Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteriophages PɸEn-CL and PɸEn-HO can Eliminate MDR Enterobacter cloacae and Enterobacter hormaechei isolated from Burn Wound Infections without Toxicity for Human Skin Cells.

The prevalence of multidrug-resistant (MDR) strains has caused serious problems in the treatment of burn infections. MDR E. cloacae and E. hormaechei have been defined as the causative agents of nosocomial infections in burn patients. In this situation, examination of phages side effects on human cell lines before any investigation on human or animal, that can provide beneficial information about the safety of isolated phages. The aim of this study was to isolate and identify the specific bacteriophages on MDR E. cloacae and E. hormaechei isolated from burn wounds and to analyze the efficacy, cell viability and cell cytotoxicity of phages on A-375 and HFSF-PI cell lines by MTT (3-(4, 5-dimethylthiazol-2-yl)2,5-diphenyl-tetrazolium bromide) colorimetric assay and lactate dehydrogenase (LDH) release assay. Phages were isolated from urban sewage Isfahan, Iran. E. cloacae strain Iau-EC100 (GenBank accession number: MZ314381) and E. hormaechei strain Iau-EHO100 (GenBank accession number: MZ348826) were sensitive to the isolated phages. Transmission electron microscopy (TEM) results revealed that PɸEn-CL and PɸEn-HO that were described had the morphologies of Myovirus and Inovirus, respectively. Overall, MTT and LDH assays showed moderate to excellent correlation in the evaluation of cytotoxicity of isolated phages. The results of MTT and LDH assays showed that, phages PɸEn-CL and PɸEn-HO had no significant toxicity effect on A375 and HFSF-PI 3 cells. Phage PɸEn-HO had a better efficacy on the two tested cell lines than other phage. Our results indicated that, there were significant differences between the two cytotoxicity assays in phage treatment compared to control.
Blind Robust Estimation With Missing Data for Smart Sensors Using UFIR Filtering

Smart sensors are often designed to operate under harsh industrial conditions with incomplete information about noise and missing data. Therefore, signal processing algorithms are required to be unbiased, robust, predictive, and desirably blind. In this paper, we propose a novel blind iterative unbiased finite impulse response (UFIR) filtering algorithm, which fits these requirements as a more robust alternative to the Kalman filter (KF). The tradeoff in robustness between the UFIR filter and KF is learned analytically. The predictive UFIR algorithm is developed to operate in control loops under temporary missing data. Experimental verification is given for carbon monoxide concentration and temperature measurements required to monitor urban and industrial environments. High accuracy and precision of the predictive UFIR estimator are demonstrated in a short time and on a long baseline.
Rescue of Notch-1 Signaling in Antigen-Specific CD8+ T Cells Overcomes Tumor-Induced T-cell Suppression and Enhances Immunotherapy in Cancer

Sierra and colleagues show that myeloid-derived suppressor cells (MDSC) blocked Notch expression in T cells via nitric oxide–dependent mechanisms, and overexpression of the Notch 1 intracellular active domain rendered the CD8+ T cells resistant to the MDSC-induced tolerogenic effect. An impaired antitumor immunity is found in patients with cancer and represents a major obstacle in the successful development of different forms of immunotherapy. Signaling through Notch receptors regulates the differentiation and function of many cell types, including immune cells. However, the effect of Notch in CD8+ T-cell responses in tumors remains unclear. Thus, we aimed to determine the role of Notch signaling in CD8+ T cells in the induction of tumor-induced suppression. Our results using conditional knockout mice show that Notch-1 and Notch-2 were critical for the proliferation and IFNγ production of activated CD8+ T cells and were significantly decreased in tumor-infiltrating T cells. Conditional transgenic expression of Notch-1 intracellular domain (N1IC) in antigen-specific CD8+ T cells did not affect activation or proliferation of CD8+ T cells, but induced a central memory phenotype and increased cytotoxicity effects and granzyme B levels. Consequently, a higher antitumor response and resistance to tumor-induced tolerance were found after adoptive transfer of N1IC-transgenic CD8+ T cells into tumor-bearing mice. Additional results showed that myeloid-derived suppressor cells (MDSC) blocked the expression of Notch-1 and Notch-2 in T cells through nitric oxide–dependent mechanisms. Interestingly, N1IC overexpression rendered CD8+ T cells resistant to the tolerogenic effect induced by MDSC in vivo. Together, the results suggest the key role of Notch in the suppression of CD8+ T-cell responses in tumors and the therapeutic potential of N1IC in antigen-specific CD8+ T cells to reverse T-cell suppression and increase the efficacy of T cell–based immunotherapies in cancer. Cancer Immunol Res; 2(8); 800–11. ©2014 AACR.
Deploying Pervasive Web Services over a P2P Overlay

Nowadays, there is an increasing need for deploying Web Services into embedded devices in pervasive computing environments. However, a number of problems arise for running pervasive web services, such as service not being accessible due to devices being located behind firewalls or NATs and therefore devices cannot offer services dynamically, and mobility problems as devices might change their location and thus the endpoints of their services. In order to address these problems, we have designed and implemented, in the scope of the Hydra Middleware Project, two components called Network Manager and SOAP tunnel, which work together to build an overlay P2P network and provide mechanisms for service registration, discovery and consumption, allowing devices to offer and consume services anywhere and anytime in a Web Service compliant form, and transparently to the application developer. A number of evaluations show that our solution is successful and usable in the pervasive service environment that Hydra is targeting.
Optimal survival time‐related cut‐point with censored data

In biomedical research and practice, continuous biomarkers are often used for diagnosis and prognosis, with a cut‐point being established on the measurement to aid binary classification. When survival time is examined for the purposes of disease prognostication and is found to be related to the baseline measure of a biomarker, employing a single cut‐point on the biomarker may not be very informative. Using survival time‐dependent sensitivity and specificity, we extend a concordance probability‐based objective function to select survival time‐related cut‐points. To estimate the objective function with censored survival data, we adopt a non‐parametric procedure for time‐dependent receiver operational characteristics curves, which uses nearest neighbor estimation techniques. In a simulation study, the proposed method, when used to select a cut‐point to optimally predict survival at a given time within a specified range, yields satisfactory results. We apply the procedure to estimate survival time‐dependent cut‐point on the prognostic biomarker of serum bilirubin among patients with primary biliary cirrhosis. Copyright © 2014 John Wiley & Sons, Ltd.
Efficient Computation of Reduced Regression Models

ABSTRACT We consider settings where it is of interest to fit and assess regression submodels that arise as various explanatory variables are excluded from a larger regression model. The larger model is referred to as the full model; the submodels are the reduced models. We show that a computationally efficient approximation to the regression estimates under any reduced model can be obtained from a simple weighted least squares (WLS) approach based on the estimated regression parameters and covariance matrix from the full model. This WLS approach can be considered an extension to unbiased estimating equations of a first-order Taylor series approach proposed by Lawless and Singhal. Using data from the 2010 Nationwide Inpatient Sample (NIS), a 20% weighted, stratified, cluster sample of approximately 8 million hospital stays from approximately 1000 hospitals, we illustrate the WLS approach when fitting interval censored regression models to estimate the effect of type of surgery (robotic versus nonrobotic surgery) on hospital length-of-stay while adjusting for three sets of covariates: patient-level characteristics, hospital characteristics, and zip-code level characteristics. Ordinarily, standard fitting of the reduced models to the NIS data takes approximately 10 hours; using the proposed WLS approach, the reduced models take seconds to fit.
Spontaneous sarcoplasmic reticulum calcium release and extrusion from bovine, not porcine, coronary artery smooth muscle.

1. We tested the hypothesis that the Ca(2+)‐loaded sarcoplasmic reticulum (SR) of coronary artery smooth muscle spontaneously releases Ca2+ preferentially toward the sarcolemma to be extruded from the cell without increasing the average free myoplasmic [Ca2+] (Ca(im)) concentration. 2. The SR of bovine cells was Ca(2+)‐loaded by depolarization‐induced Ca2+ influx. Release (unloading) of Ca2+ from the SR during recovery from depolarization was determined by Fura‐2 microfluorometry of Ca(im). The SR Ca2+ unloading was maximal following a long (14 min) recovery from depolarization, as shown by the 66% decrease in the peak caffeine‐induced Ca(im) transient compared to the Ca(im) transient after a short (2 min) recovery. No increase in Ca(im) occurred during the long recovery. No unloading of the SR Ca2+ store was noted in porcine cells. 3. Approximately 80% of the outward K+ current in bovine and porcine cells was sensitive to subsarcolemmal Ca2+ (Ca(is)) concentrations. Whole‐cell voltage clamp using pipette solutions with Ca2+ concentrations clamped between 0 and 1000 nM with Ca(2+)‐EGTA or Ca(2+)‐BAPTA buffers showed increasing K+ currents (normalized for cell membrane surface area) as a function of both membrane potential and Ca(is). Clamping of Ca(im) and Ca(is) was verified by the lack of changes in K+ current and Fura‐2 ratio in response to Ca2+ influx, Ca(2+)‐free external solution, or caffeine‐induced Ca2+ release. At +30 to +50 mV the K+ current amplitude showed a similar sensitivity to Ca2+ as Fura‐2. These data indicate that in this experimental preparation Ca(2+)‐activated K+ current is a valid estimate of Ca(is). 4. Simultaneous Ca(im) and Ca(is) measurements in bovine cells which were not Ca(2+)‐clamped (2 x 10(‐4) M‐EGTA pipette solution) showed that during the long recovery period the K+ current (reflecting Ca(is)) increased 55%, while Ca(im) did not change. 5. In quiescent bovine cells the Ca(is) was higher than Ca(im), while the higher resting Ca(is) gradient was not apparent in porcine cells. 6. The Ca(is) concentration was directly related to the amount of Ca2+ in the SR in bovine, but not porcine cells. Depletion of the SR in bovine cells by caffeine resulted in a 58% decrease in K+ current compared to the resting K+ current. 7. Caffeine‐induced Ca2+ release caused an increase in Ca(is) which preceded the increase in Ca(im) by approximately 2 s. (ABSTRACT TRUNCATED AT 400 WORDS)
Selenium and mercury concentrations in California gulls breeding on the Great Salt Lake, Utah, USA

We examined selenium (Se) and mercury (Hg) concentrations in adult California gulls (Larus californicus) nesting on the Great Salt Lake, Utah, USA, during 2006 and 2007. During 2006, the mean Se concentration (± standard error) was 18.1 ± 1.5 μg/g in blood on a dry‐weight basis and 8.1 ± 0.4 μg/g in liver. During 2007, Se concentrations were 15.7 ± 1.5 μg/g in blood and 8.3 ± 0.4 μg/g in liver; Hg concentrations were 2.4 ± 0.3 μg/g in blood and 4.1 ± 0.5 μg/g in liver. Gulls collected from a freshwater colony located within the watershed of the Great Salt Lake had similar levels of Se in the blood and liver as gulls collected on the Great Salt Lake but lower Hg concentrations. Body mass of adult gulls was not correlated with Se or Hg concentrations in their blood or liver. Selenium concentration in California gull eggs collected during 2006 was 3.0 ± 0.10 μg/g. Of 72 eggs randomly collected from Great Salt Lake colonies, only one was infertile, and none of the embryos exhibited signs of malposition or deformities. We examined 100 newly hatched California gull chicks from Great Salt Lake colonies for teratogenesis; all chicks appeared normal. Hence, the elevated Se and Hg concentrations in adult gulls nesting on the Great Salt Lake did not appear to impair gulls' health or reproductive ability.
Evidence of neutron leakage at the Fukushima nuclear plant from measurements of radioactive 35S in California

A recent earthquake and the subsequent tsunami have extensively damaged the Fukushima nuclear power plant, releasing harmful radiation into the environment. Despite the obvious implication for human health and the surrounding ecology, there are no quantitative estimates of the neutron flux leakage during the weeks following the earthquake. Here, using measurements of radioactive 35S contained in sulfate aerosols and SO2 gas at a coastal site in La Jolla, California, we show that nearly 4 × 1011 neutrons per m2 leaked at the Fukushima nuclear power plant before March 20, 2011. A significantly higher activity as measured on March 28 is in accord with neutrons escaping the reactor core and being absorbed by the coolant seawater 35Cl to produce 35S by a (n, p) reaction. Once produced, 35S oxidizes to and and was then transported to Southern California due to the presence of strong prevailing westerly winds at this time. Based on a moving box model, we show that the observed activity enhancement in is compatible with long-range transport of the radiation plume from Fukushima. Our model predicts that , the concentration in the marine boundary layer at Fukushima, was approximately 2 × 105 atoms per m3, which is approximately 365 times above expected natural concentrations. These measurements and model calculations imply that approximately 0.7% of the total radioactive sulfate present at the marine boundary layer at Fukushima reached Southern California as a result of the trans-Pacific transport.
Magnolol stimulates lipolysis in lipid‐laden RAW 264.7 macrophages

This study investigated the effect of magnolol, a compound isolated from Magnolia officinalis, on lipolysis in lipid‐laden RAW 264.7 macrophages. Treatment of macrophages with magnolol led to dissolution of lipid droplets. This phenomenon was accompanied by a dose‐dependent release of glycerol and cholesterol and a concomitant reduction in intracellular levels of glycerol and cholesterol. Furthermore, adipose differentiation‐related protein (ADRP), a lipid droplet‐associated protein, was down‐regulated by magnolol in a dose‐ and time‐dependent manner by Western blot analysis. Immunofluorescence studies also showed that ADRP became detached from the surface of lipid droplets after magnolol treatment. The lipolytic effect of magnolol was not mediated through the cAMP‐protein kinase A (PKA) system, an authentic lipolytic pathway for macrophages, since magnolol did not induce an increase of intracellular cAMP levels, and pretreatment with either of PKA inhibitors, PKI and KT5720, did not abrogate the lipolytic response to magnolol. We conclude that magnolol induce‐lipolysis of lipid‐laden macrophages by down‐regulation of ADRP expression and detachment of ADRP from the lipid droplet surface by a cAMP‐independent mechanism. Lipolysis of lipid‐laden macrophages may occur when the amount of ADRP on the surface of lipid droplets is not enough to stabilize the lipid droplets. J. Cell. Biochem. 94: 1028–1037, 2005. © 2004 Wiley‐Liss, Inc.
Development of a Basic Rate of Household Energy Consumption Considering Usage Time and Quantity of Consumer Durables

This study is a survey conducted in questionnaire format on the usage time and the quantity of consumer durables that consume energy, relevant to households in Kobe, Japan. Based on the data containing quantity and daily usage days of consumer durables obtained from the questionnaire survey, the rate of energy consumption for each household type was calculated. By using results, energy consumption of household sector in Kobe in 2010 was estimated at approximately 25,559 TJ. Taking future changes in the number of households in Kobe into consideration, the future energy consumption in 2035 would decline by approximately 6.0% from 2010. We also revealed that full electrification of residential houses would change energy consumption structures rather than overall the energy consumption.
Colonialism and the Highland Clearances

This article employs a new approach to studying internal colonialism in northern Scotland during the 18th and 19th centuries. A common approach to examining internal colonial situations within modern state territories is to compare characteristics of the internal colonial situation with attested attributes of external colonial relations. Although this article does not reject the comparative approach, it seeks to avoid criticisms that this approach can be misleading by demonstrating that promoters and managers of projects involving land use change, territorial dispossession and industrial development in the late modern Gaidhealtachd consistently conceived of their work as projects of colonization. It further argues that the new social, cultural and political structures these projects imposed on the area's indigenous population correspond to those found in other colonial situations, and that racist and racialist attitudes towards Gaels of the time are typical of those in colonial situations during the perio.
Self-consistent theory of atomic Fermi gases with a Feshbach resonance at the superfluid transition

A self-consistent theory is derived to describe the BCS-Bose-Einstein-condensate crossover for a strongly interacting Fermi gas with a Feshbach resonance. In the theory the fluctuation of the dressed molecules, consisting of both preformed Cooper pairs and bare Feshbach molecules, has been included within a self-consistent T-matrix approximation, beyond the Nozieres and Schmitt-Rink strategy considered by Ohashi and Griffin. The resulting self-consistent equations are solved numerically to investigate the normal-state properties of the crossover at various resonance widths. It is found that the superfluid transition temperature T-c increases monotonically at all widths as the effective interaction between atoms becomes more attractive. Furthermore, a residue factor Z(m) of the molecule's Green function and a complex effective mass have been determined to characterize the fraction and lifetime of Feshbach molecules at T-c. Our many-body calculations of Z(m) agree qualitatively well with recent measurments of the gas of Li-6 atoms near the broad resonance at 834 G. The crossover from narrow to broad resonances has also been studied.
Mycovirus Cryphonectria Hypovirus 1 Elements Cofractionate with trans-Golgi Network Membranes of the Fungal Host Cryphonectria parasitica

ABSTRACT The mycovirus cryphonectria hypovirus 1 (CHV1) causes proliferation of vesicles in its host, Cryphonectria parasitica, the causal agent of chestnut blight. These vesicles have previously been shown to contain both CHV1 genomic double-stranded RNA (dsRNA) and RNA polymerase activity. To determine the cellular origins of these virus-induced membrane structures, we compared the fractionation of several cellular and viral markers. Results showed that viral dsRNA, helicase, polymerase, and protease p29 copurify with C. parasitica trans-Golgi network (TGN) markers, suggesting that the virus utilizes the fungal TGN for replication. We also show that the CHV1 protease p29 associates with vesicle membranes and is resistant to treatments that would release peripheral membrane proteins. Thus, p29 behaves as an integral membrane protein of the vesicular fraction derived from the fungal TGN. Protease p29 was also found to be fully susceptible to proteolytic digestion in the absence of detergent and, thus, is wholly or predominantly on the cytoplasmic face of the vesicles. Fractionation analysis of p29 deletion variants showed that sequences in the C terminal of p29 mediate membrane association. In particular, the C-terminal portion of the protein (Met-135-Gly-248) is sufficient for membrane association and is enough to direct p29 to the TGN vesicles in the absence of other viral elements.
Metabolites of a tobacco-specific lung carcinogen in nonsmoking women exposed to environmental tobacco smoke.

BACKGROUND Environmental tobacco smoke (ETS) is associated with lung cancer in nonsmokers. Most epidemiologic studies find a higher risk for lung cancer in nonsmoking women married to smokers than in those married to nonsmokers. We measured metabolites of a tobacco-specific lung carcinogen in urine from healthy, nonsmoking women exposed to ETS. METHODS We recruited women and their partners through advertisements. Couples completed questionnaires on smoking history and demographics, and both partners provided 100 mL of urine; 23 women had male partners who smoked in the home (i.e., exposed women), and 22 women had male partners who did not smoke (i.e., unexposed women). Urine samples were analyzed for nicotine, for cotinine, for 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and its glucuronide (NNAL-Gluc), as well as for creatinine. NNAL and NNAL-Gluc are metabolites of the tobacco-specific lung carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Unpaired Student's t tests were conducted on log-transformed values. All statistical tests are two-sided. RESULTS Urinary levels of nicotine, cotinine, NNAL, and NNAL-Gluc were statistically significantly higher in exposed women than in unexposed women. Geometric means for these compounds in exposed versus unexposed women, respectively, were as follows: nicotine, 0.050 nmol/mg of creatinine (95% confidence interval [CI] = 0.033 to 0.076) versus 0.008 nmol/mg of creatinine (95% CI = 0.004 to 0.014); cotinine, 0.037 nmol/mg of creatinine (95% CI = 0.022 to 0.061) versus 0.007 nmol/mg of creatinine (95% CI = 0.004 to 0.011); NNAL, 0.013 pmol/mg of creatinine (95% CI = 0.007 to 0.024) versus 0.004 pmol/mg of creatinine (95% CI = 0.002 to 0.007); and NNAL-Gluc, 0.027 pmol/mg of creatinine (95% CI = 0.016 to 0.045) versus 0.004 pmol/mg of creatinine (95% CI = 0.003 to 0.006). CONCLUSIONS Nonsmoking women exposed to ETS take up and metabolize the tobacco-specific lung carcinogen NNK, which could increase their risk of lung cancer. Within couples, the NNAL plus NNAL-Gluc level in exposed women compared with that of their smoking partners averaged 5.6%. Notably, epidemiologic studies have estimated the excess risk for lung cancer in nonsmoking women exposed to ETS as 1%-2% of that in smokers.