Miracle-dz/UniFAR-FTUs huggingface dataset:
Cholesterol added prior to vitrification on the cryotolerance of immature and in vitro matured bovine oocytes

This study examines whether incorporating cholesterol-loaded methyl-β-cyclodextrin (CLC) in the bovine oocyte plasma membrane improves oocyte tolerance to vitrification. In vitro matured oocytes were incubated with 2 mg/ml BODIPY-labeled CLC for different time intervals in FCS or PVA supplemented medium or exposed to different CLC concentrations to examine the subcellular localization of cholesterol by confocal microscopy live-cell imaging. Subsequently, the effects of optimized CLC concentrations and incubation times prior to vitrification on early embryo development were assessed. Then, we evaluated the effects of pretreatment with 2 mg/ml CLC for 30 min before the vitrification of immature (GV) and in vitro matured (MII) oocytes on developmental competence and gene expression. Our results indicate a high plasma membrane labeling intensity after 30 min of incubation with 2 mg/ml CLC for 30 min, regardless of the holding medium used. When oocytes were incubated with 1 mg/ml, 2 mg/ml and 3 mg/ml of CLC, intense labeling was observed at the plasma membrane after 40, 30 and 20 min, respectively. CLC pre-treatment before the vitrification of bovine oocytes did not affect subsequent cleavage and embryo development rates irrespective of CLC concentrations, incubation times or meiotic stage. However, pretreatment seems to improve the quality of embryos derived from vitrified oocytes, mainly when oocytes were vitrified at the GV stage.
IFN‐β modulates the response to TLR stimulation in human DC: Involvement of IFN regulatory factor‐1 (IRF‐1) in IL‐27 gene expression

Type I IFN are cytokines which play a central role in host resistance to viral or microbial infections and are important components linking innate and adaptive immunity. We and others have previously demonstrated that the production of IFN‐β by DC following bacterial infections or TLR triggering influences, in an autocrine manner, their maturation. In this study, we investigated whether IFN‐β release modulates the phenotype of the immature DC and their response to a subsequent TLR stimulation. The induction of CD86, HLA‐DR, CD38 and B7H1 and the absence of CCR7 and CD83 expression upon IFN‐β treatment suggest that IFN‐β‐primed DC remain at the site of infection acquiring an activated phenotype. These results prompted us to investigate the response of IFN‐β‐primed DC to TLR stimulation. While IFN‐β pretreatment increases slightly the expression of maturation markers in TLR2‐ or TLR4‐stimulated DC, it is able to modulate selectively the secretion of inflammatory and immuno‐regulating cytokines. Interestingly, IL‐27p28 subunit was induced by IFN‐β alone or during LPS‐induced maturation of DC in a type I IFN‐dependent manner through IFN regulatory factor‐1 (IRF‐1) activation. Taken together, our results shed light on the capacity of IFN‐β to finely tune DC response to invading pathogens.
Repression of GCN5 Histone Acetyltransferase Activity via Bromodomain-Mediated Binding and Phosphorylation by the Ku–DNA-Dependent Protein Kinase Complex

ABSTRACT GCN5, a putative transcriptional adapter in humans and yeast, possesses histone acetyltransferase (HAT) activity which has been linked to GCN5’s role in transcriptional activation in yeast. In this report, we demonstrate a functional interaction between human GCN5 (hGCN5) and the DNA-dependent protein kinase (DNA-PK) holoenzyme. Yeast two-hybrid screening detected an interaction between the bromodomain of hGCN5 and the p70 subunit of the human Ku heterodimer (p70-p80), which is the DNA-binding component of DNA-PK. Interaction between intact hGCN5 and Ku70 was shown biochemically using recombinant proteins and by coimmunoprecipitation of endogenous proteins following chromatography of HeLa nuclear extracts. We demonstrate that the catalytic subunit of DNA-PK phosphorylates hGCN5 both in vivo and in vitro and, moreover, that the phosphorylation inhibits the HAT activity of hGCN5. These findings suggest a possible regulatory mechanism of HAT activity.
Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH

Although the enzymatic activity of cytochrome c oxidase (CcO) depends sensitively on pH over a wide range, X-ray structural analyses of bovine CcO have been conducted using crystals prepared at pH 5.7 owing to the difficulty in crystallizing this protein. Here, the structure of ligand-free reduced CcO was successfully determined at 1.99 Å resolution.
To improve the quality of cluster ensembles by selecting a subset of base clusters

Conventional clustering ensemble algorithms employ a set of primary results; each result includes a set of clusters which are emerged from data. Given a large number of available clusters, one is faced with the following questions: (a) can we obtain the same quality of results with a smaller number of clusters instead of full ensemble? (b) If so, which subset of clusters is more efficient to be used in the ensemble? In this paper, these two questions are going to be answered. We explore a clustering ensemble approach combined with a cluster stability criterion as well as a dataset simplicity criterion to discover the finest subset of base clusters for each kind of datasets. Also, a novel method is proposed in order to accumulate the selected clusters and to extract final partitioning. Although it is expected that by reducing the size of ensemble the performance decreases, our experimental results show that our selecting mechanism generally lead to superior results.
Fluorescent Differential Display Identifies Circadian Clock-Regulated Genes in Arabidopsis thaliana

Circadian rhythms in gene expression were first observed in plants more than 13 years ago, but the underlying mechanism controlling rhythmic gene expression is still not understood. The isolation of novel circadian clock-controlled genes (ccgs) is likely to provide new tools for studying circadian rhythms. Fluorescent differential display (FDD) was used to screen Arabidopsis thaliana mRNAs for cycling transcripts. Seventy PCR primer pairs were screened, and 17 different cycling bands were observed out of an estimated 10,500 bands screened. The identities of 10 bands were determined, and the rhythmic gene expression was confirmed using northern blot analysis. The 10 cycling bands represent 7 different genes, 6 of which are present in the databases and 1 that does not match anything in current databases. The rhythmic expression of the 7 genes is composed of four distinct phases of clock regulation. The results demonstrate that FDD can be used to isolate ccgs. The genes identified in this screen range from known A. thaliana ccgs, as well as genes shown to be clock controlled in other plant species, to a novel gene that may encode a pioneer protein. Further study of these ccgs is likely to increase our understanding of circadian-regulated gene expression.
Bilateral control with energy balance monitoring under time-varying communication delay

In previous work, we (1999) have proposed a control scheme based on wave variables. Unlike other methods, the proposed method could minimize the performance degradation due to the fluctuation of time delay. With this method however the system may potentially generate infinite energy in some special situations and the system stability could not be ensured rigorously. In this paper, we modify the method by introducing an energy input/output balance monitoring mechanism, which limits the energy that the system can generate. We conducted some simulation studies with a one DOF system. Simulation results show the validity of the proposed scheme.
Treatment of mucocutaneous pigmentation in Peutz–Jeghers syndrome with potassium titanyl phosphate (KTP) laser

days, her clinical condition improved. Subsequent attempts to reduce her prednisolone below 30 mg per day resulted in her skin re-flaring. Laboratory investigations revealed a persistent neutrophilia. All other haematological and biochemical parameters, including a glucose-tolerance test performed at 28 weeks’ gestation, remained within the normal ranges for pregnancy. Serial foetal ultrasound scans revealed normal growth, with all parameters on the 90th centile. Ciclosporin levels remained in the low ⁄ normal range. Following preterm premature rupture of the patient’s membranes, she gave birth at 32 weeks and 5 days to a healthy infant weighing 2.47 kg. Pustular psoriasis associated with pregnancy remains a potentially fatal disease, with a high incidence of foetal morbidity and mortality if left untreated. It is a rare, poorly documented disorder and presents particular problems because of the teratogenic and cytotoxic nature of the medications routinely used in this condition, such as methotrexate and vitamin A derivatives. Even prednisolone, although recognized as nonteratogenic, has variable efficacy in controlling pustular psoriasis, and has been associated with gestational diabetes, macrosomia and premature rupture of membranes. Despite placental transfer of ciclosporin, which appears to be dose-related, experience, predominantly with transplant recipients, suggests there is no evidence of a teratogenic effect in humans. In addition, children exposed to the drug for prolonged periods in utero have been shown to develop normal renal function. Raddadi et al. reported a similar case where ciclosporin (3.5 mg ⁄ kg) alone was used with no reported complications from 29 weeks’ gestation. A recent meta-analysis has, however, raised the possibility of its use being associated with early rupture of membranes, therefore, where ciclosporin is used, careful monitoring of serum levels and serial ultrasonography of the foetus is advisable, as is the use of the lowest possible dose.
Adherence to antiretroviral therapy, virological response, and time to resistance in the Dakar cohort

In 1998, with the launch of the Senegalese Initiative for Antiretroviral Access (ISAARV), Senegal became one of the first African countries to propose an antiretroviral access program. Our objective in this paper is to study the time to any first drug resistance, as well as predictors of the time to resistance. We propose a joint model to study the effect of adherence to the HAART therapy, and virological response on the time to resistance mutations. A logistic mixed model is used to model the time‐dependent adherence process; and a Markov model is used to study the virological response. Given the presence of missing data in the adherence process and in the virological response, the latent adherence and virological states are then included in the linear predictor of the time to resistance model. The proposed time to resistance model takes into account interval‐censored data as well as null hazard periods, during which the viral replication is very low. A Bayesian approach is used for accommodating with missing data and for prediction. We also propose model checking tools to study model adequacy. Copyright © 2009 John Wiley & Sons, Ltd.
Optimization and implementation of bio-inspired feature extraction frameworks for visual object recognition. (Optimisation et implémentation de méthodes bio-inspirées d'extraction de caractéristiques pour la reconnaissance d'objets visuels)

Industry has growing needs for so-called “intelligent systems”, capable of not only acquire data, but also to analyse it and to make decisions accordingly. Such systems are particularly useful for video-surveillance, in which case alarms must be raised in case of an intrusion. For cost saving and power consumption reasons, it is better to perform that process as close to the sensor as possible. To address that issue, a promising approach is to use bio-inspired frameworks, which consist in applying computational biology models to industrial applications. The work carried out during that thesis consisted in selecting bio-inspired feature extraction frameworks, and to optimize them with the aim to implement them on a dedicated hardware platform, for computer vision applications. First, we propose a generic algorithm, which may be used in several use case scenarios, having an acceptable complexity and a low memory print. Then, we proposed optimizations for a more global framework, based on precision degradation in computations, hence easing up its implementation on embedded systems. Results suggest that while the framework we developed may not be as accurate as the state of the art, it is more generic. Furthermore, the optimizations we proposed for the more complex framework are fully compatible with other optimizations from the literature, and provide encouraging perspective for future developments. Finally, both contributions have a scope that goes beyond the sole frameworks that we studied, and may be used in other, more widely used frameworks as well.
Characterization of a slowly proliferative cell along the oligodendrocyte differentiation pathway.

A single bipotential glial progenitor cell of newborn rat optic nerve (the O‐2A progenitor) characterized by its reactivity with antibodies to surface gangliosides (A2B5) and the presence of vimentin, can grow in microcultures in conditions which favor this progenitor's differentiation into oligodendrocytes. We selected at 8 days larger clones derived from such bipolar progenitors which had steadily proliferated on a layer of Type‐1 astrocytes during the first week. Clonal growth and ratio of progenitor cells to oligodendrocytes was measured over the next two weeks by phase microscopy and double immunofluorescence labeling for the specific markers A2B5, GC (galactocerebroside, a surface marker for differentiated oligodendrocytes), O4 (a glycolipid marker of oligodendrocytes and some progenitors), GFAP (an astrocyte specific intermediate filament protein) and vimentin. Two types of clones were identified: type A clones (the majority), which were still slowly expanding at three weeks, and type B clones (the minority), which had stopped proliferating during the second week. In type A clones, some cells became GC positive multipolar oligodendrocytes, while other multipolar cells remained GC negative for days and expressed A2B5 and O4, but not GFAP or vimentin. Type B clones contained only GC positive, vimentin negative oligodendrocytes, which were generated during the second week and then decreased in number because of their restricted lifespan. Type B clones only developed in the presence of insulin or neurons. The number of GC negative cells in type A clones increased when insulin or neurons were deleted. (ABSTRACT TRUNCATED AT 250 WORDS)
Area deprivation and trends in inequalities in self-rated health in Spain, 1987—2001

Aims: This study examined the impact that individual social position and municipal area deprivation levels had on trends in inequalities in self-rated health in Spain, between 1987 and 2001. Methods: The study was based on cross-sectional data of the National Health Surveys of Spain for the years 1987, 1993, 1995, 1997, and 2001 (n=84,567). The indicators used were educational level and occupational class, and deprivation level as the indicator of municipal areas. Multilevel logistic regression models were made, with individuals nested into municipal areas. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated. To evaluate trends, the relative index of inequality was calculated. Results: At the individual level, the likelihood of less-than-good health between those with no formal education as compared to those with graduate-level education increased from OR=2.66 (95% CI: 2.06—3.38) in 1987 to OR=3.62 (95% CI: 2.95—4.63) in 2001 among women. The values for men were OR=2.27 (95% CI: 1.89—2.72) and OR=2.94 (95% CI: 2.36—3.68) respectively. Living in areas with the highest deprivation levels as compared to the lowest systematically increased the likelihood of less-than-good health. The likelihood of reporting less-than-good health among women with no formal education as compared to women with graduate-level education in municipal areas with the highest deprivation levels increased from OR=3.61 (95% CI: 2.39—5.45) in 1987 to 4.85 (95% CI: 3.06—7.69) in 2001. Among men, the corresponding magnitudes were OR=2.07 (95% CI: 1.39—3.08) and OR=4.16 (95% CI: 2.52—6.89). Conclusions: Inequalities in self-rated health increased in Spain in this period. These inequalities may be explained by the social conditions existing throughout the period of reference, and the pattern varies according to gender, municipal area deprivation levels, and the individual indicator of social position used.
The psychological autopsy: methodological considerations for the study of adolescent suicide.

Abstract Methodological issues in the use of the psychological autopsy technique to study adolescent suicide victims were addressed in a study of 27 adolescent completed-suicide victims and a comparison group of 56 suicidal psychiatric inpatients. This report concludes that: (1) parent/parent figure descriptions of suicide victims were unaffected by the presence or severity of affective symptomatology in the informant at the time of the interview: (2) parent reports were unaffected by the time interval between the death and the interview, within a time span of 2 to 6 months: and (3) the asymmetry of informant sources must be considered in the interpretation of odds ratios for psychiatric disorder comparing completers to a live control group. In light of these findings and the convergence of several psychological autopsy studies with each other and with prospective studies, the psychological autopsy is thought to yield reliable and valid results for the study of adolescent suicide.
A Process Control System Model for Interactive Image Guided Surgery

Over the last decade, interactive image guided surgery (IIGS) has become one of the most important applications of computers in medicine. Through the interactive use of computer generated images from medical imaging and the estimated position of subcutaneous surgical instruments, the surgeon is able to perform surgery in conditions of obscuration or minimally invasive surgery without the constant use of medical imaging machinery (X-ray, MRI) in the operating room. These systems can also be used for the preoperative planning of surgical procedures and have been used to assist in the improvement of prostheses. IIGS has many benefits such as reduced recovery time for the patient and reduced stress on the surgeon as the surgical plan can be practiced ahead of time, recorded, and presented in the operating room. In the current literature, such systems were only analyzed and evaluated from limited perspectives. We review the state of the art in the analysis of IIGS systems and discuss the limitations of the models and methods that were used. We present a novel approach to model IIGS systems. We have developed our notation, modeling techniques and analysis methods so that they can be applied to domains other than surgical interactive systems.
Performance of phasor estimation algorithms in instability cases of electric power systems

The objective of this work is to evaluate performance of three phasor estimation algorithms proposed in literature, under electrical system signals. Signals obtained from electrical systems response to disturbances in which the electrical system is stable or operates in a condition of transient instability, frequency or voltage. The performance during the transient state of the system is evaluated not only by error indicators but also by how much the protections performance (of out of step, sub and over frequency and sub and over voltage) differ when processing calculated results by the phasor estimation algorithms and by processing electrical system signals. The results show the superiority of the Analytic Vector Geometry (AVG) algorithm over the others, this adequate performance in conditions of major disturbances in the electrical system allows ensuring accurate data for WAMPAC applications of supervision and control of safety and stability of electrical systems.
Detection of radiation‐induced lung injury using hyperpolarized 13C magnetic resonance spectroscopy and imaging

Radiation‐induced lung injury limits radiotherapy of thoracic cancers. Detection of radiation pneumonitis associated with early radiation‐induced lung injury (2–4 weeks postirradiation) may provide an opportunity to adjust treatment, before the onset of acute pneumonitis and/or irreversible fibrosis. In this study, localized magnetic resonance (MR) spectroscopy and imaging of hyperpolarized 13C‐pyruvate (pyruvate) and 13C‐lactate (lactate) were performed in the thorax and kidney regions of rats 2 weeks following whole‐thorax irradiation (14 Gy). Lactate‐to‐pyruvate signal ratio was observed to increase by 110% (P < 0.01), 57% (P < 0.02), and 107% (P < 0.01), respectively, in the thorax, lung, and heart tissues of the radiated rats compared with healthy age‐matched rats. This was consistent with lung inflammation confirmed using cell micrographs of bronchioalveolar lavage specimens and decreases in arterial oxygen partial pressure (paO2), indicative of hypoxia. No statistically significant difference was observed in either lactate‐to‐pyruvate signal ratios in the kidney region (P = 0.50) between the healthy (0.215 ± 0.100) and radiated cohorts (0.215 ± 0.054) or in blood lactate levels (P = 0.69) in the healthy (1.255 ± 0.247 mmol/L) and the radiated cohorts (1.325 ± 0.214 mmol/L), confirming that the injury is localized to the thorax. This work demonstrates the feasibility of hyperpolarized 13C metabolic MR spectroscopy and imaging for detection of early radiation‐induced lung injury. Magn Reson Med 70:601–609, 2013. © 2012 Wiley Periodicals, Inc.
The functional expression and characterisation of a cysteine peptidase from the invasive stage of the neuropathogenic schistosome Trichobilharzia regenti q

A transcriptional product of a gene encoding cathepsin B-like peptidase in the bird schistosome Trichobilharzia regenti was identified and cloned. The enzyme was named TrCB2 due to its 77% sequence similarity to cathepsin B2 from the important human parasite Schistosoma mansoni. The zymogen was expressed in the methylotropic yeast Pichia pastoris; procathepsin B2 underwent self-processing in yeast media. The peptidolytic activity of the recombinant enzyme was characterised using synthetic fluorogenic peptide substrates at optimal pH 6.0. Functional studies using different specific inhibitors proved the typical cathepsin B-like nature of the enzyme. The S2 subsite specificity profile of recombinant TrCB2 was obtained. Using monospecific antibodies against the recombinant enzyme, the presence of cathepsin B2 was confirmed in extracts from cercariae (infective stage) and schistosomula (early post-cercarial stage) of T. regenti on Western blots. Also, cross-reactivity was observed between T. regenti and S. mansoni cathepsins B2 in extracts of cercariae, schistosomula or adults. In T. regenti, the antisera localised the enzyme to post-acetabular penetration glands of cercariae implying an important role in the penetration of host skin. The ability of recombinant TrCB2 to degrade skin, serum and nervous tissue proteins was evident. Elastinolytic activity suggests that the enzyme might functionally substitute the histolytic role of the serine class elastase known from S. mansoni and Schistosoma haematobium but not found in Schistosoma japonicum or in bird schistosomes. 2008 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.