Miracle-dz/UniFAR-FTUs huggingface dataset:
Optogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin action

ABSTRACT Glucose transporter 4 (GLUT4; also known as SLC2A4) resides on intracellular vesicles in muscle and adipose cells, and translocates to the plasma membrane in response to insulin. The phosphoinositide 3-kinase (PI3K)–Akt signaling pathway plays a major role in GLUT4 translocation; however, a challenge has been to unravel the potentially distinct contributions of PI3K and Akt (of which there are three isoforms, Akt1–Akt3) to overall insulin action. Here, we describe new optogenetic tools based on CRY2 and the N-terminus of CIB1 (CIBN). We used these ‘Opto’ modules to activate PI3K and Akt selectively in time and space in 3T3-L1 adipocytes. We validated these tools using biochemical assays and performed live-cell kinetic analyses of IRAP–pHluorin translocation (IRAP is also known as LNPEP and acts as a surrogate marker for GLUT4 here). Strikingly, Opto-PIP3 largely mimicked the maximal effects of insulin stimulation, whereas Opto-Akt only partially triggered translocation. Conversely, drug-mediated inhibition of Akt only partially dampened the translocation response of Opto-PIP3. In spatial optogenetic studies, focal targeting of Akt to a region of the cell marked the sites where IRAP–pHluorin vesicles fused, supporting the idea that local Akt-mediated signaling regulates exocytosis. Taken together, these results indicate that PI3K and Akt play distinct roles, and that PI3K stimulates Akt-independent pathways that are important for GLUT4 translocation. Summary: Optogenetic activation with new PI3K and Akt probes support that both Akt-dependent and Akt-independent pathways are necessary for consistent GLUT4 translocation.
A wide tuning 1.3 GHz LC VCO with fast settling noise filtering voltage regulator in 0.18 µm CMOS process

This paper presents a wide tuning LC voltage controlled oscillator (VCO) with integrated voltage regulator to minimize supply pushing. The integrated voltage regulator utilizes on-chip low-corner frequency noise filters to minimize the impact of regulator noise on VCO phase noise. One shot circuit is used with low-corner frequency noise filter to ensure fast settling. The VCO achieves current consumption of 15.9 mA with single integrated low-Q LC tank, tuning range of 620.8 MHz to 1384.5 MHz, phase noise of −128 dBc/Hz at 1 MHz offset from 1.3 GHz carrier at room temperature. With the noise filter, 9 dB improvement in phase noise is demonstrated in measurement. The frequency range can be extended to 38.8 MHz – 1384.5 MHz with integrated frequency dividers.
Feature Extraction from Protein Sequences and Classification of Enzyme Function

Enzymes are biological catalysts that mediate almost all chemical reactions and are found in all tissues and fluids of the body. These enzymes play a central role in metabolic pathways, and in the prediction of metabolic pathways. Our goals in the present study were to identify new features for reliable enzyme functional classification and prediction that do not rely on sequence alignment, and to improve the accuracy or lower the error rate using the attribute selection method. In this study, we designed novel features, including PPR, NNR, PNPR, PPRDist(x, y), NNRDist(x, y), and PNPRDist(x, y), extracted from each protein sequence. Using only protein sequences, we compiled a set of 84 attributes that characterize proteins, and obtained accuracy of 72.13% through identification of optimal attributes in a given dataset. Our experiment results demonstrate that these attributes, as novel features, are useful for enzyme functional classification. In addition, we identify and analyze the biologically meaningful features of a given dataset.
A New Design of the Hash Functions With All-or-Nothing Property

All-or-nothing property is a new encryption mode proposed by Rivest and has the property that one must decrypt the entire ciphertext to determine any plaintext block. In this paper, we propose hash functions with all-or-nothing property. The proposed schemes use the existing hash functions without changing their structures, and they are secure against known attacks. Moreover, the proposed methods can be easily extended to the MAC (Message Authentication Code) for providing message confidentiality as well as authentication.
Molecular characterization of Cryptococcus neoformans isolated from the environment in Beijing, China

Abstract The molecular type of environmental Cryptococcus neoformans in Beijing was not clear. Our study aims to reveal the molecular characterization of C. neoformans complex from environment in Beijing, China. A total of 435 samples of pigeon droppings from 11 different homes in Beijing were collected from August to November in 2015. Pigeon droppings were inoculated onto caffeic acid cornmeal agar (CACA) to screen C. neoformans complex. Bruker Biotyper matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) was performed for species identification. Serotype and mating type was determined by specific primers. Restriction fragment length polymorphisms of URA5 (URA5‐RFLP) were applied to genotype. Multi‐locus sequence typing (MLST) was done for further identification and sequence type (ST) determination. Altogether, 81 isolates of C. neoformans AFLP1/VNI were recognized from 435 pigeon droppings in this study. The positive rate for C. neoformans AFLP1/VNI from pigeon droppings in different homes varied from 5.0% to 52.6%, the average was 20.2%. All of these cryptococcal strains were serotype A, MAT&agr;. They were genotyped as VNI by URA5‐RFLP and were confirmed by MLST. No other molecular types of C. neoformans and Cryptococcus gattii isolates were isolated. Their STs were identified as ST 31 (n = 54, 66.7%), followed by ST 53 (n = 10), ST 191 (n = 8), ST 5 (n = 5), ST 57 (n = 3), and ST 38 (n = 1). We concluded that not only clinical but also environmental isolates of C. neoformans need to be investigated more deeply and more extensively. The virulence difference between ST 5 and ST 31 need to be explored in the future.
The Mediating Role of Resiliency in the Relationship Between Temperament and Posttraumatic Growth

ABSTRACT The purpose of the research is to investigate the mediating role of resiliency in the relation between temperamental traits and posttraumatic growth. Data of 74 persons who have experienced the death of someone close were analyzed. The range of age of the participants was 21–74 years (M = 38.4; SD = 15.5). The Posttraumatic Growth Inventory (PTGI), the Formal Characteristics of Behavior–Temperament Inventory (FCB-TI), and the Resiliency Assessment Scale were used in the study. Resiliency plays a mediating role among four traits of temperament (Briskness, Emotional Reactivity, Endurance, and Activity) and posttraumatic growth. Resiliency seems to modify the direct impact of temperamental traits on positive posttraumatic changes.
SparkArray: An Array-Based Scientific Data Management System Built on Apache Spark

With the highly demanded requirements for manipulating large scientific datasets, scientists are in need of flexible cluster-level software to execute fast scientific data analysis. In this paper, we discuss whether the Apache Spark framework is suitable for scientific data management. We present our system SparkArray, which extends Spark with a multidimensional array data model and a set of common used array operations (e.g., filter, subarray, smooth and join). We present analysis and performance evaluation results on different implementation methods for executing array operations on clusters. We also compared the performance of SparkArray to SciDB, a recent scientific database management system, using the workloads of the Standard Science DBMS Benchmark (SS-DB). The results show that SparkArray is feasible alternative solution for large-scale scientific data management, especially when scientists require fast data loading or one-time data analysis on large scientific datasets.
Analyzing the reduced required BS density due to CoMP in cellular networks

In this paper we investigate the benefit of base station (BS) cooperation in the uplink of coordinated multi-point (CoMP) networks. Our figure of merit is the required BS density required to meet a chosen rate coverage. Our model assumes a 2-D network of BSs on a regular hexagonal lattice in which path loss, lognormal shadowing and Rayleigh fading affect the signal received from users. Accurate closed-form expressions are first presented for the sum-rate coverage probability and ergodic sum-rate at each point of the cooperation region. Then, for a chosen quality of user rate, the required density of BS is derived based on the minimum value of rate coverage probability in the cooperation region. The approach guarantees that the achievable rate in the entire coverage region is above a target rate with chosen probability. The formulation allows comparison between different orders of BS cooperation, quantifying the reduced required BS density from higher orders of cooperation.
OBDD-based evaluation of reliability and importance measures for multistate systems subject to imperfect fault coverage

Algorithms for evaluating the reliability of a complex system such as a multistate fault-tolerant computer system have become more important. They are designed to obtain the complete results quickly and accurately even when there exist a number of dependencies such as shared loads (reconfiguration), degradation, and common-cause failures. This paper presents an efficient method based on ordered binary decision diagram (OBDD) for evaluating the multistate system reliability and the Griffith's importance measures which can be regarded as the importance of a system-component state of a multistate system subject to imperfect fault-coverage with various performance requirements. This method combined with the conditional probability methods can handle the dependencies among the combinatorial performance requirements of system modules and find solutions for multistate imperfect coverage model. The main advantage of the method is that its time complexity is equivalent to that of the methods for perfect coverage model and it is very helpful for the optimal design of a multistate fault-tolerant system.
Join processing for flash SSDs: remembering past lessons

Flash solid state drives (SSDs) provide an attractive alternative to traditional magnetic hard disk drives (HDDs) for DBMS applications. Naturally there is substantial interest in redesigning critical database internals, such as join algorithms, for flash SSDs. However, we must carefully consider the lessons that we have learnt from over three decades of designing and tuning algorithms for magnetic HDD-based systems, so that we continue to reuse techniques that worked for magnetic HDDs and also work with flash SSDs. The focus of this paper is on recalling some of these lessons in the context of ad hoc join algorithms. Based on an actual implementation of four common ad hoc join algorithms on both a magnetic HDD and a flash SSD, we show that many of the "surprising" results from magnetic HDD-based join methods also hold for flash SSDs. These results include the superiority of block nested loops join over sort-merge join and Grace hash join in many cases, and the benefits of blocked I/Os. In addition, we find that simply looking at the I/O costs when designing new flash SSD join algorithms can be problematic, as the CPU cost is often a bigger component of the total join cost with SSDs. We hope that these results provide insights and better starting points for researchers designing new join algorithms for flash SSDs.
The TAU Parallel Performance System 2 Corresponding Author :

The ability of performance technology to keep pace with the g rowing complexity of parallel and distributed systems depends on robu st performance frameworks that can at once provide system-specific performance c apabilities and support high-level performance problem solving. Flexibility and portability in empirical methods and processes are influenced primarily by th e s rategies available for instrumentation and measurement, and how effectively t he are integrated and composed. This paper presents the TAU (Tuning and Analysis U tilities) parallel performance system and describe how it addresses diverse re quirements for performance observation and analysis. The TAU Parallel Performance System 4
Differential Responses to Blood Pressure and Oxidative Stress in Streptozotocin-Induced Diabetic Wistar-Kyoto Rats and Spontaneously Hypertensive Rats: Effects of Antioxidant (Honey) Treatment

Oxidative stress is implicated in the pathogenesis and/or complications of hypertension and/or diabetes mellitus. A combination of these disorders increases the risk of developing cardiovascular events. This study investigated the effects of streptozotocin (60 mg/kg; ip)-induced diabetes on blood pressure, oxidative stress and effects of honey on these parameters in the kidneys of streptozotocin-induced diabetic Wistar-Kyoto (WKY) and spontaneously hypertensive rats (SHR). Diabetic WKY and SHR were randomized into four groups and received distilled water (0.5 mL) and honey (1.0 g/kg) orally once daily for three weeks. Control SHR had reduced malondialdehyde (MDA) and increased systolic blood pressure (SBP), catalase (CAT) activity, and total antioxidant status (TAS). SBP, activities of glutathione peroxidase (GPx) and glutathione reductase (GR) were elevated while TAS was reduced in diabetic WKY. In contrast, SBP, TAS, activities of GPx and GR were reduced in diabetic SHR. Antioxidant (honey) treatment further reduced SBP in diabetic SHR but not in diabetic WKY. It also increased TAS, GSH, reduced glutathione (GSH)/oxidized glutathione (GSSG) ratio, activities of GPx and GR in diabetic SHR. These data suggest that differences in types, severity, and complications of diseases as well as strains may influence responses to blood pressure and oxidative stress.
Recursive Decision Tree Induction Based on Homogeneousness for Data Clustering

Data mining is an analytic process designed to explore data in search of consistent patterns or systematic relationships between variables. To build a model for data mining, both supervised and unsupervised learning techniques are used. In this paper we try to make use of a supervised learning technique called classification tree commonly called decision tree to cluster the similar featured attributes of large datasets. The algorithm takes an image of plotted data values as the input and inducts a decision tree accordingly. The decision factor to form the tree is a measure of homogeneousness of the data pixels in the region. Reverse merging of leaf nodes are done to make clusters based on their domain density.
Critical role of CREBH‐mediated induction of transforming growth factor β2 by hepatitis C virus infection in fibrogenic responses in hepatic stellate cells

Mechanisms of hepatic fibrogenesis induced by hepatitis C virus (HCV), one of the leading causes of liver fibrosis, are not fully understood. We studied transcriptional up‐regulation of transforming growth factor β (TGF‐β), especially TGF‐β2, which is mediated by activation of liver‐enriched transcription factor cAMP‐responsive element‐binding protein, hepatocyte specific (CREBH) triggered by HCV infection and its functional significance for induction of profibrogenic phenotypes by interaction of HCV‐infected cells with hepatic stellate cells (HSCs). Compared to TGF‐β1, expression of TGF‐β2 mRNA was induced faster and to a higher level upon HCV infection. Serum TGF‐β2 levels in hepatitis C patients were higher compared to those in healthy individuals and were positively correlated with hepatic fibrosis stages F0‐F2. TGF‐β2 promoter activity was decreased and increased, respectively, by silencing and overexpression of CREBH. CREBH recognition sites were identified in the TGF‐β2 promoter. CREBH binding to the promoter and its increase in cells expressing HCV Core‐NS2 were shown by gel mobility shift and chromatin immunoprecipitation, respectively. The active form of CREBH was detectable in HCV‐infected chimeric mice with human livers and cells expressing HCV proteins. Involvement of CREBH in HCV‐induced fibrogenic response was further demonstrated in the CREBH null‐mutant mouse model. Fibrogenic phenotypes were assessed using co‐cultures of HCV‐infected cells and HSCs. Expressions of fibrogenic factors and TGF‐β1 increasing in the co‐cultures was prevented by TGF‐β2‐ or CREBH silencing. Conclusion: CREBH was identified as a key positive regulator of TGF‐β2 transcription in HCV‐infected cells. TGF‐β2 released from infected cells potentially contributes to cross‐induction of TGF‐β in an autocrine manner through its own signaling pathway, leading to an increase in fibrogenic responses in adjacent HSCs. (Hepatology 2017;66:1430–1443).
Real-time indoor localization of service robots using fisheye camera and laser pointers

This paper presents a new real-time localization method for indoor service robots based on camera and laser. First of all, it is proved that planar motion of an upward camera in the floor plane can be solved by only two matching points with equal depth. Then, a real-time indoor localization method is proposed accordingly using an upward fisheye camera mounted on the robot and two fixed laser pointers which project red and green laser spots onto the ceiling. In addition, to improve the localization accuracy, an Extended Kalman Filter is employed with active matching to speed up laser spots recognition process. Finally, the proposed method is implemented on a mobile developer board, and tested with P3-DX platform in indoor environment. Experimental results show the excellent performance of the given method.
Does Better Inference mean Better Learning ?

Maximum Likelihood learning of graphical models is not possible in problems where inference is intractable. In such settings it is common to use approximate inference (e.g. Loopy BP) and maximize the so-called “surrogate” likelihood objective. We examine the effect of using different approximate inference methods and, therefore, different surrogate likelihoods, on the accuracy of parameter estimation. In particular, we consider methods that utilize a control parameter to trade computation for accuracy. We demonstrate empirically that cheaper, but worse quality approximate inference methods should be used in the small data setting as they exhibit smaller variance and are more robust to model mis-specification.
A Distributed Approach for Privacy Preservation in the Publication of Trajectory Data

Advancements in mobile computing techniques along with the pervasiveness of location-based services have generated a great amount of trajectory data. These data can be used for various data analysis purposes such as traffic flow analysis, infrastructure planning and understanding of human behavior. However, publishing this amount of trajectory data may lead to serious risks of privacy breach. Quasi-identifiers are trajectory points that can be linked to external information and be used to identify individuals associated with trajectories. Therefore, by analyzing quasi-identifiers, one may be able to trace anonymous trajectories back to individuals with the aid of location-aware social networking applications, for example. Most existing trajectory data anonymization approaches were proposed for centralized computing environments, so they usually present poor performance to anonymize large trajectory data sets. In this paper we propose a distributed and efficient strategy that adopts the km-anonymity privacy model and uses the scalable MapReduce paradigm, which allows finding quasi-identifiers in larger amount of data. We also present a technique to minimize the loss of information by selecting key locations from the quasi-identifiers to be suppressed. Experimental evaluation results demonstrate that our proposed approach for trajectory data anonymization is more scalable and efficient than existing works.
Multicast capacity for hybrid wireless networks

We study the multicast capacity of a random wireless network consisting of ordinary wireless nodes and base stations, known as a hybrid network. Assume that <i>n</i> ordinary wireless nodes are randomly deployed in a square region and all nodes have the uniform transmission range <i>r</i> and uniform interference range <i>R</i>><i>r</i>. We further assume that each ordinary wireless node can transmit/receive at <i>W</i> bits/second over a common wireless channel. In addition, there are <i>m</i> additional base stations (neither source nodes nor receiver nodes) placed regularly in this square region and connected by a high-bandwidth wired network. For each ordinary node <i>v</i>, we randomly pick <i>k</i>-1 nodes from the other <i>n</i>-1 ordinary nodes as the receivers of the multicast session at node <i>v</i>. The aggregated multicast capacity is defined as the total data rate of all multicast sessions in this hybrid network. We derive asymptotic upper bounds and lower bounds on multicast capacity of the hybrid wireless networks. The total multicast capacity is <i>O</i>(√<i>n</i> /√log <i>n</i> · √<i>m</i>/<i>k</i> · <i>W</i>) when <i>k</i> = <i>O</i>(<i>n</i> / log <i>n</i>), <i>k</i> = <i>O</i>(<i>m</i>), <i>k</i> / √<i>m</i> → ∞ and <i>m</i> = <i>o</i>(<i>a</i><sup>2</sup> / <i>r</i><sup>2</sup>); the total multicast capacity is Θ(√<i>n</i> / √log <i>n</i> · <i>W</i> / √<i>k</i>) when <i>k</i> = <i>O</i>(<i>n</i>/log <i>n</i>), <i>k</i> = Ω(<i>m</i>) and <i>m</i>/<i>k</i> → <i>O</i>. When <i>k</i> = <i>O</i>(<i>n</i>/log <i>n</i>) and <i>k</i> = <i>O</i>(√<i>m</i>), the upper bound for minimum multicast capacity is at most <i>O</i>(<i>r</i>·<i>n</i>/<i>a</i> · √<i>m</i> · <i>W</i>/<i>k</i>) and is at least Ω(<i>W</i>) respectively. When <i>k</i> =Ω<sup>α</sup>(<i>n</i>/log <i>n</i>), the multicast capacity is Θ(<i>W</i>).
Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity

VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, we show for the first time the structure of a member of the VapD family and present a relationship of VapD with Cas2 family and toxin–antitoxin (TA) systems. The crystal structure of HP0315 from Helicobacter pylori was solved at a resolution of 2.8 Å. The structure of HP0315, which has a modified ferredoxin-like fold, is very similar to that of the Cas2 family. Like Cas2 proteins, HP0315 shows endoribonuclease activity. HP0315-cleaved mRNA, mainly before A and G nucleotides preferentially, which means that HP0315 has purine-specific endoribonuclease activity. Mutagenesis studies of HP0315 revealed that D7, L13, S43 and D76 residues are important for RNase activity, in contrast, to the Cas2 family. HP0315 is arranged as an operon with HP0316, which was found to be an antitoxin-related protein. However, HP0315 is not a component of the TA system. Thus, HP0315 may be an evolutionary intermediate which does not belong to either the Cas2 family or TA system.
Combining PCNN with color distribution entropy and vector gradient in feature extraction

In this paper, the simplified Pulse-Coupled Neural Network (PCNN) model, widely used in image processing, is used to extract image features for image retrieval. These features include PCNN-segmentation-based color information and PCNN-gradient-based texture. On one hand, considering the spatial distribution of colors, we combine the color distribution entropy with the simplified PCNN. On the other hand, we also make use of the texture features of images produced by gradient images. Experimental results show that our method performs better than Improved Color Distribution Entropy (ICDE), Block Difference of Inverse Probabilities (BDIP), PCNN-Global Icon (PCNN-GI) and Normalized Moment of Inertia (Nmi) method respectively for recall-precision and ANMRR index.