Miracle-dz/UniFAR-FTUs huggingface dataset:
Lycopene inhibits angiogenesis both in vitro and in vivo by inhibiting MMP-2/uPA system through VEGFR2-mediated PI3K-Akt and ERK/p38 signaling pathways.

SCOPE Limited in vitro data show that lycopene may be anti-angiogenic but with unclear mechanisms. Here, we employed ex vivo and in vivo assays to substantiate the anti-angiogenic action of lycopene and determined its molecular mechanisms in human umbilical vein endothelial cells (HUVECs). METHODS AND RESULTS The anti-angiogenic activity of lycopene was confirmed by ex vivo rat aortic ring and in vivo chorioallantoic membrane assays. Furthermore, the in vivo matrigel plug assay in mice demonstrated that lycopene implanted s.c. at the highest dose used (400 μg/plug) completely inhibited the formation of vascular endothelial cells induced by vascular endothelial growth factor (VEGF). As expected, lycopene inhibited tube formation, invasion, and migration in HUVECs, and such actions were accompanied by reduced activities of matrix metalloproteinase-2, urokinase-type plasminogen activator, and protein expression of Rac1, and by enhancing protein expression of tissue inhibitors of metalloproteinase-2 and plasminogen activator inhibitor-1. Moreover, lycopene attenuated VEGF receptor-2 (VEGFR2)-mediated phosphorylation of extracellular signal-regulated kinase (ERK), p38, and Akt as well as protein expression of PI3K. CONCLUSION Our data demonstrate the anti-angiogenic effect of lycopene both in vitro and in vivo. The anti-angiogenic activity of lycopene may involve inhibition of MMP-2/uPA system through VEGFR2-mediated PI3K-Akt and ERK/p38 signaling pathways.
6. You're a real genious: irony a a miscommunication design

In a standard (rhetoric) perspective ironic communication is considered a semantic inversion between the literal (primary) meaning and the nonliteral (implicated) one. Nevertheless, in common use irony is not necessarily bound to the rhetoric concept of semantic inversion. Rather, it can be defined as an alteration of a reference aiming at stressing the reality of a fact by means of the apparent dissimulation of its true nature. In a communicative perspective, irony aims to get an effective protection of interpersonal relationships, so as to leave wide ranges of freedom for managing both meanings and interaction. The point of view herein followed concerns irony as a paradigmatic expression of miscommunication, since it is a chance in widening the psychological space available to the communicators. Irony as miscommunication fits rather well the MaCHT framework proposed by Anolli. In fact, by means of an ironic remark, the speaker can lay the responsibility of the ironic value of the utterance on the intention ascription of the interlocutor. In particular, the present chapter intends to sketch out a new theoretical perspective of ironic communication as miscommunication, by proposing the fencing game (or irony situation) model. Here irony is not considered only as a comment or remark at a linguistic level but also as a complex communicative interaction between interlocutors, depending on contextual constraints and opportunities.
Penalized logistic Regression Feature Preselection for Classification Tree : Application to the Diagnostic of Severe Imported Malaria Based on Heterogeneous Data

The actual criteria for the classification of the different forms of imported malaria are complex and do not take into account the heterogeneity of the individual profiles. Multivariate classification methods using explanatory and predictive models are necessary to characterize groups with a high risk of developing severe forms of imported malaria. We investigate two standard approaches implementing two different strategies: L1 logistic regression that models a single global solution, which is a linear combination of a subset of the input features, and classification trees that models multiple local solutions corresponding to discriminate sub regions of the feature space. As an alternative to pruning, which limits the complexity of the decision tree by removing unstable branches once the model is built, we explore an original approach known as L1 LR-Tree, which combines the two previous strategies. This combined method constrains the dimension of the initial set of features before fitting the decision tree. Through the comparison of these methods, we aim to study the influence of biological and epidemiological factors dismissed in the current clinical/biological picture used for the diagnosis of severe forms of imported malaria based on a heterogeneous population of 353 patients. This method builds sparse and stable models that can significantly differentiate the patients with moderate imported malaria from those severely affected, and the severely affected from the critically affected (p-values≤0.01 for recall and specificity scores). Moreover, it outperforms all the other methods in terms of accuracy by achieving a 70% correct classification rate through a leave-one-out evaluation. The combined models identify new risk profiles that may be useful in order to improve the diagnosis and patient treatment.
All-optical inverted and noninverted wavelength conversion using two-cascaded semiconductor optical amplifiers

A two-cascaded semiconductor optical amplifier configuration in a counterpropagating topology is proposed for an all-optical wavelength conversion operation. The attractive issue of the proposed method is that the converted signal can be obtained simultaneously with an inverted and noninverted signal. The all-optical noninverted wavelength conversion feasibility is also demonstrated delivering an extinction ratio higher than 7 dB over a wide range of wavelengths.
The biocompatibility of fluorescent nanodiamonds and their mechanism of cellular uptake

The labeling of cells with fluorescent nanoparticles is promising for various biomedical applications. The objective of this study is to evaluate the biocompatibility and the mechanism of the cellular uptake of fluorescent nanodiamonds (FNDs) in cancer cells (HeLa) and pre-adipocytes (3T3-L1). With flow cytometry and the use of a battery of metabolic and cytoskeletal inhibitors, we found that the mechanism of the FND uptake in both cells is by energy-dependent clathrin-mediated endocytosis. In addition, the surface charge of FND influences its cellular uptake, as the uptake of poly-L-lysine-coated FNDs is better than that of oxidative-acid-purified FNDs at the same concentration in regular medium with or without serum. We also confirm that the proliferative potential of FND-treated and untreated cells does not exhibit any significant differences when measured at bulk cultures, and more stringently at clonal cell density. Further biocompatibility studies indicate that the in vitro differentiation of 3T3-L1 pre-adipocytes and 489-2 osteoprogenitors is not affected by the FND treatment. Our results show that FNDs are biocompatible and ideal candidates for potential applications in human stem cell research.
Two different snoRNAs are encoded in introns of amphibian and human L1 ribosomal protein genes.

We previously reported that the third intron of the X.laevis L1 ribosomal protein gene encodes for a snoRNA called U16. Here we show that four different introns of the same gene contain another previously uncharacterized snoRNA (U18) which is associated with fibrillarin in the nucleolus and which originates by processing of the pre-mRNA. The pathway of U18 RNA release from the pre-mRNA is the same as the one described for U16: primary endonucleolytic cleavages upstream and downstream of the U18 coding region produce a pre-U18 RNA which is subsequently trimmed to the mature form. Both the gene organization and processing of U18 are conserved in the corresponding genes of X.tropicalis and H.sapiens. The L1 gene thus has a composite structure, highly conserved in evolution, in which sequences coding for a ribosomal protein are intermingled with sequences coding for two different snoRNAs. The nucleolar localization of these different components suggests some common function on ribosome biosynthesis.
The Influence of Cochlear Implant Electrode Position on Performance

Objectives: To study the relation between variables related to cochlear implant electrode position and speech perception performance scores in a large patient population. Design: The study sample consisted of 203 patients implanted with a CII or HiRes90K implant with a HiFocus 1 or 1J electrode of Advanced Bionics. Phoneme and word score averages for the 1- and 2-year follow-up were calculated for 41 prelingually deaf and 162 postlingually deaf patients. Analyses to reveal correlations between these performance outcomes and 6 position-related variables (angle of most basal electrode contact, surgical insertion angle, surgical insertion, wrapping factor, angular insertion depth, linear insertion depth) were executed. The scalar location, as an indication for the presence of intracochlear trauma, and modiolus proximity beyond the basal turn were not evaluated in this study. In addition, different patient-specific variables (age at implantation, age at onset of hearing loss, duration of deafness, preoperative phoneme and word scores) were tested for correlation with performance. Results: The performance scores of prelingual patients were correlated with age at onset of hearing loss, duration of deafness and preoperative scores. For the postlingual patients, performance showed correlations with all 5 patient-specific variables. None of the 6 position-related variables influenced speech perception in cochlear implant patients. Conclusions: Although several patient-specific variables showed correlations with speech perception outcomes, not one of the studied angular and linear position-related variables turned out to have a demonstrable influence on performance.
Assessment of blind predictions of protein–protein interactions: Current status of docking methods

The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional structure is assessed from a first major evaluation of blind predictions. This evaluation was performed as part of a communitywide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Seven newly determined structures of protein–protein complexes were available as targets for this experiment. These were the complexes between a kinase and its protein substrate, between a T‐cell receptor β‐chain and a superantigen, and five antigen‐antibody complexes. For each target, the predictors were given the experimental structures of the free components, or of one free and one bound component in a random orientation. The structure of the complex was revealed only at the time of the evaluation. A total of 465 predictions submitted by 19 groups were evaluated. These groups used a wide range of algorithms and scoring functions, some of which were completely novel. The quality of the predicted interactions was evaluated by comparing residue–residue contacts and interface residues to those in the X‐ray structures and by analyzing the fit of the ligand molecules (the smaller of the two proteins in the complex) or of interface residues only, in the predicted versus target complexes. A total of 14 groups produced predictions, ranking from acceptable to highly accurate for five of the seven targets. The use of available biochemical and biological information, and in one instance structural information, played a key role in achieving this result. It was essential for identifying the native binding modes for the five correctly predicted targets, including the kinase‐substrate complex where the enzyme changes conformation on association. But it was also the cause for missing the correct solution for the two remaining unpredicted targets, which involve unexpected antigen‐antibody binding modes. Overall, this analysis reveals genuine progress in docking procedures but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility. Proteins 2003;52:51–67. © 2003 Wiley‐Liss, Inc.
Commodity Forward Curve Dynamics with Inventory Information

In this paper we introduce a new two-factor commodity term structure model for which inventories serve as a second state variable. We derive a closed-form formula for futures prices and empirically analyze the model's properties. Besides being economically appealing, our model also outperforms the well-known Gibson and Schwartz (1990) model in terms of hedging abilities.
Measurement of homocysteine concentrations and stable isotope tracer enrichments in human plasma.

Elevated levels of plasma homocysteine have been established as an independent risk factor for cardiovascular disease. Homocysteine is in low concentration in plasma (5-15 microM) and is bound to other thiols (e.g., cysteine in plasma proteins) via disulfide bonds. Existing methods for measuring homocysteine have difficulty in reducing and maintaining the reduction of homocysteine for measurement. We describe a GC/MS method that first reduces the disulfides in the physiological sample matrix and then immediately alkylates the free thiols with 4-vinylpyridine to prevent the reformation of the disulfide bonds. We use a deuterated internal standard, [3,3,3',3',4,4,4',4'-2H8]homocystine to account for losses associated with the isolation, derivatization, and measurement of the natural homocysteine. The amino acids are separated and derivatized to form the tert-butyldimethylsilyl derivatives. This method requires only 50 microL of plasma to measure homocysteine concentrations to 5 microM. Total homocysteine concentrations in plasma can be measured routinely from 0.5-mL samples with relative intra- and interday precisions of 1.3 and 4.0%, respectively. This method is sensitive enough to determine tracer enrichments of [1-13C]homocysteine with a detection limit of < 0.3 mol% excess and an average tracer precision of 0.6%.
Pricing of Long-Dated Commodity Derivatives with Stochastic Volatility and Stochastic Interest Rates

Aiming to study pricing of long-dated commodity derivatives, this paper presents a class of models within the Heath, Jarrow, and Morton (1992) framework for commodity futures prices that incorporates stochastic volatility and stochastic interest rate and allows a correlation structure between the futures price process, the futures volatility process and the interest rate process. The functional form of the futures price volatility is specified so that the model admits finite dimensional realisations and retains affine representations, henceforth quasi-analytical European futures option pricing formulae can be obtained. A sensitivity analysis reveals that the correlation between the interest rate process and the futures price process has noticeable impact on the prices of long-dated futures options, while the correlation between the interest rate process and the futures price volatility process does not impact option prices. Furthermore, when interest rates are negatively correlated with futures prices then option prices are more sensitive to the volatility of interest rates, an effect that is more pronounced with longer maturity options.
MODELLING AND AURALISATION OF SOUND FIELDS IN ROOMS-AN OVERVIEW –

The subject of room simulation attracted the attention for the last few decades. Methods for acoustic simulation of rooms have been developed for purposes of analysis, design, and virtual performance. Geometrical-acoustics based methods, the mirror-image method and the ray-tracing method, have been mainly used. In this paper, the application of diffusion in room acoustics computer models is discussed. The paper specifies the specular-radiant method to calculate the acoustic response of rooms. This method integrates the geometrical and the radiant approaches to predict the sound field in those rooms with boundaries of partially specular reflectivity. Furthermore, the room impulse response is auralised for given sources and receiver positions. Finally, evaluation tests are presented.
HER-3 peptide vaccines/mimics: Combined therapy with IGF-1R, HER-2, and HER-1 peptides induces synergistic antitumor effects against breast and pancreatic cancer cells

The human epidermal growth factor receptor 3 (HER-3/ErbB3) is a unique member of the human epidermal growth factor family of receptors, because it lacks intrinsic kinase activity and ability to heterodimerize with other members. HER-3 is frequently upregulated in cancers with epidermal growth factor receptor (EGFR/HER-1/ErbB1) or human epidermal growth factor receptor 2 (HER-2/ErBB2) overexpression, and targeting HER-3 may provide a route for overcoming resistance to agents that target EGFR or HER-2. We have previously developed vaccines and peptide mimics for HER-1, HER-2 and vascular endothelial growth factor (VEGF). In this study, we extend our studies by identifying and evaluating novel HER-3 peptide epitopes encompassing residues 99–122, 140–162, 237–269 and 461–479 of the HER-3 extracellular domain as putative B-cell epitopes for active immunotherapy against HER-3 positive cancers. We show that the HER-3 vaccine antibodies and HER-3 peptide mimics induced antitumor responses: inhibition of cancer cell proliferation, inhibition of receptor phosphorylation, induction of apoptosis and antibody dependent cellular cytotoxicity (ADCC). Two of the HER-3 epitopes 237–269 (domain II) and 461–479 (domain III) significantly inhibited growth of xenografts originating from both pancreatic (BxPC3) and breast (JIMT-1) cancers. Combined therapy of HER-3 (461–471) epitope with HER-2 (266–296), HER-2 (597–626), HER-1 (418–435) and insulin-like growth factor receptor type I (IGF-1R) (56–81) vaccine antibodies and peptide mimics show enhanced antitumor effects in breast and pancreatic cancer cells. This study establishes the hypothesis that combination immunotherapy targeting different signal transduction pathways can provide effective antitumor immunity and long-term control of HER-1 and HER-2 overexpressing cancers.
An Approach to Evaluating and Comparing Biomarkers for Patient Treatment Selection

Abstract Despite the heightened interest in developing biomarkers predicting treatment response that are used to optimize patient treatment decisions, there has been relatively little development of statistical methodology to evaluate these markers. There is currently no unified statistical framework for marker evaluation. This paper proposes a suite of descriptive and inferential methods designed to evaluate individual markers and to compare candidate markers. An R software package has been developed which implements these methods. Their utility is illustrated in the breast cancer treatment context, where candidate markers are evaluated for their ability to identify a subset of women who do not benefit from adjuvant chemotherapy and can therefore avoid its toxicity.
Assessing the allergenic potential of molds found in water-damaged homes in a mouse model

Abstract Damp/moldy indoor environments, which have resulted from flooding events and may increase as a result of climate change, have been associated with asthma exacerbation. Certain molds found in significantly higher or lower concentrations in asthmatics’ homes compared to control homes have been categorized as Group 1 (G1) and Group 2 (G2) molds, respectively. We have compared the allergic potential of selected G1/G2 molds to house dust mite (HDM) in a mouse model. BALB/c mice were exposed to mold (0–80 µg) or HDM (20 µg) extract by intratracheal aspiration either 4X over 4 weeks (allergenicity) or 1X (non-specific responses). Airflow limitation (methacholine challenge) was measured (Day 1) and serum and bronchoalveolar lavage fluid were collected (Day 2) after the final exposure. The G1 molds induced low-to-moderate responses and required higher doses to achieve antigen-specific IgE results similar to those induced by HDM. Compared to HDM responses, the G2 mold in this study required lower doses to induce a similar response. Acute exposure responses suggest some molds may exacerbate asthmatic responses. These studies demonstrate the differing capacities of molds to induce responses associated with allergic asthma, including differences in the threshold dose for allergy induction. Therefore, molds must be evaluated individually for allergic/asthmatic potential. These studies along with our previous studies with G1 (Stachybotrys chartarum)/G2 (Penicillium chrysogenum) molds suggest that the G1/G2 categorization is not indicative of allergic potential but they do not preclude this categorization’s utility in determining unhealthy building dampness.
Kinetic study of the quenching reaction of singlet oxygen by seven rice bran extracts in ethanol solution. Development of a singlet oxygen absorption capacity (SOAC) assay method

Measurements of singlet oxygen (1O2) quenching rates (kQ (S)) and the relative singlet oxygen absorption capacity (SOAC) values were performed for seven rice bran extracts 1–7, which contained different concentrations of antioxidants (AOs) (such as α-, β-, γ-, and δ-tocopherols and -tocotrienols, three carotenoids (lutein, β-carotene, and zeaxanthin), and γ-oryzanol), in ethanol at 35 °C using UV–vis spectrophotometry. The concentrations of four tocopherols and four tocotrienols, three carotenoids, and γ-oryzanol contained in the extracts were determined using HPLC-MS/MS, UV-HPLC, and UV–vis absorption spectroscopy, respectively. Furthermore, comparisons of kQ (S) (Obsd.) values observed for the above extracts 1–7 with the sum of the product { [AO-i]} of the values obtained for each AO-i and the concentration ([AO-i]) of AO-i contained in extracts 1–7 were performed. From the results, it has been ascertained that the SOAC method is applicable to general food extracts to evaluate their 1O2-quenching activity. Graphical abstract Measurements of the quenching rate (kQ) of singlet oxygen were performed for seven rice bran extracts in ethanol to evaluate their singlet oxygen quenching activity.
CLINICAL METHOD FOR ELECTRICAL AND MECHANICAL RECORDING OF THE MECHANICALLY AND ELECTRICALLY ELICITED ANKLE REFLEX

A method for quantitative evaluation of the ankle stretch reflex in man has been developed. The method includes recording of the mechanical and electrical stimulus intensity and of the electrical and mechanical reflex response. In addition, it offers the possibility of reflex latency recording. The size of the tendon tap was recorded by a reflex hammer incorporating an accelerometer which converts the retardation force, experienced by the hammer head when it strikes the tendon, to an electrical signal. The output signal has a linear relationship with the moment of force imposed upon the tendon‐muscle system by the tap and can therefore be used as an indicator of muscle stretch. The strength of the electrical stimulus was estimated in milliamperes by the voltage drop across a serial resistor in the stimulating circuit. The electrical reflex response was recorded by surface electrodes over the triceps surae muscle, and the best recording electrode placement was determined. The reflex contraction was recorded by a general purpose myograph allowing isotonic as well as isometric recordings. The method described is easy to use, is not painful to the patient, and offers considerable precision and accuracy in ankle reflex recording.
Evaluation of a fever‐management algorithm in a pediatric cancer center in a low‐resource setting

In low‐ and middle‐income countries (LMICs), inconsistent or delayed management of fever contributes to poor outcomes among pediatric patients with cancer. We hypothesized that standardizing practice with a clinical algorithm adapted to local resources would improve outcomes. Therefore, we developed a resource‐specific algorithm for fever management in Davao City, Philippines. The primary objective of this study was to evaluate adherence to the algorithm.