Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization of Hypoxia‐Inducible Factor 1α‐p300 Interactions in Live Cells by Fluorescence Resonance Energy Transfer

Hypoxia‐inducible factor (HIF)‐1α mediates the hypoxia response signaling pathway essential for maintaining cellular homeostasis in low oxygen environments through its complex formation with CBP/p300 in the nucleus. Employing fluorescence resonance energy transfer (FRET), we devised a live‐cell interaction assay based on reporter proteins by tagging fluorescent proteins onto the carboxy termini of HIF‐1α and p300. The nature of the constructed reporter protein was verified by observing localized distribution, degradation, and stabilization kinetics in cells transfected with the HIF‐1α containing plasmid. A mutant HIF‐1α incapable of binding to p300 was then utilized to demonstrate insignificant FRET efficiency, thereby confirming that our constructs could effectively probe the direct interaction between HIF‐1α and p300. We further examined the effects of small molecules known to modulate the HIF‐1α‐p300 interaction and transcriptional activity on FRET. Finally, by inhibiting activities of two HIF‐specific hydroxylases, HIF‐specific prolyl hydroxylase (PHD) 2 and factor inhibiting HIF‐1 (FIH‐1) with their specific siRNAs, we explored how these HIF‐specific hydroxylases contribute to the HIF‐1α‐p300 interaction by FRET measurements along with HIF‐1 mediated transcriptional activation. Therefore, this technique would provide a way to study selective inhibition of either PHD2 or FIH‐1 within living cells, and to screen specific inhibitors of HIF‐mediated transcription activity for therapeutic applications. J. Cell. Biochem. 115: 271–280, 2014. © 2013 Wiley Periodicals, Inc.
Classification of Traffic Flows into QoS Classes by Unsupervised Learning and KNN Clustering

Traffic classification seeks to assign packet flows to an appropriate quality of service (QoS) class based on flow statistics without the need to examine packet payloads. Classification proceeds in two steps. Classification rules are first built by analyzing traffic traces, and then the classification rules are evaluated using test data. In this paper, we use self-organizing map and K-means clustering as unsupervised machine learning methods to identify the inherent classes in traffic traces. Three clusters were discovered, corresponding to transactional, bulk data transfer, and interactive applications. The K-nearest neighbor classifier was found to be highly accurate for the traffic data and significantly better compared to a minimum mean distance classifier.
Distributive and self-sustainable scheduling algorithm for wireless sensor networks

Scheduling or allocation of resources becomes one of the fundamental problems in wireless networks when several nodes contend to access a single and a common medium. To design a scalable wireless network, the slot scheduling algorithm must be computationally simple and distributive. In the past, many scheduling algorithms were proposed. However, when these techniques were implemented in dense networks, they often lacked the scalability factor due to node failure and dynamic topology changes. Thus, the design of optimal distributed scheduling algorithm has remained a challenge for the last few decades. In this paper, we propose a distributive and self-sustainable scheduling algorithm (DSSA). DSSA is a schedule based protocol and the objective of the algorithm is to assign the time slots to the nodes and avoid collision. DSSA is a simple, distributed and performance optimal scheduling algorithm and overcomes a variety of slot scheduling problems. DSSA resolves slot scheduling challenges by presenting a novel heuristic approach. The proposed technique is not centralized, hence it is distributive. It is fair and simple in terms of implementation, because the node which REQUEST first is given a priority to schedule its slot. Moreover, it is robust against any dynamic change without incurring extra message overhead and, utilizes minimal resources to provide an optimal collision free transmission. Simulation results show that DSSA is more performance optimal than the distributed randomized scheduling algorithm DRAND in terms of energy consumption, message overhead and execution time.
Distributed Charging Control of Plug-In Electric Vehicles via the Stochastic Alternating Direction Method of Multipliers

Plug-in electric vehicles (PEVs) are likely to become very popular in the future. With a large number of PEVs across the world, the batteries of PEVs may form a huge energy storage system which can serve as both controllable power loads and power sources. This can help the power grid to regulate the frequency by minimizing the expected imbalance between load and generation under the circumstance of high load uncertainty. In this paper, we propose a distributed algorithm to solve this stochastic minimization problem. The algorithm is very easy to implement. Simulation results show that our proposed algorithm works well and can benefit the power grid in helping frequency regulation.
Maltotriose is the inducer of the maltose regulon of Escherichia coli

In a cell-free system programmed with a plasmid bearing a malP'-'lacZ gene fusion under the control of malPp, beta-galactosidase synthesis was strictly dependent on the presence of both the MalT activator protein and the inducer of the Escherichia coli maltose regulon. We show that, among all maltodextrins tested (from maltose to maltoheptaose), only maltotriose was able to induce beta-galactosidase synthesis. Likewise, in an in vitro transcription system, initiation of transcription at malPp required the presence of the MalT protein and maltotriose along with the RNA polymerase holoenzyme; neither maltose nor maltotetraose could substitute for maltotriose.
Stabilizing controller design for uncertain nonlinear systems using fuzzy models

A Lyapunov-based stabilizing control design method for uncertain nonlinear dynamical systems using fuzzy models is proposed. The controller is constructed using a design model of the dynamical process to be controlled. The design model is obtained from the truth model using a fuzzy modeling approach. The truth model represents a detailed description of the process dynamics. The truth model is used in a simulation experiment to evaluate the performance of the controller design. A method for generating local models that constitute the design model is proposed. Sufficient conditions for stability and stabilizability of fuzzy models using fuzzy state feedback controllers are given. The results obtained are illustrated with a numerical example involving a four-dimensional nonlinear model of a stick balancer.
Construction of genomic libraries from Neurospora crassa with the BigEasy TM v 2 . 0 Linear Cloning System

Introduction The complete genome sequence of the filamentous fungus Neurospora crassa has been difficult to assemble, because a large amount of AT-rich “genomic dark matter” is lost from traditional shotgun, cosmid, and BAC libraries (1-3). This situation is typical of most repeat-rich eukaryotic genomes. Various novel direct sequencing approaches promise to reduce some of these errors. However, preliminary results from 454 pyrosequencing of the Neurospora crassa genome (1, 2) suggest that new sequencing methodology alone will likely not be sufficient to generate finished sequence of even a relatively small eukaryotic genome (~40 Mb), simply because assembly of AT-rich repeats proves to be a major obstacle.
An Increase in Dietary Quality Is Associated with Favorable Plasma Biomarkers of the Brain-Adipose Axis in Apparently Healthy US Women.

BACKGROUND The associations between long-term dietary quality and biomarkers of the brain-adipose axis have not been examined. OBJECTIVE We evaluated both cross-sectional and longitudinal associations between dietary quality and several biomarkers involved in the brain-adipose axis. METHODS In the Nurses' Health Study II, 831 women [baseline mean age: 45 y; body mass index (BMI; in kg/m(2)): 24.6] were randomly selected from women who provided 2 fasting blood samples in 1996-1999 and 2010-2011 to measure plasma concentrations of leptin, soluble leptin receptor (sOB-R), adiponectin, insulin, retinol binding protein-4 (RBP-4), interleukin-6 (IL-6), and C-reactive protein (CRP). Dietary quality was assessed by the Alternative Healthy Eating Index (AHEI-2010) with the use of semiquantitative food-frequency questionnaires administered in 1995 and 2011. We used linear mixed models to evaluate the cross-sectional associations between dietary quality and biomarker concentrations. We also examined change in dietary quality in relation to change in biomarker concentrations. RESULTS In cross-sectional analyses that compared the highest with the lowest quintile of AHEI-2010, we observed significantly lower leptin (P-trend < 0.0001), insulin (P-trend < 0.0001), and CRP (P-trend = 0.02) and significantly higher sOB-R (P-trend < 0.0001) and adiponectin (P-trend = 0.0003). These associations, except for CRP, remained significant after adjustment for BMI. In longitudinal analyses, women in the highest quintile of AHEI-2010 score change (most improvement) had a 13% increase in leptin, compared with a 42% increase (P-trend < 0.0001) in the lowest quintile (least improvement). The corresponding multivariable-adjusted percentage changes for other biomarkers were 4% compared with -1% for sOB-R (P-trend = 0.04), 14% compared with 6% for adiponectin (P-trend = 0.02), and -11% compared with 16% for CRP (P-trend = 0.02). Adjustment for interim weight change attenuated these associations. No associations were observed for RBP-4 or IL-6. CONCLUSION Improvement in dietary quality was associated with favorable profiles of several biomarkers of the brain-adipose axis in women.
B4GAT1 is the priming enzyme for the LARGE-dependent functional glycosylation of α-dystroglycan

Recent studies demonstrated that mutations in B3GNT1, an enzyme proposed to be involved in poly-N-acetyllactosamine synthesis, were causal for congenital muscular dystrophy with hypoglycosylation of α-dystroglycan (secondary dystroglycanopathies). Since defects in the O-mannosylation protein glycosylation pathway are primarily responsible for dystroglycanopathies and with no established O-mannose initiated structures containing a β3 linked GlcNAc known, we biochemically interrogated this human enzyme. Here we report this enzyme is not a β-1,3-N-acetylglucosaminyltransferase with catalytic activity towards β-galactose but rather a β-1,4-glucuronyltransferase, designated B4GAT1, towards both α- and β-anomers of xylose. The dual-activity LARGE enzyme is capable of extending products of B4GAT1 and we provide experimental evidence that B4GAT1 is the priming enzyme for LARGE. Our results further define the functional O-mannosylated glycan structure and indicate that B4GAT1 is involved in the initiation of the LARGE-dependent repeating disaccharide that is necessary for extracellular matrix protein binding to O-mannosylated α-dystroglycan that is lacking in secondary dystroglycanopathies. DOI: http://dx.doi. org/10.7554/eLife.03943. 001
Interactive consistency with multiple failure modes

The authors address the problem of reaching Byzantine agreement in a distributed system in the presence of different types of faults and show that significant improvements in reliability and performance are possible if faults can be partitioned into disjoint classes. They show that, in a distributed system, to guarantee Byzantine agreement requires N>2a+2s+b+r where N is the total number of processors, a is the number of malicious asymmetric faults (a<or=r), s the number of malicious symmetric faults, b the number of nonmalicious or intercepted faults, and r an algorithm-dependent term. The practical value of this unified model in designing ultrareliable systems is demonstrated by examples. <<ETX>>
Exploring Active and Passive Team-Based Coordination

As human-robot teamwork becomes increasingly common, a key challenge is to fluidly and intuitively coordinate team members’ interactions. In this work, we explore two modalities of human-robot coordination: active, where agents intentionally attempt to understand and influence the plans of human teammates, and passive, where agents simply react to their human teammates’ varying behavior. In our Productivity and Wellness Pal (PaWPal) project, we seek to develop an agent that actively elicits a teammate’s constraints, preferences, and goals in order to nudge them towards better behavior. Conversely, in our Coordinating HumanRobot Teamwork project, we take a distributed approach to scheduling where agents passively adapt to teammates’ plan executions. Our research hypothesis is that human-robot coordination techniques will lead to more natural and effective human-robot teamwork if they recognize and respect the inclinations of all teammates.
Offset-free Energy-optimal Model Predictive Control for point-to-point motions

This paper discusses Offset-free Energy-optimal Model Predictive Control (offset-free EOMPC) which is a MPC algorithm to realize time-constrained energy-optimal point-to-point motion control with high positioning accuracy for linear time-invariant (LTI) systems. The offset-free EOMPC approach is developed based on our previous research - Energy-optimal Model Predictive Control (EOMPC) - which aims at performing energy-optimal point-to-point motions within a given motion time. A drawback of the EOMPC method is that it cannot achieve high positioning accuracy in the presence of unmodelled disturbances or model-plant mismatch. In order to cope with this problem, a `disturbance model' strategy is adopted: the system state is augmented with disturbance variables. Based on the `disturbance model', the disturbances are estimated and the effects of which are cancelled. Experimental validation of the offset-free EOMPC on a linear motor with coulomb friction and cogging disturbances has been implemented and the results show that time-constrained energy-optimal point-to-point motion with high positioning accuracy is achieved.
Incidental Histopathological Findings in Hearts of Control Beagle Dogs in Toxicity Studies

In preclinical studies of pharmaceutical agents, the beagle dog is a commonly used model for the detection of cardiotoxicity. Incidental findings, postmortem changes, and artifacts must be distinguished histopathologically from test item–related findings in the heart. In this retrospective analysis, cardiac sections from 88 control beagles (41 male, 47 female; ages 5–18 months) in preclinical studies were examined histopathologically. The most common finding was thickening of the tunica media of intramural coronary arteries, most likely a postmortem change. The second most common finding was the presence of vacuoles within Purkinje fibers. Dilated lymphatic and blood vessels at the insertion of chordae tendineae were noted more commonly in males than in females and were considered a normal anatomic feature. Mesothelial-lined papillary fronds along the epicardial surface of the atria were present in several dogs, as were small infiltrates of inflammatory cells usually within the myocardium. In summary, control beagles’ hearts frequently have incidental findings that must be differentiated from test item–related pathologic changes. Historical control data can be useful for the interpretation of incidental and test item–related findings in the beagle heart.
A Structured Clinical Interview for Kleptomania (SCI‐K): preliminary validity and reliability testing

Kleptomania presents difficulties in diagnosis for clinicians. This study aimed to develop and test a DSM‐IV‐based diagnostic instrument for kleptomania. To assess for current kleptomania the Structured Clinical Interview for Kleptomania (SCI‐K) was administered to 112 consecutive subjects requesting psychiatric outpatient treatment for a variety of disorders. Reliability and validity were determined. Classification accuracy was examined using the longitudinal course of illness. The SCI‐K demonstrated excellent test‐retest (Phi coefficient = 0.956 (95% CI = 0.937, 0.970)) and inter‐rater reliability (phi coefficient = 0.718 (95% CI = 0.506, 0.848)) in the diagnosis of kleptomania. Concurrent validity was observed with a self‐report measure using DSM‐IV kleptomania criteria (phi coefficient = 0.769 (95% CI = 0.653, 0.850)). Discriminant validity was observed with a measure of depression (point biserial coefficient = −0.020 (95% CI = −0.205, 0.166)). The SCI‐K demonstrated both high sensitivity and specificity based on longitudinal assessment. The SCI‐K demonstrated excellent reliability and validity in diagnosing kleptomania in subjects presenting with various psychiatric problems. These findings require replication in larger groups, including non‐psychiatric populations, to examine their generalizability. Copyright © 2006 John Wiley & Sons, Ltd.
Turning Point Prediction of Oscillating Time Series using Local Dynamic Regression Models

In the prediction of oscillating time series, the interest is in the turning points of successive oscilla- tions rather than the samples themselves. For this purpose a scheme has been proposed; the state space reconstruction is limited to the turning points and the local (nearest neigh- bor) model is modified in order to predict the turning point magnitudes and times. This approach is extended here us- ing a local dynamic regression model on both turning point magnitudes and times. Simulations on oscillating nonlin- ear systems show that the proposed approach gives better predictions of turning points than the standard local model applied to all the samples of the oscillating time series.
A note on fitting a marginal model to mixed effects log-linear regression data via GEE.

Marginal generalized linear models for correlated data are often fit by generalized estimating equations (Liang, K.Y. and Zeger, S.L., 1986, Biometrika 73, 13-22), which requires the marginal expectation to be correctly specified while the covariance structure is allowed to be misspecified. This note is concerned with the correct specification of the marginal mean for data from a mixed log-linear regression model and the relationship between the true subject-specific parameters and the true marginal parameters.
On the inverse kinematics of an a priori unknown general 6R-Robot

SUMMARY This paper looks at the inverse kinematics problem of an a priori unknown 6R-Robot from the representation point of view. It describes a new representation of the Euclidean motion group. With this representation, the inverse kinematics problem can be treated entirely numerical. No symbolical methods are required.
Toward Distributed Relay Selection for Opportunistic Amplify-and-Forward Transmission

Opportunistic relaying in cooperative communication depends on careful relay selection. However the traditional centralized method used for opportunistic Amplify-and-Forward (OAF) protocols requires precise measurements of channel state information (CSI) at the destination (CSI-OAF). In this paper, we propose a distributed relay selection framework for opportunistic AF (D-OAF) cooperative communications and offer an accurate performance analysis based on exact statistics of the local signal-to-noise ratios of the best relay. Furthermore, we validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures, and we compare our new results with their CSI-based counterparts.
Identification of Genes Differentially Expressed in Cultured Human Osteoblasts Versus Human Fibroblasts by DNA Microarray Analysis

Little is known about patterns of gene expression from cells populating the connective tissues. This study investigated the possible variance of gene expression profile between human osteoblasts (HO) and human fibroblasts (HF) in vitro, using DNA microarray technology. Clustering identification was used to compare expression patterns between HO and HF for biological significance. Our results showed that genes encoding the extracellular matrix or apoptosis-related proteins tended to be expressed in greater abundance in HO, while more proteolysis-related proteins were expressed in higher level in HF. Significant differences in expression were also noted with genes related to signaling pathways. To confirm the array results, three genes (periostin, MFG-E8, MMP-10) were selected and analyzed independently by RT-PCR and northern blot. The results were found consistent with the array data in HO and HF. The present findings suggest that HO and HF differ not only phenotypically but in the expression level of tissue specific genes to assure the turnover and homeostasis of their respective tissues.
Lysine and protein metabolism in young women. Subdivision based on the novel use of multiple stable isotopic labels.

A multitracer stable isotope study of lysine kinetics was carried out in fasted adult female volunteers to determine whether a multicompartmental model that partitions protein synthesis and breakdown into at least two types of tissue components can be constructed from plasma and breath data. Five female subjects, maintained on formula diets, received L-[13C1]lysine (27 mumol/kg) as an i.v. bolus and L-[15N2]lysine (27 mumol/kg) as an oral bolus 4 h postprandially. Plasma and breath samples were collected for 6 h. On an alternate day, subjects received NaH13CO3 (10 mumol/kg) as an i.v. bolus and breath samples were collected for 6 h. Plasma tracer lysine levels were determined by gas chromatography-mass spectrometry isotope ratiometry, and breath 13CO2 levels were measured by mass spectrometric gas isotope ratiometry. The tracer data could be fitted to a mammillary multicompartmental model that consisted of a lysine central compartment and slow- and fast-exchanging peripheral compartments containing 37, 38, and 324 mumol/kg, respectively. The rates of lysine oxidation, incorporation into protein, and release by protein breakdown were 21, 35, and 56 mmol/kg/h, respectively, in the fast-exchanging compartment, whereas the rates of protein synthesis and breakdown in the slow compartment were both 53 mmol/kg/min. These values corresponded to a whole-body lysine flux of 106 mmol/kg/h. The kinetic parameters were in excellent agreement with reported values obtained by constant-infusion methods. The measurements indicated that it will be possible to detect changes in amino acid pool sizes and protein synthesis and breakdown associated with the mobilization of protein stores from plasma and breath measurements in multitracer stable isotope experiments.
A deck for sound design in games: enhancements based on a design exercise

In the context of an initiative to empower non-expert practitioners to perform sound design in games, we have been working on a collection of design patterns and in a deck of cards that function as tokens to those patterns. The deck serves both practitioners and researchers. Practitioners may appreciate a presentation of potential sound explorations in a format that is literally handy, with no need to be familiar with the formalism of design patterns. Researchers who are willing to evolve such patterns may explore the usage of cards as part of a setting designed to be auditable. This paper presents the results of a first experiment with the deck in a scenario of a game design session. The goal is to evidence information supporting foremost enhancements to the deck itself, to the process in which it has being explored and audited, and to the inscribed collection of patterns.