Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning, Nucleotide Sequence, and Heterologous Expression of the Biosynthetic Gene Cluster for R1128, a Non-steroidal Estrogen Receptor Antagonist

R1128 substances are anthraquinone natural products that were previously reported as non-steroidal estrogen receptor antagonists with in vitro and in vivopotency approaching that of tamoxifen. From a biosynthetic viewpoint, these polyketides possess structurally interesting features such as an unusual primer unit that are absent in the well studied anthracyclic and tetracyclic natural products. The entire R1128 gene cluster was cloned and expressed in Streptomyces lividans, a genetically well developed heterologous host. In addition to R1128C, a novel optically active natural product, designated HU235, was isolated. Nucleotide sequence analysis of the biosynthetic gene cluster revealed genes encoding two ketosynthases, a chain length factor, an acyl transferase, three acetyl-CoA carboxylase subunits, two cyclases, two oxygenases, an amidase, and remarkably, two acyl carrier proteins. Feeding studies indicate that the unusual 4-methylvaleryl side chain of R1128C is derived from valine. Together with the absence of a dedicated ketoreductase, dehydratase, or enoylreductase within the R1128 gene cluster, this suggests a functional link between fatty acid biosynthesis and R1128 biosynthesis in the engineered host. Specifically, we propose that the R1128 synthase recruits four subunits from the endogenous fatty acid synthase during the biosynthesis of this family of pharmacologically significant natural products.
The actions of leptin on survival and hydrogen peroxide toxicity in primary mixed glial cells of rat

Studies indicate that leptin is involved in not only energy expenditure and food intake, but also in protection against apoptosis, in inflammation and in stimulation of proliferation in many cell types. However, leptin treatment increases the oxidative stress in many cell culture studies. This contradiction evoked a question of whether leptin acts as an oxidant or antioxidant on glial cells. We investigated the effect of leptin on glial cell survival and hydrogen peroxide (H2O2)-induced toxicity in vitro. The survival rate of the cells was determined by using 3-(4,5-D-methylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, thyazolyl blue (MTT) method. The cells obtained from the whole brain of 1–3 day-old rat were treated with 1, 10, 100 and 1000 ng/mL leptin for 24 or 72 h. Either the pretreatment of leptin alone for 5 h or leptin combined simultaneously with H2O2 or well known antioxidant glutathione (GSH) were applied to the cells. Malondialdehyde (MDA) levels were measured in cell lysates to which leptin was added for 24 h. The 100 and 1000 ng/mL leptin treatment for 72 h increased the glial viability by 19% and 36%, respectively. The dose of H2O2 that killed 75% of the cells was determined as 100 µM. GSH at different doses was applied as a positive control to the cells and the dose of 500 µM completely eliminated toxic effect of 100 µM H2O2. Either the pretreatment of leptin alone for 5 h or leptin combined simultaneously with H2O2 could not eliminate H2O2-caused toxicity. Furthermore, respective leptin doses did not change the glia MDA level. We suggest that leptin can increase glia survival dose dependently, but can not eliminate H2O2-induced oxidation in primary mixed glial cell culture.
A well‐balanced Runge–Kutta discontinuous Galerkin method for the shallow‐water equations with flooding and drying

We build and analyze a Runge–Kutta discontinuous Galerkin method to approximate the one‐ and two‐dimensional shallow‐water equations. We introduce a flux modification technique to derive a well‐balanced scheme preserving steady states at rest with variable ground elevation and a slope modification technique to deal satisfactorily with flooding and drying. Numerical results illustrating the performance of the proposed scheme are presented. Copyright © 2007 John Wiley & Sons, Ltd.
Shading and Highlight Invariant Color Image Segmentation

A new color image segmentation algorithm is presented in this paper. This algorithm is invariant to highlights and shading. This is accomplished in two steps. First, the average pixel intensity is removed from each RGB coordinate. This transformation mitigates the effects of highlights. Next, the Mixture of Principal Components algorithm is used to perform the segmentation. The MPC is implicitly invariant to shading due to the inner vector product or vector angle being used as similarity measure. Since the new coordinate system contains negative numbers, it is necessary to modify the MPC algorithm since in its original form it does not distinguish between positive and negative color space coordinates. Results on artificial and real images illustrate the effectiveness of the method. Finally, the use of the total within-cluster variance is investigated as possible criterion for selecting the number of clusters for the new algorithm. Note: This report is an overview of the work published in [16] which was carried out while I was a Foreign Researcher in Prof. Tominaga’s lab at the Osaka Electro-Communications University on an IEEE NNC scholarship. PROBLEM STATEMENT In recent years, color constancy the perception of objects in the real world without illumination effects has been a major concern in the research community of image science and technology. Humans perceive object surfaces in a scene in spite of shading and highlight effects. Can machines do a similar feat?
Improving the Hybrid model MPI+Threads through Applications, Runtimes and Performance tools. (Amélioration du modèle hybride MPI+Threads à travers les applications, les supports d'exécution et outils d'analyse de performance)

To provide increasing computational power for numerical simulations, supercomputers evolved and arenow more and more complex to program. Indeed, after the appearance of shared memory systemsemerged architectures such as NUMA (Non Uniform Memory Access) systems, providing several levelsof parallelism. Another constraint, the decreasing amount of memory per compute core, has to bementioned. Therefore, parallel models such as Message Passing Interface (MPI) are no more sufficientto enable scalability of High Performance applications, and have to be coupled with another modeladapted to shared memory architectures. OpenMP, as a de facto standard, is a good candidate to bemixed with MPI. The principle is to use this model to augment legacy codes already parallelized withMPI. But hybridizing scientific codes is a complex task, bottlenecks exist and need to be identified. Thisthesis tackles these limitations and proposes different contributions following various aspects. Our firstcontribution reduces the overhead of the OpenMP layer by optimizing the creation and synchronizationof threads for MPI+OpenMP codes. On a second time, we target MPI collective operations. Our contributionconsists in proposing a technique to exploit idle cores in order to help the operation, with theexample of MPI Allreduce collective. We also introduce unified Collectives involving both MPI tasks andOpenMP threads. Finally, we focus on performance analysis of hybrid MPI+OpenMP codes, and ourlast contribution consists in the implementation of OpenMP Tools API (OMPT), an instrumentation tool,inside the OpenMP runtime of MPC framework. This tool allows us to instrument and profile OpenMPconstructs and allows the analysis of both runtime and application sides
Task Independent Privacy Preserving Data Mining on Medical Dataset

In this era of data digitization, data mining is essential for getting valuable information. However, privacy and security issues remain major barriers during this process. Since medical records are related to human subjects, privacy protection is taken more seriously than other data mining tasks. As required by the Health Insurance Portability and Accountability Act (HIPAA), it is necessary to protect the privacy of patients and ensure the security of the medical data. The privacy issues are handled by many algorithms and techniques in literature. But, always there exists a trade off between privacy and information. So, to preserve the accuracy of results and to reduce loss of information, task based privacy preserving techniques are developed. Our aim is to implement a task independent technique which preserves the information, privacy and utility of the data. Our algorithm is applied on the original data table to alter only the sensitive raw data before applying any mining methods. The experimental results prove that our simple technique yields excellent results as if worked on the original data set.
Disruption of Rpn4-Induced Proteasome Expression in Saccharomyces cerevisiae Reduces Cell Viability Under Stressed Conditions

The proteasome homeostasis in Saccharomyces cerevisiae is regulated by a negative feedback circuit in which the transcription activator Rpn4 upregulates the proteasome genes and is rapidly degraded by the assembled proteasome. Previous studies have shown that rpn4Δ cells are sensitive to a variety of stresses. However, the contribution of the loss of Rpn4-induced proteasome expression to the rpn4Δ phenotypes remains unclear because Rpn4 controls numerous genes other than the proteasome genes. Here we construct a yeast strain in which one of the essential proteasome genes, PRE1, is no longer induced by Rpn4. We show that the active proteasome level is lower in this strain than in the wild-type counterpart. Moreover, we demonstrate that loss of Rpn4-induced proteasome expression leads to cell-cycle delay in G2/M and sensitizes cells to various stresses. To our knowledge, this is the first report that explicitly reveals the physiological function of Rpn4-induced proteasome expression. This study also provides a tool for understanding the interactions between proteasome homeostasis and other cellular processes.
Performance Comparison of DC Link Voltage Controllers in Vector Controlled Boost Type PWM Converter for Wind Turbine System

This paper presents control algorithms to regulate the DC link voltage in a vector controlled boost type PWM converter with particular applications to a wind energy conversion system. The algorithms provide near- sinusoidal input currents and unity power factor and low output voltage ripple. Moreover, the designed PWM exhibits fast transient response to load variations, and is capable of regenerative operation. An experiment with the 7.5 kW converter is set up to investigate and compare the control performances of three designed DC link voltage controllers comprising PI-fuzzy, PI-fuzzy with measured load current feed-forward and PI-fuzzy with observed load current feed-forward.
Nail Drug Delivery System-A Novel Approaches For Drug Delivery System

Topical therapy is highly desirable in treating nail disorders due to its localized effects, which results in minimal adverse systemic events and possibly improved adherence. However, the effectiveness of topical therapies is limited by minimal drug permeability through the nail plate. Infections of foot and hand nails by fungi are a very common condition in millions of people. They account for about half of all nail disorders and are estimated to occur in over 10% of the population. Such infections may be difficult to treat, and currently prescribed oral antifungal medications may cause side effects ranging from skin rashes to liver damage. Other treatment modalities include the use of antifungal lacquers and topical medications. Topical trans-nail delivery of antifungal drugs is limited by several physicochemical and physiological factors. Use of chemical permeation enhancers has been a common approach for enhancing trans-nail delivery of drugs. The potential of physical permeation enhancement techniques has been found to be higher than the potential of chemical permeation enhancers in transdermal delivery of hydrophilic drugs and macromolecular therapeutic agents. However, application of physical permeation enhancement techniques has not been explored for trans-nail drug delivery. In the current work, iontophoresis was applied across human nail in vitro to assess its efficiency in enhancing drug delivery. This new therapy may reduce the need for hazardous systemic administration of oral antifungal drugs for nail infections. A novel ultrasound-mediated drug delivery system has been developed for treatment of a nail fungal disorder (onychomycosis) by improving delivery to the nail bed using ultrasound to increase the permeability of the nail. The slip-in device consists of ultrasound transducers and drug delivery compartments above each toenail. The device is connected to a computer, where a software interface allows users to select their preferred course of treatment. Keyword: Topical Trans-Nail Delivery, Human Nail, Antifungal Drugs, Iontophoresis.
A Word Embeddings Model for Sentence Similarity

Currently, word embeddings (Bengio et al, 2003; Mikolov et al, 2013) have had a major boom due to its performance in di(cid:27)erent Natural Language Processing tasks. This technique has overpassed many conventional methods in the literature. From the obtained embedding vectors, we can make a good grouping of words and surface elements. It is common to represent top-level elements such as sentences, using the idea of composition (Baroni et al, 2014) through vectors sum, vectors product or through de(cid:28)ning a linear operator representing the composition. Here, we propose the representation of sentences through a matrix containing the word embedding vectors of such sentence. However, this involves obtaining a distance between matrices. To solve this, we use a Frobenius inner product. We show that this sentence representation overtakes traditional composition methods.
Explorer Tracking and monitoring horses in the wild using wireless sensor networks

The Retuerta is one of the oldest breed of horses in Europe, which roams wild in the Donana National Park, Andalusia, Spain. Thirty-two of these horses were marked with wireless sensors to gather spatio-temporal data on their behaviour over a period of several months. This paper describes our experiences of tracking and monitoring these wild horses attached with body-worn sensors and operating in a harsh and challenging environment. Analysis of this data for the first two months has revealed rare insights into the horses’ social behaviour, such as the group dynamics (group sizes and memberships), dispersal and home ranges which are of interest to both animal ethologists and practitioners managing the ecology of their wild habitats. The paper introduces the Virtual Beacon Time Division Multiple Access (VB-TDMA) protocol for orchestrating the data collection, and describes the choices that were made for addressing the many technical challenges for an extended deployment, such as in the design of the sensor platform, wireless data collection and battery lifetime issues. Our experiences point to the virtue of simplicity in design of wireless sensor networks to support core functionalities for achieving good average case performances.
Going back to basics in design science: from the information technology artifact to the information systems artifact

The concept of the ‘information technology (IT) artifact’ plays a central role in the information systems (IS) research community's discourse on design science. We pose the alternative concept of the ‘IS artifact’, unpacking what has been called the IT artifact into a separate ‘information artifact’, ‘technology artifact’ and ‘social artifact’. Technology artifacts (such as hardware and software), information artifacts (such as a message) and social artifacts (such as a charitable act) are different kinds of artifacts that together interact in order to form the IS artifact. We illustrate the knowledge value of the IS artifact concept with material from three cases. The result is to restore the idea that the study of design in IS needs to attend to the design of the entire IS artifact, not just the IT artifact. This result encourages an expansion in the use of design science research methodology to study broader kinds of artifacts.
A pair-wise key establishment scheme without predistributing keys for ad-hoc networks

This paper deals with a pair-wise key establishment scheme without pre-distributing keys for ad-hoc networks. The scheme is based on the Diffie-Hellman key exchange protocol. It makes use of the one-time password to prevent a falsification of Diffie-Hellman values. Additionally, it forces each node to prove its long-term secret key ownership to provide mutual authentication. Security analyses prove that it is secure against various attacks. Also, simulation results show that it significantly reduces the number of messages to be exchanged over the probabilistic key pre-distribution scheme.
Sildenafil versus Endothelin Receptor Antagonist for Pulmonary Hypertension (SERAPH) study.

RATIONALE Phosphodiesterase type 5 (PDE5) inhibition has been proposed for the treatment for pulmonary arterial hypertension (PAH). OBJECTIVE This study compared adding sildenafil, a PDE5 inhibitor, to conventional treatment with the current practice of adding bosentan, an endothelin receptor antagonist. METHODS Twenty-six patients with PAH, idiopathic or associated with connective tissue disease, World Health Organization (WHO) functional class III, were randomized in a double-blind fashion to receive sildenafil (50 mg twice daily for 4 weeks, then 50 mg three times daily) or bosentan (62.5 mg twice daily for 4 weeks, then 125 mg twice daily) over 16 weeks. MEASUREMENTS Changes in right ventricular (RV) mass (using cardiovascular magnetic resonance), 6-minute walk distance, cardiac function, brain natriuretic peptide, and Borg dyspnea index. MAIN RESULTS When analyzed by intention to treat, there were no significant differences between the two treatment groups. One patient on sildenafil died suddenly. Patients on sildenafil who completed the protocol showed significant changes from baseline, namely, reductions in RV mass (-8.8 g; 95% confidence interval [CI], -2, -16; n = 13, p = 0.015) and plasma brain natriuretic peptide levels (-19.4 fmol x ml(-1); 95% CI, -5, -34; p = 0.014) and improvements in 6-minute walk distance (114 m; 95% CI, 67, 160; p = 0.0002), cardiac index (0.3 L x min(-1) x m(-2); 95% CI, 0.1, 0.4; p = 0.008), and systolic left ventricular eccentricity index (-0.2; 95% CI, -0.02, -0.37; p = 0.031). Bosentan improved 6-minute walk distance (59 m; 95% CI, 29, 89; n = 12, p = 0.001) and cardiac index (0.3; 95% CI, 0.1, 0.4; p = 0.008). CONCLUSIONS Sildenafil added to conventional treatment reduces RV mass and improves cardiac function and exercise capacity in patients with PAH, WHO functional class III. Safety monitoring is important until more experience is obtained.
Weakly-supervised word learning is improved by an active online algorithm

When infants learn words, they do not generally occur in isolation but as parts of continuous utterances and with several possible related meanings. Details of the efficient learning techniques of infants remain unknown. In this paper we introduce a dynamic concept matrix (DCM) algorithm that learns acoustic models for a set of keywords from given pairs of continuous utterances and related keyword labels. DCM is an incremental, active online algorithm. Specifically, each training utterance is first recognized with the current word models, and the recognition result is used to guide training further. In low-noise conditions DCM shows significant improvement in convergence rate and final recognition scores to an earlier passive CM model on TIDIGITS and CAREGIVER UK Y2 datasets. The results suggest that in ambiguous learning situations it may be beneficial for the learner to observe the learning situation, make hard decisions if some known words/objects were recognized and update the models based on the decisions.
Feedback Power Control with Bit Error Outage Probability QoS Measure on the Rayleigh Fading Channel

We propose to use the probability of instantaneous bit error outage (IBEO) as a new performance measure in the design of an actual feedback power control system. It is defined as the probability that the instantaneous bit error probability (IBEP) exceeds an IBEP threshold. We propose the IBEO-based power control law where the transmitted power is adjusted according to the variations of the channel such that the IBEO probability is kept within some quality of service (QoS)-specified threshold. It ensures that in the long term, no more than a certain fraction of received bits would have IBEP exceeding some IBEP threshold. Therefore, the instantaneous QoS is guaranteed. Based on a practical system model with channel estimation and prediction, we develop the traditional average bit error probability (ABEP)-based power control law and the new IBEO-based power control law. For both laws, we derive explicit ABEP and IBEO probability results. The IBEO-based law shows a remarkable gain over the ABEP-based law in terms of IBEO probability, and sacrifices only a little in the ABEP performance.
Interactive Time-Dependent Particle Tracing Using Tetrahedral Decomposition

Streak lines and particle traces are effective visualization techniques for studying unsteady fluid flows. For real time applications, accuracy is often sacrificed to achieve interactive frame rates. Physical space particle tracing algorithms produce the most accurate results although they are usually too expensive for interactive applications. An efficient physical space algorithm is presented which was developed for interactive investigation and visualization of large, unsteady, aeronautical simulations. Performance has been increased by applying tetrahedral decomposition to speed up point location and velocity interpolation in curvilinear grids. Preliminary results from batch computations showed that this approach was up to six times faster than the most common algorithm which uses the Newton-Raphson method and trilinear interpolation. Results presented show that the tetrahedral approach also permits interactive computation and visualization of unsteady particle traces. Statistics are given for frame rates and computation times on single and multiprocessors. The benefits of interactive feature detection in unsteady flows are also demonstrated.