Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of IL-8 Promoter Activity by Verrucarin A in Human Monocytic THP-1 Cells

Macrocyclic trichothecenes have been frequently detected in fungi in water-damaged buildings and exhibited higher toxicity than the well-studied trichothecenes; however, the mechanism underlying their toxicity has been poorly understood. In this study, transcriptional regulation of the cytokine interleukin (IL)-8 by a macrocyclic trichothecene, verrucarin A (VA), in human monocytic THP-1 cells is reported. Consistent with previous findings, VA was 100-fold more cytotoxic than deoxynivalenol (DON), while ochratoxin A (OA) was not cytotoxic. In cells transduced with the wild-type IL-8 promoter luciferase construct, VA induced a biphasic dose response composed of an upregulation of luciferase expression at low concentrations of 0.01−1 ng/ml and a downregulation at high levels of 10 ng/ml and higher. In contrast, DON induced a sigmoid-shaped dose response with the EC50 of 11.6 ng/ml, while OA did not markedly affect the IL-8 expression. When cells were transduced with IL-8 promoter with a mutation of transcription factor nuclear factor-κB (NF-κB)-binding site, VA (1 ng/ml), DON (1000 ng/ml), and tumor necrosis factor (TNF) α (20 ng/ml)-induced luciferase expression were impaired. In addition, the NF-κB inhibitor caffeic acid phenethyl ester inhibited VA-, DON-, and TNFα-induced luciferase expression. Mutation of the CCAAT/enhancer-binding protein (CEBP) β binding site of the IL-8 promoter affected only DON-, but not VA- and TNFα-induced luciferase expression. Taken together, these results suggested that VA activated IL-8 promoter via an NF-κB-dependent, but not CEBPβ-dependent, pathway in human monocytes.
Missense mutations in the human SDHB gene increase protein degradation without altering intrinsic enzymatic function

Mutations of succinate dehydrogenase subunit B (SDHB) play a crucial role in the pathogenesis of the most aggressive and metastatic pheochromocytomas (PHEOs) and paragangliomas (PGLs). Although a variety of missense mutations in the coding sequence of the SDHB gene have been found in PHEOs and PGLs, it has been unclear whether these mutations impair mRNA expression, protein stability, subcellular localization, or intrinsic protein function. RT‐PCR and Western blot analysis of SDHB mRNA and protein expression from SDHB‐related PHEOs and PGLs demonstrated intact mRNA expression but significantly reduced protein expression compared to non‐SDHB PHEOs and PGLs. A pulse‐chase assay of common SDHB missense mutations in transfected HeLa cell lines demonstrated that the loss of SDHB function was due to a reduction in mutant protein half‐life, whereas colocalization of SDHB with mitochondria and immunoprecipitation with SDHA demonstrated intact subcellular localization and complex formation. The half‐life of the SDHB protein increased after treatment with histone deacetylase inhibitors (HDACis), implicating the protein quality control machinery in the degradation of mutant SDHB protein. These findings provide the first direct mechanism of functional loss resulting from SDHB mutations and suggest that reducing protein degradation with HDACis may serve as a novel therapeutic paradigm for preventing the development of SDHB‐related tumors. —Yang, C. , Matro, J. C. , Huntoon, K. M. , Ye, D. Y. , Huynh, T. T. , Fliedner, S. M. J., Breza, J., Zhuang, Z. , Pacak, K. Missense mutations in the human SDHB gene increase protein degradation without altering intrinsic enzymatic function. FASEB J. 26, 4506–4516 (2012). www.fasebj. org
Systems biology: model based evaluation and comparison of potential explanations for given biological data

Systems biology and its usage of mathematical modeling to analyse biological data is rapidly becoming an established approach to biology. A crucial advantage of this approach is that more information can be extracted from observations of intricate dynamics, which allows nontrivial complex explanations to be evaluated and compared. In this minireview we explain this process, and review some of the most central available analysis tools. The focus is on the evaluation and comparison of given explanations for a given set of experimental data and prior knowledge. Three types of methods are discussed: (a) for evaluation of whether a given model is sufficiently able to describe the given data to be nonrejectable; (b) for evaluation of whether a slightly superior model is significantly better; and (c) for a general evaluation and comparison of the biologically interesting features in a model. The most central methods are reviewed, both in terms of underlying assumptions, including references to more advanced literature for the theoretically oriented reader, and in terms of practical guidelines and examples, for the practically oriented reader. Many of the methods are based upon analysis tools from statistics and engineering, and we emphasize that the systems biology focus on acceptable explanations puts these methods in a nonstandard setting. We highlight some associated future improvements that will be essential for future developments of model based data analysis in biology.
Building a microgrid laboratory

Microgrids are local area power systems, and are attracting increased attention due to their potential to provide a solution to integrate renewable energy into the wider grid. In order to facilitate experimental research, a microgrid laboratory has been built by CSIRO in Australia. Experiments have been carried out which investigate issues of integrating distributed generation, including renewable energy, into the electricity network. This paper describes some of the challenges involved in setting up such a facility and provides examples of experimental results. This facility is unique in its incorporation of three types of solar PV technologies, two types of wind power, three types of battery storage, and a programmable load bank. The availability of a flexible facility such as this is essential in advancing the science in this area, and is leading to valuable insights into microgrid operation.
A Lower Bound on the Error Probability for Signals in White Gaussian Noise

In this correspondence we apply a recent inequality by de Caen (1997) to derive a lower bound on the probability of error for M-ary signals derived from a binary linear code and used on the additive white Gaussian noise channel with a maximum-likelihood decoder. This bound depends only on the weight enumerator of the code and the signal-to-noise ratio E/sub b//N/sub 0/. We show that this bound converges to the union upper bound as E/sub b//N/sub 0/ goes to infinity. Finally, by means of examples, we compare our lower bound with those of Shannon and Swaszek and with Poltyrev's upper bound.
A fast‐activated inward calcium current in twitch muscle fibres of the frog (Rana montezume).

Voltage‐clamp experiments were performed at 18 degrees C in intact twitch muscle fibres of the frog using the three micro‐electrode technique. Membrane currents were recorded in the presence of 120 mM‐tetraethylammonium‐methanesulphonate and 10 mM‐Ca2+. The recording solution was made hypertonic by adding 350 mM‐sucrose to avoid contraction. Two components of inward current in the absence of external Na+ were observed. Depolarization induced a fast‐activated inward current of small amplitude in addition to the well‐known slow, transient Ca2+ current (ICa,s). Both components of inward current persisted in the presence of tetrodotoxin. They practically disappeared on replacing external Ca2+ with Mg2+ and were blocked by millimolar additions of Cd2+ to the bath. Thus, the fast‐activated component of inward current was also carried by Ca2+ (ICa,f). Neither ICa,f nor ICa,s were reduced by 5 microM‐diltiazem. During 400 ms depolarizations ICa,f was detected at approximately ‐60 mV, 30 mV more negative than the membrane potentials at which ICa,s appeared. At about 0 mV the time constant for activation was 5 ms for ICa and 150 ms for ICa,s. ICa,f did not significantly decline during depolarizations up to 2s in duration at membrane potentials between ‐60 and ‐30 mV. ICa,f tended to disappear as a function of time on exposure to the hypertonic recording solution. Its maximum amplitude decreased from about ‐25 microA/cm2 during the first 5 min to about ‐5 microA/cm2 after 25 min while ICa.s remained practically unchanged (maximum peak amplitude of about ‐60 microA/cm2). These results indicate the existence of two types of voltage‐dependent CA2+ channels in intact muscle fibres. The kinetic properties of fast‐activated Ca2+ channels suggest that they significantly activate during a single twitch.
Bacteriocin and antibiotic resistance plasmids in Bacillus cereus and Bacillus subtilis

A number of plasmids have been isolated as covalently closed circular DNAs from strains of Bacillus cereus and B. subtilis. From 12 out of 15 strains of B. cereus, plasmids could be isolated. Most of the B. cereus strains contained two or more plasmids. Their molecular weights ranged from 1.6 X 10(6) to 105 X 10(6). Bacteriocin production could be attributed to a 45 X 10(6)-dalton plasmid (pBC7) from B. cereus DSM 336, and tetracycline resistance to a 2.8 X 10(6) plasmid (pBC16) from B. cereus GP7. Two streptomycin-resistant strains of B. subtilis harbored plasmids of 5.2 X 10(6) and 9 X 10(6), respectively, which were, however, not correlated with the antibiotic resistance. The plasmid carrying resistance to tetracycline, pBC16, which was originally isolated from B. cereus, could be subsequently transformed in B. subtilis, where it is stably maintained.
LTR control based on GA-BP neural network for hammerstein model of pH neutralization process

A loop transfer recovery (LTR) control method based on Genetic Algorithm (GA) — Back Propagation (BP) neural network is proposed for Hammerstein model of pH neutralization process with typical nonlinear characteristics in this paper. GA-BP neural network is used to establish the inverse model of nonlinear part, so that the LTR control based on inverse system method can be used to recover the performance of the system. The simulation results shows that this method is efficient in Hammerstein model of pH neutralization process and the robustness and track performance of the proposed controller has also been demonstrated.
Application of Spatial Interpolation Method for Estimating the Spatial Variability of Rainfall in Semiarid New Mexico, USA

Spatial interpolation of rain gauge data is important for ecohydrology study or modelling of land degradation. The monthly rainfall data recorded at 68 stations in Jornada basin was analysed to study the spatial patterns of rainfall. The inverse distance weighting spatial interpolation method was applied to model the spatial variability of rainfall for a wet (1992) and dry (1994) years. The rainfall interpolation was tested for the basin wide region and by constraining the rainfall-interpolation within the study area boundary. The accuracy of the interpolation result was measured by adopting the leave-one-out cross validation method. The result indicates that the rainfall displayed a strong spatial variability trend from the southwest to the northeast. The result from the CV analysis of the total data points for both year showed that the IDW interpolation method produced from data points within the study area boundary produced better fits compared to the CV result from all the data points within the Jornada basin. The result from constraining the rainfall-interpolation within the study-area boundary showed that the interpolation error from the edge effects can be minimised and result of the predicted values showed a closer fit to the measured values. DOI: 10.5901/mjss.2015. v6n4s3p108
Quantitative Compositional Mapping of Core-Shell Polymer Microspheres by Soft X-ray Spectromicroscopy

Core−shell polymer microspheres have been prepared by a two-step precipitation polymerization. These microspheres consist of 3.2 μm polydivinylbenzene-55 (DVB55) cores coated with ∼0.4−0.9 μm wide shells composed of poly(DVB55-co-EDMA), a random copolymer of DVB55 and ethylene glycol dimethyl acrylate (EDMA). The chemical composition, core−shell morphology, and porosity of these structured microspheres have been studied quantitatively with scanning transmission X-ray microscopy (STXM) at a spatial resolution of 100 nm. Images recorded at selected energies through the C 1s absorption region were analyzed using singular value decomposition to obtain quantitative maps of the DVB55 and EDMA components. The EDMA concentration in the shell determined by STXM was found to be in good agreement with that predicted from the comonomer composition over the range of 10−90% EDMA. The precision of chemical quantification at high spatial resolution is shown to be adequate for STXM to be useful in guiding the development .
Multi‐functional DNA proteins in yeast: The factors GFI and GFII are identical to the ARS‐binding factor ABFI and the centromere‐binding factor CPF1 respectively

GFI and GFII are abundant DNA‐binding proteins in the yeast Saccharomyces cerevisiae. Binding sites for GFI conform to the sequence 5′‐RTCRYNNNNNACG‐3′. This consensus can also accommodate the recognition sequence for the ARS1‐binding factor ABFI. Results of retardation‐competition assays, limited proteolysis experiments, molecular weight determinations based on denaturation–renaturation procedures and mobility shift assays of protein–DNA complexes formed in the presence of a monoclonal antibody raised against ABFI suggest strongly that GFI and ABFI are the same protein. Similarly, GFII appears to be identical to the centromere‐binding protein CPFI (alias CP1), since both proteins bind to the CDEI motif of yeast centromeres (5′‐RTCACRTG‐3′) and cannot be detected in a cpf1 disruption mutant yeast strain. In addition, based on denaturation–renaturation studies, both factors appear to have molecular weights in the same range of 53–62 kDa.
Vasa expression in a colonial ascidian, Botrylloides violaceus

SUMMARY Evolution of solitary or colonial life histories in tunicates is accompanied by dramatic developmental changes that affect morphology and reproduction. We compared vasa expression in a solitary ascidian and a closely related colonial ascidian, in an effort to uncover developmental mechanisms important during the evolution of these contrasting life histories, including the ability to reproduce by budding. In this study, we explored the origin of germ cells in new buds developing by asexual reproduction in a colonial ascidian, Botrylloides violaceus and compared it to the source of germ cells in a solitary ascidian Boltenia villosa. We studied expression by in situ hybridization of vasa, a DEAD box RNA helicase gene found in germ cells across the metazoans. In B. villosa, bv‐vasa mRNA was expressed in putative germ cells and oocytes of adult gonads, and was sequestered into a posterior lineage during embryogenesis. In mature colonies of the ascidian B. violaceus, bot‐vasa mRNA was expressed in putative spermatogonia, in oocytes of zooids, and in some circulating cells in the zooids and differentiating buds. We propose that expression of vasa in cells other than gonadal germ cells of zooids in a colonial ascidian may serve as a source of germ‐line stem cells in the colony.
Detection of quorum sensing signal molecules in the family Vibrionaceae

Aims: The aim of this study was to detect the production of three kinds of quorum sensing (QS) signal molecules, i.e. the N‐acyl‐homoserine lactone (AHL), the autoinducer‐2 (AI‐2) and the cholerae autoinducer‐1‐like (CAI‐1‐like) molecules in 25 Vibrionaceae strains.
Applying an Influence Measurement Framework to Large Social Network

Predicting influential users is one of the important research problems on social network analysis. It helps to understand many complicated phenomena including information dissemination. It can be employed in many real world applications such as viral marketing. Influential users can influence social network users using their attributes, strategic locations or expertises. In this paper, we tackle this problem by proposing a novel hybrid framework that is used to predict influential users on social network. In this framework, we integrate users’ attributes and their strategic location to measure influence. We apply several centrality analysis algorithms to find user’s strategic locations, while we adapt a real world attribute measure that is used by Flickr based on users’ attributes. We employ our framework to a large dataset crawled from real world social network, i.e., Digg. We evaluate the proposed framework in term of correlation. We further show that the proposed framework outperforms other measurements
Temporal deletion of Aqp11 in mice is linked to the severity of cyst-like disease.

Aquaporin 11 (AQP11) is a channel protein with unknown biological function that is expressed in multiple tissues, including the kidney proximal tubule (PT) epithelium. Constitutive deletion of Aqp11 in mice (Aqp11-/-) results in early postnatal vacuolization in the PT and development of apparent cysts at 2 wk of age. Electron microscopy of adult Aqp11-/- mouse PT cells revealed a dilated rough endoplasmic reticulum. These changes may cause renal failure and premature death. This study examined 1) whether postnatal deletion of Aqp11 affects PT injury and cyst formation, 2) the temporal role of Aqp11 deletion on cyst development, and 3) the nature of apparent cysts. Tamoxifen-inducible Aqp11-/- mice were generated (Ti-Aqp11-/-). Deletion of Aqp11 at postnatal days (P) P2, P4, P6, P8, and P12 was investigated. Deranged renal development, especially in kidney cortex, PT cell vacuolization, and apparent tubular cysts developed only in mice where Aqp11 gene disruption was induced until P8. Aqp11 gene deletion from P12 onward did not result in a clear deficiency in renal development, PT injury, or cyst formation. Intraperitoneal injection of biotinylated-dextran (10 kDa) into adult mice resulted in extensive endocytic dextran uptake in both cystic Aqp11-/- and control PT epithelium, respectively. This suggests that apparent cysts are not membrane-enclosed structures but represent PT dilations. We conclude that Aqp11-/- mice develop cyst-like dilated proximal tubules without documented cysts at time of death.
Co-localization of glutamic acid decarboxylase and vesicular GABA transporter in cytochrome oxidase patches of macaque striate cortex

Abstract The patches in primary visual cortex constitute hot spots of metabolic activity, manifested by enhanced levels of cytochrome oxidase (CO) activity. They are also labeled preferentially by immunostaining for glutamic acid decarboxylase (GAD), γ-aminobutyric acid (GABA), and parvalbumin. However, calbindin shows stronger immunoreactivity outside patches. In light of this discrepancy, the distribution of the vesicular GABA transporter (VGAT) was examined in striate cortex of two normal macaques. VGAT immunoreactivity was strongest in layers 4B, 4Cα, and 5. In tangential sections, the distribution of CO, GAD, and VGAT was compared in layer 2/3. There was a close match between all three labels. This finding indicates that GABA synthesis is enriched in patches, and that inhibitory synapses are more active in patches than interpatches.
Design of 1 kW bidirectional half-bridge CLLC converter for electric vehicle charging systems

DC-DC converters are utilized in many applications such as automobiles, chargers, uninterrupted power supplies (UPS), and renewable energy systems. Galvanically isolated DC-DC converters are usually selected in electric vehicle (EV) battery charging systems. The converters typically interface between a DC link and a high voltage battery pack. Resonant CLLC DC-DC converters can achieve galvanic isolation, bidirectional power flow, and high efficiency, which make them good candidates for bidirectional EV charging systems. In this paper, a bidirectional half-bridge CLLC converter is designed and evaluated. An optimal soft-switching feature is applied in the design. The operating principle, design methodology and some considerations are presented. The prototype with 1 kW power rating interfaces a 300 – 600 V DC link and a high voltage battery pack (200 – 400 V). The performance in terms of efficiency, control complexity, component stress and cost is analyzed.
Protein composition of Rhodopseudomonas sphaeroides outer membrane

The outer membrane polypeptide profile of Rhodopseudmonas sphaeroides was characterized. Solubilization of the outer membrane at 75 or 100 degrees C as opposed to room temperature resulted in the dissociation of 75-, 72-, and 68-kilodalton (kdal) polypeptide aggregates into 29-, 26.5-, and 21.5-kdal polypeptides, respectively, and a shared 47-kdal subunit. Similarly, an 88.5-kdal polypeptide dissociates into a 45-kdal monomeric form, and the electrophoretic mobility of a 58.5-kdal polypeptide was altered to 83 kdal.Lysozyme treatment of outer membrane fractions altered the 21.5-kdal polypeptide mobility to 23 kdal. The presence of lipid in both the 47-kdal polypeptide and an 8- to 10-kdal polypeptide was demonstrated by lipid staining and [14C]acetate incorporation. The lipid component of the 47-kdal polypeptide was neither lipopolysaccharide nor phospholipid. The 8- to 10-kdal polypeptide may be the equivalent of the Braun lipoprotein. Outer membrane fractions isolated from R. sphaeroides-specific phage RS1-resistant mutants were deficient in several of the high-molecular-weight aggregates involving the 47-kdal polypeptide.
Different magnitude representations in left and right hemisphere: Evidence from the visual half field technique

The differences between left and right hemispheric magnitude representations were investigated in two lateralised priming experiments using single-digit (Experiment 1) and two-digit numbers (Experiment 2). Based on recent brain-imaging and TMS studies, some authors have argued that the magnitude representation in the left hemisphere (LH) is more precise than the one in the right hemisphere (RH). In two experiments a prime number preceded a target number that had to be classified as smaller or larger than a fixed standard. In order to reveal hemispheric differences in magnitude representation, the priming distance effect, i.e., faster responses to targets preceded by numerically closer primes, was analysed in both visual half fields (VHF). Using single-digit numbers no hemispheric differences were found for the priming distance effect, supporting an equally precise magnitude representation in both hemispheres. However, the experiment using two-digit numbers revealed a significantly steeper priming curve when targets were presented in the left visual field (LVF) compared to targets presented in the RVF. These results suggest a less precise magnitude representation in the RH, due to a larger overlap of magnitude representations.
Survey of emm-Like Gene Sequences from Pharyngeal Isolates of Group C and Group G Streptococci Collected in Spain

ABSTRACT We conducted a nationwide surveillance of the variable 5′ emm-like (M-like protein gene) sequences from 214 pharyngeal group C and group G streptococci. Almost 75% of the isolates exhibited emm or emm-like sequences previously described. We identified six new 5′ emm-like regions, and almost 23% of the isolates were nontypeable. Five emm-like sequences accounted for more than 50% of the isolates in group C and group G, suggesting horizontal gene transfer between strains of different species.