Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosides

Objective:To determine if particular components of antiretroviral drug regimens are associated with greater insulin resistance, dyslipidemia, and peripheral lipoatrophy. Methods:Metabolic and body composition variables were measured prospectively over 64 weeks in 334 antiretroviral-naive, HIV-infected subjects who were randomized to receive nelfinavir, efavirenz, or both, combined with zidovudine/lamivudine or didanosine/stavudine in a factorial design, multicenter trial. Subjects assigned to efavirenz (n = 110) were compared with those assigned to nelfinavir (n = 99); subjects assigned to zidovudine/lamivudine (n = 154) were compared with those assigned to didanosine/stavudine (n = 180). A subset of 157 subjects had serial dual-energy X-ray absorptiometry (DEXA) scans. Results:Lipid measures increased in all groups. Greater increases in high density lipoprotein (HDL) cholesterol occurred with efavirenz than with nelfinavir. Greater increases in total cholesterol, non-HDL cholesterol and HDL cholesterol occurred with stavudine and didanosine than with zidovudine/lamivudine. There were no differences in insulin resistance in the comparisons. After initial increases in the first 16 weeks, median limb fat decreased. Greater changes in percentage changes in limb fat occurred with didanosine/stavudine (−16.8%) than with zidovudine/lamivudine (+4.0%; P < 0.001 for overall change from baseline) and with nelfinavir (−13.1%) compared with efavirenz (+1.8%; P = 0.003). Conclusions:Over 64 weeks, all regimens were associated with increases in lipids but insulin resistance did not differ between groups. Regimens containing didanosine/stavudine and regimens containing nelfinavir were associated with greater loss of limb fat.
The Interplay between Information Acquisition and Quality Disclosure

This study investigates the interactions between a manufacturer's information acquisition and quality disclosure strategies in a supply chain setting in which the manufacturer privately knows his product quality but is uncertain about consumer preferences. We argue that the manufacturer should treat his information acquisition and quality disclosure decisions as an integrated process because these decisions can significantly influence a retailer's rational inferences about product quality and can have conflicting effects on his own profitability. Although information acquisition helps a manufacturer subsequently craft better pricing and quality disclosure strategies, it also leaks certain product information to the retailer, thus helping the retailer better estimate product quality. Therefore, in equilibrium, a manufacturer may choose not to acquire any consumer information, even when such acquisition is costless. Moreover, we find that this adverse effect of acquisition is highly dependent on the cost of disclosure and consumers’ preference differentiation. Increased consumer preference differentiation may have a non‐monotonic relationship with the manufacturer's profit, and information acquisition can become detrimental to the manufacturer once the disclosure cost is sufficiently high.
WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

WebMaBoSS is an easy-to-use web interface for conversion, storage, simulation and analysis of Boolean models that allows to get insight from these models without any specific knowledge of modeling or coding. It relies on an existing software, MaBoSS, which simulates Boolean models using a stochastic approach: it applies continuous time Markov processes over the Boolean network. It was initially built to fill the gap between Boolean and continuous formalisms, i.e., providing semi-quantitative results using a simple representation with a minimum number of parameters to fit. The goal of WebMaBoSS is to simplify the use and the analysis of Boolean models coping with two main issues: 1) the simulation of Boolean models of intracellular processes with MaBoSS, or any modeling tool, may appear as non-intuitive for non-experts; 2) the simulation of already-published models available in current model databases (e.g., Cell Collective, BioModels) may require some extra steps to ensure compatibility with modeling tools such as MaBoSS. With WebMaBoSS, new models can be created or imported directly from existing databases. They can then be simulated, modified and stored in personal folders. Model simulations are performed easily, results visualized interactively, and figures can be exported in a preferred format. Extensive model analyses such as mutant screening or parameter sensitivity can also be performed. For all these tasks, results are stored and can be subsequently filtered to look for specific outputs. This web interface can be accessed at the address: https://maboss.curie. fr/webmaboss/ and deployed locally using docker. This application is open-source under LGPL license, and available at https://github.com/sysbio-curie/WebMaBoSS.
Listening to the blue: the time-resolved thermodynamics of the bacterial blue-light receptor YtvA and its isolated LOV domain

YtvA is a bacterial flavo-protein related to plant phototropin. The photochemistry of YtvA and of its isolated LOV domain (YtvA-LOV) has been characterized by optical, mass spectrometric and photocalorimetric methods. The energy content ( E 390 ) of the FMN-C4a-thiol photoadduct (YtvA 390 and YtvA-LOV 390 ) and its structural volume change (Δ V 390 ), with respect to the parent state, have been determined by means of Laser Induced Optoacoustic Spectroscopy (LIOAS). The high value of E 390 , 136 and 115 kJ mol^−1, respectively, ensures a large driving force for the dark recovery to the unphotolyzed state and points to a strained conformation of the protein or/and the chromophore in the photoadduct. The value of Δ V 390 is significantly different for the two proteins, Δ V 390 = −12.5 ml mol^−1 in YtvA and −17.2 ml mol^−1 in YtvA-LOV. The kinetics of the dark recovery reaction for YtvA-LOV is slower than for full-length YtvA, with τ rec = 3900 and 2600 s at 25 °C, respectively, and shows a different temperature dependence. A similarly slow kinetics can be induced in YtvA by high ionic strength. Minor differences are observed in the fluorescence and photoadduct formation quantum yield. The overall stability is higher for YtvA than for YtvA-LOV. The data as a whole are indicative of an interaction between the two domains of YtvA, most probably mediated by electrostatic interactions that renders the full-length protein a compact and more rigid unit. The results reported here support the idea that the formation of the photoadduct changes the dynamics of the protein, depending on the conformational flexibility of the parent state. Flashing of the photoadduct induces a negligible Δ V , with 96% of the excitation energy dissipated as heat in <20 ns, indicating that the photoadduct does not undergo a photocycle on the LIOAS time scale, or that the photoinduced reactions occur with very low yield.
Impact of Feature Selection on Micro-Text Classification

Social media datasets, especially Twitter tweets, are popular in the field of text classification. Tweets are a valuable source of micro-text (sometimes referred to as "micro-blogs"), and have been studied in domains such as sentiment analysis, recommendation systems, spam detection, clustering, among others. Tweets often include keywords referred to as "Hashtags" that can be used as labels for the tweet. Using tweets encompassing 50 labels, we studied the impact of word versus character-level feature selection and extraction on different learners to solve a multi-class classification task. We show that feature extraction of simple character-level groups performs better than simple word groups and pre-processing methods like normalizing using Porter's Stemming and Part-of-Speech ("POS")-Lemmatization.
Hypoxia inhibits the migratory capacity of human monocyte‐derived dendritic cells

Hypoxia, a prominent characteristic of inflammatory tissue lesions and solid tumour microenvironments, is a crucial stimulus capable of modulating the expression of specific genes involved in leucocyte recruitment. Although studies have shown that hypoxia can affect leucocyte migration by influencing the expression of migration‐related genes, such as matrix metalloproteinases (MMP) and their endogenous tissue inhibitors of matrix metalloproteinases (TIMP), it remains unclear whether hypoxia can affect the migration of dendritic cells (DC). In this study, we showed that human monocyte‐derived DC under hypoxic conditions in a transwell system have significantly reduced migratory capacity compared to normoxic controls. A moderate phenotypic change of hypoxic DC was observed. In hypoxic DC, we detected a twofold increase in TIMP‐1 transcript levels, and downregulated expression of MMP‐9 and membrane type 1‐MMP genes by threefold and 17‐fold, respectively. Our results suggest that hypoxia may inhibit DC migratory activity by regulating the balance between MMP and TIMP gene expression.
Curative liver resection for metastatic breast cancer.

AIMS Hepatic resection is a standard procedure in the treatment of colorectal liver metastases. Liver metastases are frequent in breast cancer, but resectional treatment is rarely possible and few reports have addressed the results of surgical treatment for metastatic breast cancer. The aim of our study was to analyse the outcome of patients with metastatic breast cancer after resection of isolated hepatic secondaries and possibly to identify selection criteria for patients who may benefit from surgery. METHODS Between 1984 and 1998, 90 patients with a history of breast cancer and suspected liver metastases were referred for surgical evaluation. Fifty-four patients also had extrahepatic disease or metastases from another primary tumour; multiple liver metastases were not amenable to surgical treatment in 20 patients. Five patients were treated by regional chemotherapy via an intra-arterial port catheter; after liver resection two patients were found to have liver metastases from intercurrent colorectal cancer. Thus only nine liver resections for metastatic breast cancer could be performed with curative intent. RESULTS No patient died post-operatively after liver resection. In the follow-up period, four of the nine patients who were treated with curative intent received systemic chemotherapy. At a median follow-up of 29 months, four patients died from tumour recurrence. Five patients are currently alive. Five-year survival in the resection group was calculated as 51% (Kaplan-Meier estimate). Node-negative primary breast cancer and a long interval between treatment of the primary and liver metastases appeared to be associated with long survival after liver resection. CONCLUSIONS These observations suggest that careful follow-up and adequate patient selection could offer some patients with isolated liver metastases from breast cancer a chance of long-term survival.
Learning from Stories: Narrative Interviewing in Cross-cultural Research

This paper argues for the importance of eliciting stories when trying to understand the point of view and personal experience of one's informants. It also outlines one approach to eliciting and analyzing narrative data as part of a complex and multi-faceted ethnographic study. The paper draws upon ethnographic research among African-American families who have children with serious illnesses or disabilities. However, it is not a report of research findings per se. Rather, it is primarily a conceptual paper that addresses narrative as a research method. Features that distinguish a story from other sorts of discourse are sketched and current discussions in the occupational therapy and social science literature concerning the importance of narrative are examined. The heart of the paper focuses on a single narrative interview and examines what we learn about the client and family caregiver perspective through stories.
Modelling Realized Volatility in Electricity Spot Prices: New Insights and Application to the Japanese Electricity Market

The paper analyzes volatility of the electricity prices in the Japanese day-ahead market using realized volatility. We use several jump tests to decompose total realized variation into jump and continuous components. Then, we estimate several HAR models that show the time-dependence structure of the volatility. Our results show that even though that market is narrow, it is relevant to identify jumps in volatility. Besides, modelling residuals improve estimation results. The time-dependent structure of the prices is present in volatility as well.
Numerical Analysis of Bulk Superconducting Magnet Magnetized by Pulsed-Field Considering a Partial Difference of Superconducting Characteristics

On the pulsed-fleld magnetization (PFM) of superconducting bulk magnets, a detailed analysis taking into account the difference in superconducting characteristics between a growth sector boundary (GSB) and a growth sector region (GSR) parts of the material was carried out. The current density was defined in each part and a magnetic field induced by the local current was calculated. The entire magnetic field distribution was obtained by adding individual distributions. The experiment with a Sm123 bulk superconductor was performed and it was confirmed that the calculated distribution agreed with the experimental result.
A Current-Fed Isolated Bidirectional DC–DC Converter

This paper proposes a current-fed isolated bidirectional dc–dc converter (CF-IBDC) that has the advantages of wide input voltage range, low input current ripple, low conduction losses, and soft switching over the full operating range. Compared with conventional CF-IBDCs, the voltage spikes of the low-voltage (LV) side switches in the proposed converter can be eliminated without additional clamp circuits. The converter adopts the pulse width modulation plus hybrid phase-shift control scheme such that the bus voltage can match the output voltage by means of the transformer. Thus, the current stresses and conduction losses of the converter become lower. In addition, the practical zero voltage switching (ZVS) of the secondary-side switches can be realized by adjusting the phase-shift angle within the secondary side when in light load or no load condition. The operating principles and characteristics including the power transfer, root-mean-square (RMS) current, and soft switching are investigated in detail. Then the design guidelines of inductors are also given. Finally an experimental prototype with 30–60 V input and 400 V/2.5 An output is built to verify the correctness of theoretical analyses.
Oil, inflation, and financial markets

The economy’s heavy dependence on fossil energy links oil prices to real economic activities, inflation, and financial markets. This dissertation studies the extent to which fluctuations in oil prices are related to inflation and the prices and expected returns of Treasury bonds. Chapter 2 shows that the correlation between U.S. core inflation and oil price changes exhibits a timevarying pattern since the 1970s. The significant resurgence of the positive correlation after the 2007 financial crisis is puzzling, given the subdued macroeconomic impact of oil price shocks since the mid-1980s. A twosector DSGE model illustrates that the relation between the price of oil and core inflation depends on the type of shocks embedded in oil price changes. Oil supply shocks cause the price of oil and core inflation to co-move, whereas the aggregate demand shocks driven by economic growth lead to opposing changes in the price of oil and core inflation. The economic mechanisms uncovered in the model and historical geopolitical events together provide a consistent and logical explanation of the time-varying correlations observed in the data. Chapter 3 examines the economic impact of oil prices on Treasury bond returns. I find novel evidence that growth rates of crude oil prices can explain contemporaneous excess returns on nominal U.S. Treasury bonds and inflation swaps, and also predict expected future excess returns on inflation swaps. Empirical results suggest that the impact of oil prices on nominal bonds is through the impact on expected inflation. I then build a two-sector New Keynesian model to study theoretical interactions between the economic drivers of oil prices, expected inflation, and bond yields. The model shows that oil supply and demand shocks have opposite impacts on bond yields and expected inflation. The conventional wisdom that high oil prices lead to high expected inflation and nominal yields is true only if high oil prices are driven by a negative shock to the supply of oil. In contrast, when oil prices are driven by a positive shock to productivity growth, high oil prices can lead to low expected inflation and nominal yields.
A multicenter, randomized, double-blind, controlled trial of nebulized epinephrine in infants with acute bronchiolitis.

BACKGROUND The treatment of infants with bronchiolitis is largely supportive. The role of bronchodilators is controversial. Most studies of the use of bronchodilators have enrolled small numbers of subjects and have examined only short-term outcomes, such as clinical scores. METHODS We conducted a randomized, double-blind, controlled trial comparing nebulized single-isomer epinephrine with placebo in 194 infants admitted to four hospitals in Queens-land, Australia, with a clinical diagnosis of bronchiolitis. Three 4-ml doses of 1 percent nebulized epinephrine or three 4-ml doses of normal saline were administered at four-hour intervals after hospital admission. Observations were made at admission and just before, 30 minutes after, and 60 minutes after each dose. The primary outcome measures were the length of the hospital stay and the time until the infant was ready for discharge. The secondary outcome measures were the degree of change in the respiratory rate, the heart rate, and the respiratory-effort score and the time that supplemental oxygen was required. RESULTS There were no significant overall differences between the groups in the length of the hospital stay (P=0.16) or the time until the infant was ready for discharge (P=0.86). Among infants who required supplemental oxygen and intravenous fluids, the time until the infant was ready for discharge was significantly longer in the epinephrine group than in the placebo group (P=0.02). The need for supplemental oxygen at admission had the greatest influence on the score for severity of illness and strongly predicted the length of the hospital stay and the time until the infant was ready for discharge (P<0.001). There were no significant changes in the respiratory rate, blood pressure, or respiratory-effort scores from before each treatment to after each treatment. The heart rate was significantly increased after each treatment with epinephrine (P=0.02 to P<0.001). CONCLUSIONS The use of nebulized epinephrine did not significantly reduce the length of the hospital stay or the time until the infant was ready for discharge among infants admitted to the hospital with bronchiolitis.
Risk of non‐AIDS‐defining events among HIV‐infected patients not yet on antiretroviral therapy

Certain non‐AIDS‐related diseases have been associated with immunodeficiency and HIV RNA levels in HIV‐infected patients on combination antiretroviral therapy (cART). We aimed to investigate these associations in patients not yet on cART, when potential antiretroviral‐drug‐related effects are absent and variation in RNA levels is greater.
Optical measurement of osmotic water transport in cultured cells. Role of glucose transporters

Methodology was developed to measure osmotic water permeability in monolayer cultured cells and applied to examine the proposed role of glucose transporters in the water pathway (1989. Proc. Natl. Acad. Sci. USA. 86:8397-8401). J774 macrophages were grown on glass coverslips and mounted in a channel-type perfusion chamber for rapid fluid exchange without cell detachment. Relative cell volume was measured by 45 degrees light scattering using an inverted microscope; measurement accuracy was validated by confocal imaging microscopy. The time required for greater than 90% fluid exchange was less than 1 s. In response to a decrease in perfusate osmolality from 300 to 210 mosM, cells swelled without lag at an initial rate of 4.5%/s, corresponding to a water permeability coefficient of (6.3 +/- 0.4) x 10(-3) cm/s (SE, n = 20, 23 degrees C), assuming a cell surface-to-volume ratio of 4,400 cm-1. The initial rate of cell swelling was proportional to osmotic gradient size, independent of perfusate viscosity, and increased by amphotericin B (25 micrograms/ml), and had an activation energy of 10.0 +/- 1 kcal/mol (12-39 degrees C). The compounds phloretin (20 microM) and cytochalasin B (2.5 micrograms/ml) inhibited glucose transport by greater than 85% but did not influence Pf in paired experiments in which Pf was measured before and after inhibitor addition. The mercurials HgCl2 (0.1 mM) and p-chloromercuribenzoate (1 mM) did not inhibit Pf. A stopped-flow light scattering technique was used to measure Pf independently in J774 macrophages grown in suspension culture. Pf in suspended cells was (4.4 +/- 0.3) x 10(-3) cm/s (assuming a surface-to-volume ratio of 8,800 cm-1), increased more than threefold by amphotericin B, and not inhibited by phloretin and cytochalasin B under conditions of strong inhibition of glucose transport. The glucose reflection coefficient was 0.98 +/- 0.03 as measured by induced osmosis, assuming a unity reflection coefficient for sucrose. These results establish a quantitative method for measurement of osmotic water transport in adherent cultured cells and provide evidence that glucose transporters are not involved in the water transporting pathway.
Evaluation of cytotoxic effects of several novel tetralin derivatives against Hela, MDA-MB-468, and MCF-7 cancer cells

Background: The inhibitors of the enzymes estrone sulfatase and 17-β-hydroxysteroid dehydrogenase (17-β-HSD) could provide a means of blocking estrogen biosynthesis leading to regression of estrogen-dependent tumors. We evaluated the cytotoxicity of several tetralin derivatives, 2-(4-halo-phenylmethylene)-3,4-dihydronaphthalene-1-ones, as potential inhibitors of these two enzymes, on Hela, MDA-MB-468, and MCF-7 cancer cell lines. Materials and Methods: The cell lines were cultured in RPMI medium and the cytotoxic effect of tested compounds (compounds 1 to 5) was screened at the concentrations of 0.1, 1, and 10 μM either alone or in combination with doxorubicin (100 μM), using MTT assay. The mixtures of cell suspension with solvent (1% DMSO in PBS) and doxorubicin (100 μM) were used as negative and positive controls, respectively. Each concentration of compounds was assayed in four wells and repeated in at least three independent experiments for each cell line. The cytotoxic effect of each particular concentration of tested compounds was expressed as the percent of cell survival. Results: None of the compounds exhibited cytotoxic effect (reduction of cell survival to less than 50%) on tested cell lines. However, statistically significant reduction in cell survival was observed for some compounds against particular cell lines. Among all tested combinations of compounds with doxorubicin against cell lines, only compound 4 at 10 μM concentration showed synergistic cytotoxic effect with doxorubicin against Hela cells. Conclusion: With the exception of compound 2, other tested compounds have potential for further cytotoxicity evaluation. Synthesizing other tetralin derivatives similar to compound 4 and studying their structure-activity relationships (SARs) would be encouraged.