statistically significant differences were observed between the counts obtained at both sampling times in those media in which growth was detected. In all of the culture media, bacterial counts in pump-collected samples were higher than in those obtained by manual expression. Staphylococci and streptococci were the predominant bacteria in both fresh and frozen samples, Staphylococcus epidermidis being the most abundant species at both sampling times. Lactic acid bacteria and bifidobacteria were also present in fresh and frozen breast milk samples, but among them, only 1 species (Lactobacillus gasseri) could be isolated at both sampling times. Conclusions:The results of this study suggest that cold storage of milk at −20°C for 6 weeks does not significantly affect either the quantitative or the qualitative bacterial composition of breast milk.