Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic analysis of the hierarchical structure of regulatory networks

A fundamental question in biology is how the cell uses transcription factors (TFs) to coordinate the expression of thousands of genes in response to various stimuli. The relationships between TFs and their target genes can be modeled in terms of directed regulatory networks. These relationships, in turn, can be readily compared with commonplace “chain-of-command” structures in social networks, which have characteristic hierarchical layouts. Here, we develop algorithms for identifying generalized hierarchies (allowing for various loop structures) and use these approaches to illuminate extensive pyramid-shaped hierarchical structures existing in the regulatory networks of representative prokaryotes (Escherichia coli) and eukaryotes (Saccharomyces cerevisiae), with most TFs at the bottom levels and only a few master TFs on top. These masters are situated near the center of the protein–protein interaction network, a different type of network from the regulatory one, and they receive most of the input for the whole regulatory hierarchy through protein interactions. Moreover, they have maximal influence over other genes, in terms of affecting expression-level changes. Surprisingly, however, TFs at the bottom of the regulatory hierarchy are more essential to the viability of the cell. Finally, one might think master TFs achieve their wide influence through directly regulating many targets, but TFs with most direct targets are in the middle of the hierarchy. We find, in fact, that these midlevel TFs are “control bottlenecks” in the hierarchy, and this great degree of control for “middle managers” has parallels in efficient social structures in various corporate and governmental settings.
Pseudoephedrine enhances performance in 1500-m runners.

UNLABELLED Pseudoephedrine is an over-the-counter drug to relieve nasal and sinus congestion. Although it has been suggested that pseudoephedrine could be a stimulant and ergogenic aid, pseudoephedrine was recently removed from the banned substance list by the International Olympic Committee and placed on the monitoring program (from January 2004). It was felt that evidence was lacking for an ergogenic effect, although few studies have investigated the effects of pseudoephedrine on exercise performance. This study, therefore, aimed to investigate the effects of pseudoephedrine on 1500-m running performance. METHODS In a double-blind, randomized crossover design, seven male athletes completed two 1500-m running trials on an outdoor track after having completed a familiarization trial. All trials were 7 d apart. After a 12-h overnight fast, subjects reported to the laboratory and received a standardized breakfast (energy asymptotically equal to 500 kcal 50% CHO). Subjects were given either 2.5 mg.kg(-1) bw pseudoephedrine or 2.5 mg.kg(-1) bw maltodextrins (placebo) in gelatin capsules 70 min before the start of the warm-up, which started 20 min before they ran 1500 m all-out. Pre- and postexercise blood samples were collected and analyzed for lactate and glucose concentrations, partial pressure of oxygen (PO2) and carbon dioxide (PCO2), and percent oxygen saturation. RESULTS Pseudoephedrine significantly decreased time to completion of 1500-m time trials in the present study by 2.1% (from 279.65 +/- 4.36 s with placebo to 273.86 +/- 4.36 s with pseudoephedrine) with no reported side effects. No changes in the measured blood parameters were found, suggesting a central effect of pseudoephedrine rather than a metabolic effect. CONCLUSION The finding was that 2.5 mg.kg(-1) bw pseudoephedrine ingested 90 min preexercise improves 1500-m running performance.
Impact of channel modeling on accurate estimation of on-body channel capacity

This paper investigates the impact of on-body channel modeling on the accurate estimation of BAN system performance. Channel capacity is used as a measure of the on-body system performance. The actual channel capacity is calculated based on signal measurements conducted in an indoor environment. Then it is compared to the channel capacity calculated for five theoretical channel models obtained through statistical analysis of the measured data.
Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms

Many bacterial mRNAs are regulated at the transcriptional or translational level by ligand-binding elements called riboswitches. Although they both bind adenine, the adenine riboswitches of Bacillus subtilis and Vibrio vulnificus differ by controlling transcription and translation, respectively. Here, we demonstrate that, beyond the obvious difference in transcriptional and translational modulation, both adenine riboswitches exhibit different ligand binding properties and appear to operate under different regulation regimes (kinetic versus thermodynamic). While the B. subtilis pbuE riboswitch fully depends on co-transcriptional binding of adenine to function, the V. vulnificus add riboswitch can bind to adenine after transcription is completed and still perform translation regulation. Further investigation demonstrates that the rate of transcription is critical for the B. subtilis pbuE riboswitch to perform efficiently, which is in agreement with a co-transcriptional regulation. Our results suggest that the nature of gene regulation control, that is transcription or translation, may have a high importance in riboswitch regulatory mechanisms.
Monadic concurrent linear logic programming

Lolli is a logic programming language based on the asynchronous propositions of intuitionistic linear logic. It uses a backward chaining, backtracking operational semantics. In this paper we extend Lolli with the remaining connectives of intuitionistic linear logic restricted to occur inside a monad, an idea taken from the concurrent logical framework (CLF). The resulting language, called LolliMon, has a natural forward chaining, committed choice operational semantics inside the monad, while retaining Lolli's semantics outside the monad. LolliMon thereby cleanly integrates both concurrency and saturation with logic programming search. We illustrate its expressive power through several examples including an implementation of the pi-calculus, a call-by-need lambda-calculus, and several saturating algorithms presented in logical form.
Position Sensorless Control of Switched Reluctance Generator for Wind Energy Conversion

This paper presents a novel sensorless control system of switched reluctance generator (SRG) in order to reduce cost, simplify system structure and increase reliability. Considering nonlinear characteristics of SRG and robustness of sliding mode observer (SMO), sensorless control method of SRG based on SMO is proposed and analyzed. For wind energy conversion system (WECS), a voltage-source PWM inverter is used to make power output of SRG connect to the grid (or ac load). The SRG phase current was regulated by current chopping control method (CCC). An 18.5 kW three-phase 12/8 SRG experimental prototype was constructed and wind turbine mover was emulated using a DC motor drive. Test results using dual TMS320F2812 DSP as control core verified validity and feasibility of the proposed system.
Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds' (D R) genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.
Graphical editing support for QuickCheck models

QuickCheck can test a system by specifying a state machine for the API exported by that system. This state machine specification includes a list of possible API calls. Each call is accompanied by a precondition, a postcondition, a generator for the arguments, and a description of how the state is changed. Based on this specification QuickCheck generates a random sequence of API calls. The preconditions ensure that a generated sequence is valid, and the postconditions check that the system behaves as expected. Many systems require an initialisation call before other calls, describing the transition from an uninitialized to an initialised state. QuickCheck offers two ways of specifying transitions between states: using preconditions or a finite state machine abstraction. In this paper we show, by means of an example, that the latter approach is to be preferred. In addition, we present a recent extension to QuickCheck that allows a user to graphically create and edit a finite state machine specification. This extension simplifies and speeds up the specification of a finite state machine, which can be regarded as a formal model of the system, considerably. The graphical representation makes the formal model easier to understand, and visualises the distribution of API calls. Moreover, the extension allows the user to change this distribution.
Topic Classification for Suicidology

Computational techniques for topic classification can support qualitative research by automatically applying labels in preparation for qualitative analyses. This paper presents an evaluation of supervised learning techniques applied to one such use case, namely, that of labeling emotions, instructions and information in suicide notes. We train a collection of one-versus-all binary support vector machine classifiers, using cost-sensitive learning to deal with class imbalance. The features investigated range from a simple bag-of-words and n-grams over stems, to information drawn from syntactic dependency analysis and WordNet synonym sets. The experimental results are complemented by an analysis of systematic errors in both the output of our system and the gold-standard annotations. Category: Smart and intelligent computing
Electrotactile Feedback Improves Performance and Facilitates Learning in the Routine Grasping Task

Aim of this study was to investigate the feasibility of electrotactile feedback in closed loop training of force control during the routine grasping task. The feedback was provided using an array electrode and a simple six-level spatial coding, and the experiment was conducted in three amputee subjects. The psychometric tests confirmed that the subjects could perceive and interpret the electrotactile feedback with a high success rate. The subjects performed the routine grasping task comprising 4 blocks of 60 grasping trials. In each trial, the subjects employed feedforward control to close the hand and produce the desired grasping force (four levels). First (baseline) and the last (validation) session were performed in open loop, while the second and the third session (training) included electrotactile feedback. The obtained results confirmed that using the feedback improved the accuracy and precision of the force control. In addition, the subjects performed significantly better in the validation vs. baseline session, therefore suggesting that electrotactile feedback can be used for learning and training of myoelectric control.
Reduction of epoxy derivatives of benzo(a)pyrene by microsomal cytochrome P-450.

Abstract Benzo( a )pyrene 4,5-oxide was rapidly reduced to benzo( a )pyrene by rat liver microsomes in the presence of reduced nicotinamide adenine dinucleotide phosphate when incubated anaerobically. The activity of benzo( a )pyrene 4,5-oxide reductase was increased about seven times by pretreatment of rats with 3-methylcholanthrene. The addition of riboflavin to the incubation mixture resulted in the increase (up to 10-fold) in the reduced nicotinamide adenine dinucleotide phosphate-supported reduction of benzo( a )pyrene 4,5-oxide. Moreover, the xanthine oxidase-supported reduction of benzo( a )pyrene 4,5-oxide was increased up to 20-fold by riboflavin. Both stimulations by riboflavin were completely blocked by carbon monoxide. Benzo( a )pyrene 7,8-oxide was reduced by rat liver microsomes as rapidly as was benzo( a )pyrene 4,5-oxide, but phenanthrene 9,10-oxide and trans -stilbene oxide were reduced at slower rates. No detectable reductase activities were seen when benzo( a )pyrene 7β,8α-diol-9α,10α-epoxide, benzo( a )pyrene 7β,8α-diol-9β,10β-epoxide, styrene oxide, and several other epoxide compounds were used as the substrates. The activity of microsomal benzo( a )pyrene 4,5-oxide reductase was markedly depressed when incubated under an atmosphere of air. The inhibition by oxygen of the benzo( a )pyrene 4,5-oxide reductase was partially reversed by the addition of a liver 105,000 × g supernatant fraction to the incubations containing microsomes. These results suggested that epoxide metabolites formed by microsomal cytochrome P-450 were reduced to the parent hydrocarbon at significant rates in physiological environments.
Motion planning implemented in ROS for mobile robot

In a dynamic environment, the automatic mobile robot requires a real-time independent path planning for safe navigation. To solve this problem, this paper represents a hybrid path planning approach combining the safe global path planning and a new improved adaptive window approach. The improved adaptive window approach base on the concept of safe path which improves the accuracy of obstacle avoidance significantly. Based on the robot operating system, all works in this paper are validated both in the virtual environment and the real world. The experiments show that the hybrid path planning can safely control the mobile robot in a dynamic environment.
Draft Genome Sequence of Bacillus fengqiuensis FJAT-14578, Isolated from a Soil Sample in China

ABSTRACT Here, we report the first high-quality draft genome sequence of Bacillus fengqiuensis FJAT-14578, isolated from a soil sample collected from China. The genome size was 5,569,389 bp, with a 40.93 mol% G+C content. The number of tRNAs was 69 and of rRNAs was 10 (5S, 16S, and 23S).
Why Did They #Unfollow Me?: Early Detection of Follower Loss on Twitter

Having more followers has become a norm in recent social media and micro-blogging communities. This battle has been taking shape from the early days of Twitter. Despite this strong competition for followers, many Twitter users are continuously losing their followers. This work addresses the problem of identifying the reasons behind the drop of followers of users in Twitter. As a first step, we extract various features by analyzing the content of the posts made by the Twitter users who lose followers consistently. We then leverage these features to early detect follower loss. We propose various models and yield an overall accuracy of 73% with high precision and recall. Our model outperforms baseline model by 19.67% (w.r.t accuracy), 33.8% (w.r.t precision) and 14.3% (w.r.t recall).
Accurate DEM Reconstruction from Permanent Scatterers and Multi-baseline Interferometry

The application of the Permanent Scatterers (PS) Technique in multi-temporal data-sets, namely the identification and exploitation of sparse coherent targets, has shown that it is possible to estimate and remove interferometric phase components due to atmospheric effects and orbital fringes. So far, the application of the PS technique has been focused on the extraction of the motion field of the area of interest. However, it is also known that PS relative elevations can be estimated with sub-meter precision while smooth errors can be removed using a coarse resolution DEM or the data of the Shuttle Radar Topography Mission (SRTM). In this paper, we describe a new approach combining the PS Technique and standard interferometry to improve the quality of lnSAR DEM's. ERS Tandem interferograms are exploited to increase the number of coherent pixels, while atmospheric effects are estimated and subtracted by means of the sparse PS grid. Prior information and PS elevation are used to reduce the probability of phase-unwrapping errors. Preliminary results are reported and the key-factors for its successful application (e.g. the number of Tandem acquisitions available, PS density) are discussed.
Distinctiveness-sensitive nearest-neighbor search for efficient similarity retrieval of multimedia information

Nearest neighbor (NN) search in high dimensional feature space is widely used for similarity retrieval of multimedia information. However recent research results in the database literature reveal that a curious problem happens in high dimensional space. Since high dimensional space has a high degree of freedom, points could be scattered so that every distance between them might yield no significant difference. In this case, we can say that the NN is indistinctive because many points exist at the similar distance. To make matters worse, indistinctive NNs require more search cost because search completes only after choosing the NN from plenty of strong candidates. In order to circumvent the handful effect of indistinctive NNs, the paper presents a new NN search algorithm which determines the distinctiveness of the NN during search operation. This enables us not only to cut down search cost but also to distinguish distinctive NNs from indistinctive ones. These advantages are especially beneficial to interactive retrieval systems.
Survey of DOS defense mechanisms

The Denial of Service (DOS) attacks hinder the availability of service to the genuine client from the server. The DOS attacks can cause severe damage to the interconnected systems such as web servers, database servers, cloud computing servers, etc. This paper surveys the different defense mechanisms available for the denial of service attacks.
S TORE F ORMAT C HOICE AND S HOPPING T RIP TYPES

Purpose: The purpose of the paper is to identify store format attributes that impact on store format choice when consumers conduct fill-in or major trips to buy groceries. By doing so, we take into consideration that consumers patronise multiple (store-based) formats depending on the shopping situation operationalised by the type of shopping trip. Design/methodology/approach: The paper adopts the conceptual framework of random utility theory via application of a multinomial logit modelling framework. The analysis is based on a survey of 408 consumers representing households in a clearly defined central European retail area. Findings: The results reveal a considerable moderating effect of the shopping situation on the relationship between perceived store format attributes and store format choice. Consumers' utilities are significantly higher for discount stores and hypermarkets when conducting major trips. To the contrary, supermarkets are preferred for fill-in trips in the focused retail market. Merchandise-related attributes of store formats have a higher impact on the utility formation regarding major-trips, whereas service-and convenience-related attributes do so regarding fill-in trips. Research limitations: The findings can only be generalised to retail markets having similar characteristics like the one under study. It is highly concentrated, contains considerable share of small size retail stores, it is urban and has clear cut boundaries due to its geographical location. Originality/value: This paper considers the fact that consumers patronise multiple store formats and investigates the moderating effect of the shopping situation – operationalised by different types of shopping trips – on store format choice.
A Modular Algorithm for the Dynamics of Multiple Flexible robots

This paper presents an efficient modular algorithm for the dynamic simulation of systems of multiple flexible robots with multiple concurrent constraints. This research represents an important extension of previous work in the modular dynamic simulation of complex rigid-body systems. In addition to a summary of the algorithm, the treatment of potentially critical nonlinear strain and kinematic effects is also discussed. The algorithm is validated through several examples, including both series and parallel robot configurations.
Sparse Boosting

We propose Sparse Boosting (the SparseL2Boost algorithm), a variant on boosting with the squared error loss. SparseL2Boost yields sparser solutions than the previously proposed L2Boosting by minimizing some penalized L2-loss functions, the FPE model selection criteria, through small-step gradient descent. Although boosting may give already relatively sparse solutions, for example corresponding to the soft-thresholding estimator in orthogonal linear models, there is sometimes a desire for more sparseness to increase prediction accuracy and ability for better variable selection: such goals can be achieved with SparseL2Boost. We prove an equivalence of SparseL2Boost to Breiman's nonnegative garrote estimator for orthogonal linear models and demonstrate the generic nature of SparseL2Boost for nonparametric interaction modeling. For an automatic selection of the tuning parameter in SparseL2Boost we propose to employ the gMDL model selection criterion which can also be used for early stopping of L2Boosting. Consequently, we can select between SparseL2Boost and L2Boosting by comparing their gMDL scores.
Semi-autonomous indoor positioning using MEMS-based inertial measurement units and building information

State-of-the-art indoor positioning systems are based on short-range wireless technologies such as ultra-wideband (UWB) and wireless local area network (WLAN). Additional information produced by a low-cost inertial measurement unit (IMU) or selected from low-grade floor plans is frequently used to improve the positioning accuracy. Therefore absolute and relative positioning systems (e.g. WLAN and IMU) are typically integrated using a Kalman filter (KF) or a particle filter (PF). In this case, all the buildings have to be equipped with a large number of transmitters and receivers which may render inoperable during emergency situations and induce substantial costs both in terms of setup and maintenance. Hence, in this paper we present and assess the prototype of a self-contained indoor positioning system. Our prototype consists of a micro-electro-mechanical system- (MEMS) based IMU and a mobile computer which includes a database with characteristic building information. A novel combination of methods is proposed to increase the distance between positions where absolute repositioning is still mandatory.