Miracle-dz/UniFAR-FTUs huggingface dataset:
A Lipopolysaccharide-Specific Enhancer Complex Involving Ets, Elk-1, Sp1, and CREB Binding Protein and p300 Is Recruited to the Tumor Necrosis Factor Alpha Promoter In Vivo

ABSTRACT The tumor necrosis factor alpha (TNF-α) gene is rapidly activated by lipopolysaccharide (LPS). Here, we show that extracellular signal-regulated kinase (ERK) kinase activity but not calcineurin phosphatase activity is required for LPS-stimulated TNF-α gene expression. In LPS-stimulated macrophages, the ERK substrates Ets and Elk-1 bind to the TNF-α promoter in vivo. Strikingly, Ets and Elk-1 bind to two TNF-α nuclear factor of activated T cells (NFAT)-binding sites, which are required for calcineurin and NFAT-dependent TNF-α gene expression in lymphocytes. The transcription factors ATF-2, c-jun, Egr-1, and Sp1 are also inducibly recruited to the TNF-α promoter in vivo, and the binding sites for each of these activators are required for LPS-stimulated TNF-α gene expression. Furthermore, assembly of the LPS-stimulated TNF-α enhancer complex is dependent upon the coactivator proteins CREB binding protein and p300. The finding that a distinct set of transcription factors associates with a fixed set of binding sites on the TNF-α promoter in response to LPS stimulation lends new insights into the mechanisms by which complex patterns of gene regulation are achieved.
Reliability-Enhanced Hybrid CMOS/MTJ Logic Circuit Architecture

Benefitting from its non-volatility, nearly infinite endurance, good scalability, and great CMOS compatibility, magnetic tunnel junction (MTJ) embedded in conventional CMOS logic circuits has been proposed as one potentially powerful solution to introduce non-volatility in today’s programmable logic circuits, which is envisioned to achieve low power and high area efficiency. However, the recently proposed hybrid CMOS/MTJ logic circuits and prototypes based on such a logic-in-memory architecture suffers from a severe reliability issue, which is the precise transformation from MTJ resistance to electric signals due to its limited tunnel magnetoresistance ratio (TMR $\leq$ 150%), i.e., the requirement of nearly zero sensing error for logic applications. In this paper, to overcome this sensing reliability issue, a novel sense amplifier (SA) with high sensing margin is proposed for such hybrid CMOS/MTJ logic circuit architecture. By using a commercial CMOS 40 nm design kit and a physics-based MTJ compact model, hybrid CMOS/MTJ transient and Monte Carlo statistic simulations have been conducted to demonstrate the functionality of the proposed SA and evaluate its performance, respectively.
Optimal Jamming Attack Scheduling in Networked Sensing and Control Systems

This paper investigates the optimal jamming attack scheduling in Networked Sensing and Control Systems (NSCS). From viewpoint of the attacker, we formulate an optimization problem which maximizes the Linear Quadratic Gaussian (LQG) control cost with attacking energy constraint in a finite time horizon. For two special cases, we obtain that the optimal jamming attack schedule is to consecutively attack in the given time horizon. For the general case, we propose an algorithm to find the optimal schedules. Finally, we study the effectiveness of our proposed attack strategies on our established semiphysical testbed.
Biological inactivation of adhering Listeria monocytogenes by listeriaphages and a quaternary ammonium compound

The use of listeriaphages as a means of disinfecting contaminated stainless-steel and polypropylene surfaces was investigated. Surfaces artificially contaminated with L. monocytogenes 10401 and 8427 were sanitized with suspensions of listeriaphages (H387, H387-A, and 2671), all belonging to the Siphoviridae family. Phage suspensions at concentrations of up to 3.5 x 10(8) PFU/ml were at least as efficient as a 20 ppm solution of a quaternary ammonium compound (QUATAL) in reducing L. monocytogenes populations. A synergistic activity was observed when two or more phages were used in combination and when phages were suspended in QUATAL. The biological activity of the three phages was not affected by QUATAL concentrations of 50 ppm and a contact time of 4 h.
Method for Growth and Purification of Bacteriophage 643 on Streptococcus lactis ML3

The yield of bacteriophage 643 was increased by infecting cultures of Streptococcus lactis ML3 in late-log phase growth, harvesting the infected cells, and suspending them in fresh, phosphate-buffered minimal medium. The cells lysed after this treatment and produced high titers of bacteriophage. The phage particles were dissociated from debris by 2 M NaCl and purified by differential and CsCl band centrifugation.
An importance of clinical proteomics for personalized medicine of lung cancer subtypes

Mass spectrometry-based clinical proteomic analysis, combined with collection of taegeted cancerous cells laser-microdissected (LMD) from formalin-fixed paraffinembedded (FFPE) tissues, has been promising to unveil both proteins expressed and their functional networks in lung cancer subtypes. Among lung cancer subtypes, both large cell neuroendocrine carcinoma (LCNEC) of the lung and small cell lung carcinoma (SCLC) are now classified to neuroendocrine tumor (NET) but pre-therapeutic histological distinction between LCNEC and SCLC has so far been problematic, leading to adverse clinical outcome. Protein biomarker candidates for LCNEC were found to be interestingly known as cancer stem cell (CSC) markers including aldehyde dehydrogenase 1 family member A1 (ALDH1A1), and those for SCLC included novel NET marker candidates, brain acid soluble protein 1 (BASP1) and secretagogin (SEGN), and a known NET marker, neural cell adhesion molecule (CD56). For three types of lung adenocarcinomas (ACs), which are adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and lepidic predominant invasive asenocarcinoma (LEP), their preliminary clinical proteomic analyses revealed protein expression profiles characterizing those lung cancer subtypes. The STRING protein-protein interaction (PPI) network analysis followed by gene set enrichment (GSE) for proteins expressed significantly to the three lung AC subtypes manifested characteristic associations of cancer-related pathways, which might play consertedly important roles in progression of disease mechanisms, and which would be quite useful to understand carcinogenic processes of lung adenocarcinom. Thus outcomes from clinical proteomic analysis reveal not only biomarker protein candidates expressed significantly to a disease but also serve to elucidate disease-oriented protein-protein interaction (PPI) networks including functional networks predicted from experimentally obtained proteome datasets. Abbreviations: LCNEC: Large-Cell Neuroendocrine Lung Carcinoma, OLC: Other Large-Cell Lung Cancer, SCLC: Small-Cell Lungcancer, GGO: Focal Ground-Glass Opacity, AIS: Adenocarcinoma In Situ, MIA: Minimally Invasive Adenocarcinoma, LEP: Lepidic Predominant Invasive Adenocarcinoma, FFPE: Formalin-Fixed and Paraffin-Embedded tissue sections, MS: Mass Spectrometry, PPI: Comparative Proteomics, Protein-Protein Interaction
Evolution of aromatic beta-glucoside utilization by 1 successive mutational steps in Escherichia coli

5 Department of Molecular Reproduction, Development and Genetics 6 Indian Institute of Science, Bangalore -560012, India 7 *Corresponding author 8 Address for correspondence: 9 Department of Molecular Reproduction, Development and Genetics 10 Indian Institute of Science, Bangalore -560012 India 11 E-mail: mahi@mrdg.iisc. ernet.in 12 Tel: +91 8
Feature Extraction in Pet Images for the Diagnosis of Alzheimer's Disease

Alzheimerâs disease accounts for an estimated 60% to 80% of cases of dementia. Recently, several computer-aided diagnosis systems have been developed, based on extracting information from FDG-PET scans. 3-dimensional FDG-PET images, under a voxel-as-feature approach, lead to high-dimensional features spaces which results in system performance problems. We propose a new approach for feature extraction of 3-dimensional images to improve the performance of a diagnosis system, and compare it with Gaussian pyramid technique. To evaluate the performance of our approach we applied it to a data base obtained from the Alzheimerâs Disease Neuroimaging Initiative (ADNI). Experimental results have shown that the proposed approach is a good option for image feature extraction, outperforming the Gaussian pyramid technique.
Multi-objective genetic algorithm-based optimization of an asynchronous data-flow security processor

The architecture of a recently proposed Globally Asynchronous Locally Synchronous (GALS) processor dedicated to security programs is considered. Operations are performed using a number of Functional Units (FUs) grouped into a number of Execution Regions (ERs) working with independent clocks. The selection of the number of ERs as well as the distribution of the FUs among regions is approached as a multi-objective optimization problem with the objective functions selected as area, delay, and energy. This problem is solved using the NSGA-II algorithm. The obtained solutions are compared with those obtained in the case of operating all regions with the same clock. It is shown that for the case of AES encryption and with high communication delay overheads the synchronous case achieves a better performance. However, by reducing these overheads and speeding up the instruction region, execution delay with asynchronous operation can be reduced to 56% of the delay in the synchronous case.
A novel third harmonic current injection method to optimize the air-gap flux for multiphase induction machine

This paper presents a novel harmonic current injection method to optimize air-gap flux density distribution for multiphase induction machine. The control objective is to generate a nearly rectangular air-gap flux for better iron utilization. The proposed method uses air-gap field-oriented control and rotor field-oriented control to realize a real-time adjustment of the third harmonic current under various loads. The control concept is valid for any number of planes with a higher number of phases, and each plane requires two PI controllers. The robustness and effectiveness of the proposed scheme has been validated by experiments.
American Basket and Spread Option Pricing by a Simple Binomial Tree

The return on a portfolio is the weighted average of the returns on the individual assets in the portfolio. But the dynamics of portfolio returns are not so simple. The standard assumption that the underlying asset for an option follows geometric Brownian motion is convenient for individual stocks, but it runs into trouble for combinations of stocks, because a linear combination of lognormal returns does not have a lognormal distribution. Luckily, the true portfolio return distribution can be closely approximated by a generalized lognormal using the technique of matching moments, even when some weights are negative, as in a spread trade. This makes it easy to price European options on baskets of stocks or spreads. In this article, the authors show how to extend the same basic idea to construct a binomial tree for the portfolio return, which allows for efficient pricing of contracts with American exercise.
Overcoming drug resistance with alginate oligosaccharides able to 1 potentiate the action of selected antibiotics 2 3 4

29 The uncontrolled, often inappropriate use of antibiotics has resulted in the increasing 30 prevalence of antibiotic-resistant pathogens, with major cost implications for both US and 31 European healthcare systems. We describe the utilization of a low molecular weight 32 oligosaccharide nanomedicine (OligoG) based on the biopolymer alginate, which is able to 33 perturb multi-drug resistant (MDR) bacteria by modulating biofilm formation/persistence 34 and reducing resistance to antibiotic treatment; evident using conventional and robotic MIC 35 screening and microscopic analyses of biofilm structure. OligoG increased the efficacy of 36 conventional antibiotics (up to 512-fold) against important MDR pathogens including 37 Pseudomonas, Acinetobacter and Burkholderia spp. , appearing to be effective with several 38 classes of antibiotic (i.e. macrolides, β-lactams, tetracyclines). Using confocal laser 39 scanning microscopy (CLSM) and scanning electron microscopy (SEM) increasing 40 concentrations of alginate oligomer (2, 6 and 10%) were shown have a direct effect on the 41 quality of the biofilms produced and on the health of the cells within that biofilm. Biofilm 42 growth was visibly weakened in the presence of 10% OligoG as seen by decreased biomass 43 and increased intercellular spaces, with the bacterial cells themselves becoming distorted and 44 uneven due to apparently damaged cell membranes. This study demonstrates the feasibility 45 of reducing the tolerance of wound biofilms to antibiotics with the use of specific alginate 46
Binding of Shc to the NPXY Motif Is Mediated by Its N-terminal Domain (*)

Shc is an SH2-containing adapter protein that binds to and is phosphorylated by a large number of growth factor receptors. Phosphorylated Shc is able to interact with the Grb2-Sos complex which is responsible for mediating nucleotide exchange on Ras. We have shown previously that binding of Shc to the epidermal growth factor (EGF)-like receptor, c-ErbB-3, is through an NPXY motif (Prigent, S. A., and Gullick, W. J.(1994) EMBO J. 13, 2831−2841) shared by middle T antigen, TrkA, and EGF receptor. It has recently been reported that a region distinct from the SH2 domain is able to bind to tyrosine-phosphorylated proteins. In this paper we have used fusion proteins of various Shc domains to show that it is the N-terminal domain of Shc that is primarily responsible for binding EGF receptor and c-ErbB-3. Furthermore, by competition studies with synthetic phosphopeptides we have shown that this N-terminal domain binds to the previously identified NPXY motif.
Big data, big metadata and quantitative study of science: A workflow model for big scientometrics

Large cyberinfrastructure‐enabled data repositories generate massive amounts of metadata, enabling big data analytics to leverage on the intersection of technological and methodological advances in data science for the quantitative study of science. This paper introduces a definition of big metadata in the context of scientific data repositories and discusses the challenges in big metadata analytics due to the messiness, lack of structures suitable for analytics and heterogeneity in such big metadata. A methodological framework is proposed, which contains conceptual and computational workflows intercepting through collaborative documentation. The workflow‐based methodological framework promotes transparency and contributes to research reproducibility. The paper also describes the experience and lessons learned from a four‐year big metadata project involving all aspects of the workflow‐based methodologies. The methodological framework presented in this paper is a timely contribution to the field of scientometrics and the science of science and policy as the potential value of big metadata is drawing more attention from research and policy maker communities.
Using neural networks for estimation of aquifer dynamical behavior

The systems of water distribution from groundwater wells can be monitored using the changes observed on its dynamical behavior. In this paper, artificial neural networks are used to estimate the depth of the dynamical water level of groundwater wells in relation to water flow, operation time and rest time. Simulation results are presented to demonstrate the validity of the proposed approach. These results have shown that artificial neural networks can be effectively used for the identification and estimation of parameters related to systems of water distribution.
Towards an Integrative Model of User Acceptance of E-Commerce Website

This paper addresses why users accept the e-commerce website and how user’s two important beliefs PU and PEOU are affected by the website quality. In this study, we also introduce perceived playfulness as a new factor that reflects the user's intrinsic belief in user acceptance of e-commerce website. A survey of 356 users was conducted to test our model. Information quality of e-commerce website is an important factor in affecting the user’s two beliefs, but system quality and service quality have direct effect on PEOU. Additionally, in terms of predictive power, the model accounts for 57% of the variance in attitude and 60% of the variance in behavioral intention. Keywordsperceived playfulness, website quality, TPB, TAM
Clustering Web Visitors by Fast, Robust and Convergent Algorithms

The identification of categories of visitors to a Web-site is very useful towards improved Web designs and improved Web applications. However, the large volume involved in mining access-logs and visitation paths, and the uncertainty to fully identify the visitor demand efficient clustering algorithms that are also resistant to noise and outliers. Also, visitation paths are discrete, and dissimilarity between visitation paths involves sophisticated evaluation and results in attribute-vectors with large dimension. We provide randomized, iterative clustering algorithms for generic dissimilarity in paths. Our algorithms are robust because they use medians rather than means as estimators of location, and the resulting representative of a cluster is actually a path in the data set. We demonstrate mathematically that our algorithms converge and have subquadratic complexity. We also show experimentally that they are resistant to noise by recovering clusters from synthetic data generated by a mixture of distributions of paths in a graph. Our non-crisp method proposed generalizes approaches that allow a data item to have a degree of membership in a cluster.
A coplanar 94 GHz low-noise amplifier MMIC using 0.07 /spl mu/m metamorphic cascode HEMTs

A 94 GHz low-noise amplifier MMIC (LNA) has been developed, based on a coplanar technology utilizing 0.07 /spl mu/m depletion type metamorphic HEMTs (MHEMTs). The realized single stage cascode LNA achieved a small-signal gain of more than 12 dB and an average noise figure of 23 dB over the bandwidth from 80 to 100 GHz. With an indium content of 80% in the channel, a 2/spl times/30 /spl mu/m MHEMT device has shown a transit frequency (f/sub t/) of 290 GHz, an extrinsic transconductance of 1450 mS/mm and a maximum stable gain (MSG) of 11 dB at 94 GHz. Using two HEMTs connected in cascode configuration, the MSG could be increased to 22 dB. To stabilize the cascode device and to increase the bandwidth of the amplifier circuit, a resistive feedback was integrated into the HEMT in common-gate configuration. Coplanar topology in combination with cascode transistors resulted in a chip-size of only 1/spl times/1 mm/sup 2/.
Inhomogeneous electronic state near the insulator-to-metal transition in the correlated oxide VO2

We investigate the percolative insulator-to-metal transition IMT in films of the correlated material vanadium dioxide VO2. Scattering-type scanning near-field infrared microscopy and atomic force microscopy were used to explore the relationship between the nucleation of metallic regions and the topography in insulating VO2. We demonstrate that the IMT begins within 10 nm from grain boundaries and crevices by using mean curvature and statistical analysis. We also observe coexistence of insulating and metallic domains in a single crystalline grain that points to intrinsic inhomogeneity in VO2 due to competing electronic phases in the IMT regime.
Porphyrin-Mediated Cell Surface Heme Capture from Hemoglobin by Porphyromonas gingivalis

ABSTRACT The porphyrin requirements for growth recovery of Porphyromonas gingivalis in heme-depleted cultures are investigated. In addition to physiologically relevant sources of heme, growth recovery is stimulated by a number of noniron porphyrins. These data demonstrate that, as for Haemophilus influenzae, reliance on captured iron and on exogenous porphyrin is manifest as an absolute growth requirement for heme. A number of outer membrane proteins including some gingipains contain the hemoglobin receptor (HA2) domain. In cell surface extracts, polypeptides derived from HA2-containing proteins predominated in hemoglobin binding. The in vitro porphyrin-binding properties of a recombinant HA2 domain were investigated and found to be iron independent. Porphyrins that differ from protoporphyrin IX in only the vinyl aspect of the tetrapyrrole ring show comparable effects in competing with hemoglobin for HA2 and facilitate growth recovery. For some porphyrins which differ from protoporphyrin IX at both propionic acid side chains, the modification is detrimental in both these assays. Correlations of porphyrin competition and growth recovery imply that the HA2 domain acts as a high-affinity hemophore at the cell surface to capture porphyrin from hemoglobin. While some proteins involved with heme capture bind directly to the iron center, the HA2 domain of P. gingivalis recognizes heme by a mechanism that is solely porphyrin mediated.
The mechanism underlying lexical selection: Evidence from the picture–picture interference paradigm

In two experiments using the picture–picture and picture–word interference paradigms, we compared predictions from the swinging lexical network and the response exclusion hypothesis to determine whether the process of word selection is competitive. Further, we suggest that previous categorical effects in the picture–picture interference paradigm were due to stimuli confounds, thus readdressing the debate concerning categorical effects in the paradigm. Consistent with both hypotheses, in Experiment 1 we found faster picture naming times when distractor pictures were associatively related than when they were unrelated, explained as a result of a spread of activation at the conceptual level with little (swinging lexical network) or no (response exclusion hypothesis) contribution from lexical competition. In Experiment 2, we found a significant categorical interference effect in the picture–word interference paradigm, and this effect significantly decreased but was not facilitatory when distractors were pictures. We discuss how these results are consistent with the swinging lexical network and conclude that the process to select a word is a competitive one.
CNT-count Failure Characteristics of Carbon Nanotube FETs under Process Variations

Carbon Nanotube Field Effect Transistors (CNFET) are promising nano-scaled devices for implementing high performance, very dense and low power circuits. Chemical synthesis and lithography processes are exploited to fabricate CNFETs. Hence, in the presence of sub-wave length lithographic inaccuracies and chemical synthesis imperfections, CNT-count per CNFET deviates and may result in CNFET failure. In this paper, a parameterized model for CNT-count deviation under combined of lithographic and chemical imperfections is presented. The proposed CNT-count model takes advantage of a new CNT density metric which is easily and accurately extractable. We use the proposed model to quantify the impact of process variations on failure probability of CNFETs. Results indicate that the CNFET width variation plays a dominant role in defining the CNT-count failure of CNFETs in addition to CNT density variation.