Miracle-dz/UniFAR-FTUs huggingface dataset:
Brachyury cooperates with Wnt/β-Catenin signalling to elicit Primitive Streak like behaviour in differentiating mouse ES cells

The formation of the Primitive Streak is the first visible sign of gastrulation, the process by which the three germ layers are formed from a single epithelium during early development. Embryonic Stem Cells (ESCs) provide a good system to understand the molecular and cellular events associated with these processes. Previous work, both in embryos and in culture, has shown how converging signals from both Nodal/TGFβR and Wnt/β-Catenin signalling pathways specify cells to adopt a Primitive Streak like fate and direct them to undertake an epithelial to mesenchymal transition (EMT). However, many of these approaches have relied on genetic analyses without taking into account the temporal progression of events within single cells. In addition, it is still unclear as to what extent events in the embryo are able to be reproduced in culture. Here, we combine flow-cytometry and a quantitative live single-cell imaging approach to demonstrate how the controlled differentiation of mouse ESCs (mESCs) towards a Primitive Streak fate in culture results in cells displaying many of the characteristics observed during early mouse development including transient Brachyury expression, EMT and increased motility. We also find that the EMT initiates the process, and this is both fuelled and terminated by the action of Bra, whose expression is dependent on the EMT and ß-Catenin activity. As a consequence of our analysis, we propose that a major output of Brachyury expression is in controlling the velocity of the cells that are transiting out of the Primitive Streak.
Using Economic Theory to Build Optimal Portfolios

Given expected returns and return covariances, portfolio weights are known in closed form in a mean-variance framework. The real difficulty is in estimating these parameters. Using recent advances in Bayesian techniques, we show how investors can incorporate any prior information for optimal portfolio selection. We apply our method to 27 domestic and international data sets. We find that our tangency portfolios have three essential and attractive features. i) They perform better in terms of out-of-sample Sharpe ratio. ii) Their weights are guaranteed to be economically "reasonable": positive, stable, and without extravagant position in any asset. iii) Turnover is very low.
Distributed Self-Organization Of Swarms To Find Globally $\epsilon$-Optimal Routes To Locally Sensed Targets

The problem of near-optimal distributed path planning to locally sensed targets is investigated in the context of large swarms. The proposed algorithm uses only information that can be locally queried, and rigorous theoretical results on convergence, robustness, scalability are established, and effect of system parameters such as the agent-level communication radius and agent velocities on global performance is analyzed. The fundamental philosophy of the proposed approach is to percolate local information across the swarm, enabling agents to indirectly access the global context. A gradient emerges, reflecting the performance of agents, computed in a distributed manner via local information exchange between neighboring agents. It is shown that to follow near-optimal routes to a target which can be only sensed locally, and whose location is not known a priori, the agents need to simply move towards its "best" neighbor, where the notion of "best" is obtained by computing the state-specific language measure of an underlying probabilistic finite state automata. The theoretical results are validated in high-fidelity simulation experiments, with excess of $10^4$ agents.
Analysis of prosody increment induced by pitch accents for automatic emphasis correction

We are interested in developing an automatic emphasis correction system, which converts any unemphasized word in an ut-terance into emphasized. Analyzing how prosody changes from unaccented to accented is crucial for the task. While previous works on prosody reconstruction only model the prosody contour itself instead of the increment, we propose a framework to study the prosody increment induced by pitch accents from real speech in a statistically rigorous manner. This framework also infers the degree of emphasis of each word to account for the additional prosody variations due to metalinguistic factors. According to the analysis results, this framework provides a lot of useful insights into the prosody increment, which are consistent with many existing studies on pitch accent and emphasis.
Voltage Drop Aware Power Pad Assignment and Floorplanning for Multi-voltage SoC Designs

Multi-voltage technique is an effective way of power saving in system-on-a-chip (SoC) designs. However, as the technology nodes continue to shrink, the voltage drop constraint in multiple power domains presents serious obstacles in power/ground (P/G) network design of wire-bonding package. In this paper, a voltage drop aware power pad assignment and floor planning method for multi-voltage SoC designs is proposed. In order to reduce the voltage drop, we develop a fast method to calculate the location of power pad for each power domain based on the spring model. During floor planning iterations, a static voltage drop analysis is performed to update the voltage drop distribution, and then number of violation nodes in the P/G network is obtained. To speed up the floor planning algorithm, instead of time-consuming matrix computation to obtain voltage drops, we use the weighted distance from blocks to power pads as an optimization objective. Experimental results on GSRC benchmark suites indicate that the proposed approach generates an optimized placement of power pads and floor planning of blocks.
Exorciser: Automatic generation and interactive grading of structured excercises in the theory of computation

For almost two centuries educators and technicians hcve been designing and evaluating teaching devices having the capability to coach, support learning processes and to asses the student's mastery of new skills by means of tests and exercises. Withouta personal tutor, 'paperand pencii" exercises follow a presentation-activation-feedbackpattern that takes days before the Student receives feedback on her Performance. The concept of an automated tutor that conveys exercises (presentation), demands a response (activation), and then informs the student Df the correctness of her response (feedback),aims to replace the linear activation-feedback phase by an interactive process that allows the student :o makeintelligent adjustmentsbased on available feedback. In a suitable domainof knowledge the techniques developedin this the¬ sis lead to an effectiveautomatedtutor, able to reliably and quickly check details, and to provide feedbackjust in time—freeing t ie human tutor to address more demanding and thought-stimulating activities. The key idea is to design both a class of exercises and a Solution spacs within which the student's Solution is confined. This is possible in selected mathematically structured domainsof knowledge where Solutions and their processes can be verified algorithmically. The validity of this approach is demonstrated in our system ExorCISER, which contains 25 examples of such interactive exercises and which has been in use for several years. We have tested the usubility and verified the effectiveness of Exorciserin actual instructional settings by means of a comparative study. The opportunity to receive immediate individual feedback, together with the possibility of generating an unlimited number of exercise instances of various levels of dimculty, combined with the possibility to look at the Solution of an exercise on request, makes ExORClSER'steach¬ ing capabilities truly interactive and attraetive. Further reasons for the student's aeeeptanceof the Exorciserenvironment is its intuitive user interface and the fact that the student always mainUins control of the system.
Metabolism of 2-Chloro-4-Nitrophenol in a Gram Negative Bacterium, Burkholderia sp. RKJ 800

A 2-Chloro-4-nitrophenol (2C4NP) degrading bacterial strain designated as RKJ 800 was isolated from a pesticide contaminated site of India by enrichment method and utilized 2C4NP as sole source of carbon and energy. The stoichiometric amounts of nitrite and chloride ions were detected during the degradation of 2C4NP. On the basis of thin layer chromatography, high performance liquid chromatography and gas chromatography-mass spectrometry, chlorohydroquinone (CHQ) and hydroquinone (HQ) were identified as major metabolites of the degradation pathway of 2C4NP. Manganese dependent HQ dioxygenase activity was observed in the crude extract of 2C4NP induced cells of the strain RKJ 800 that suggested the cleavage of the HQ to γ-hydroxymuconic semialdehyde. On the basis of the 16S rRNA gene sequencing, strain RKJ 800 was identified as a member of genus Burkholderia. Our studies clearly showed that Burkholderia sp. RKJ 800 degraded 2-chloro-4-nitrophenol via hydroquinone pathway. The pathway identified in a gram negative bacterium, Burkholderia sp. strain RKJ 800 was differed from previously reported 2C4NP degradation pathway in another gram-negative Burkholderia sp. SJ98. This is the first report of the formation of CHQ and HQ in the degradation of 2C4NP by any gram-negative bacteria. Laboratory-scale soil microcosm studies showed that strain RKJ 800 is a suitable candidate for bioremediation of 2C4NP contaminated sites.
Towards Communication Strategies for Platooning

—Platooning, the act of cars autonomously following their leaders to form a road train, has huge potentials to improve trafﬁc ﬂow efﬁciency and driving experience on freeways, and most importantly road trafﬁc safety. The challenges of this application are numerous, as witnessed by the number of projects working on this topic from the eighties till nowadays. Platooning indeed encompasses control theory, vehicle dynamics, transportation engineering, and wireless networking, making it one of the widest and most challenging research topics. Wireless communication is a fundamental building block for this application, as it is needed to manage and maintain the platoons and, clearly, have strict constraints in terms of update frequency and reliability. While control theory and vehicle dynamics already provide strong theoretical and practical basis, questions regarding robust and timely communication are still open. In this paper we study concepts for platooning systems and identify speciﬁc challenges in wireless networking. In particular, we present a platooning simulation framework that can be used to analyze such systems, describe approaches for communication protocols, and present preliminary results outlining the potentials of our ideas.
Multivariate random forests

Random forests have emerged as a versatile and highly accurate classification and regression methodology, requiring little tuning and providing interpretable outputs. Here, we briefly outline the genesis of, and motivation for, the random forest paradigm as an outgrowth from earlier tree‐structured techniques. We elaborate on aspects of prediction error and attendant tuning parameter issues. However, our emphasis is on extending the random forest schema to the multiple response setting. We provide a simple illustrative example from ecology that showcases the improved fit and enhanced interpretation afforded by the random forest framework. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 80‐87 DOI: 10.1002/widm.12
Following Traces of Lost Models

In modern statistics, the variety of models available for classification or regression is huge. Due to advances in computational technology and broadly available statistical software, we are now able to fit many models to the given data. Ensemble methods such as bagging or boosting take advantage of this development to improve prediction accuracy, but individual models are lost in the quantity of ensemble elements. Tools available for the analysis of multiple models or model ensembles are, however, rare. In this paper, we present a visualization method that is part of a larger framework for exploratory model analysis. This visualization tool allows us to compare many tree-based models using Trace Plots with respect to variables used and cut-points chosen. It can be used for both analysis of model properties and finding special subgroups in the data. It is suitable for analyzing model ensembles or comparing individual models. The method can accommodate a large number of tree models. We will illustrate the method in a practical application.
Productivity Analysis of UK Auditing Firms

This study analyses the productivity change in the United Kingdom (UK) of auditing firms over the period 2005–2012, using a Malmquist index with a technological bias. Productivity is the rate at which goods or services are produced relative to the input. A common measure of productivity is the ratio of output per unit of labour used in the production. Productivity change is the change in the total output relative to the change in the total input and it is composed of technical efficiency change (managerial practices and scale effects) and technological change (innovation and investment in new technologies). Until 2005, the auditing profession in the UK employed a regime of self-regulation; after a brief hiatus, the country adopted the new European Statutory Audit Directive in April 2008, changing the regulatory framework. This study analyses the productivity change among UK auditing companies both before and after the regulation change. Our results indicate that the productivity change among UK auditing companies is mixed and not dictated by regulation. Furthermore, the traditional growth accounting method, which assumes Hicks-neutral technological change, is not appropriate for an analysis of the productivity change in auditing firms.
A New Approach to the Allocation of Aid Among Developing Countries: Is the USA more Selfish than the Rest?

This paper attempts to explain the factors that determine the geographical allocation of foreign aid. It develops a theoretical model and uses panel data taking account of the truncated nature of the dependent variable. We run regressions for different groups of donors (USA, non-USA bilateral and multilateral). We find that all the donors respond to recipient need in their allocation of aid, but compared to the rest the USA puts less emphasis on need and more emphasis on donor interest e.g. geopolitical, commercial, and other links with specific recipients. We conclude that the USA is a more selfish aid donor than other bilateral and multilateral donors when allocating its aid. JEL Classification: F35, C23, C24.
GPU-in-Hadoop: Enabling MapReduce across distributed heterogeneous platforms

As the size of high performance applications increases, four major challenges including heterogeneity, programmability, failure resilience, and energy efficiency have arisen in the underlying distributed systems. To tackle with all of them without sacrificing performance, traditional approaches in resource utilization, task scheduling and programming paradigm should be reconsidered. As Hadoop has handled data-intensive applications well in Clouds, GPU has demonstrated its acceleration effectiveness for computation-intensive ones. This paper intends to integrate Hadoop with CUDA to exploit both CPU and GPU resources. Hadoop will schedule MapReduce's Map and Reduce functions across multiple nodes, whereas CUDA code helps accelerate them further on local GPUs. All available heterogeneous computational power will be utilized. MapReduce in Hadoop will ease the programming task by hiding communication details. Hadoop Distributed File System will help achieve data-level fault resilience. GPU's energy efficiency characteristics help reduce the power consumption of the whole system. To achieve Hadoop and GPU integration, four approaches including Jcuda, JNI, Hadoop Streaming, and Hadoop Pipes, have been accomplished. Experimental results have demonstrated their effectiveness.
Seção de Software

Muitos problemas interessantes de otimização não podem ser resolvidos de forma exata, utilizando a computação convencional (seqüencial) dentro de um tempo razoável, inviabilizando sua utilização em muitas aplicações reais na engenharia e na indústria. Embora os computadores estejam cada vez mais velozes, existem limites físicos e a velocidade dos circuitos não pode continuar melhorando indefinidamente. Por outro lado nos últimos anos tem-se observado uma crescente aceitação e uso de implementações paralelas nas aplicações de alto desempenho como também nas de propósito geral, motivados pelo surgimento de novas arquiteturas que integram dezenas de processadores rápidos e de baixo custo. Essas arquiteturas compõem ambientes com memória distribuída como, por exemplo, estações de trabalho ou PCs conectados em rede.
Performance improvement of induction motor by Selective Harmonic Elimination (SHE) using Newton Raphson (N-R) method

The paper presents an induction motor model with improvised performance by unified approach for selective Harmonic Elimination (SHE) of 3-Phase Voltage Source Inverter (VSI). Due to switching in inverters harmonics are present, the performance of inverter can be improved by reducing the harmonics. At this stage of time where everyone focus on increasing the level of inverter, lose their attention towards harmonic reduction. AS we know several modulation methods have been implemented to multilevel inverters. The modulation methods with higher switching frequency reduce filter size but increases switching losses. The Step modulation method operates with low switching frequency has less switching losses but the required filter size is large. To reduce the filter size the number of levels of the inverter has to be increased but it increases the cost of the system. This paper presents a novel modulation method where additional notches are introduced in the multi-level output voltage. The projected work investigates the Selective Harmonics Elimination (SHE) to eliminate harmonics produced by Pulse Width Modulation (PWM) [1] inverter. The model presented here eliminate the even order harmonics due to the symmetry of the wave, 3rd and multiple of 3rd order harmonics are eliminated due to fact that the harmonics wave of all 3 phases are in space phase, but differ in time phase by 120 degree, along with this 5th and 7th harmonics are eradicated by using SHE technique. The proposed modulation method is verified through MATLAB Simulink simulation.
THE FLORIDA STATE UNIVERSITY FAMU–FSU COLLEGE OF ENGINEERING OPTIMAL SPACE TIME TRELLIS CODE DESIGN FOR FAST FADING CHANNELS By

The demand for high-speed mobile wireless communications is rapidly growing. MIMO technology promises to be a key technique for achieving the high date capacity and spectral efficiency for wireless communication systems of the near future. This dissertation presents an overview of Multiple Input Multiple Output (MIMO) systems. A simple mathematical model is used to describe MIMO systems. Systems’ capacity improvement is derived. Various Benefits achievable by MIMO system are discussed. History and open problems in this field are presented as well. An investigation of Space Time Trellis Code (STTC) design criteria is presented.There are four sets of design criteria which apply to different channel models. Design Criteria Set I and Criteria Set II apply to slow fading channels and design Criteria Set III and Criteria Set VI apply to fast fading channels. If a code has small diversity order, design Criteria Set I and Criteria Set III will apply and in the case of large diversity order, Criteria Set II and Criteria Set VI apply. Based on these design criteria, this dissertation developed a construction method of optimal STTC codes for fast fading channels.when the diversity order is large,trace criteria is applicable. Set partition idea is extended to symbol group partition. A set of design rules are developed to construct optimal STTC. The optimality is proved as well. This dissertation also provides simulation results of optimal STTC over other claimed STTC. The simulation results showed that the optimal STTC outperformed all other codes. And at the same times, using the simulation results, the effect of number of transmitting antennas and number of receivering antennas on the performance of STTC are also studied. Finally, open problems for future research are discussed.
Contribution of Fdh3 and Glr1 to Glutathione Redox State, Stress Adaptation and Virulence in Candida albicans

The major fungal pathogen of humans, Candida albicans, is exposed to reactive nitrogen and oxygen species following phagocytosis by host immune cells. In response to these toxins, this fungus activates potent anti-stress responses that include scavenging of reactive nitrosative and oxidative species via the glutathione system. Here we examine the differential roles of two glutathione recycling enzymes in redox homeostasis, stress adaptation and virulence in C. albicans: glutathione reductase (Glr1) and the S-nitrosoglutathione reductase (GSNOR), Fdh3. We show that the NADPH-dependent Glr1 recycles GSSG to GSH, is induced in response to oxidative stress and is required for resistance to macrophage killing. GLR1 deletion increases the sensitivity of C. albicans cells to H2O2, but not to formaldehyde or NO. In contrast, Fdh3 detoxifies GSNO to GSSG and NH3, and FDH3 inactivation delays NO adaptation and increases NO sensitivity. C. albicans fdh3⎔ cells are also sensitive to formaldehyde, suggesting that Fdh3 also contributes to formaldehyde detoxification. FDH3 is induced in response to nitrosative, oxidative and formaldehyde stress, and fdh3Δ cells are more sensitive to killing by macrophages. Both Glr1 and Fdh3 contribute to virulence in the Galleria mellonella and mouse models of systemic infection. We conclude that Glr1 and Fdh3 play differential roles during the adaptation of C. albicans cells to oxidative, nitrosative and formaldehyde stress, and hence during the colonisation of the host. Our findings emphasise the importance of the glutathione system and the maintenance of intracellular redox homeostasis in this major pathogen.
Layered space-time equalization for wireless MIMO systems

We investigate layered space-time equalization (LSTE) architectures for multiple-input multiple-output (MIMO) frequency-selective channels. At each stage or layer of detection, a MIMO delayed decision feedback sequence estimator (MIMO-DDFSE) is used to tentatively detect a group of selected data streams, among which a subgroup of data streams are output and are canceled from the received signals. With the proposed architectures, the numbers of the tentatively detected data streams and output data streams can be different at different LSTE stages, while the MIMO-DDFSE can also reduce to the special cases of multiple-input single-output decision feedback equalizer (MISO-DFE), MISO-DDFSE, and MIMO-DFE, allowing tradeoffs between performance and complexity. We also derive the equalizer coefficients, discuss timing recovery, and consider channel estimation. Simulation results demonstrate the performance of the proposed LSTE structures and the tradeoffs between performance and complexity of the multistage structure and the single-stage version. We also demonstrate the impact of imperfect channel estimation, imperfect interference cancellation, the number of receive antennas, filter length, and oversampling on performance.