Miracle-dz/UniFAR-FTUs huggingface dataset:
Freeze-Thaw Bayesian Optimization

In this paper we develop a dynamic form of Bayesian optimization for machine learning models with the goal of rapidly finding good hyperparameter settings. Our method uses the partial information gained during the training of a machine learning model in order to decide whether to pause training and start a new model, or resume the training of a previously-considered model. We specifically tailor our method to machine learning problems by developing a novel positive-definite covariance kernel to capture a variety of training curves. Furthermore, we develop a Gaussian process prior that scales gracefully with additional temporal observations. Finally, we provide an information-theoretic framework to automate the decision process. Experiments on several common machine learning models show that our approach is extremely effective in practice.
Cardiovascular magnetic resonance measurement of myocardial extracellular volume in health and disease

Objective To measure and assess the significance of myocardial extracellular volume (ECV), determined non-invasively by equilibrium contrast cardiovascular magnetic resonance, as a clinical biomarker in health and a number of cardiac diseases of varying pathophysiology. Design Prospective study. Setting Tertiary referral cardiology centre in London, UK. Patients 192 patients were mainly recruited from specialist clinics. We studied patients with Anderson–Fabry disease (AFD, n=17), dilated cardiomyopathy (DCM, n=31), hypertrophic cardiomyopathy (HCM, n=31), severe aortic stenosis (AS, n=66), cardiac AL amyloidosis (n=27) and myocardial infarction (MI, n=20). The results were compared with those for 81 normal subjects. Results In normal subjects, ECV (mean (95% CI), measured in the septum) was slightly higher in women than men (0.273 (0.264 to 0.282 vs 0.233 (0.225 to 0.244), p<0.001), with no change with age. In disease, the ECV of AFD was the same as in normal subjects but higher in all other diseases (p<0.001). Mean ECV was the same in DCM, HCM and AS (0.280, 0.291, 0.276 respectively), but higher in cardiac AL amyloidosis and higher again in MI (0.466 and 0.585 respectively, each p<0.001). Where ECV was elevated, correlations were found with indexed left ventricular mass, end systolic volume, ejection fraction and left atrial area in apparent disease-specific patterns. Conclusions Myocardial ECV, assessed non-invasively in the septum with equilibrium contrast cardiovascular magnetic resonance, shows gender differences in normal individuals and disease-specific variability. Therefore, ECV shows early potential to be a useful biomarker in health and disease.
Synthesis and characterization of thermally responsive polymer layers

ii DEDICATION.v ACKNOWLEDGMENTS . vi LIST OF FIGURES . xiii LIST OF TABLES . xx CHAPTER 1: INTRODUCTION . 1 CHAPTER 2: LITERATURE REVIEW . 7 2.1: Polymer Brushes. Definition and General Properties: . 7 2.2: Formation of Polymer Brushes: . 9 2.2.1: Physisorption . 10 2.2.2: “Grafting from” Technique . 13 2.2.3: Preparation of Polymer Brushes by “Grafting to” Technique: . 15 2.3: Thermally Responsive Polymer Brushes: . 18 2.3.1: Polymers Governed by UCST Solution Behavior: . 19 2.3. 2: Polymers Governed by LCST Behavior: . 23 2.4: Poly (N-isopropylacrylamide) Brushes . 25 2.5: References . 33 CHAPTER 3: EXPERIMENTAL 1 . 46 3.1: Chemical Reagents Used . 46
Fuels from microalgae: Technology status, potential, and research requirements

Although numerous options for the production of fuels from microalgae have been proposed, our analysis indicates that only two qualify for extensive development - gasoline and ester fuel. In developing the comparisons that support this conclusion, we have identified the major areas of microalgae production and processing that require extensive development. Technology success requires developing and testing processes that fully utilize the polar and nonpolar lipids produced by microalgae. Process designs used in these analyses were derived from fragmented, preliminary laboratory data. These results must be substantiated and integrated processes proposed, tested, and refined to be able to evaluate the commercial feasibility from microalgae. The production of algal feedstocks for processing to gasoline or ester fuel requires algae of high productivity and high lipid content that efficiently utilize saline waters. Species screening and development suggest that algae can achieve required standards taken individually, but algae that can meet the integrated requirements still elude researchers. Effective development of fuels from microalgae technology requires that R and D be directed toward meeting the integrated standards set out in the analysis. As technology analysts, it is inappropriate for us to dictate how the R and D effort should proceed to meet these standards.more » We end our role by noting that alternative approaches to meeting the feasibility targets have been identified, and it is now the task of program managers and scientists to choose the appropriate approach to assure the greatest likelihood of realizing a commercially viable technology. 70 refs., 39 figs., 35 tabs. « less
Automatic Detection, Estimation, and Validation of Harmonic Components in Measured Power Spectra: All-in-One Approach

The detection of periodic components buried in noise is a general problem in various engineering fields. The amplitudes in the frequency domain of a disturbed signal follow Rice distribution, which is fully described by two parameters. Most methods are restricted to automatically detecting the harmonic components. In this paper, we extend the methodology to detect significant harmonics in measured spectra such that, aside from detection, the magnitude of the harmonic component is also estimated, together with the probability that the harmonic component was incorrectly detected.
Inhibition of Bacterial Ammonia Oxidation by Organohydrazines in Soil Microcosms

Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO) is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB). Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homolog in known ammonia-oxidizing archaea (AOA). In this study, the effects of three organohydrazines on activity, abundance, and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 μmol g−1 dry weight soil completely suppressed the activity of soil nitrification. Denaturing gradient gel electrophoresis fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA) clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear.
Microbiological study of cosmetic products during their use by consumers: health risk and efficacy of preservative systems

Aim: To evaluate the microbial contamination of 91 cosmetics (23 o/w emulsions, 47 tensiolytes, 21 aqueous pastes) in three different states of use (intact, in‐use, ending product) and the protection efficacy of the preservative systems most frequently used in the analysed cosmetic formulations.
Secure Systems Faster, Easier Updates

unscrupulous. They're creating independent agents—mobile pro-grams—that, once released, take on lives of their own. Their attacks are becoming more sophisticated every day, and the situation will likely become much worse unless we, as defenders , take drastic steps. We can't hope to completely defeat all our attackers. For every individual we arrest, every worm we successfully eradicate, another virus writer and his or her program will propagate on the Internet. In an evolutionary arms race, the best we can hope for is to stay in the game no matter how the adversaries change and adapt. This game is ultimately one of survival, and so far, our computers aren't very good at playing it on their own. To keep up with malware writers, software producers in both the commercial and open-source software worlds have adopted various automatic software update mechanisms. Some of these mechanisms distribute updates after requesting a user's permission; others install updates automatically. Although such systems provide some short-term relief, they will likely soon become ineffective, and further, they will also become extremely dangerous once they are inevitably co-opted by attackers. If we want the Internet to remain a viable way to communicate and collaborate , we must adopt another, perhaps radically different, model for securing our computers. To better understand this conclusion , we should first reexamine why developers and users are embracing automated update systems. Automated update mechanisms are designed to solve one simple problem: humans can't be counted on to download and install anything in a timely fashion. Home users forget to update their systems (if they know to do it at all), and administrators already have too much to do. Yet, malicious code can spread across the Internet in minutes. Thus, software companies such as Microsoft, Sy-mantec, and Red Hat have created systems that remind users to initiate automated update processes or that bypass the user completely and install necessary updates on their own. To date, almost every virus or worm epidemic has exploited a security vulnerability for which there was an existing software patch or virus signature. However, before software developers can distribute a fix, they must identify the problem, craft a solution, and test that solution to ensure no untoward side effects. If McAfee makes a mistake with a virus signature, it could disable or even delete legitimate users' applications (legitimate applications have already been disabled by virus scanners; see http://news.com.com/2100-7350-5361660.html). If Microsoft …
DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase

Escherichia coli DNA polymerase V (pol V), a heterotrimeric complex composed of UmuD′2C, is marginally active. ATP and RecA play essential roles in the activation of pol V for DNA synthesis including translesion synthesis (TLS). We have established three features of the roles of ATP and RecA. (1) RecA-activated DNA polymerase V (pol V Mut), is a DNA-dependent ATPase; (2) bound ATP is required for DNA synthesis; (3) pol V Mut function is regulated by ATP, with ATP required to bind primer/template (p/t) DNA and ATP hydrolysis triggering dissociation from the DNA. Pol V Mut formed with an ATPase-deficient RecA E38K/K72R mutant hydrolyzes ATP rapidly, establishing the DNA-dependent ATPase as an intrinsic property of pol V Mut distinct from the ATP hydrolytic activity of RecA when bound to single-stranded (ss)DNA as a nucleoprotein filament (RecA*). No similar ATPase activity or autoregulatory mechanism has previously been found for a DNA polymerase. DOI: http://dx.doi. org/10.7554/eLife.02384. 001
2D-Confined Nanochannels Fabricated by Conventional Micromachining

Two new methods have been developed to fabricate nanochannels by conventional micromachining. We succeeded in restricting the width of the channels to the submicrometer scale, while using standard photolithography with a resolution in the order of 1 m. The first method is based on the sacrificial etching of a nanowire, which was formed on the side wall of a step. The second method is based on the adhesion of the capping layer to the substrate after removal of a sacrificial strip separating the two. The fabricated nanochannels are localized and can be connected to microchannels and reservoirs.
The Efficacy and Safety of the Combination of Total Glucosides of Peony and Leflunomide for the Treatment of Rheumatoid Arthritis: A Systemic Review and Meta-Analysis

Objective. To evaluate the efficacy and safety of the total glucosides of peony (TGP) and leflunomide (LEF) for the treatment of rheumatoid arthritis (RA). Methods. Randomized controlled trials (RCTs) on the efficacy and safety of the combination of TGP and LEF versus LEF alone for the treatment of RA were retrieved by searching PubMed, EMBASE, Cochrane Library, the China National Knowledge Infrastructure database, and Wanfang database. Results. Eight RCTs including 643 RA patients were included in the present meta-analysis. The quality of included studies was poor. The levels of ESR (P < 0.0001), CRP (P < 0.0001), and RF (P < 0.0001) in RA patients who received the combination of TGP and LEF were significantly lower than RA patients who received LEF therapy alone. The pooled results suggest that the combination of TGP and LEF caused less abnormal liver function than LEF alone (P = 0.02). No significant difference in the gastrointestinal discomfort was identified between the combination of TGP and LEF and LEF alone groups (P = 0.18). Conclusion. The combination of TGP and LEF in treatment of RA presented the characteristics of notably decreasing the levels of laboratory indexes and higher safety in terms of liver function. However, this conclusion should be further investigated based on a larger sample size.
Addition of the keto functional group to the genetic code of Escherichia coli

Although the keto group is the most versatile of the functional groups in organic chemistry, it is absent in the genetically encoded amino acids. To overcome this natural limitation on protein biosynthesis, we have evolved an orthogonal tRNA-synthetase pair that makes possible the efficient incorporation of a keto amino acid, p-acetyl-l-phenylalanine, into proteins in E. coli with high translational fidelity in response to the amber nonsense codon. To demonstrate the utility of this keto amino acid, we have used it to modify a protein selectively with a small molecule fluorophore and biotin derivative. This additional genetically encoded amino acid should greatly expand our ability to manipulate protein structure and function both in vitro and in living cells.
A Dietary-Wide Association Study (DWAS) of Environmental Metal Exposure in US Children and Adults

Background A growing body of evidence suggests that exposure to toxic metals occurs through diet but few studies have comprehensively examined dietary sources of exposure in US populations. Purpose Our goal was to perform a novel dietary-wide association study (DWAS) to identify specific dietary sources of lead, cadmium, mercury, and arsenic exposure in US children and adults. Methods We combined data from the National Health and Nutrition Examination Survey with data from the US Department of Agriculture's Food Intakes Converted to Retail Commodities Database to examine associations between 49 different foods and environmental metal exposure. Using blood and urinary biomarkers for lead, cadmium, mercury, and arsenic, we compared sources of dietary exposure among children to that of adults. Results Diet accounted for more of the variation in mercury and arsenic than lead and cadmium. For instance we estimate 4.5% of the variation of mercury among children and 10.5% among adults is explained by diet. We identified a previously unrecognized association between rice consumption and mercury in a US study population – adjusted for other dietary sources such as seafood, an increase of 10 g/day of rice consumption was associated with a 4.8% (95% CI: 3.6, 5.2) increase in blood mercury concentration. Associations between diet and metal exposure were similar among children and adults, and we recapitulated other known dietary sources of exposure. Conclusion Utilizing this combination of data sources, this approach has the potential to identify and monitor dietary sources of metal exposure in the US population.
Application of a Mathematical Model to Describe the Effects of Chlorpyrifos on Caenorhabditis elegans Development

Background The nematode Caenorhabditis elegans is being assessed as an alternative model organism as part of an interagency effort to develop better means to test potentially toxic substances. As part of this effort, assays that use the COPAS Biosort flow sorting technology to record optical measurements (time of flight (TOF) and extinction (EXT)) of individual nematodes under various chemical exposure conditions are being developed. A mathematical model has been created that uses Biosort data to quantitatively and qualitatively describe C. elegans growth, and link changes in growth rates to biological events. Chlorpyrifos, an organophosphate pesticide known to cause developmental delays and malformations in mammals, was used as a model toxicant to test the applicability of the growth model for in vivo toxicological testing. Methodology/Principal Findings L1 larval nematodes were exposed to a range of sub-lethal chlorpyrifos concentrations (0–75 µM) and measured every 12 h. In the absence of toxicant, C. elegans matured from L1s to gravid adults by 60 h. A mathematical model was used to estimate nematode size distributions at various times. Mathematical modeling of the distributions allowed the number of measured nematodes and log(EXT) and log(TOF) growth rates to be estimated. The model revealed three distinct growth phases. The points at which estimated growth rates changed (change points) were constant across the ten chlorpyrifos concentrations. Concentration response curves with respect to several model-estimated quantities (numbers of measured nematodes, mean log(TOF) and log(EXT), growth rates, and time to reach change points) showed a significant decrease in C. elegans growth with increasing chlorpyrifos concentration. Conclusions Effects of chlorpyrifos on C. elegans growth and development were mathematically modeled. Statistical tests confirmed a significant concentration effect on several model endpoints. This confirmed that chlorpyrifos affects C. elegans development in a concentration dependent manner. The most noticeable effect on growth occurred during early larval stages: L2 and L3. This study supports the utility of the C. elegans growth assay and mathematical modeling in determining the effects of potentially toxic substances in an alternative model organism using high-throughput technologies.
Laser Surface Estimation for Microwave Breast Imaging Systems

Microwave breast imaging techniques involve collecting measurements from a breast that is positioned in a scanner. While the patient interface typically includes a hole through which the breast is placed when the patient lies in the prone position, the exact location and shape of breast are not known. In this paper, we explore the addition of a laser sensor and associated algorithms in order to provide a rapid and accurate estimate of the breast surface location. We demonstrate that the laser is capable of estimating surfaces with improved accuracy compared to microwave measurements. The impact of accurate surface estimation on images is shown, and results obtained from human scans are presented.
Energy-Efficient Power Allocation in Dynamic Multi-Carrier Systems

We propose an online power allocation algorithm for optimizing energy efficiency (throughput per unit of transmit power) in multi-user, multi-carrier systems that evolve dynamically over time (e.g. due to changes in the wireless environment or the users' load). Contrary to the static/ergodic regime, a fixed optimal power allocation profile (either static or in the mean) does not exist, so we draw on exponential learning techniques to design an algorithm that is able to adapt to system changes "on the fly". Specifically, the proposed transmit policy leads to no regret, i.e., it is asymptotically optimal in hindsight, irrespective of the system's evolution over time. Importantly, despite the algorithm's simplicity and distributed nature, users are able to track their individually optimum transmit profiles as they vary with time, even under rapidly changing network conditions.
Modelling of Migration from Printing Inks on Paper Packaging

The migration model of contaminants from inks on paper packaging to food is developed based on the penetration of ink in paper and Fick's diffusion. The printed paper is divided as ink layer and paper layer. The mass transfer coefficient hm and partition coefficient KF,P in the interface between paper and food are considered in the model. The model equation is solved, and the migration expression is obtained by using the method of separation of variables. The fitting method is used between the model and the migration experimental data to obtain the diffusion coefficients and mass transfer coefficients for dibutyl phthalate (DBP) and acetyl tributyl citrate (ATBC). It is found that there exist linear relationships between ln(DP) and 1/T, and also between ln(hm) and 1/T for DBP and ATBC. The migrations of DBP in the paper sample 2402 at different temperatures and of ATBC in the paper sample 2401 at 50°C are predicted by using the model, and a good agreement is obtained between the model predictions and the migration experimental data. Copyright © 2014 John Wiley & Sons, Ltd.
Characterization of Proline-Serine-Rich Carboxyl Terminus in Human Sulfotransferase 2B1b: Immunogenicity, Subcellular Localization, Kinetic Properties, and Phosphorylation

The human sulfotransferase (SULT) 2B1 gene is a member of the SULT2 gene family and encodes two isoforms, SULT2B1a and SULT2B1b. Although messages for both SULT2B1a and SULT2B1b are detectable in human tissues, only SULT2B1b has been identified immunologically. Compared with other human SULTs, SULT2B1b has an extension at the proline- and serine-rich carboxyl (PSC) end of about 53 amino acids. The structure and function of this unique PSC extension were investigated. Constructs of full-length SULT2B1b as well as truncated SULT2B1b without the PSC extension were expressed in Escherichia coli. Removal of the PSC extension significantly decreased the thermostability of the expressed enzyme as well as decreasing the rate of dehydroepiandrosterone sulfation. Rabbit polyclonal antibodies were raised against both the full-length and truncated SULT2B1b proteins. Immunoblot analysis showed that antibodies raised to full-length SULT2B1b immunoreact only with full-length SULT2B1b, whereas antibodies raised to truncated SULT2B1b react with both full-length and truncated SULT2B1b. Unlike full-length SULT2B1b, truncated SULT2B1b was incapable of translocation to nuclei in transfected human BeWo choriocarcinoma cells. Phosphorylated serines were detected in the PSC extension of full-length SULT2B1b expressed in BeWo cells but not in truncated SULT2B1b. At least one phosphorylated serine was detected in expressed SULT2B1b via two-dimensional gel electrophoresis, immunoblot analysis, and mass spectroscopic analysis. Bacterially expressed full-length SULT2B1b but not truncated SULT2B1b was phosphorylated by casein kinase or Cdc2 protein kinase in vitro. This study suggests that the PSC extension of SULT2B1b is an important site in the immunogenicity, nuclear translocation, kinetic activity, and thermostability of this SULT isoform.
Basic Principles of Capillarity in Relation to Crystal Growth

The fi rst part of this chapter (1.1) contains a brief defi nition of characteristic energies of surfaces and interfaces, as well as of capillary pressure. The second part (1.2) presents the basic principles of wettability and selected data for surface tension and contact angle for liquids of interest in crystal growth on various solid substrates. The third part (1.3) deals with growth angles, i.e. the contact angles formed by liquids on their own crystal, and the role of these angles in melt growth processes.