Miracle-dz/UniFAR-FTUs huggingface dataset:
The control of inflammation via the phosphorylation and dephosphorylation of tristetraprolin: a tale of two phosphatases

Twenty years ago, the first description of a tristetraprolin (TTP) knockout mouse highlighted the fundamental role of TTP in the restraint of inflammation. Since then, work from several groups has generated a detailed picture of the expression and function of TTP. It is a sequence-specific RNA-binding protein that orchestrates the deadenylation and degradation of several mRNAs encoding inflammatory mediators. It is very extensively post-translationally modified, with more than 30 phosphorylations that are supported by at least two independent lines of evidence. The phosphorylation of two particular residues, serines 52 and 178 of mouse TTP (serines 60 and 186 of the human orthologue), has profound effects on the expression, function and localisation of TTP. Here, we discuss the control of TTP biology via its phosphorylation and dephosphorylation, with a particular focus on recent advances and on questions that remain unanswered.
Thermal expansion behaviour of coupling reagent treated carbon fibre reinforced polyamide composite

A comparison was made of the effects of coupling reagent surface modification and air oxidation on the improvement of the interfacial adhesion of carbon fibres in reinforced polyamide composites. Results showed that coupling reagent modification greatly strengthens the adhesion between the reinforcement and matrix and is superior to improvements produced by surface oxidation in air. The optimum interfacial adhesion was reached at 0·3 wt-% coupling reagent concentration. The thermal expansion behaviour of the carbon fibre reinforced polyamide composite also showed that coupling reagent modification improved the interfacial adhesion.
A Practical Vision Based Approach to Unencumbered Direct Spatial Manipulation in Virtual Worlds

We present a practical approach for developing interactive environments that allows humans to interact with large complex 3D models without them having to manually operate input devices. The system provides support for scene manipulation based on hand tracking and gesture recognition and for direct 3D interaction with the 3D models in the display space if a suitably registered 3D display is used. Being based on markerless tracking of a user’s two hands, the system does not require users to wear any input or output devices. 6DOF input is provided by using both hands simultaneously, making the tracker more robust since only tracking of position information is required. The effectiveness of the method is demonstrated with a simple application for model manipulation on a large stereo display, in which rendering constraints are met by employing state-of-the-art multiresolution techniques.
ILD preservation in the multichannel wiener filter for binaural hearing aid applications

This work presents a new method for noise reduction in binaural hearing aid applications that preserves the interaural level difference. A bounded symmetrical approximation of the logarithm is employed to estimate the interaural level difference, resulting in identical values for symmetrical (left/right) frontal angles. It proposes a new cost function to be used in association with the multichannel Wiener filter technique to provide a trade-off between noise reduction and distortion of the localization cues. Simulations of a binaural setup and comparisons with a previously developed technique show that the new method gives a signal to noise ratio improvement of up to 9.6 dB better than the baseline technique, for the same maximum-tolerated binaural-cue distortion.
Improved Resource Allocation Algorithm Based on Partial Solution Estimation for SC-FDMA Systems

Single carrier frequency division multiple access (SC-FDMA) has been adopted as the standard multiple access scheme for 3GPP LTE uplink. In comparison to orthogonal frequency division multiple access (OFDMA), the subcarriers assigned to each user are required to be consecutive in SC-FDMA localized scheme, which imposes more difficulties on resource allocation problem. Subject to this constraint, various optimization objectives, such as utility maximization and power minimization, have been studied for SC-FDMA resource allocation. In this paper, we focus on developing a general algorithm framework with near-optimal performance and polynomial-time complexity to maximize the total utility for SC-FDMA systems. The proposed algorithm is based on low-complexity estimation for the partial solution space. Compared with existing algorithms, simulation results show that our algorithm improves the system utility significantly and has less deviation to global optimum. In addition, the proposed algorithm framework allows a flexible trade-off between computational effort and solution performance by varying the complexity of estimation approaches.
Freeze-Thaw Enhancement of the Drainage and Consolidation of Fine-Grained Dredged Material in Confined Disposal Areas.

Abstract : Fine-grained dredged material obtained from disposal sites in the Great Lakes region was subjected to controlled freeze-thaw cycling in a special laboratory consolidometer. Volume changes and permeabilities were observed after full consolidation and freeze-thaw cycling for applied pressures in the range of 0.93 to 30.73 kPa. It was observed that as much as 20 percent or more volume reduction results when dredged material with liquid limits in the range of 60 to 90 percent is subjected to one cycle of freezing and thawing. The degree of overconsolidation by freezing and thawing appears to decrease with increasing amounts of coarse materials and with increasing plasticity. The vertical permeability of all materials examined was increased as much as two orders of magnitude, the greatest increase in permeability occurring for the fine-grained materials at the lowest stress levels. The application of the phenomenon of overconsolidation by freezing and thawing to disposal sites is discussed and site management procedures are suggested. The process appears to be particularly adaptable to regions of cold winters where material frost penetrations of more than 1 m can be obtained, but it can be applied to regions of more moderate winters such as in the Great Lakes region by sequentially depositing and freezing dredged material during the winter months. (Author)
A Genomic Map of Viroid RNA Motifs Critical for Replication and Systemic Trafficking[W]

RNA replication and systemic trafficking play significant roles in developmental regulation and host–pathogen interactions. Viroids are the simplest noncoding eukaryotic RNA pathogens and genetic units that are capable of autonomous replication and systemic trafficking and offer excellent models to investigate the role of RNA structures in these processes. Like other RNAs, the predicted secondary structure of a viroid RNA contains many loops and bulges flanked by double-stranded helices, the biological functions of which are mostly unknown. Using Potato spindle tuber viroid infection of Nicotiana benthamiana as the experimental system, we tested the hypothesis that these loops/bulges are functional motifs that regulate replication in single cells or trafficking in a plant. Through a genome-wide mutational analysis, we identified multiple loops/bulges essential or important for each of these biological processes. Our results led to a genomic map of viroid RNA motifs that mediate single-cell replication and systemic trafficking, respectively. This map provides a framework to enable high-throughput studies on the tertiary structures and functional mechanisms of RNA motifs that regulate viroid replication and trafficking. Our model and approach should also be valuable for comprehensive investigations of the replication and trafficking motifs in other RNAs.
An Adaptive-FocusingAlgorithm for a Microwave Planar Phased-Array Hyperthermia System

• We have experimentally investigated the use of adaptive-focusing techniques in the hyperthermia treatment of cancer. Gradient-search adaptive-focusing software developed at Lincoln Laboratory has been implemented on a commercial microwave hyperthermia planar phased-array antenna system at the University of California at San Francisco (UCSF). The system, manufactured by Labthermics Technologies, Inc., consists of 16 independent amplitude/phasecontrolled waveguide antenna elements operating at 915 MHz. In the experiments, conducted at UCSF, a method of steepest-ascent gradient-search feedback algorithm was used to control the hyperthermia array phase shifters and focus the transmitted radiation beam at a hypothetical tumor site in a muscle-equivalent sugar/saline liquid phantom. A feedback probe, embedded in the phantom, measured the resulting electric field (E-field) generated by the antenna array. The measured data indicate a significant increase in the focal-region field strength with a rapid convergence of the adaptive-focusing algorithm in 10 to 15 iterations. From the measurements, the maximum useful heating depth in thesugarlsaline phantom is estimated for the 915-MHz system at about 3 em.
American Option Pricing with Transaction Costs

In this paper we examine the problem of finding investors' reservation option prices and corresponding early exercise policies of American- style options in the market with proportional transaction costs using the utility based approach proposed by Davis and Zariphopoulou (1995). We present a model, where investors have a CARA utility, and derive some properties of reservation option prices. We discuss the numerical algorithm and propose a new formulation of the problem in terms of quasi-variational HJB inequalities. Based on our formulation, we suggest original discretization schemes for computing reservation prices of American-style option. The discretization schemes are then implemented for computing prices of American put and call options. We examine the effects on the reservation option prices and the corresponding early exercise policies of varying the investor's ARA and the level of transaction costs. We find that in the market with transaction costs the holder of an American-style option exercises this option earlier as compared to the case with no transaction costs. This phenomenon concerns both put and call options written on a non-dividend paying stock. The higher level the transaction costs is, or the higher risk avers the option holder is, the earlier an American option is exercised.
Pulse Pattern-Modulated Strategy for Harmonic Current Components Reduction in Three-Phase AC–DC Converters

Generated harmonic current as a consequence of employing power electronics converter is known as an important power quality issue in distribution networks. From industry point of view, complying with international standards is mandatory; however, cost and efficiency are two other important features, which need to be considered in order to be competitive in the market. Therefore, having a flexibility to meet various requirements imposed by the standard recommendations or costumer needs is at most desirable. This makes the generated harmonic current mitigation a challenging task especially with three-phase diode-bridge rectifier, which is still preferred in many power electronic systems. This paper addresses a novel current modulation strategy using a single-switch boost three-phase diode-bridge rectifier. The proposed method can selectively mitigate current harmonics, which makes it suitable for different applications. The obtained results at experimental and simulation levels verify and confirm the robustness of the proposed approach.
5G systems: The mmMAGIC project perspective on use cases and challenges between 6–100 GHz

mmMAGIC (Millimetre-Wave Based Mobile Radio Access Network for Fifth Generation Integrated Communications) is an EU funded 5G-PPP project, whose overall objective is to design and pre-develop a mobile radio access technology (RAT) operating in the 6-100 GHz range, capable of impacting standards and other relevant fora. The focus of the project is on extreme Mobile Broadband, which is expected to drive the 5G requirements for massive increase in capacity and data-rates. This paper elaborates on some 5G key research areas such as: identification of the most compelling use-cases and Key Performance Indicators (KPIs) for future 5G systems, advantages and challenges of millimeter-wave (mmWave) technologies, channel measurements and channel modeling, network architecture; and the design of a new mobile radio interface including multi-node and multi-antenna transceiver architecture.
Decreases of Metallothionein and Aminopeptidase N in Renal Cancer Tissues1

Abstract Good molecular markers for investigating the biochemical differences between renal cancer and surrounding tissues have not yet been developed. Sixteen kidney samples (clear cell RCC) were investigated to determine the differences in the protein components between renal cancer and surrounding tissues, using HPLC analysis. The metallothionein (MT) and zinc levels were consistently lower in renal cancer tissues compared with in surrounding tissues. The mean concentration of MT in normal tissues surrounding renal tumors was about 15 times higher than that in cancer tissues. An immunohistochemical study confirmed that the expression of MT in renal cancer tissues was lower than that in adjacent normal tissues. The activities of aminopeptidases (APs) were significantly decreased in renal cancer tissues compared with in adjacent normal tissues. An immunohistochemical study and Western blot analysis confirmed that the expression of AP-N in renal cancer tissues was also lower than in adjacent normal tissues. These results suggest that the immunohistochemical detection of MT and AP-N could provide useful information as a pathological diagnostic tool for classifying renal cancer and surrounding tissues.
Purification and characterization of an enzyme produced by Treponema denticola capable of hydrolyzing synthetic trypsin substrates

An enzyme from Treponema denticola that hydrolyzes a synthetic trypsin substrate, N-alpha-benzoyl-L-arginine-p-nitroanilide (BAPNA), was purified to near homogeneity, as judged by gel electrophoresis. The molecular weight of the enzyme was estimated to be ca. 69,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and ca. 50,000 by gel filtration on Sephadex G-100. The pH optimum for the hydrolysis of BAPNA was around 8.5. The enzyme was heat labile and irreversibly inactivated at low pH values. Enzyme activity was enhanced by Ca2+, Mg2+, and Ba2+ but inhibited by Mn2+, Hg2+, Co2+, and Zn2+. Metal chelators and sulfhydryl reagents had no effect on this activity. The enzyme was inhibited by certain protease inhibitors such as diisopropyl fluorophosphate, N-alpha-p-tosyl-L-lysine chloromethyl ketone, phenylmethylsulfonyl fluoride, L-1-tosylamide-2-phenylethylchloromethyl ketone, alpha-1-antitrypsin, and soybean trypsin inhibitor. The Km values for BAPNA and N-alpha-benzoyl-L-arginine ethyl ester were 0.05 and 0.12 mM, respectively, and the Vmax values were higher than those observed with trypsin. Although the purified enzyme hydrolyzed some low-molecular-weight synthetic trypsin substrates, it did not hydrolyze casein, hemoglobin, azocasein, azocoll, bovine serum albumin, or gelatin. Thus, this enzyme is probably not a protease but is capable of hydrolyzing ester, amide, and peptide bonds involving the carboxyl group of arginine and lysine.
Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete pipeline for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). We applied these methods to hematopoiesis, including a new single cell dataset in which transcription factors (TFs) involved in the earliest branchpoint of blood differentiation were individually up- and down-regulated. We could identify two unique sub-populations within a seemingly homogenous group of hematopoietic stem cells. In addition, we could predict regulatory mechanisms controlling the expression levels of eighteen key hematopoietic transcription factors throughout differentiation. Detailed information about gene regulatory mechanisms can therefore be obtained simply from high throughput single cell gene expression data, which should be widely applicable given the rapid expansion of single cell genomics.
Mesenchymal stem cell expression of stromal cell‐derived factor‐1β augments bone formation in a model of local regenerative therapy

Bone has the potential for spontaneous healing. However, this process often fails in patients with co‐morbidities requiring clinical intervention. Numerous studies have revealed that bone marrow‐derived mesenchymal stem/stromal cells (BMSCs) hold great potential for regenerative therapies. Common problems include poor cell engraftment, which can be addressed by irradiation prior to transplantation. Increasing evidence suggests that stromal cell‐derived factor‐1 (SDF‐1) is involved in bone formation. However, osteogenic contributions of the beta splice variant of SDF‐1 (SDF‐1β), which is highly expressed in bone, remain unclear. Using the tetracycline (Tet)‐regulatory system we have shown that SDF‐1β enhances BMSC osteogenic differentiation in vitro. Here we test the hypothesis that SDF‐1β augments bone formation in vivo in a model of local BMSC transplantation following irradiation. We found that SDF‐1β, expressed at high levels in Tet‐Off‐SDF‐1β BMSCs, augments the cell‐mediated therapeutic effects resulting in enhanced bone formation, as evidenced by ex vivo μCT and bone histomorphometry. The data demonstrate the specific contribution of SDF‐1β to BMSC‐mediated bone formation, and validate the feasibility of the Tet‐Off technology to regulate SDF‐1β expression in vivo. In conclusion, SDF‐1β provides potent synergistic effects supporting BMSC‐mediated bone formation and appears a suitable candidate for optimization of bone augmentation in translational protocols. Published 2014. This article has been contributed to by US Government employees and their work is in the public domain in the USA. J Orthop Res 33:174–184, 2015.
A Novel Chimeric Lysin Shows Superiority to Mupirocin for Skin Decolonization of Methicillin-Resistant and -Sensitive Staphylococcus aureus Strains

ABSTRACT Staphylococcus aureus is a major human pathogen responsible for a number of serious and sometimes fatal infections. One of its reservoirs on the human body is the skin, which is known to be a source of invasive infection. The potential for an engineered staphylococcus-specific phage lysin (ClyS) to be used for topical decolonization is presented. We formulated ClyS into an ointment and applied it to a mouse model of skin colonization/infection with S. aureus. Unlike the standard topical antibacterial agent mupirocin, ClyS eradicated a significantly greater number of methicillin-susceptible S. aureus (MSSA) and -resistant S. aureus (MRSA) bacteria: a 3-log reduction with ClyS as opposed to a 2-log reduction with mupirocin in our model. The use of ClyS also demonstrated a decreased potential for the development of resistance by MRSA and MSSA organisms compared to that from the use of mupirocin in vitro. Because antibodies may affect enzyme function, we tested antibodies developed after repeated ClyS exposure for their effect on ClyS killing ability. Our results showed no inhibition of ClyS activity at various antibody titers. These data demonstrate the potential of developing ClyS as a novel class of topical antimicrobial agents specific to staphylococcus.
Conversion: multi-version concurrency control for main memory segments

We present Conversion, a multi-version concurrency control system for main memory segments. Like the familiar Subversion version control system for files, Conversion provides isolation between processes that each operate on their own working copy. A process retrieves and merges any changes committed to the trunk by calling update(), and a call to commit() pushes any local changes to the trunk. Conversion operations are fast, starting at a few microseconds and growing linearly (by less than 1 μs) with the number of modified pages. This is achieved by leveraging virtual memory hardware, and efficient data structures for keeping track of which pages of memory were modified since the last update. Such extremely low-latency operations make Conversion well suited to a wide variety of concurrent applications. Below, in addition to a micro-benchmark and comparative evaluation, we retrofit Dthreads [28] with a Conversion-based memory model as a case study. This resulted in a speedup (up to 1.75x) for several benchmark programs and reduced the memory management code for Dthreads by 80%.
Editorial: Reward- and aversion-related processing in the brain: translational evidence for separate and shared circuits

The dynamic evaluation of experience is existentially essential. Assigning value to events and objects drives neural development and plasticity and impacts our changing perceptual interpretations of the world and future behaviors (Nelson et al., 2014). The affective foundation of behavior provides more than a mere phenomenological “coloring” of experience. In fact, affect may be an inseparable component of sensation and cognition instead of an oft-considered byproduct (Inzlicht et al., 2015), and translational neuroanatomical evidence suggests that the major brain areas and tracts involved appear largely conserved across species (Panksepp, 2011).
Greedy Step Averaging: A parameter-free stochastic optimization method

In this paper we present the greedy step averaging(GSA) method, a parameter-free stochastic optimization algorithm for a variety of machine learning problems. As a gradient-based optimization method, GSA makes use of the information from the minimizer of a single sample's loss function, and takes average strategy to calculate reasonable learning rate sequence. While most existing gradient-based algorithms introduce an increasing number of hyper parameters or try to make a trade-off between computational cost and convergence rate, GSA avoids the manual tuning of learning rate and brings in no more hyper parameters or extra cost. We perform exhaustive numerical experiments for logistic and softmax regression to compare our method with the other state of the art ones on 16 datasets. Results show that GSA is robust on various scenarios.