Miracle-dz/UniFAR-FTUs huggingface dataset:
A UDP glucosyltransferase from Bacillus subtilis successively transfers up to four glucose residues to 1,2‐diacylglycerol: expression of ypfP in Escherichia coli and structural analysis of its reaction products

We have isolated the ypfP gene (accession number P54166) from genomic DNA of Bacillus subtilis Marburg strain 60015 (Freese and Fortnagel, 1967) using PCR. After cloning and expression in E. coli, SDS–PAGE showed strong expression of a protein that had the predicted size of 43.6 kDa. Chromatographic analysis of the lipids extracted from the transformed E. coli revealed several new glycolipids. These glycolipids were isolated and their structures determined by nuclear magnetic resonance (NMR) and mass spectrometry. They were identified as 3‐[O‐β‐D‐glucopyranosyl‐(1→6)‐O‐β‐D‐glucopyranosyl]‐1,2‐diacylglycerol, 3‐[O‐β‐D‐glucopyranosyl‐(1→6)‐O‐β‐D‐glucopyranosyl‐(1→6)‐O‐β‐D‐glucopyranosyl]‐1,2‐diacylglycerol and 3‐[O‐β‐D‐glucopyranosyl‐(1→6)‐O‐β‐D‐glucopyranosyl‐(1→6)‐O‐β‐D‐glucopyranosyl‐(1→6)‐O‐β‐D‐glucopyranosyl]‐1,2‐diacylglycerol. The enzymatic activity expected to catalyse the synthesis of these compounds was confirmed by in vitro assays with radioactive substrates. In these assays, one additional glycolipid was formed and tentatively identified as 3‐[O‐β‐D‐glucopyranosyl]‐1,2‐diacylglycerol, which was not detected in the lipid extract of transformed cells. Experiments with some of the above‐described glycolipids as 14C‐labelled sugar acceptors and unlabelled UDP‐glucose as glucose donor suggest that the ypfP gene codes for a new processive UDP‐glucose: 1,2‐diacylglycerol‐3‐β‐D‐glucosyl transferase. This glucosyltransferase can use diacylglycerol, monoglucosyl‐diacylglycerol, diglucosyldiacylglycerol or triglucosyldiacylglycerol as sugar acceptor, which, apart from the first member, are formed by repetitive addition of a glucopyranosyl residue in β (1→6) linkage to the product of the preceding reaction.
ACHIEVEMENT GOAL ORIENTATIONS AND MATH ATTITUDES

The purpose of this research is to examine the relationships between achievement goal orientations and math attitudes. Participants were 569 university students. The 2X2 Achievement Goal Orientations Scale and Mathematics Attitudes Scale were used as measures. The relationships between achievement goal orientations and math attitudes were examined using correlation analysis and multiple regression analysis. According to the results negative attitudes were predicted positively by learning-avoidance and performance-approach/avoidance goal orientations. Furthermore, positive attitudes were predicted positively by learning-approach/avoidance goal orientations and negatively by performance-approach/avoidance goal orientations. The results were discussed in the light of literature.
Plasticity of Surface Structures and &bgr;2-Adrenergic Receptor Localization in Failing Ventricular Cardiomyocytes During Recovery From Heart Failure

Background— Cardiomyocyte surface morphology and T-tubular structure are significantly disrupted in chronic heart failure, with important functional sequelae, including redistribution of sarcolemmal &bgr;2-adrenergic receptors (&bgr;2AR) and localized secondary messenger signaling. Plasticity of these changes in the reverse remodeled failing ventricle is unknown. We used AAV9.SERCA2a gene therapy to rescue failing rat hearts and measured z-groove index, T-tubule density, and compartmentalized &bgr;2AR-mediated cAMP signals, using a combined nanoscale scanning ion conductance microscopy-Förster resonance energy transfer technique. Methods and Results— Cardiomyocyte surface morphology, quantified by z-groove index and T-tubule density, was normalized in reverse-remodeled hearts after SERCA2a gene therapy. Recovery of sarcolemmal microstructure correlated with functional &bgr;2AR redistribution back into the z-groove and T-tubular network, whereas minimal cAMP responses were initiated after local &bgr;2AR stimulation of crest membrane, as observed in failing cardiomyocytes. Improvement of &bgr;2AR localization was associated with recovery of &bgr;AR-stimulated contractile responses in rescued cardiomyocytes. Retubulation was associated with reduced spatial heterogeneity of electrically stimulated calcium transients and recovery of myocardial BIN-1 and TCAP protein expression but not junctophilin-2. Conclusions— In summary, abnormalities of sarcolemmal structure in heart failure show plasticity with reappearance of z-grooves and T-tubules in reverse-remodeled hearts. Recovery of surface topology is necessary for normalization of &bgr;2AR location and signaling responses.
Computer design: Generalized measures of computer system performance

GENERALIZED measures of computer system performance are being developed as part of a comprehensive information service. The need for standardized performance criteria is emphasized by the wide range of commercially available computers, the varied configurations each can assume, the great variety of tasks and methods of implementing them, and the ever-present limitations upon time and money for the selection, programming, and operation of the system.
TheDUTT1Gene, a Novel NCAM Family Member Is Expressed in Developing Murine Neural Tissues and Has an Unusually Broad Pattern of Expression

A new member of the NCAM family mapping to 3p12 has been isolated and predicted to be arranged in five immunoglobulin-like domains and three fibronectin-like domains which are particularly homologous to L1. There is a transmembrane domain and a long cytoplasmic region with no detectable homology to other sequences. Although less closely related to DCC, another family member, both share a loop of positively charged amino acids within the first immunoglobulin domain, unique to these two members of this very large gene family. Preliminary studies of expression in mouse embryos support an inferred role in neural development, but the observation of widespread gene expression in adult human tissues indicates that this protein has additional functions to those performed in neural cells.
Pre‐term delivery and the growth of the eye An oculometric study of eye size around term‐time

Abstract Refraction and axial eye dimensions, evaluated by ultrasound measurements, were investigated in 101 pre‐term infants and 25 full‐term controls. Gestational ages in the pre‐term group ranged from 25 to 34 weeks, birth weights from 728 to 2480 g. All were seen in the eye clinic due to risk of developing retinopathy of prematurity. Age at examination was 36–54 weeks (gestational/conceptional) in the pre‐terms and 37.3–50 weeks in the term infants. Adjusted to a 40 weeks axial length value (based on an assumed avarage eye elongation of 0.14 mm per week) the term‐values were similar, 17.02 and 17.03 mm in the two groups. Within the premature group, however, the 40‐week ajusted axial lengths were shorter, the shorter the gestational age. The study demonstrated more foetal anterior segment proportions, with flatter anterior chambers and thicker, more spheroid lenses in the preterm infants. Probably this explains the early preponderance of myopia in that group, at feature eventually to disappear, and not to be confused with myopia of prematurity. As compared to the full‐terms a correlational disturbance by pre‐term delivery was further indicated by the absence of the usual correlation between axial length and refractive value.
Inhibition of Glioblastoma Growth by the Thiadiazolidinone Compound TDZD-8

Background Thiadiazolidinones (TDZD) are small heterocyclic compounds first described as non-ATP competitive inhibitors of glycogen synthase kinase 3β (GSK-3β). In this study, we analyzed the effects of 4-benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8), on murine GL261 cells growth in vitro and on the growth of established intracerebral murine gliomas in vivo. Methodology/Principal Findings Our data show that TDZD-8 decreased proliferation and induced apoptosis of GL261 glioblastoma cells in vitro, delayed tumor growth in vivo, and augmented animal survival. These effects were associated with an early activation of extracellular signal-regulated kinase (ERK) pathway and increased expression of EGR-1 and p21 genes. Also, we observed a sustained activation of the ERK pathway, a concomitant phosphorylation and activation of ribosomal S6 kinase (p90RSK) and an inactivation of GSK-3β by phosphorylation at Ser 9. Finally, treatment of glioblastoma stem cells with TDZD-8 resulted in an inhibition of proliferation and self-renewal of these cells. Conclusions/Significance Our results suggest that TDZD-8 uses a novel mechanism to target glioblastoma cells, and that malignant progenitor population could be a target of this compound.
An Efficient Approach for Outlier Analysis over Big Data

Outlier analysis was used since a year decade for removing the irregular annotations from data sets. Outlier exists in data sets due to unexpected faults, activities, fake behavior, human intervention error, sensor error due to atmospheric interference etc. These detections are required to identify the system faults, irregular behavior of data in some specific application for decision making and to identify the frauds. The numbers of research have been proposed by the researchers but with limited solutions. Proposed detection techniques are not quite sufficient to resolve the current issues like performance and detect the accurate outlier from the big data. This paper entails an architecture and algorithm for outlier analysis over big data. We proposed an architecture and algorithm for outlier analysis which can be useful to resolve the current issues.
Social Networks Meet Distributed Systems: Towards a Robust Sybil Defense under Churn

This paper examines the impact of heavy churn on the robustness of decentralized social network-based Sybil defense (SNSD) schemes. Our analysis reveals that (i) heavy churn disintegrates the social overlay network that is fundamental to these schemes into multiple disconnected components, resulting in poor network connectivity, and (ii) a naive solution that adds links from each node to all its 2-hop neighbors improves network connectivity but comes at a significant cost of poor attack resilience of these schemes. We propose a new design point in the trade-off between network connectivity and attack resilience of SNSD schemes, where each node adds links to only a selective few of all its 2-hop neighbors based on a minimum expansion contribution (MinEC) heuristic. Extensive evaluation through simulations shows that our approach fares as good as the naive 2-hop solution in terms of network connectivity, while making little compromise on the attack resilience. Moreover, our approach preserves the fast-mixing property that is fundamental to many SNSD schemes even at high levels of churn. This result suggests that existing and potential future SNSD schemes relying on this property can incorporate our approach into their designs with minimal changes.
Activation of Na (cid:1) /H (cid:1) Exchanger 1 Is Sufficient to Generate Ca 2 (cid:1) Signals That Induce Cardiac Hypertrophy and Heart Failure

—Activation of the sarcolemmal Na (cid:1) /H (cid:1) exchanger (NHE)1 is increasingly documented as a process involved in cardiac hypertrophy and heart failure. However, whether NHE1 activation alone is sufficient to induce such remodeling remains unknown. We generated transgenic mice that overexpress a human NHE1 with high activity in hearts. The hearts of these mice developed cardiac hypertrophy, contractile dysfunction, and heart failure. In isolated transgenic myocytes, intracellular pH was elevated in Hepes buffer but not in physiological bicarbonate buffer, yet intracellular Na (cid:1) concentrations were higher under both conditions. In addition, both diastolic and systolic Ca 2 (cid:1) levels were increased as a consequence of Na (cid:1) -induced Ca 2 (cid:1) overload; this was accompanied by enhanced sarcoplasmic reticulum Ca 2 (cid:1) loading via Ca 2 (cid:1) /calmodulin-dependent protein kinase (CaMK)II-dependent phosphorylation of phospholamban. Negative force–frequency dependence was observed with preservation of high Ca 2 (cid:1) , suggesting a decrease in myofibril Ca 2 (cid:1) sensitivity. Furthermore, the Ca 2 (cid:1) -dependent prohypertrophic molecules calcineurin and CaMKII were highly activated in transgenic hearts. These effects observed in vivo and in vitro were largely prevented by the NHE1 inhibitor cariporide. Interestingly, overexpression of NHE1 in neonatal rat ventricular myocytes induced cariporide-sensitive nuclear translocation of NFAT (nuclear factor of activated T cells) and nuclear export of histone deacetylase 4, suggesting that increased Na (cid:1) /H (cid:1) exchange activity can alter hypertrophy-associated gene expression. However, in transgenic myocytes, contrary to exclusive translocation of histone deacetylase 4, NFAT only partially translocated to nucleus, possibly because of marked activation of p38, a negative regulator of NFAT signaling. We conclude that activation of NHE1 is sufficient to initiate cardiac hypertrophy and heart failure mainly through activation of CaMKII–histone deacetylase pathway. ( Circ Res . 2008;103:891-899.) at 35ºC. To measure the steady-state pH i under physiological transfection, indirect
Feeling is Understanding: From Affective to Semantic Spaces

Motivated by theories of language development we investigate the contribution of affect to lexical semantics in the context of distributional semantic models (DSMs). The relationship between semantic and affective spaces is computationally modeled for the task of semantic similarity computation between words. It is shown that affective spaces contain salient information for lexical semantic tasks. We further investigate specific semantic relationships whe re affective information plays a prominent role. The relations between semantic similarity and opposition are studied in the framework of a binary classification problem applied for the discrimination of synonyms and antonyms. For the case of antonyms, the use of affective features results in 33% relat ive improvement in classification accuracy compared to the use of semantic features.
3D-mapping-aided gnss localization for integrity monitoring in urban environments

In order to foster the development of Global Navigation Satellite Systems (GNSS) for land navigation services, there is a pressing need for providing a trust level of the localization solution, especially for liability critical applications. In view of such need, integrity monitoring aims to compute protection levels that successfully bounds positioning errors in nominal conditions. Conventional Receiver Autonomous Integrity Monitoring (RAIM) algorithms have been widely used for integrity monitoring especially for aircraft navigation. Conventional RAIM starts out by supposing a Gaussian measurement errors model with known means and variances. However, this assumption does not hold in dense urban environment. Therefore, we propose novel algorithms that dispenses with this classical assumption. We use external information provided by a 3D GNSS simulation to characterize GNSS errors in urban areas. We propose two approaches for protection levels computation based on comparison between predicted 3D pseudo-ranges bias and computed thresholds. These approaches give a new vision on integrity control based on indicators on the pseudo-ranges bias. Experimental results show that proposed algorithms give an acceptable success rate on integrity monitoring in a harsh areas.
Logic encryption: A fault analysis perspective

The globalization of Integrated Circuit (IC) design flow is making it easy for rogue elements in the supply chain to pirate ICs, overbuild ICs, and insert hardware trojans; the IC industry is losing approximately $4 billion annually [1], [2]. One way to protect the ICs from these attacks is to encrypt the design by inserting additional gates such that correct outputs are produced only when specific inputs are applied to these gates. The state-of-the-art logic encryption technique inserts gates randomly into the design [3] and does not necessarily ensure that wrong keys corrupt the outputs. Our technique ensures that wrong keys corrupt the outputs. We relate logic encryption to fault propagation analysis in IC testing and develop a fault analysis based logic encryption technique. This technique achieves 50% Hamming distance between the correct and wrong outputs (ideal case) when a wrong key is applied. Furthermore, this 50% Hamming distance target is achieved by using a smaller number of additional gates when compared to random logic encryption.
A robust framework for detecting structural variations in a genome

Motivation: Recently, structural genomic variants have come to the forefront as a significant source of variation in the human population, but the identification of these variants in a large genome remains a challenge. The complete sequencing of a human individual is prohibitive at current costs, while current polymorphism detection technologies, such as SNP arrays, are not able to identify many of the large scale events. One of the most promising methods to detect such variants is the computational mapping of clone-end sequences to a reference genome. Results: Here, we present a probabilistic framework for the identification of structural variants using clone-end sequencing. Unlike previous methods, our approach does not rely on an a priori determined mapping of all reads to the reference. Instead, we build a framework for finding the most probable assignment of sequenced clones to potential structural variants based on the other clones. We compare our predictions with the structural variants identified in three previous studies. While there is a statistically significant correlation between the predictions, we also find a significant number of previously uncharacterized structural variants. Furthermore, we identify a number of putative cross-chromosomal events, primarily located proximally to the centromeres of the chromosomes. Availability: Our dataset, results and source code are available at http://compbio.cs.toronto.edu/structvar/ Contact:seunghak@cs.toronto.edu,echeran@cs.toronto.edu,brudno@cs.toronto.edu
Fluent temporal logic for discrete-time event-based models

Fluent model checking is an automated technique for verifying that an event-based operational model satisfies some state-based declarative properties. The link between the event-based and state-based formalisms is defined through "fluents" which are state predicates whose value are determined by the occurrences of initiating and terminating events that make the fluents values become true or false, respectively.The existing fluent temporal logic is convenient for reasoning about untimed event-based models but difficult to use for timed models. The paper extends fluent temporal logic with temporal operators for modelling timed properties of discrete-time event-based models. It presents two approaches that differ on whether the properties model the system state after the occurrence of each event or at a fixed time rate. Model checking of timed properties is made possible by translating them into the existing untimed framework.
Distributed Fault Detection and Isolation Resilient to Network Model Uncertainties

The ability to maintain state awareness in the face of unexpected and unmodeled errors and threats is a defining feature of a resilient control system. Therefore, in this paper, we study the problem of distributed fault detection and isolation (FDI) in large networked systems with uncertain system models. The linear networked system is composed of interconnected subsystems and may be represented as a graph. The subsystems are represented by nodes, while the edges correspond to the interconnections between subsystems. Considering faults that may occur on the interconnections and subsystems, as our first contribution, we propose a distributed scheme to jointly detect and isolate faults occurring in nodes and edges of the system. As our second contribution, we analyze the behavior of the proposed scheme under model uncertainties caused by the addition or removal of edges. Additionally, we propose a novel distributed FDI scheme based on local models and measurements that is resilient to changes outside of the local subsystem and achieves FDI. Our third contribution addresses the complexity reduction of the distributed FDI method, by characterizing the minimum amount of model information and measurements needed to achieve FDI and by reducing the number of monitoring nodes. The proposed methods can be fused to design a scalable and resilient distributed FDI architecture that achieves local FDI despite unknown changes outside the local subsystem. The proposed approach is illustrated by numerical experiments on the IEEE 118-bus power network benchmark.
Isolation of herpes simplex virus regulatory protein ICP4 as a homodimeric complex

The viral polypeptide ICP4 (or Vmw175) is synthesized during the immediate early phase of infection by herpes simplex virus and regulates the transcription of delayed early and late viral genes. We obtained a partially purified preparation of soluble ICP4 under nondenaturing conditions. Physical constants for native ICP4 were empirically determined by molecular sieve chromatography and sucrose density gradient ultracentrifugation. The Stokes radius of native ICP4 was 8.72 X 10(-7) cm. The sedimentation coefficient of native ICP4 was 9.00S. From these values, the calculated molecular weight of native ICP4 was 342,000, a value which is twice that of monomeric ICP4, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The failure of any other polypeptides to specifically coprecipitate with native ICP4 in the presence of anti-ICP4 antibody indicates that the 342,000-dalton complex is a homodimer of ICP4. The frictional coefficient ratio of native ICP4, which is 1.9, indicates that the homodimer is a highly elongated molecule.
Designing and Applying Adaptation Patterns Embedded in the Script

CeLS is a web-based system designed to enable teachers and researchers to create, enact and test multi-stage CSCL scripts in actual educational settings. The paper presents CeLS approach and potential for adaptive collaboration scripting, aimed to tailor the activity according to students' performance, personal characteristics and preferences. We specifically focus on two aspects: 'on the fly' adaptations according to enactment events and Adaptation Patterns: pre-designed processes that are embedded in the script definition.
Plasmacytoid dendritic cells sense hepatitis C virus–infected cells, produce interferon, and inhibit infection

Hepatitis C virus (HCV), a member of the Flaviviridae family, is a single-stranded positive-sense RNA virus that infects >170 million people worldwide and causes acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Despite its ability to block the innate host response in infected hepatocyte cell lines in vitro, HCV induces a strong type 1 interferon (IFN) response in the infected liver. The source of IFN in vivo and how it is induced are currently undefined. Here we report that HCV-infected cells trigger a robust IFN response in plasmacytoid dendritic cells (pDCs) by a mechanism that requires active viral replication, direct cell-cell contact, and Toll-like receptor 7 signaling, and we show that the activated pDC supernatant inhibits HCV infection in an IFN receptor-dependent manner. Importantly, the same events are triggered by HCV subgenomic replicon cells but not by free virus particles, suggesting the existence of a novel cell-cell RNA transfer process whereby HCV-infected cells can activate pDCs to produce IFN without infecting them. These results may explain how HCV induces IFN production in the liver, and they reveal a heretofore unsuspected aspect of the innate host response to viruses that can subvert the classical sensing machinery in the cells they infect, and do not infect or directly activate pDCs.