Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression

Introgression is the effective exchange of genetic information between species through natural hybridization. Previous genetic analyses of the Drosophila yakuba—D. santomea hybrid zone showed that the mitochondrial genome of D. yakuba had introgressed into D. santomea and completely replaced its native form. Since mitochondrial proteins work intimately with nuclear‐encoded proteins in the oxidative phosphorylation (OXPHOS) pathway, we hypothesized that some nuclear genes in OXPHOS cointrogressed along with the mitochondrial genome. We analyzed nucleotide variation in the 12 nuclear genes that form cytochrome c oxidase (COX) in 33 Drosophila lines. COX is an OXPHOS enzyme composed of both nuclear‐ and mitochondrial‐encoded proteins and shows evidence of cytonuclear coadaptation in some species. Using maximum‐likelihood methods, we detected significant gene flow from D. yakuba to D. santomea for the entire COX complex. Interestingly, the signal of introgression is concentrated in the three nuclear genes composing subunit V, which shows population migration rates significantly greater than the background level of introgression in these species. The detection of introgression in three proteins that work together, interact directly with the mitochondrial‐encoded core, and are critical for early COX assembly suggests this could be a case of cytonuclear cointrogression.
Iterative Detection and Decoding with PIC Algorithm for MIMO-OFDM Systems

In this paper, we propose a new iterative detection and decoding scheme based on parallel interference cancel (PIC) for coded MIMO-OFDM systems. The performance of proposed receiver is improved through the joint PIC MIMO detection and iterative detection and decoding. Its performance is evaluated based on com-puter simulation. The simulation results indicate that the performance of the proposed receiver is greatly im-proved compared to coded MIMO-OFDM systems based on VBLAST detection scheme.
A Genomic Duplication is Associated with Ectopic Eomesodermin Expression in the Embryonic Chicken Comb and Two Duplex-comb Phenotypes

Duplex-comb (D) is one of three major loci affecting comb morphology in the domestic chicken. Here we show that the two Duplex-comb alleles, V-shaped (D*V) and Buttercup (D*C), are both associated with a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES). EOMES is a T-box transcription factor that is involved in mesoderm specification during gastrulation. In D*V and D*C chicken embryos we find that EOMES is ectopically expressed in the ectoderm of the comb-developing region as compared to wild-type embryos. The confinement of the ectopic expression of EOMES to the ectoderm is in stark contrast to the causal mechanisms underlying the two other major comb loci in the chicken (Rose-comb and Pea-comb) in which the transcription factors MNR2 and SOX5 are ectopically expressed strictly in the mesenchyme. Interestingly, the causal mutations of all three major comb loci in the chicken are now known to be composed of large-scale structural genomic variants that each result in ectopic expression of transcription factors. The Duplex-comb locus also illustrates the evolution of alleles in domestic animals, which means that alleles evolve by the accumulation of two or more consecutive mutations affecting the phenotype. We do not yet know whether the V-shaped or Buttercup allele correspond to the second mutation that occurred on the haplotype of the original duplication event.
The c-Jun NH2-terminal Kinase Promotes Insulin Resistance during Association with Insulin Receptor Substrate-1 and Phosphorylation of Ser307 *

Tumor necrosis factor α (TNFα) inhibits insulin action, in part, through serine phosphorylation of IRS proteins; however, the phosphorylation sites that mediate the inhibition are unknown. TNFα promotes multipotential signal transduction cascades, including the activation of the Jun NH2-terminal kinase (JNK). Endogenous JNK associates with IRS-1 in Chinese hamster ovary cells. Anisomycin, a strong activator of JNK in these cells, stimulates the activity of JNK bound to IRS-1 and inhibits the insulin-stimulated tyrosine phosphorylation of IRS-1. Serine 307 is a major site of JNK phosphorylation in IRS-1. Mutation of serine 307 to alanine eliminates phosphorylation of IRS-1 by JNK and abrogates the inhibitory effect of TNFα on insulin-stimulated tyrosine phosphorylation of IRS-1. These results suggest that phosphorylation of serine 307 might mediate, at least partially, the inhibitory effect of proinflammatory cytokines like TNFα on IRS-1 function.
A vector-based system for the differentiation of mouse embryonic stem cells toward germ-line cells

Objective(s): To culture the in vitro mouse embryonic stem cells (mESCs) and to direct their differentiation to germ-line cells; in present study we used a vector backbone containing the fusion construct Stra8-EGFP to select differentiated ES cells that entered meiosis. Retinoic acid was used to differentiate embryonic stem cells to germ cells. Materials and Methods: A fragment of Stra8 gene promoter (-1400 to +7) was inserted in ScaI/HindIII multiple cloning site of pEGFP-1 vector. The electroporation was done on embryonic stem cells and positive colonies were selected as puromycin-resistant after three weeks of treatment with puromycin. All-trans retinoic acid (RA) was used for differentiation of mESCs at final concentration of 10-5M. The expression of protamine 1 (Prm1) gene was checked as post meiotic marker in differentiated mESCs after 5, 10, 15, 21 and 30 days after RA induction. Results: The PCR amplification by specific primers for Stra8-EGFP fusion gene was detected in DNA sample from mESCs after electroporation and puromycin treatment. GFP-positive mESC colonies were observed after 72 hr RA induction. The protamine 1 gene was expressed after 21 days of RA induction. Conclusion: In this study, we demonstrated the in vitro generation of mouse embryonic stem cells to germ cells by using a backbone vector containing the fusion gene Stra8-EGFP. The Stra8 gene is a retinoic acid-responsive protein and is able to regulate meiotic initiation.
Hopf Algebraic Structures in the Cutting Rules

Since the Connes--Kreimer Hopf algebra was proposed, revisiting present quantum field theory has become meaningful and important from algebraic points. In this paper, the Hopf algebra in the cutting rules is constructed. Its coproduct contains all necessary ingredients for the cutting equation crucial to proving perturbative unitarity of the S-matrix. Its antipode is compatible with the causality principle. It is obtained by reducing the Hopf algebra in the largest time equation which reflects partitions of the vertex set of a given Feynman diagram. First of all, the Connes--Kreimer Hopf algebra in the BPHZ renormalization instead of the dimensional regularization and the minimal subtraction is described so that the strategy of setting up Hopf algebraic structures of Feynman diagrams becomes clear.
Non-Steroidal Anti-Inflammatory Drugs in the Carcinogenesis of the Gastrointestinal Tract

It is estimated that underlying infections and inflammatory responses are linked to 15–20% of all deaths from cancer worldwide. Inflammation is a physiologic process in response to tissue damage resulting from microbial pathogen infection, chemical irritation, and/or wounding. Tissues injured throughout the recruitment of inflammatory cells such as macrophages and neutrophils, generate a great amount of growth factors, cytokines, and reactive oxygen and nitrogen species that may cause DNA damage that in turn predisposes to the transformation from chronic inflammation to neoplasia. Cyclooxygenase (COX), playing a key role in cell homeostasis, angiogenesis and tumourigenesis, may represent the link between inflammation and cancer. Currently COX is becoming a pharmacological target for cancer prevention and treatment.
Learning Object Models on a Robot using Visual Context and Appearance Cues

Visual object recognition is an important challenge to widespread deployment of mobile robots in real-world domains characterized by partial observability and unforeseen dynamic changes. This paper describes an algorithm that enables robots to use motion cues to identify (and focus on) a set of interesting objects, automatically extracting appearance-based and contextual cues from a small number of images to efficiently learn representative models of these objects. Object models learned from relevant image regions consist of: (a) relative spatial arrangement of gradient features; (b) graph-based models of neighborhoods of gradient features; (c) parts-based models of image segments; (d) color distribution statistics; and (e) probabilistic models of local context. An energy minimization algorithm and a generative model of information fusion use the learned models to reliably and efficiently recognize these objects in novel scenes. All algorithms are evaluated on wheeled robots in indoor and outdoor domains.
Mobile Recommender Systems

Mobile phones are becoming a primary platform for information access and when coupled with recommender systems technologies they can become key tools for mobile users both for leisure and business applications. Recommendation techniques can increase the usability of mobile systems providing personalized and more focussed content, hence limiting the negative effects of information overload. In this paper we review the major issues and opportunities that the mobile scenario opens to the application of recommender systems especially in the area of travel and tourism. We overview major techniques that have been proposed in the last years and we illustrate the supported functions. We also illustrate specific computational models that have been proposed for mobile recommender systems and we close the paper by presenting some possible future developments and extension in this area.
Mitigation of Flooding Based Denial of Service Attack against Session Initiation Protocol Based VoIP System

The Session Initiation Protocol (SIP) is the most popular signaling protocol used in Voice over Internet Protocol (VoIP). The flooding based DoS attack can be performed by sending only hundreds of SIP messages per second to a SIP server. In this paper, we have proposed a new mitigation scheme for SIP based VoIP system which can protect it from flooding based DoS attack. This scheme is based on the INVITE and BYE messages of the SIP protocol. A prototype system for the flooding based DoS attack on SIP server and a mitigation mechanism has been designed and implemented. The performance of the proposed system has been evaluated and found to be better than other existing mechanisms.
Cellular Phone Users- Willingness to Shop Online

This study aims to identify cellular phone usersâ€™ shopping motivating factors towards online shopping. 100 university students located in Klang Valley, Malaysia were involved as the respondents. They were required to complete a set of questionnaire and had to own a cellular phone in order to be selected as sample in this study. Three from five proposed hypotheses were supported: purchasing information, shopping utilities and service quality. As a result, marketers and retailers should concentrate more on the less important factors in order to encourage and create willingness of the consumers to purchase online. Recommendation for future research is also presented.
Intelligent event processing for emergency medical assistance

The main objective of Emergency Medical Assistance services is to attend patients with sudden diseases at any possible location within an area of influence. Especially for severe emergency patients, the potential of such systems to reduce mortality is directly related to the response time, e.g., the time a patient has to wait for an ambulance. An efficient coordination of the ambulance fleet is crucial for reducing the response times of a service. And this requires complete, real-time information about the current state of the ambulance fleet. Such information is usually transmitted by the ambulance crew members. However, due to the often stressful work of those professionals, the information is frequently not sent in a timely manner. In this paper we present an approach that addresses this problem. We use a Complex Event Processing architecture to automatically identify and transmit incidents and changes in the operational states of ambulances. As a result, the availability of information in the control centre and, thus, the effectiveness of the service is improved. The system is inspired by the operational model of SUMMA112, the Emergency Medical Coordination Centre of the Autonomous Region of Madrid in Spain.
Test-Driven Development of IEEE 1451 Transducer Services and Application

— IEEE 1451 standard defines the methods of integrating smart transducers into communicating networks. Interface between a user application and a field of transducers, known as Transducer Services API is defined by standrad IEEE 1451.0. This paper presents the use of Test-Driven Design (TDD) in developing methods for accessing transducer services using Transducer Services API and developing web applications which access this services over the network. The characteristics of TDD and its benefits are presented and the way of realization for one method is shown using Java and JUnit framework to run tests. I. INTRODUCTION ENSORS have been used in a wide range of applications, such as industrial and home automation, military, healthcare, security, agriculture and environment monitoring. Rapid technological development contributed to the reduction of their dimension and power consumption. Over the time, besides basic measuring functionality, sensors were equipped with other functionalities such as: self-calibration, self-configuration, signal processing. These functionalities provided standalone intelligence and such sensors became known as smart transducers. In order to measure some event within an area of interest, smart transducers were aggregated into communication networks in order to efficiently collect and present measured data to the user [1]. In early days, networking of such smart transducers was difficult because vendors independently developed communication interfaces which in most cases weren't compatible. Shortly afterwards, a family of IEEE 1451 standards was introduced in order to define standardization of transducers interface and overcome compatibility issues. The IEEE 1451 standard is composed of several sub
Forecasting trading volume in the Chinese stock market based on the dynamic VWAP

We investigate the modeling and forecasting of the intra-daily volume time series in Chinese stock market with an application to dynamic Volume Weighted Average Price (VWAP) method. The empirical results show that: (1) This method performs better than the traditional static VWAP strategy; (2) By adjusting time scale (time window) and the composition of the stock portfolio according to the principal component analysis method, we can further improve the forecasting accuracy of the stock turnover series; (3) There is significant long memory characteristic in the special component of the turnover series when using the dynamic VWAP method, however, we find that it can not improve the prediction of turnover series by using ARFIMA model on these series. We also analyze the reasons and provide some explanations.
Rolling droplets

When a rigid circular cylinder or sphere is placed on rough inclined plane it will roll down the plane. When th experiment is repeated with a rigid cube it will slide dow the plane. If the object is deformable a variety of motio become possible; the motion of elastic bodies and fluid dr depends on the interfacial energies of the materials, roughness of the interfaces, the size of the objects, etc. is because a deformable body maintains contact with the face over a finite area. For a viscous fluid droplet, two p sible motions may ensue. If the droplet partially wets t surface it slides along it, while if the droplet is nonwetting, can roll on the surface, much like an elastic body wh viewed from the exterior. Here we consider the motion o small nonwetting droplet forced by a weak gravitation field. A classic example of this motion is exhibited by droplet of mercury on an inclined plane and is probably origin of the name quicksilver, after the Latin Argentum Vivum for the swiftly moving droplet of the silvery liquid. For such motions to be observable, we must have liqu with high surface tension moving on very clean hydropho surfaces. Until recently, only chemically treated surfac were amenable to such experiments that allowed for la contact angles; however, these surfaces were easily cont nated. Recently it has become possible to vary the sur roughness 9 to achieve contact angles very close to 180° th making robust experiments in the high contact angle reg more accessible. A small droplet rolling down such an cline then would reach a steady velocity determined by balance between the rate of energy dissipation due to inte viscous motions and the rate of change of gravitational tential energy.
Wheelchair.q, a mechanical concept for a stair climbing wheelchair

This paper present Wheelchair.q, a concept for a stair climbing wheelchair able to move in structured and unstructured environment, to climb over obstacles and to go up and down stairs. The wheelchair passively changes its locomotion, from a rolling on wheels to a stepping on legs one. The different locomotions are triggered only by local and dynamic conditions and not by an external command and so only one motor for each locomotion unit is necessary. A four-bar linkage moves and rotates the chair, in order to avoid wheelchair turning over and to guarantee a comfortable posture to the passenger.
Performance evaluation of EANT in the robocup keepaway benchmark

Several methods have been proposed for solving reinforcement learning (RL) problems. In addition to temporal difference (TD) methods, evolutionary algorithms (EA) are among the most promising approaches. The relative performance of these approaches in certain subdomains of the general RL problem remains an open question at this time. In addition to theoretical analysis, benchmarks are one of the most important tools for comparing different RL methods in certain problem domains. A recently proposed RL benchmark problem is the Keepaway benchmark, which is based on the RoboCup Soccer Simulator. This benchmark is one of the most challenging multiagent learning problems because its state-space is continuous and high dimensional, and both the sensors and actuators are noisy. In this paper we analyze the performance of the neuroevolutionary approach called evolutionary acquisition of neural topologies (EANT) in the Keepaway benchmark, and compare the results obtained using EANT with the results of other algorithms tested on the same benchmark.
A new method based on wavelet and greedy pusuit analysis for neuro-spike detection

This paper introduces a novel greedy model for spike detection system aimed to neural signal obtained from the brain such as EEG, ECOG. This Presented algorithm combines wavelet transform and simultaneous orthogonal matching pursuit (SOMP). The proposed method is capable of data compression for spike detection. The spike detection experiment demonstrates the TPR in ROC curve is up to 98.76% and the compact factor reaches 42.52 when the length of window we used is 500. Moreover, our method is simple for low power system design and real-time hardware realization.
An Intact Dorsomedial Hypothalamic Nucleus, but Not the Subzona Incerta or Reuniens Nucleus, Is Necessary for Short-Day Melatonin Signal-Induced Responses in Siberian Hamsters

Siberian hamsters provide a useful model to define mechanisms underlying obesity reversal as they naturally transition from their extreme seasonal obesity in long ‘summer-like’ days (LDs) to a leaner state in short ‘winter-like’ days (SDs). These day length changes are coded into durational melatonin (MEL) signals by the pineal gland resulting in stimulation of MEL receptors (MEL1a-Rs). MEL1a-R mRNA is colocalized centrally in sympathetic nervous system (SNS) outflow neurons comprising a chain of neurons that ultimately innervates white adipose tissue (WAT). Neural components in this circuit include the subzona incerta (subZI), dorsomedial hypothalamic nucleus (DMH) and thalamic reuniens nucleus (ReN). SD, long-duration MEL signals induce gonadal regression and increase WAT SNS drive triggering lipolysis and thereby reversing LD obesity. We attempted to block the reversal of SD MEL signal-induced obesity by making electrolytic or sham lesions of the subZI, ReN or DMH in LD-housed hamsters. To create SD-like, long-duration MEL signals, we injected MEL 3 h before lights out, thereby lengthening the naturally occurring nocturnal duration of circulating MEL. ReN and subZI lesions did not block SD-like MEL signal-induced decreases in body, WAT, testicular masses or food intake; by contrast, DMH lesions blocked decreases in WAT and testicular mass. This nonresponsiveness was not due to lesion-induced inappropriate nocturnal LD MEL secretion that would have altered our creation of SD-like signals. Therefore, the DMH appears to participate in the control of both SD energy and reproductive responses, and joins the suprachiasmatic nucleus as sites necessary for SD responses in this species.
Consistent Network Update without tagging

Designing of network update algorithms is urgent for development of SDN control software. A particular case of Network Update Problem is that of adding a set of forwarding rules into flow-tables of SDN switches (say, to install new paths in the network) or restoring seamlessly a given network configuration after some packet forwarding rules have been disabled (say, at the expiry of their time-outs). Some algorithms provide solutions to these problems but only with the help of tagging techniques. But is it possible to perform a consistent network update without tagging? We study this problem in the framework of a formal model of SDN, develop correct and safe network updating algorithms, and show that in some cases it is impossible to update consistently network configurations without resorting either to tagging or to priorities of packet forwarding rules.
Leveraging Weighted Automata in Compositional Reasoning about Concurrent Probabilistic Systems

We propose the first sound and complete learning-based compositional verification technique for probabilistic safety properties on concurrent systems where each component is an Markov decision process. Different from previous works, weighted assumptions are introduced to attain completeness of our framework. Since weighted assumptions can be implicitly represented by multi-terminal binary decision diagrams (MTBDD's), we give an L*-based learning algorithm for MTBDD's to infer weighted assumptions. Experimental results suggest promising outlooks for our compositional technique.