Miracle-dz/UniFAR-FTUs huggingface dataset:
Sorting Out Antibiotics' Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors

ABSTRACT In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double-reporter system for not only antimicrobial activity detection but also simultaneous sorting of potential antimicrobials into those that cause ribosome stalling and those that induce the SOS response due to DNA damage. In this reporter system, the red fluorescent protein gene rfp was placed under the control of the SOS-inducible sulA promoter. The gene of the far-red fluorescent protein, katushka2S, was inserted downstream of the tryptophan attenuator in which two tryptophan codons were replaced by alanine codons, with simultaneous replacement of the complementary part of the attenuator to preserve the ability to form secondary structures that influence transcription termination. This genetically modified attenuator makes possible Katushka2S expression only upon exposure to ribosome-stalling compounds. The application of red and far-red fluorescent proteins provides a high signal-to-background ratio without any need of enzymatic substrates for detection of the reporter activity. This reporter was shown to be efficient in high-throughput screening of both synthetic and natural chemicals.
Ammonium nitrate surface modification through spraying and drying technology

Polymer and coupling agent were used to coat phase stabilized ammonium nitrate(PSAN) by mens of spraying and drying technology in order to lower moisture absorption of AN. The characterization of the modified PSAN were performed by measurements of hygroscopicity, contact angle, mass fraction of coating layer, XPS and SEM. The results show that the composite modification of both polymer and coupling agent can restrain effectively moisture absorption of PSAN and relatively average moisture absorption rate of the modified PSAN was up to 46 % , average reduces 3 % compared with the liquid phase separation techniques, and the mass of coating layer redues 76 % . It indicated that the effect of spraying and drying technology is better than that of the liquid phase separation techniques.
iVoLVER: A Visual Language for Constructing Visualizations from In-the-Wild Data

iVoLVER, the Interactive Visual Language for Visualization Extraction and Reconstruction, is a web-based pen-and-touch interface that graphically supports construction of interactive visualizations. iVoLVER is designed to enable data extraction from different types of artifacts (e.g., photos) and to use that data to generate original representations of that data. People can create visualizations from data that is not structured in traditional formats without the need of textual programming or sitting at their desk. This demonstration shows how iVoLVER visualizations are constructed and also demonstrates the possible uses of iVoLVER in several contexts.
EEG-fMRI Fusion: Adaptations of the Kalman Filter for Solving a High-Dimensional Spatio-Temporal Inverse Problem

Recording the dynamics of human brain activity is a key topic for both neuroscience fundamental research and medicine. The two main techniques used, Electroand Magneto-encephalography (EEG/MEG) on the one hand, functional Magnetic Resonance Imaging (fMRI) on the other hand, measure different aspects of this activity, and have dramatically different temporal and spatial resolutions. There is an important literature dedicated to the analysis of EEG/MEG (REF) and fMRI data (REF). Indeed, the both techniques provide partial and noisy measures of the hidden neural activity, and sophisticated methods are needed to reconstruct this activity as precisely as possible. Adaptive filtering algorithms seem well-adapted to this reconstruction, since the problem can easily be formulated as a dynamic system, but it is only recently that such formulations have been proposed for EEG analysis (Jun et al., 2005), fMRI analysis (Johnston et al., 2008; Murray & Storkey, 2008; Riera et al., 2004), or EEG-fMRI fusion (Deneux & Faugeras, 2006b; Plis et al., 2010). In this chapter, we focus on the so-called "EEG-fMRI fusion", i.e. the joint analysis of EEG/MEG and fMRI data obtained on the same experiment. For more than a decade, EEGfMRI fusion has become a hot topic, because it is believed that both techniques used together should provide higher levels of information on brain activity, by taking advantage of the high temporal resolution of EEG, and spatial resolution of fMRI. However, the two modalities and their underlying principles are so different from each other that the proposed solutions were often ad hoc, and lacked a common formalism. We show here how the use of dynamic system formulation and adaptive filter algorithms appears to be a natural way to achieve the EEG-fMRI fusion. However, not only do adaptive filtering techniques offer new possibilities for the EEGfMRI fusion, but also this specific problem brings new challenges and fosters the development of new filtering algorithms. These challenges are mostly a very high
Subjective Evaluation: A Comparison of Several Statistical Techniques

ABSTRACT Evaluation of subjective examinations using computerized tools has been a topic of research for more than four decades. Several statistical and mathematical techniques have been proposed by various researchers. In this research work, the several methods proposed earlier like Latent Semantic Analysis (LSA), Generalized Latent Semantic Analysis (GLSA), Bilingual Evaluation Understudy (BLEU), and Maximum Entropy (MaxEnt) are compared on common input data. The techniques are implemented using Java programming language, MatLab, and other open source tools. Experiments have been conducted and developed prototypes are tested using a database of 4500 answers with approximately 50 questions of computer science. Comparison of these techniques on a common database is not available in the literature as far as the authors' review is concerned. The database used for testing is collected by conducting tests of students of graduate level in the field of computer science. The pros and cons of each technique on the basis of experiments are discussed in the paper.
CCCS: a top-down associative classifier for imbalanced class distribution

In this paper we propose CCCS, a new algorithm for classification based on association rule mining. The key innovation in CCCS is the use of a new measure, the "Complement Class Support (CCS)" whose application results in rules which are guaranteed to be positively correlated. Furthermore, the anti-monotonic property that CCS possesses has very different semantics vis-a-vis the traditional support measure. In particular, "good" rules have a low CCS value. This makes CCS an ideal measure to use in conjunction with a top-down algorithm. Finally, the nature of CCS allows the pruning of rules without the setting of any threshold parameter! To the best of our knowledge this is the first threshold-free algorithm in association rule mining for classification.
Flyback Inverter Using Voltage Sensorless MPPT for Photovoltaic AC Modules

A flyback inverter using voltage sensorless maximum power point tracking (MPPT) for photovoltaic (PV) AC modules is presented. PV AC modules for a power rating from 150 W to 300 W are generally required for their small size and low price because of the installation on the back side of PV modules. In the conventional MPPT technique for PV AC modules, sensors for detecting PV voltage and PV current are required to calculate the PV output power. However, system size and cost increase when the voltage sensor and current sensor are used because of the addition of the auxiliary circuit for the sensors. The proposed method uses only the current sensor to track the MPP point. Therefore, the proposed control method overcomes drawbacks of the conventional control method. Theoretical analysis, simulation, and experiment are performed to verify the proposed control method.
Security Interrogation and Defense for SAR Analog to Digital Converter

Nowadays, the analog and mixed-signal intellectual property (IP) cores play an important role in system on chip (SoC) design due to their capabilities in performing critical functions. These IPs can be the target of adversaries similar to their digital counterparts. In this work, we study the security aspects of a tunnel field effect transistor (TFET)-based six-bit successive approximation register (SAR) analog to digital converter (ADC) through proposing two threats and two countermeasures that target the output signals of the ADC datapath and its control unit. The datapath-based threat manipulates the exiting signals from the register file, and its countermeasure attempts to filter the ADC output based on the convention of having ± 1 least significant bit variation (at maximum) between the adjacent sampled data points. The control-based threat manipulates the exiting signals from the control unit, and its countermeasure is a trustworthy replication of a part of the ADC circuit that is used to provide reference data for security examination and output filtering.
MONTE CARLO SIMULATION OF SEMICONDUCTOR DEVICES AND PROCESSES

The Monte Carlo method (MC) can be considered as a very general mathematical tool for the solution of a great variety of problems [1-4]. In its present form, the method is attributed to Fermi, Von Neumann, and Ulam, who developed it for the solution of problems related to neutron transport . Among the various applications of the method the following are probably the most important: * Integro-differential equations * Matrix inversion * Transport of nuclear particles * Transport in semiconductors * Modeling of semiconductor devices * Process simulation Being based on random numbers, the results obtained with a MC procedure are never exact, but rigorous in a statistical sense: the exact result lies in given intervals with given probabilities. The applications of MC methods can be divided into two major groups. One consists of direct reproduction on a computer of the microscopic dynamics of the physical
X-ray Structure of TMP Kinase from Mycobacterium tuberculosis Complexed with TMP at 1 . 95 AÊ Resolution

Present address: I. Li de la Sierra d'Enzymologie et de Biochimie Stru Bat. 34, Avenue de la Terrasse, 9119 France. Abbreviations used: TMPK, thym TMPKMtub, thymidylate kinase from tuberculosis; TMPKEcoli, thymidylate Escherichia coli; TMPKYeast, thymidy yeast; CMPK, cytidylate kinase; UM kinase; AMPK, adenylate kinase; N monophosphate kinase; TMP, thym monophosphate; TDP, thymidine d thymidine triphosphate; TB, tubercu immunode®ciency virus; MIR, mult replacement; HSV, herpes simplex v E-mail address of the correspond delarue@pasteur.fr
The External Financing of Investment

Abstract This paper investigates the impact of investment characteristics on the financing choice. We investigate instances of seasoned equity, bank debt, straight non-bank debt, and convertible issues by U.S. firms where the stated use of proceeds is capital expenditure and where we are able to hand-collect and classify the characteristics of the investment. Controlling for a firm's existing assets, capital structure and valuation, we document a strong empirical link between an investment's characteristics and the choice between debt and equity financing. Factor analysis indicates that the principal determinant of the financing choice is whether an investment's payoffs can be described as a hit or miss.
Current noise in a vibrating quantum dot array

We develop methods for calculating the zero-frequency noise for quantum shuttles, i.e., nanoelectromechanical devices where the mechanical motion is quantized. As a model system we consider a three-dot array, where the internal electronic coherence both complicates and enriches the physics. Two different formulations are presented: (i) quantum regression theorem and (ii) the counting variable approach. It is demonstrated, both analytically and numerically, that the two formulations yield identical results, when the conditions of their respective applicability are fulfilled. We describe the results of extensive numerical calculations for current and current noise (Fano factor), based on a solution of a Markovian generalized master equation. The results for the current and noise are further analyzed in terms of Wigner functions, which help to distinguish different transport regimes (in particular, shuttling versus cotunneling). In the case of weak interdot coupling, the electron transport proceeds via sequential tunneling between neighboring dots. A simple rate equation with the rates calculated analytically from the $P(E)$ theory is developed and shown to agree with the full numerics.
Height, Body Mass Index, and Ovarian Cancer: A Pooled Analysis of 12 Cohort Studies

Background: Although many studies have investigated the association between anthropometry and ovarian cancer risk, results have been inconsistent. Methods: The associations of height, body mass index (BMI), and ovarian cancer risk were examined in a pooled analysis of primary data from 12 prospective cohort studies from North America and Europe. The study population consisted of 531,583 women among whom 2,036 epithelial ovarian cancer cases were identified. To summarize associations, study-specific relative risks (RR) were estimated using the Cox proportional hazards model and then combined using a random-effects model. Results: Women with height ≥1.70 m had a pooled multivariate RR of 1.38 [95% confidence interval (95% CI), 1.16-1.65] compared with those with height <1.60 m. For the same comparison, multivariate RRs were 1.79 (95% CI, 1.07-3.00) for premenopausal and 1.25 (95% CI, 1.04-1.49) for postmenopausal ovarian cancer (Pinteraction = 0.14). The multivariate RR for women with a BMI ≥30 kg/m2 was 1.03 (95% CI, 0.86-1.22) compared with women with a BMI from 18.5 to 23 kg/m2. For the same comparison, multivariate RRs were 1.72 (95% CI, 1.02-2.89) for premenopausal and 1.07 (95% CI, 0.87-1.33) for postmenopausal women (Pinteraction = 0.07). There was no statistically significant heterogeneity between studies with respect to height or BMI. BMI in early adulthood was not associated with ovarian cancer risk. Conclusion: Height was associated with an increased ovarian cancer risk, especially in premenopausal women. BMI was not associated with ovarian cancer risk in postmenopausal women but was positively associated with risk in premenopausal women. (Cancer Epidemiol Biomarkers Prev 2008;17(4):902–12)
Anti-biofilm and remineralization effects of chitosan hydrogel containing amelogenin-derived peptide on initial caries lesions

Abstract In this study, we have designed a more clinically powerful anti-caries treatment by applying the amelogenin-derived peptide QP5 to the antibacterial carrier material chitosan in a hydrogel (CS-QP5 hydrogel), and characterized its effects on the inhibition of a cariogenic biofilm and the promotion of the remineralization of the initial caries lesions. The results indicated that the CS-QP5 hydrogel sustainably inhibited the growth of the Streptococcus mutans biofilm, lactic acid production and the metabolic activity over a prolonged period of time. Moreover, the CS-QP5 hydrogel promoted the remineralization of early enamel lesions, which were indicated by surface micro-hardness (, polarized light microscopy and transverse microradiography. In conclusion, the CS-QP5 hydrogel shows good potential for caries control in the clinic because of its antibacterial effects as well as the remineralization of initial enamel carious lesions even in a biofilm model over a prolonged period of time.
Serum Total Bilirubin Levels Provide Additive Risk Information over the Framingham Risk Score for Identifying Asymptomatic Diabetic Patients at Higher Risk for Coronary Artery Stenosis

Background The diagnosis of coronary artery disease (CAD) is often delayed in patients with type 2 diabetes. Serum total bilirubin levels are inversely associated with CAD. However, no studies have examined whether this can be used as a biochemical marker for identifying asymptomatic diabetic patients at higher risk for having obstructive CAD. Methods We performed a cross-sectional study of 460 consecutive asymptomatic patients with type 2 diabetes. All patients underwent coronary computed tomographic angiography, and their serum total bilirubin levels were measured. Obstructive CAD was defined as ≥50% diameter stenosis in at least one coronary artery. Results Serum total bilirubin tertiles showed an inverse association with the prevalence of obstructive CAD. In multivariate logistic regression analysis, the odds ratio for the highest versus the lowest tertile of total bilirubin was 0.227 (95% confidence interval [CI], 0.130 to 0.398), and an increment of 1 µmol/L in serum total bilirubin level was associated with a 14.6% decrease in obstructive CAD after adjustment for confounding variables. Receiver operating characteristic curve analysis showed that the area under the curve for the Framingham Risk Score (FRS) plus serum total bilirubin level was 0.712 (95% CI, 0.668 to 0.753), which is significantly greater than that of the FRS alone (P=0.0028). Conclusion Serum total bilirubin level is inversely associated with obstructive CAD and provides additive risk information over the FRS. Serum total bilirubin may be helpful for identifying asymptomatic patients with type 2 diabetes who are at higher risk for obstructive CAD.
Residual abilities in age-related macular degeneration to process spatial frequencies during natural scene categorization

Abstract Age-related macular degeneration (AMD) is characterized by a central vision loss. We explored the relationship between the retinal lesions in AMD patients and the processing of spatial frequencies in natural scene categorization. Since the lesion on the retina is central, we expected preservation of low spatial frequency (LSF) processing and the impairment of high spatial frequency (HSF) processing. We conducted two experiments that differed in the set of scene stimuli used and their exposure duration. Twelve AMD patients and 12 healthy age-matched participants in Experiment 1 and 10 different AMD patients and 10 healthy age-matched participants in Experiment 2 performed categorization tasks of natural scenes (Indoors vs. Outdoors) filtered in LSF and HSF. Experiment 1 revealed that AMD patients made more no-responses to categorize HSF than LSF scenes, irrespective of the scene category. In addition, AMD patients had longer reaction times to categorize HSF than LSF scenes only for indoors. Healthy participants’ performance was not differentially affected by spatial frequency content of the scenes. In Experiment 2, AMD patients demonstrated the same pattern of errors as in Experiment 1. Furthermore, AMD patients had longer reaction times to categorize HSF than LSF scenes, irrespective of the scene category. Again, spatial frequency processing was equivalent for healthy participants. The present findings point to a specific deficit in the processing of HSF information contained in photographs of natural scenes in AMD patients. The processing of LSF information is relatively preserved. Moreover, the fact that the deficit is more important when categorizing HSF indoors, may lead to new perspectives for rehabilitation procedures in AMD.
Dorsal versus ventral hippocampal contributions to trace and contextual conditioning: Differential effects of regionally selective nmda receptor antagonism on acquisition and expression

The dorsal and ventral subregions of the hippocampus likely play dissociable roles in some forms of learning. For example, we have previously demonstrated that temporary inactivation of ventral, but not dorsal, hippocampus dramatically impaired the acquisition of trace fear conditioning, while temporary inactivation of dorsal, but not ventral, hippocampus impaired spatially guided reinforced alternation (Czerniawski et al. (2009) Hippocampus 19:20–32). Importantly, emerging data suggest that lesions, temporary inactivation, and NMDA receptor antagonism within these subregions can produce quite different patterns of behavioral effects when administered into the same region. Specifically, while neither lesions nor temporary inactivation of dorsal hippocampus impair the acquisition of trace fear conditioning, learning in this paradigm is severely impaired by pre‐training administration of the NMDA receptor antagonist dl‐2‐phosphonovaleric acid (APV) in dorsal hippocampus; the effect of NMDA receptor antagonism within ventral hippocampus on the acquisition and expression of trace conditioning, or on learning in general, has not yet been systematically explored. The present study extends our previous work examining the differential effect of lesions or inactivation of the dorsal and ventral hippocampal subregions by systematically examining the effect of regionally selective pre‐training or pre‐testing administration of APV on the acquisition and expression of trace and contextual fear conditioning. The results of these studies demonstrate that while pre‐training NMDA receptor antagonism within either the dorsal or ventral subregion of the hippocampus impaired the acquisition of both trace and contextual conditioning, pre‐testing NMDA receptor antagonism within ventral, but not dorsal, hippocampus impaired the expression of previously‐acquired trace and contextual fear conditioning. These data suggest that selectively manipulating the integrity of individual subregions may result in compensatory mechanisms that can support learning, and that NMDA‐dependent plasticity within both dorsal and ventral hippocampus is normally required for the acquisition and maintenance of memory in trace and contextual fear conditioning. © 2011 Wiley Periodicals, Inc.
Antibacterial activity of aqueous extract from selectedmacroalgae of southwest coast of India

Aqueous extract of seven species of marine macroalgae were screened for their antimicrobial potency against ten pathogenic bacterial strains. Ulva fasciata, Gracilaria corticata, Sargassum wightii and Padina tetrastromatica showed significantly higher activity against 70% of the tested bacterial isolates. The maximum zone of inhibition was noted for the red alga G.corticata against Proteus mirabilis (17mm) and brown alga P. tetrastromatica against the pathogens Staphylococcus aureus and Vibrio harveyi (15mm). The general trend of inhibitory activity was higher towards Gram negative bacteria.