Miracle-dz/UniFAR-FTUs huggingface dataset:
The Yeast Translation Release Factors Mrf1p and Sup45p (eRF1) Are Methylated, Respectively, by the Methyltransferases Mtq1p and Mtq2p*

The translation release factors (RFs) RF1 and RF2 of Escherichia coli are methylated at the N5 -glutamine of the GGQ motif by PrmC methyltransferase. This motif is conserved in organisms from bacteria to higher eukaryotes. The Saccharomyces cerevisiae RFs, mitochondrial Mrf1p and cytoplasmic Sup45p (eRF1), have sequence similarities to the bacterial RFs, including the potential site of glutamine methylation in the GGQ motif. A computational analysis revealed two yeast proteins, Mtq1p and Mtq2p, that have strong sequence similarity to PrmC. Mass spectrometric analysis demonstrated that Mtq1p and Mtq2p methylate Mrf1p and Sup45p, respectively, in vivo. A tryptic peptide of Mrf1p, GGQHVNTTDSAVR, containing the GGQ motif was found to be ∼50% methylated at the glutamine residue in the normal strain but completely unmodified in the peptide from mtq1-Δ. Moreover, Mtq1p methyltransferase activity was observed in an in vitro assay. In similar experiments, it was determined that Mtq2p methylates Sup45p. The Sup45p methylation by Mtq2p was recently confirmed independently (Heurgue-Hamard, V., Champ, S., Mora, L., Merkulova-Rainon, T., Kisselev, L. L., and Buckingham, R. H. (2005) J. Biol. Chem. 280, 2439–2445). Analysis of the deletion mutants showed that although mtq1-Δ had only moderate growth defects on nonfermentable carbon sources, the mtq2-Δ had multiple phenotypes, including cold sensitivity and sensitivity to translation fidelity antibiotics paromomycin and geneticin, to high salt and calcium concentrations, to polymyxin B, and to caffeine. Also, the mitochondrial mit– mutation, cox2-V25, containing a premature stop mutation, was suppressed by mtq1-Δ. Most interestingly, the mtq2-Δ was significantly more resistant to the anti-microtubule drugs thiabendazole and benomyl, suggesting that Mtq2p may also methylate certain microtubule-related proteins.
Regulation of Osteoblast-Like Cell Behaviors on Hydroxyapatite by Electrical Polarization

The osteoblast adhesion to the substrates are recognized to play a fundamental role in osteoconduction process. The purpose of this study was to evaluate the in vitro behavior of osteoblasts cultured on polarized hydroxyapatite (HA), having the enhanced osteobonding abilities. Osteoblast-like cells were seeded onto the polarized HA and investigated the adhesion and motility. The polarization had no effects on the percentage of the number of the spreaded cells against all the adhered cells, but had significant effects on the elongation of adhered cells from fluorescent observation and on the cell motility showed by the wound healing assay. The charges induced on the HA surface accelerated the cytoskeleton reorganization of the adhered cells cultured on HA specimens. The acceleration was emerged as the cells shape, actin filament pattern such as stress fiber formation, and the prolongation of the cell movement distances.
Polybrominated Diphenyl Ethers Induce Developmental Neurotoxicity in a Human in Vitro Model: Evidence for Endocrine Disruption

Background Polybrominated diphenyl ethers (PBDEs) are persistent and bioaccumulative flame retardants, which are found in rising concentrations in human tissues. They are of concern for human health because animal studies have shown that they possess the potential to be developmentally neurotoxic. Objective Because there is little knowledge of the effects of PBDEs on human brain cells, we investigated their toxic potential for human neural development in vitro. Moreover, we studied the involvement of thyroid hormone (TH) disruption in the effects caused by PBDEs. Methods We used the two PBDE congeners BDE-47 and BDE-99 (0.1–10 μM), which are most prominent in human tissues. As a model of neural development, we employed primary fetal human neural progenitor cells (hNPCs), which are cultured as neurospheres and mimic basic processes of brain development in vitro: proliferation, migration, and differentiation. Results PBDEs do not disturb hNPC proliferation but decrease migration distance of hNPCs. Moreover, they cause a reduction of differentiation into neurons and oligodendrocytes. Simultaneous exposure with the TH receptor (THR) agonist triiodothyronine rescues these effects on migration and differentiation, whereas the THR antagonist NH-3 does not exert an additive effect. Conclusion PBDEs disturb development of hNPCs in vitro via endocrine disruption of cellular TH signaling at concentrations that might be of relevance for human exposure.
Pestivirus Internal Ribosome Entry Site (IRES) Structure and Function: Elements in the 5′ Untranslated Region Important for IRES Function

ABSTRACT The importance of certain structural features of the 5′ untranslated region of classical swine fever virus (CSFV) RNA for the function of the internal ribosome entry site (IRES) was investigated by mutagenesis followed by in vitro transcription and translation. Deletions made from the 5′ end of the CSFV genome sequence showed that the IRES boundary was close to nucleotide 65: thus, the IRES includes the whole of domain II but no sequences upstream of this domain. Deletions which invaded domain II even to a small extent reduced activity to about 20% that of the full-length structure, and this 20% residual activity persisted with more extensive deletions until the whole of domain II had been removed and the deletions invaded the pseudoknot, whereupon IRES activity fell to zero. The importance of both stems of the pseudoknot was verified by making mutations in both sides of each stem; this severely reduced IRES activity, but the compensating mutations which restored base pairing caused almost full IRES function to be regained. The importance of the length of the loop linking the two stems of the pseudoknot was demonstrated by the finding that a reduction in length from the wild-type AUAAAAUU to AUU almost completely abrogated IRES activity. Random A→U substitutions in the wild-type sequence showed that IRES activity was fairly proportional to the number of A residues retained in this pseudoknot loop, with a preference for clustered neighboring A residues rather than dispersed As. Finally, it was found that the sequence of the highly conserved domain IIIa loop is, rather surprisingly, not important for the maintenance of full IRES activity, although amputation of the entire domain IIIa stem and loop was highly debilitating. These results are interpreted in the light of recent models, derived from cryo-electron microscopy, of the interaction of the closely related hepatitis C virus IRES with 40S ribosomal subunits.
A 130nm canary SRAM for SRAM dynamic write VMIN tracking across voltage, frequency, and temperature variations

With device scaling in bulk technologies, process variation increases and SRAM VMIN scaling faces a bottleneck. Using peripheral assist techniques, we can lower the VMIN at the cost of energy and area. However, the SRAM VMIN is highly dependent on voltage, temperature, and operating frequency fluctuations, which are hard to determine in real time. Prior work shows theoretically that canary SRAMs using reverse assist can track SRAM dynamic write VMIN. In this paper, we show the first silicon results of a working 512b canary SRAM using bitline and wordline type reverse assists in a 130nm bulk technology. It has distinct canary failure trends across voltage, frequency, and temperature variations to track an 8Kb SRAM's dynamic write VMIN.
Microstructure and Mechanical Property of Fe-Al2O3 Nanocomposites Synthesized by Reactive Milling Followed by Spark Plasma Sintering

The in-situ Fe based nanocomposite containing Al2O3 particle is synthesized by reactive milling of Fe2O3-Al-Fe powder mixture in toluene medium followed by consolidation of powders using Spark Plasma Sintering process. Transmission electron microscopy investigation of consolidated Fe-Al2O3 nanocomposites has shown heterogenous grain structure of Fe consisting of nano, submicron and micron size grains together with nanometer Al2O3 particles. The hardness of Fe-Al2O3 nanocomposites consolidated at 800°C is 795 MPa.
CHARACTERIZATION OF POLY(METHYL METHACRYLATE BASED NANOCOMPOSITES ENHANCED WITH CARBON NANOTUBES

OF THESIS CHARACTERIZATION OF POLY(METHYL METHACRYLATE)-BASED NANOCOMPOSITES ENHANCED WITH CARBON NANOTUBES The viscoelastic relaxation dynamics of a series of poly(methyl methacrylate) [PMMA] based nanocomposites filled with carbon nanotubes have been studied using dynamic mechanical analysis and broadband dielectric spectroscopy. The networks were prepared using four methods: (i) melt mixing, (ii) solution processing, (iii) in-situ polymerization, and (iv) polymer grafting. Nanotube modifications included surface oxidation via acid exposure and surface functionalization for polymer grafting. The effect of variations in processing method and nanotube modification on glass transition temperature (Tg) and relaxation dynamics was investigated. The relaxation behavior of the nanocomposites was sensitive to processing method and nanotube functionalization. Nanotube loading (to 5 wt%) led to a progressive increase in rubbery modulus, with the increase more pronounced in the solution-processed samples owing to enhanced nanotube dispersion. In the case of the oxidized nanotubes, loading led to an increase in modulus, but also a systematic decrease in Tg of ~ 15°C with 3 wt% nanotubes. For in-situ polymerized (PMMA/MWNT-ox) nanocomposites, there was no readily discernable trend in Tg. Composites prepared via in-situ polymerization in the presence of methyl methacrylate functionalized tubes (i.e., polymer grafting) displayed a positive shift in Tg of nearly 20°C at 1 wt% loading. Investigation of the dielectric relaxation of the PMMA/MWNT composites indicated a percolation threshold between 0.3 and 0.4 wt% MWNT.
Applying Pitch Target Model to Convert F0 Contour for Expressive Mandarin Speech Synthesis

In the paper, pitch target model is employed to represent and convert F0 contour for synthesizing an emotional Mandarin speech from a neutral speech. Compared with conventional F0 transforming methods, the proposed method converts F0 patterns described by pitch target parameters rather than F0 contours themselves, and uses Gaussian Mixture Model(GMM) and Classification and Regression Trees (CART) methods to build mapping functions for well-chosen pitch target parameters. Other prosodic parameters such as duration and intensity are also converted. Listening tests prove that these converted speeches express corresponding emotional states.
Development of intelligent user behavior based adaptive rule based system

This paper investigates attributes of user search behavior and develops dasiasearch satisfaction metricspsila to determine user satisfaction with search engine. Unlike most previous Web studies that have analyzed user behavior through search engine logs, this work focuses primarily on remotely observing user as he queries search engine. A survey was conducted to identify pattern of search among large sample of users. User generally queries search engine with different types of queries namely informational, transactional and navigational. Our analysis suggests that the user search pattern differs for various types of queries. User tendency to click even when search is successful has been investigated. This has been observed to be a common behavior for open ended informational and transactional queries. A rule based model has been proposed to determine the user satisfaction for a search session. The application of the system in determining user satisfaction, search results relevancy and query complexity has been illustrated.
Device-to-Device Communications for 5G Internet of Things

The proliferation of heterogeneous devices connected through large-scale networks is a clear sign that the vision of the Internet of Things (IoT) is getting closer to becoming a reality. Many researchers and experts in the field share the opinion that the next-to-come fifth generation (5G) cellular systems will be a strong boost for the IoT deployment. Device-to-Device (D2D) appears as a key communication paradigm to support heterogeneous objects interconnection and to guarantee important benefits. In this paper, we thoroughly discuss the added-value features introduced by cellular/non-cellular D2D communications and its potential in efficiently fulfilling IoT requirements in 5G networks. State-of-the-art solutions, enabling radio technologies, and current standardization activities for D2D communications are surveyed and their pros and cons with reference to manifold IoT use cases pointed out. Future research directions are then presented towards a fully converged 5G IoT ecosystem.
Effects of asymmetric dimethylarginine on bovine retinal capillary endothelial cell proliferation, reactive oxygen species production, permeability, intercellular adhesion molecule-1, and occludin expression

Purpose Asymmetric dimethylarginine (ADMA), an endogenous competitive inhibitor of nitric oxide synthase, is associated with impaired endothelial dysfunction, such as chronic heart failure, hypertension, diabetes, and pulmonary hypertension. The effects of ADMA on cell proliferation, reactive oxygen species (ROS) production, cell permeability, intercellular adhesion molecule-1 (ICAM-1), and tight-junction protein occludin levels in bovine retinal capillary endothelial cells (BRCECs) were investigated. Methods A cell proliferation assay was performed using the novel tetrazolium compound 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium and an electron coupling reagent. Intracellular ROS levels were determined using the fluorescent probe CM-H2DCFDA. Horseradish peroxidase was used for a permeability assay. ICAM-1 and tight-junction protein occludin were assessed by western blotting and quantitative real-time PCR. Results Cell proliferation was significantly inhibited by ADMA. ADMA increased intracellular ROS generation in BRCECs. The increased ROS production induced by ADMA was markedly inhibited by the angiotensin II receptor-blocker telmisartan, the angiotensin-converting enzyme inhibitor benazepril, the reduced form of nicotinamide-adenine dinucleotide phosphate (NADPH) oxidase inhibitor diphenyliodonium (DPI), or the antioxidant and free-radical scavenger N-acetyl-l-cysteine (NAC). ADMA significantly increased horseradish peroxidase (HRP) permeability in BRCECs. Benazepril, telmisartan, DPI, and NAC downregulated cell permeability. ADMA markedly upregulated ICAM-1 expression in BRCECs, which were downregulated by telmisartan, DPI, and NAC. ADMA significantly downregulated occludin expression in BRCECs. Benazepril and telmisartan upregulated occludin expression in BRCECs exposed to ADMA. Conclusions Our results provide the first reported evidence that ADMA has potent adverse effects on cell proliferation, intracellular ROS generation, cell permeability, levels of ICAM-1, and the tight-junction protein occludin. Angiotensin-converting enzyme inhibitors, angiotensin II receptor blockers, and antioxidants are effective inhibitors of the adverse effects of ADMA.
CNS invasion by CD14+/CD16+ peripheral blood-derived monocytes in HIV dementia: perivascular accumulation and reservoir of HIV infection

Increases in circulating CD14+/CD16+ monocytes have been associated with HIV dementia; trafficking of these cells into the CNS has been proposed to play an important role in the pathogenesis of HIV-induced neurological disorders. This model suggests that events outside the CNS leading to monocyte activation initiate the process leading to HIV dementia. To investigate the role of this activated monocyte subset in the pathogenesis of HIV dementia, we examined brain specimens from patients with HIV encephalopathy (HIVE), HIV without encephalopathy, and seronegative controls. An accumulation of perivascular macrophages was observed in HIVE. The majority of these cells identified in microglial nodules and in the perivascular infiltrate were CD14+/CD16+. P24 antigen colocalized with both CD14 and CD16 suggesting that the CD14+/CD16+ macrophage is a major reservoir of HFV-1 infection in CNS. Using CD45/LCA staining, the perivascular macrophage was distinguished from resident microglia. In addition to perivascular and nodular localizations, CD16 also stained ramified cells throughout the white matter. These cells were more ramified and abundant than cells positive for CD14 in white matter. Double staining for p24 and CD16 suggests that these cells were often infected with HIV-1. The prominent distribution of CD14+ cells in HIVE prompted our analysis of soluble CD14 levels in cerebrospinal fluid. Higher levels of soluble CD14 (sCD14) were observed in patients with moderate-to-severe HIV dementia, suggesting the utility of sCD14 as a surrogate marker. CD14+/CD16+ monocytes may play a role in other neurological disorders and sCDl4 may be useful for evaluating these conditions.
■ REVIEW : Parallel Processing, Asynchronous Perception, and a Distributed System of Consciousness in Vision

The primate visual brain is characterized by a set of parallel, multistage systems that are specialized to process different attributes of the visual scene. They occupy spatially distinct positions in the visual brain and do not project to a unique common area. These processing systems are also perceptual systems, because the result of activity in each leads to the perception of the relevant visual attribute. But the different processing-perceptual systems require different times to complete their tasks, thus leading to another char acteristic of the visual brain, a temporal hierarchy for perception. Together, these two characteristics—of parallel processing and temporal hierarchy—suggest that each processing-perceptual system can act with fair autonomy. Studies of the diseased human brain show that activity in separate processing-perceptual systems—especially those concerned with color and motion—can lead to the perception of the relevant attribute even when the other processing systems are inactive and that activity in individual processing- perceptual systems has a conscious experience as a correlate, which suggests that consciousness itself is a modular, distributed system. NEUROSCIENTIST 4:365-372, 1998
A Note on Approximate Nearest Neighbor Methods

A number of authors have described randomized algorithms for solving the epsilon-approximate nearest neighbor problem. In this note I point out that the epsilon-approximate nearest neighbor property often fails to be a useful approximation property, since epsilon-approximate solutions fail to satisfy the necessary preconditions for using nearest neighbors for classification and related tasks.
Mitochondrial ROMK Channel Is a Molecular Component of MitoKATP

Rationale: Activation of the mitochondrial ATP-sensitive potassium channel (mitoKATP) has been implicated in the mechanism of cardiac ischemic preconditioning, yet its molecular composition is unknown. Objective: To use an unbiased proteomic analysis of the mitochondrial inner membrane to identify the mitochondrial K+ channel underlying mitoKATP. Methods and Results: Mass spectrometric analysis was used to identify KCNJ1(ROMK) in purified bovine heart mitochondrial inner membrane and ROMK mRNA was confirmed to be present in neonatal rat ventricular myocytes and adult hearts. ROMK2, a short form of the channel, is shown to contain an N-terminal mitochondrial targeting signal, and a full-length epitope-tagged ROMK2 colocalizes with mitochondrial ATP synthase &bgr;. The high-affinity ROMK toxin, tertiapin Q, inhibits mitoKATP activity in isolated mitochondria and in digitonin-permeabilized cells. Moreover, short hairpin RNA—mediated knockdown of ROMK inhibits the ATP-sensitive, diazoxide-activated component of mitochondrial thallium uptake. Finally, the heart-derived cell line, H9C2, is protected from cell death stimuli by stable ROMK2 overexpression, whereas knockdown of the native ROMK exacerbates cell death. Conclusions: The findings support ROMK as the pore-forming subunit of the cytoprotective mitoKATP channel.
Inefficient Quality Control of Thermosensitive Proteins on the Plasma Membrane

Background Misfolded proteins are generally recognised by cellular quality control machinery, which typically results in their ubiquitination and degradation. For soluble cytoplasmic proteins, degradation is mediated by the proteasome. Membrane proteins that fail to fold correctly are subject to ER associated degradation (ERAD), which involves their extraction from the membrane and subsequent proteasome-dependent destruction. Proteins with abnormal transmembrane domains can also be recognised in the Golgi or endosomal system and targeted for destruction in the vacuole/lysosome. It is much less clear what happens to membrane proteins that reach their destination, such as the cell surface, and then suffer damage. Methodology/Principal Findings We have tested the ability of yeast cells to degrade membrane proteins to which temperature-sensitive cytoplasmic alleles of the Ura3 protein or of phage lambda repressor have been fused. In soluble form, these proteins are rapidly degraded upon temperature shift, in part due to the action of the Doa10 and San1 ubiquitin ligases and the proteasome. When tethered to the ER protein Use1, they are also degraded. However, when tethered to a plasma membrane protein such as Sso1 they escape degradation, either in the vacuole or by the proteasome. Conclusions/Significance Membrane proteins with a misfolded cytoplasmic domain appear not to be efficiently recognised and degraded once they have escaped the ER, even though their defective domains are exposed to the cytoplasm and potentially to cytoplasmic quality controls. Membrane tethering may provide a way to reduce degradation of unstable proteins.
Residual stress field in steel samples during plastic deformation and recovery processes

An X-ray diffraction method was applied to measure residual stresses and stored elastic energy in deformed and annealed polycrystalline ferritic and austenitic steel samples. The orientation distribution of plastic incompatibility second-order stresses created during elastoplastic deformation was determined and presented in Euler space. Using deformation models, these stresses were correlated with different types of intergranular interactions occurring in the studied materials. An important decrease of the first- and the second-order residual stresses was observed during recovery and recrystallisation processes. Diffraction peak widths, related to dislocation density, were studied and correlated with stress variation during annealing process. Differences in stress relaxation between ferritic and austenitic samples were explained by different values of the stacking fault energy, which influences dislocation climb and cross-slip.