Miracle-dz/UniFAR-FTUs huggingface dataset:
Binding of glycated ovocystatin to rat renal brush border membranes.

Glycated proteins are considered as one of the factors involved in the pathogenesis of diabetic complications, including nephropathy. These proteins are formed endogenously under conditions of hyperglycemia, as well as being provided with food containing sugars, which was subjected to high temperature. Examples are egg products. One of the proteins found in eggs in a relatively high concentration is chicken cystatin (ovocystatin). It is now believed that some proteins can passage the intestinal epithelium by transcytosis directly into the bloodstream. Thus, glycated protein present in food can be an additional source of glycotoxins. The aim of this study was to compare the affinity of native and glycated cystatin to the brush border membranes of rat kidney. Kinetic analysis was performed with surface plasmon resonance technique using sensor chip L1. Dissociation constants for native and glycated cystatin (Kd ) were 2.76 μmol/L and 3.82 μmol/L, respectively. The results of our study indicate that glycation only slightly affects binding of cystatin to brush border membranes. This suggests that glycated cystatin and other glycated proteins may also be efficiently taken up in the kidney proximal tubule. The observation may be important for understanding the mechanisms involved in the development of diabetic nephropathy.
Recent Advances on the Posttranslational Modifications of EXTs and Their Roles in Plant Cell Walls

The genetic set up and the enzymes that define the O-glycosylation sites and transfer the activated sugars to cell wall glycoprotein Extensins (EXTs) have remained unknown for a long time. We are now beginning to see the emerging components of the molecular machinery that assembles these complex O-glycoproteins on the plant cell wall. Genes conferring the posttranslational modifications, i.e., proline hydroxylation and subsequent O-glycosylation, of the EXTs have been recently identified. In this review we summarize the enzymes that define the O-glycosylation sites on the O-glycoproteins, i.e., the prolyl 4-hydroxylases (P4Hs), the glycosyltransferases that transfer arabinose units (named arabinosyltransferases, AraTs), and the one responsible for transferring a single galactose (galactosyltransferase, GalT) on the protein EXT backbones. We discuss the effects of posttranslational modifications on the structure and function of extensins in plant cell walls.
Smart Refresh: An Enhanced Memory Controller Design for Reducing Energy in Conventional and 3D Die-Stacked DRAMs

DRAMs require periodic refresh for preserving data stored in them. The refresh interval for DRAMs depends on the vendor and the design technology they use. For each refresh in a DRAM row, the stored information in each cell is read out and then written back to itself as each DRAM bit read is self-destructive. The refresh process is inevitable for maintaining data correctness, unfortunately, at the expense of power and bandwidth overhead. The future trend to integrate layers of 3D die-stacked DRAMs on top of a processor further exacerbates the situation as accesses to these DRAMs will be more frequent and hiding refresh cycles in the available slack becomes increasingly difficult. Moreover, due to the implication of temperature increase, the refresh interval of 3D die-stacked DRAMs will become shorter than those of conventional ones. This paper proposes an innovative scheme to alleviate the energy consumed in DRAMs. By employing a time-out counter for each memory row of a DRAM module, all the unnecessary periodic refresh operations can be eliminated. The basic concept behind our scheme is that a DRAM row that was recently read or written to by the processor (or other devices that share the same DRAM) does not need to be refreshed again by the periodic refresh operation, thereby eliminating excessive refreshes and the energy dissipated. Based on this concept, we propose a low-cost technique in the memory controller for DRAM power reduction. The simulation results show that our technique can reduce up to 86% of all refresh operations and 59.3% on the average for a 2 GB DRAM. This in turn results in a 52.6% energy savings for refresh operations. The overall energy saving in the DRAM is up to 25.7% with an average of 12.13% obtained for SPLASH-2, SPECint2000, and Biobench benchmark programs simulated on a 2 GB DRAM. For a 64 MB 3D DRAM, the energy saving is up to 21% and 9.37% on an average when the refresh rate is 64 ms. For a faster 32 ms refresh rate the maximum and average savings are 12% and 6.8% respectively.
Granular Computing: Perspectives and Challenges

Granular computing, as a new and rapidly growing paradigm of information processing, has attracted many researchers and practitioners. Granular computing is an umbrella term to cover any theories, methodologies, techniques, and tools that make use of information granules in complex problem solving. The aim of this paper is to review foundations and schools of research and to elaborate on current developments in granular computing research. We first review some basic notions of granular computing. Classification and descriptions of various schools of research in granular computing are given. We also present and identify some research directions in granular computing.
Isocitrate Dehydrogenase (IDH)1/2 Mutations as Prognostic Markers in Patients With Glioblastomas

AbstractThe purpose of this study was to perform a meta-analysis examining the association of isocitrate dehydrogenase (IDH)1/2 mutations with overall survival (OS) and progression-free survival (PFS) in patients with glioblastomas.Medline, Cochrane, EMBASE, and Google Scholar were searched from inception to January 28, 2015, using combinations of the following keywords: IDH mutation, brain tumor, glioma, glioblastoma, oligodendroglioma, prognosis. Randomized controlled trials, and prospective and retrospective studies of patients with glioblastomas that provided IDH mutation and survival data were included. OS and PFS were used to evaluate the association of IDH1 and IDH1/2 mutations and prognosis. Hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) for OS and PFS were calculated and compared between patients with and without mutations.Of 165 studies that were identified, 136 nonrelevant studies were excluded. Twenty-nine full-text articles were assessed, and of these, 5 were excluded as they did not provide a quantitative outcome. Therefore, 24 studies were included in the qualitative synthesis. The pooled HR of 0.358 (95% CI 0.264–0.487, P < 0.001) indicated that IDH mutations were associated with better OS. Similarly, the pooled HR of 0.322 (95% CI 0.24200.455, P < 0.001) indicated that IDH mutations were associated with better PFS. When patients were stratified by surgery versus no surgery or IDH1 versus IDH1/2 mutations, the results also indicated that the presence of IDH mutations was associated with better OS and PFS.The IDH mutations are associated with improved survival in patients with glioblastomas.
From plasma to nanoparticles: optical and particle emission of a spark discharge generator

The increased demand for high purity nanoparticles (NPs) of defined geometry necessitates the continuous development of generation routes. One of the most promising physical techniques for producing metal, semiconductor or alloy NPs in the gas phase is spark discharge NP generation. The technique has a great potential for up-scaling without altering the particles. Despite the simplicity of the setup, the formation of NPs in a spark discharge takes place via complex multi-scale processes, which greatly hinders the investigation via conventional NP measurement techniques. In the present work, time-resolved optical emission spectroscopy (OES) was used to provide information on the species present in the spark from as early as approximately 100 ns after the initiation of the discharge. We demonstrate that operando emission spectroscopy can deliver valuable insights into NP formation. The emission spectra of the spark are used to identify, among others, the main stages of material erosion and to calculate the quenching rate of the generated metal vapour. We demonstrate that the alteration of key control parameters, that are typically used to optimize NP generation, clearly affect the emission spectra. We report for Cu and Au NPs that the intensity of spectral lines emitted by metal atoms levels off when spark energy is increased above an energy threshold, suggesting that the maximum concentration of metal vapour produced in the generator is limited. This explains the size variation of the generated NPs. We report a strong correlation between the optical and particle emission of the spark discharge generator, which demonstrate the suitability of OES as a valuable characterization tool that will allow for the more deliberate optimization of spark-based NP generation.
Preliminary Phytochemical Screening and Biological Activities of Bulbine abyssinica Used in the Folk Medicine in the Eastern Cape Province, South Africa

Bulbine abyssinica A. Rich. is used in traditional medicine to treat rheumatism, dysentery, bilharzia, cracked lips, back pain, infertility, diabetes mellitus, and gastrointestinal, vaginal, and bladder infections. Therefore, preliminary phytochemical screening, antioxidant, anti-inflammatory, and antibacterial properties of the whole plant (acetone and aqueous extracts) were determined using standard procedures. The in vitro antioxidant model assays revealed that the plant possesses free radical scavenging potential varying with free radical species. The species showed significant protein denaturation inhibitory activity with good protection against erythrocyte membrane lysis indicating anti-inflammatory potential. The results also showed that the species was active against the growth of all the selected eight diabetic status opportunistic bacteria except one. Moreover, the species is characterized by appreciable amounts of total phenols, flavonoids, flavanols, proanthocyanidins, and alkaloids. Traces amounts of saponins and tannins were also observed. Amongst the identified phytochemicals present, empirical searches identified them being antioxidant, anti-inflammatory, and antimicrobial agents. The identification of these phytochemical constituents with their known pharmacological properties indicates that this plant is a good source of the free radical scavenging, anti-inflammatory, and antimicrobial agents. These findings also account for the multipharmacological use of B. abyssinica in fork medicine.
Map-Based Probabilistic Visual Self-Localization

Accurate and efficient self-localization is a critical problem for autonomous systems. This paper describes an affordable solution to vehicle self-localization which uses odometry computed from two video cameras and road maps as the sole inputs. The core of the method is a probabilistic model for which an efficient approximate inference algorithm is derived. The inference algorithm is able to utilize distributed computation in order to meet the real-time requirements of autonomous systems in some instances. Because of the probabilistic nature of the model the method is capable of coping with various sources of uncertainty including noise in the visual odometry and inherent ambiguities in the map (e.g., in a Manhattan world). By exploiting freely available, community developed maps and visual odometry measurements, the proposed method is able to localize a vehicle to 4 m on average after 52 seconds of driving on maps which contain more than 2,150 km of drivable roads.
Detection of biological threat agents by real-time PCR: comparison of assay performance on the R.A.P.I.D., the LightCycler, and the Smart Cycler platforms.

BACKGROUND Rapid detection of biological threat agents is critical for timely therapeutic administration. Fluorogenic PCR provides a rapid, sensitive, and specific tool for molecular identification of these agents. We compared the performance of assays for 7 biological threat agents on the Idaho Technology, Inc. R.A. P.I. D. , the Roche LightCycler, and the Cepheid Smart Cycler. METHODS Real-time PCR primers and dual-labeled fluorogenic probes were designed to detect Bacillus anthracis, Brucella species, Clostridium botulinum, Coxiella burnetii, Francisella tularensis, Staphylococcus aureus, and Yersinia pestis. DNA amplification assays were optimized by use of Idaho Technology buffers and deoxynucleotide triphosphates supplemented with Invitrogen Platinum Taq DNA polymerase, and were subsequently tested for sensitivity and specificity on the R.A. P.I. D. , the LightCycler, and the Smart Cycler. RESULTS Limit of detection experiments indicated that assay performance was comparable among the platforms tested. Exclusivity and inclusivity testing with a general bacterial nucleic acid cross-reactivity panel containing 60 DNAs and agent-specific panels containing nearest neighbors for the organisms of interest indicated that all assays were specific for their intended targets. CONCLUSION With minor supplementation, such as the addition of Smart Cycler Additive Reagent to the Idaho Technology buffers, assays for DNA templates from biological threat agents demonstrated similar performance, sensitivity, and specificity on all 3 platforms.
Quantitative microleakage evaluation of fissure sealants applied with or without a bonding agent: results after four-year water storage in vitro.

PURPOSE To evaluate the effect of long-term water storage on the microleakage of a fissure sealant applied with or without different bonding agents. MATERIALS AND METHODS Extracted human third molars were randomly assigned into 8 groups (n = 24/each). The occlusal surfaces were sealed with a fluoride fissure sealant material (Helioseal F) after one of the following pretreatments: (1) phosphoric acid etching only; (2) phosphoric acid etching + Single Bond; (3) phosphoric acid etching + Prime & Bond NT; (4) Clearfil SE Bond; (5) FL Bond; (6) One Up Bond F; (7) Prompt L-Pop; (8) Mac Bond II. All specimens were thermocycled (1000X), after which half of them (n=96) were stored in distilled water for 48 h (group A), and the remaining half (n=96) for 48 months (group B). The specimens were immersed in 0.5% basic fuchsin solution, sectioned, and digitally photographed. Microleakage was evaluated quantitatively using an open-source image analysis toolkit (ImageJ), and the data were analyzed statistically. RESULTS Four-year water storage significantly increased the amount of leakage in all test groups (p < 0.001). In both the absence and presence of water aging, the etch-and-rinse adhesives yielded the lowest microleakage scores (p < 0.001). In the 48-h group, the following ranking was achieved in terms microleakage values: phosphoric acid + Prime & Bond NT = phosphoric acid + Single Bond < Prompt L-Pop = phosphoric acid etching only < FL Bond < Clearfil SE Bond < Mac Bond II = One Up Bond F. In the 48-month group, the ranking changed as follows: phosphoric acid + Prime & Bond NT = phosphoric acid + Single Bond < Prompt L-Pop = FL Bond < Clearfil SE Bond = Mac Bond II = One Up Bond F < phosphoric acid etching only. CONCLUSION Long-term water storage significantly increased the microleakage of Helioseal F applied alone and with a bonding agent. Regardless of the storage term, the use of etch-and-rinse adhesives resulted in significantly less microleakage compared to that achieved with self-etching adhesives or acid etching alone. The sealants placed without a prior bonding agent showed the greatest amount of leakage after four years.
A Reward-Modulated Hebbian Learning Rule Can Explain Experimentally Observed Network Reorganization in a Brain Control Task

It has recently been shown in a brain–computer interface experiment that motor cortical neurons change their tuning properties selectively to compensate for errors induced by displaced decoding parameters. In particular, it was shown that the three-dimensional tuning curves of neurons whose decoding parameters were reassigned changed more than those of neurons whose decoding parameters had not been reassigned. In this article, we propose a simple learning rule that can reproduce this effect. Our learning rule uses Hebbian weight updates driven by a global reward signal and neuronal noise. In contrast to most previously proposed learning rules, this approach does not require extrinsic information to separate noise from signal. The learning rule is able to optimize the performance of a model system within biologically realistic periods of time under high noise levels. Furthermore, when the model parameters are matched to data recorded during the brain–computer interface learning experiments described above, the model produces learning effects strikingly similar to those found in the experiments.
N‐terminal extension changes the folding mechanism of the FK506‐binding protein

Many of the protein fusion systems used to enhance the yield of recombinant proteins result in the addition of a small number of amino acid residues onto the desired protein. Here, we investigate the effect of short (three amino acid) N‐terminal extensions on the equilibrium denaturation and kinetic folding and unfolding reactions of the FK506‐binding protein (FKBP) and compare the results obtained with data collected on an FKBP variant lacking this extension. Isothermal equilibrium denaturation experiments demonstrated that the N‐terminal extension had a slight destabilizing effect. NMR investigations showed that the N‐terminal extension slightly perturbed the protein structure near the site of the extension, with lesser effects being propagated into the single α‐helix of FKBP. These structural perturbations probably account for the differential stability. In contrast to the relatively minor equilibrium effects, the N‐terminal extension generated a kinetic‐folding intermediate that is not observed in the shorter construct. Kinetic experiments performed on a construct with a different amino acid sequence in the extension showed that the length and the sequence of the extension both contribute to the observed equilibrium and kinetic effects. These results point to an important role for the N terminus in the folding of FKBP and suggest that a biological consequence of N‐terminal methionine removal observed in many eukaryotic and prokaryotic proteins is to increase the folding efficiency of the polypeptide chain.
Delayed removal of a deeply migrated pigtail pancreatic stent in a normal pancreatic duct

A 57-year-old man underwent endoscopic retrograde cholangiopancreatography (ERCP) for multiple bile duct and gallbladder stones. During the ERCP, we attempted to insert a prophylactic 5-Fr, single pigtail pancreatic stent (Cook Endoscopy, Winston-Salem, North Carolina, United States) because biliary cannulation is difficult and the pancreatic duct is frequently cannulated unintentionally; however the pancreatic stent migrated deep into the normal pancreatic duct and the pigtail portion of the stent curled into the inner pancreatic duct (●" Fig.1a). We attempted to remove the stent immediately using endobiliary biopsy forceps, a conventional snare, and a Dormia basket (●" Fig.2), as reported in various cases [1–4]; however these methods all failed because the pancreatic duct was of normal size and it was difficult to advance the devices past the neck of the pancreatic duct. Moreover, the curved pigtail head made capture impossible. The repeated attempts at removal only pushed the stent more deeply into the pancreatic duct. Consequently, we inserted a second 9cm-long pancreatic stent to prevent postERCP pancreatitis, removed the biliary stones, and then performed a laparoscopic cholecystectomy. Again, we tried to remove the migrated pancreatic stent, but failed despite trying various methods, Fig.1 Unintentionally migrated pigtail pancreatic stent in a 57-year-old man who underwent endoscopic retrograde cholangiopancreatography (ERCP) for multiple bile duct and gallbladder stones. a Unintentional deep inward migration of a pigtail pancreatic stent up to the neck of the normal pancreatic duct. b A second long pancreatic duct stent inserted to prevent post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis.
Resting‐state networks in awake five‐ to eight‐year old children

During the first 6–7 years of life children undergo a period of major neurocognitive development. Higher‐order cognitive functions such as executive control of attention, encoding and retrieving of stored information and goal‐directed behavior are present but less developed compared to older individuals. There is only very limited information from functional magnetic resonance imaging (fMRI) studies about the level of organization of functional networks in children in the early school period. In this study we perform continuous resting‐state functional connectivity MRI in 5‐ to 8‐year‐old children in an awake state to identify and characterize resting‐state networks (RSNs). Temporal concatenation independent component analysis (ICA) approach was applied to analyze the data. We identified 14 components consisting of regions known to be involved in visual and auditory processing, motor function, attention control, memory, and the default mode network (DMN). Most networks, in particular those supporting basic motor function and sensory related processing, had a robust functional organization similar to mature adult patterns. In contrast, the DMN and other RSNs involved in higher‐order cognitive functions had immature characteristics, revealing incomplete and fragmented patterns indicating less developed functional connectivity. We therefore conclude that the DMN and other RSNs involved in higher order cognitive functioning are detectable, yet in an immature state, at an age when these cognitive abilities are mastered. Hum Brain Mapp, 2011. © 2011 Wiley‐Liss, Inc.
Methylation of histone H3 and H4 by PRMT5 regulates ribosomal RNA gene transcription

In an effort to understand the epigenetic regulation of ribosomal RNA gene (rDNA) expression we have previously demonstrated the role of DNA methyltransferases and methyl CpG binding proteins in rRNA synthesis. Here, we studied the role of protein arginine methyltransferase PRMT5 and the two methylated histones H3R8Me2 and H4R3Me2, in rDNA expression in Epstein Barr virus‐ transformed primary B‐cells (LCLs) and in HeLa cells responding to serum‐regulated growth. Chromatin immunoprecipitation assay showed that histones H3 and H4 associated with rRNA promoters were differentially methylated at arginine residues 8 and 3, respectively, depending on its transcriptional activity. Association of PRMT5 and methylated H3 with the unmethylated promoters in resting B‐cells was significantly reduced in rapidly growing LCLs. Unlike PRMT5 and H3R8Me2, histone H4 associated with both methylated and unmethylated rRNA promoters in resting B‐cells was methylated at the R3 residue. However, a dramatic decrease in R3 methylation of H4 recruited to the unmethylated rRNA promoters was observed in LCLs while it remained unaltered in the fraction bound to the methylated promoters. Differential interaction of PRMT5 and methylation of H3 and H4 associated with the rRNA promoters was also observed when serum starved HeLa cells were allowed to grow in serum replenished media. Ectopic expression of PRMT5 suppressed activity of both unmethylated and methylated rRNA promoter in transient transfection assay whereas siRNA mediated knockdown of PRMT5 increased rRNA synthesis in HeLa cells. These data suggest a key role of PRMT5 and the two methylated histones in regulating rRNA promoter activity. J. Cell. Biochem. 109: 553–563, 2010. © 2009 Wiley‐Liss, Inc.