Miracle-dz/UniFAR-FTUs huggingface dataset:
Interchain disulfide bonds and subunit organization in human serum cholinesterase.

Highly purified “usual” human serum cholinesterase was studied. The enzyme is a tetramer with a molecular weight of approximately 340,000. Its four subunits appear to be identical. On 1% sodium dodecyl sulfate (SDS) gel electrophoresis the enzyme had a molecular weight of about 180,000 when dissolved in 1% SDS, but it had a molecular weight of about 90,000 when dissolved in 1% SDS and 40 mM dithiothreitol. This was evidence that the subunits were arranged as a dimer of dimers ((cw)&, with each (a)~ dimer composed of two identical subunits joined by interchain disulfide bonds. Purified “atypical” cholinesterase had the same dimer of dimers structure and the same molecular weight on SDS-gel electrophoresis as usual cholinesterase. Additional structural experiments were conducted with purified usual choline&erase. The number of interchain disulfide bonds was quantitated by selectively reducing these bonds in the absence of a denaturant, followed by alkylation with [l-‘4C]iodoacetate. One SH per subunit was alkylated. As the enzyme contains no free SH groups, the alkylated residues must previously have been components of disulfide bonds. It was shown that the alkylated -SH groups arose from interchain disulfide bonds, for on SDS-gel electrophoresis of the alkylated enzyme, the labeled product all migrated with the subunit molecular weight of 90,000. It was concluded that each dimer contained only one interchain disulfide bond between two subunits. After reduction and alkylation of the interchain disulfide bonds, the enzyme was still a tetramer and was fully active. Therefore, it was concluded that the interchain disulfides were not necessary for either the tetramerit structure or for activity, and that the four subunits were held together by noncovalent bonds. The interchain disulfide bonds stabilized the enzyme as shown by measurements of rates of heat inactivation. Native enzyme had a half-life of 54 min at 55”C, whereas enzyme that had been selectively reduced and [14C]carboxymethylated, had a half-life of 16 min at 55°C. The interchain disulfide bonds were easily reduced and alkylated, suggesting that these bonds are located near the surface of the molecule. In addition to the single interchain disulfide bond, each subunit contains several (three to five) pairs of intrachain disulfide bonds.
Intelligent Memory: An Architecture for Lock-Free Synchronization (Special Issue on Parallel and Distributed Supercomputing)

This paper presents intelligent memory, a new memory architecture capable of providing e cient lock-free synchronization. In the intelligent memory, a sequence of operations on a shared object associated with that memory module can be processed without any intervention so that an environment for the synchronization can be provided by executing a critical section itself in that memory module. For this, we present a memory architecture for intelligent memory having minimal instruction set and develop a programming model, called Critical Section Procedure (CSP), which consists of a shared data structure and operations on it. Intelligent memory is intended to eliminate waste of processing time such as busy waiting in spin lock and retry due to process contention in existing lock-free synchronization schemes. Simulation results show that intelligent memory provides better throughput compared with a spin lock and the existing lock-free synchronization.
Blind Color Decomposition of Histological Images

Cancer diagnosis is based on visual examination under a microscope of tissue sections from biopsies. But whereas pathologists rely on tissue stains to identify morphological features, automated tissue recognition using color is fraught with problems that stem from image intensity variations due to variations in tissue preparation, variations in spectral signatures of the stained tissue, spectral overlap and spatial aliasing in acquisition, and noise at image acquisition. We present a blind method for color decomposition of histological images. The method decouples intensity from color information and bases the decomposition only on the tissue absorption characteristics of each stain. By modeling the charge-coupled device sensor noise, we improve the method accuracy. We extend current linear decomposition methods to include stained tissues where one spectral signature cannot be separated from all combinations of the other tissues' spectral signatures. We demonstrate both qualitatively and quantitatively that our method results in more accurate decompositions than methods based on non-negative matrix factorization and independent component analysis. The result is one density map for each stained tissue type that classifies portions of pixels into the correct stained tissue allowing accurate identification of morphological features that may be linked to cancer.
Numerical prediction of laminar nanofluid flow in rectangular microchannel

Numerical simulation of laminar nanofluid flow in Three-dimensional (3D) straight rectangular microchannel heat sink is carried out. In this study the behavior and effect of using pure water and Fe3O4-H2O as working fluids in the microchannel are examined. Fe3O4-H2O with volume fraction range of 0.4% - 0.8% are used in this simulation to evaluate the cooling performance of microchannel heat sink. Fluent, a Computational Fluid Dynamic (CFD) is used as the solver of simulation. A rectangular microchannel with hydraulic diameter of 86 µm and length of 10mm under the boundary condition of constant heat flux and uniform inlet velocity is set on this analysis. The Results of present work show that using Fe3O4-H2O as coolant resulted in to higher efficiency of heat transfer in microchannel heat sink in comparison to Pure water. However, using Fe3O4-H2O with 0.8% volume fraction provide a high heat transfer enhancement of 30% as compared to 0.4% and 0.6% volume fractions of the same Fe3O4-H2O. Numerical results show that increasing the thermal conductivity of working fluid can enhanced heat transfer. Therefore, it is equally important to note that the presence of nanoparticles could enhance the cooling of MCHS. Meanwhile, higher Nusselt number is found as fluid enters the channel inlet. This could be anticipated as a result of the development of thermal entry region at the channel and the values of Nusselt number tend to stabilize after fully develop region has been achieved
Effects of exercise training on breast cancer metastasis in a rat model

Exercise training is thought to play a protective role against cancer development and metastasis, either by reducing hormonal stimulation of hormone‐dependent cancers or by reducing the permeability of vascular walls towards invading metastatic cells. The purpose of this work was to evaluate the role of long‐term exercise training in the development and metastasis of breast cancer, in an immune‐competent 1‐methyl‐1‐nitrosourea (MNU) induced rat model. A single MNU dose was administered to Sprague‐Dawley rats at 50 days of age and the rats were subjected to exercise training on a treadmill at 20 m/min, 60 min/day, 5 days/week for 35 weeks. Exercised animals developed slightly less (2.30 ± 1.42) tumours per animal than sedentary animals (2.55 ± 1.44) and did not develop any metastasis, while two pulmonary metastases were observed in the sedentary group. All primary neoplasms and their metastases were positive for oestrogen (ER) α and progesterone (PR) receptors, indicating high hormonal sensitivity. Interestingly, exercise training increased circulating oestrogen levels, thus suggesting that the mechanism might involve either or both of a protective hormone‐independent effect and modulation of tumoural vascularization.
Magnesium-based biodegradable materials : from surface functionalization to cellular evaluation

Magnesium (Mg) alloys are a new generation of biodegradable materials with good osseointegration and elastic modulus similar to that of human bone. These properties make them attractive materials to produce biodegradable implants for bone repairing applications that require temporary support. However, Mg alloys degrade rapidly in the in vivo environment making necessary to control their corrosion rate to accompany the tissue healing processes. Several approaches have been proposed for reducing corrosion rate and improving biocompatibility of Mg alloys. The most used ones are conversion films and surface coatings. This project proposes a synergistic approach that combines both decreased corrosion rate and improved biocompatibility of Mg alloys: we developed novel bi-layered coatings to functionalize the surface of AZ31 and ZE41 Mg alloys for bone repair applications. First, a bottom silane-TiO2 coating was formulated and deposited on both alloys by the dip-coating technique. The silane-based coating was effective in slowing down the corrosion rate of the substrates in simulated body fluid (SBF) and in Dulbecco’s Modified Eagle’s Medium (DMEM). Secondly, top layers of type I collagen and/or chitosan were developed. Cell in vitro tests, with fibroblasts and osteoblasts, revealed that the biopolymers enhanced the biological response of the silane-TiO2 coating. Furthermore, the findings showed that there is a combined effect of the bi-layered coatings and the nature of the alloys on their final corrosion response and on the fate of the cells. In the same way, this work contributes to elucidating corrosion processes of Mg alloys in organic solutions in the long-term.
THERMODYNAMIC PROPERTIES OF A QUANTUM GROUP BOSON GAS GLp,q(2)

An approach is proposed enabling to effectively describe the behaviour of a bosonic system. The approach uses the quantum group GLp,q(2) formalism. In effect, considering a bosonic Hamiltonian in terms of the GLp,q(2) generators, it is shown that its thermodynamic properties are connected to deformation parameters p and q. For instance, the average number of particles and the pressure have been computed. If p is fixed to be the same value for q, our approach coincides perfectly with some results developed recently in this subject. The ordinary results, of the present system, can be found when we take the limit p = q = 1.
Adeno-associated virus type 2 as an oncogenic virus in human hepatocellular carcinoma

ABSTRACT Adeno-associated virus type 2 (AAV2) is a defective DNA virus that was previously considered to be non-pathogenic. We identified somatic AAV2 integration in a subset of 11 hepatocellular carcinomas (HCC) that mainly developed in normal liver without known etiology through recurrent insertional mutagenesis in cancer driver genes such as telomerase reverse transcriptase (TERT), cyclin A2 (CCNA2), cyclin E1 (CCNE1), tumor necrosis factor (ligand) superfamily, member 10 (TNFSF10), and lysine (K)-specific methyltransferase 2B (KMT2B).
Bar of Soap

I can’t imagine a bar of soap singing opera, but now I’m imagining daytime television about the soap’s lament—lavender professing his love to lemon, lemon caught cheating by pine, all while exaggerating face for imaginary nosebleed seats. Cover Page Footnote "Bar of Soap" was originally published at Booth. This article is available in Booth: http://digitalcommons.butler. edu/booth/vol8/iss8/4 September 23, 2016 Bar of Soap by Rachel Janis I can’t imagine a bar of soap singing opera, but now I’m imagining daytime television about the soap’s lament—lavender professing his love to lemon, lemon caught cheating by pine, all while exaggerating face for imaginary nosebleed seats. Then again, in this world, Kleenex has become recognized as a word deserving a capital K, leaving tissue behind as the thing we remove from gifts to pack away in the basement closet till we again need something to articulate full. When I tell my scientist brother this, he says, thank god for that, thank god for the organs we pack away for later. I don’t know why I’m suddenly crying, suddenly in need of Kleenex when imagining an alternate universe where the tumor in his head wins, where the portions of brain left over skip the icebox, tossed in toxic waste: a process everything like an employer separating resumes and nothing like an employer separating resumes, and suddenly the factoids my brother sang by the hour are gone: I can’t, for the life of him, gather them. Was it the chicken or the egg, was it Freud or Adler who said we roadtrip toward death, how many times can our blood vessels, unraveled, bag the Earth, and how fast can a sneeze tie its own noose? This all connects, I promise. My scientist brother is still here, our great aunt has been buying him bars of soap every holiday season, and he will smell like lavender and rosemary during Christmas dinner this year. He will ask me in between salad and meat did I know that the average American spends five years of her life waiting in line? Try making a poem speak that. 1 Janis: Bar of Soap Published by Digital Commons @ Butler University, 2016 Rachel Janis holds a BA from Knox College and lives above a coffee shop in Galesburg, Illinois. This is her first publication. 2 Booth, Vol. 8 [2016], Iss. 8, Art. 4 http://digitalcommons.butler. edu/booth/vol8/iss8/4
Systematic Analysis of Cis-Elements in Unstable mRNAs Demonstrates that CUGBP1 Is a Key Regulator of mRNA Decay in Muscle Cells

Background Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific. Principal Findings We have established the rates of decay for over 7000 transcripts expressed in mouse C2C12 myoblasts. We found that GU-rich (GRE) and AU-rich (ARE) elements are over-represented in the 3′UTRs of short-lived mRNAs and that these mRNAs tend to encode factors involved in cell cycle and transcription regulation. Stabilizing elements were also identified. By comparing mRNA decay rates in C2C12 cells with those previously measured for pluripotent and differentiating embryonic stem (ES) cells, we identified several groups of transcripts that exhibit cell-type specific decay rates. Further, whereas in C2C12 cells the impact of GREs on mRNA decay appears to be greater than that of AREs, AREs are more significant in ES cells, supporting the idea that cis elements make a cell-specific contribution to mRNA stability. GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. We therefore utilized RNA immunoprecipitation followed by microarray (RIP-Chip) to identify CUGBP1-associated transcripts. These mRNAs also showed dramatic enrichment of GREs in their 3′UTRs and encode proteins linked with cell cycle, and intracellular transport. Interestingly several CUGBP1 substrate mRNAs, including those encoding the myogenic transcription factors Myod1 and Myog, are also bound by the stabilizing factor HuR in C2C12 cells. Finally, we show that several CUGBP1-associated mRNAs containing 3′UTR GREs, including Myod1, are stabilized in cells depleted of CUGBP1, consistent with the role of CUGBP1 as a destabilizing factor. Conclusions Taken together, our results systematically establish cis-acting determinants of mRNA decay rates in C2C12 myoblast cells and demonstrate that CUGBP1 associates with GREs to regulate decay of a wide range of mRNAs including several that are critical for muscle development.
Multitask Learning : an application to Incremental Face Recognition

Usually face classification applications suffer from two important problems: the number of training samples from each class is reduced, and the final system usually must be extended to incorporate new people to recognize. In this paper we introduce a face recognition method that extends a previous boosting-based classifier adding new classes and avoiding the need of retraining the system each time a new person joins the system. The classifier is trained using the multitask learning principle and multiple verification tasks are trained together sharing the same feature space. The new classes are added taking advantage of the previous learned structure, being the addition of new classes not computationally demanding. Our experiments with two different data sets show that the performance does not decrease drastically even when the number of classes of the base problem is multiplied by a factor of 8.
Comparison of two interferon-γ release assays and tuberculin skin test for detecting latent tuberculosis in patients with immune-mediated inflammatory diseases

Biological agents interfering with proinflammatory tumour necrosis factor α (TNFα) signalling have become an established tool in the treatment of rheumatoid arthritis and other chronic inflammatory conditions. Their use is associated with an increased risk for some infections including the reactivation of latent tuberculosis infection (LTBI). 1 Consequently, screening for LTBI prior to onset of anti-TNFα therapy is recommended. Interferon γ release assays (IGRAs) are novel diagnostic tools for the diagnosis of LTBI and show a high specificity compared with the tuberculin skin test (TST). 2 However, optimal screening procedures are still a matter of debate.1 Furthermore, questions remain with regard to the performance of IGRAs in patients receiving immunosuppressive therapy and the comparative performance of the two commercially available IGRAs.2 To address these questions, 90 successive patients from the outpatient department of rheumatology (representing an LTBI low prevalence patient group) at the University Hospital of Wurzburg, Germany were prospectively screened for LTBI using TST, TSPOT.TB (TSPOT; Oxford Immunotec, Abingdon, Oxfordshire, UK) and Quantiferon Gold (QFT; Cellestis Europe, Darmstadt, Germany) before initiation of anti-TNF treatment). Underlying disease entities included ankylosing spondylitis (n=18 patients), rheumatoid arthritis (n=51), psoriatic arthritis (n=10) and other autoimmune diseases (n=11). Nineteen patients were receiving a steroid regimen of ≥7.5 mg prednisone equivalent and …
The Role of Dispute Settlement Procedures in International Trade Agreements

Although disputes are typically treated as synonymous with concerns about enforcement in economic models of trade agreements, in reality most WTO disputes seem to concern the interpretation of vague provisions, or instances where the agreement is silent. And some have suggested that the WTO's Dispute Settlement Body (DSB) could usefully grant exceptions to rigid contractual obligations. These activist DSB roles could help "complete" an incomplete contract. But how activist should the DSB be? Should DSB rulings set precedent? We address these questions by characterizing the optimal choice of contract form and DSB mandate under various contracting conditions. JEL Codes: D02, D78, D86, F13, K12, K33. Copyright 2011, Oxford University Press.
Multicarrier Interleaved PWM Strategies for a Five-Level NPC Inverter Using a Three-Phase Coupled Inductor

Multicarrier interleaved pulsewidth modulation (PWM) techniques are presented for a five-level neutral point clamped inverter using a three-phase coupled inductor. The inverter operation is demonstrated using a simple multicarrier interleaved PWM algorithm. Since both the inverter and inductor power losses are closely linked to the magnitude of the inductor current ripple, improved multilevel interleaved PWM techniques are presented based upon the concept of interchangeability of switching states in each phase. The proposed PWM techniques, which are easier to implement when compared to multilevel space-vector PWM techniques, also exploit the use of switching states with a high-effective winding inductance to minimize the inductor current ripple. Simulation results are presented to illustrate the improvements obtained in the inverter waveforms and their harmonic spectrum. Experimental results demonstrate how the inductor current ripple and the related power losses are significantly reduced using the proposed PWM scheme.
The effects of Doppler spreads in OFDM(A) mobile radio systems

We analyze the effects of Doppler spread in mobile channels on orthogonal frequency division multiplex (OFDM) systems. This is important, since channel variations during one OFDM symbol cause inter sub-carrier interference (ICI) in OFDM systems, which degrades the performance, since ICI can be seen as additional near-Gaussian noise. The analysis is outlined, and closed-form results given for numerous important practical Doppler spread encountered in mobile channels. We also show that for the case of asymmetrical Doppler spreads, the frequency correction of the receiver can be adjusted so as to minimize the ICI. To extend our work to OFDM(A) mobile radio systems in the uplink case where many users' contributions to the ICI overlap, we have introduced the concept of an equivalent single-user which causes the total ICI, in order to use the same analytical framework. For some channel examples, we simulated the Doppler spread of this equivalent user. Simulation results confirm our analysis and show the importance of the analytical tool to perform realistic system analysis without having to resort to time consuming time-domain simulations.
Competitive or noncompetitive, that's the question: research toward histone deacetylase inhibitors

Histone deacetylase (HDAC) catalyze deacetylation of acetylated lysine residues on histones and a growing number of nonhistone proteins including many transcription factors, playing an important role in the upstream control of gene transcription, cell cycle progression, and apoptosis. It has been wildly recognized that HDACs are promising targets for cancer therapy. At least 10 HDAC inhibitors are currently in clinical evaluation. However, none of them is practically isoform selective. More and more evidence suggests that acetylation modification occurring in ∼85% of eukaryotic proteins should be a general mechanism for altering protein structures or protein-protein interactions. Unselectively inhibiting the deacetylation activity of HDACs and the consequent modulation of the acetylation status of so many substrates might have multiple mechanisms of action in vivo, resulting in both therapeutic responses and unanticipated side effects. Lack of selectivity for the existing HDAC inhibitors is somewhat logical for the highly conserved residues in the catalytic site and the malleable structure in the rim of the active site of HDAC enzymes. For further advancements in the development of HDAC inhibitors, clues for selectivity will have to be considered. [Mol Cancer Ther 2008;7(5):1007–12]