Miracle-dz/UniFAR-FTUs huggingface dataset:
Alignment Constrained Sampling

We present ALICO (ALIgnment COnstrainted) null set generator: a framework to generate randomized versions of an input multiple sequence alignment that preserve some of its crucial features including its dependence structure. In particular, we show that, on average, ALICO samples approximately preserve the PIDs (percent identities) between every pair of input sequences. At the same time our examples demonstrate that the average k-mer composition of each of the sampled sequences show great resemblance to the k-mer composition of our genomic training data. Of note is that ALICO requires only pairwise alignment training data rather than multiple alignment training data. We demonstrate the utility of ALICO in predicting the correct results returned by the "homology-aware" finders PhyloCon, MEME with conservation prior and PRIORITY-C, as well as by our "naive" finder GibbsMarkov, applied to the MacIsaac orthologous yeast data. Finally, we show that using ALICO sampling derived p-values to combine results from multiple finders often outperforms its best individual component. Supplementary Material is available at www.liebertonline. com/cmb .
Methodology of a Population-Based Stroke and TIA Incidence and Outcomes Study: The Auckland Regional Community Stroke Study (ARCOS IV) 2011–2012

Background Stroke is a leading cause of death and disability worldwide. Stroke burden is immense as it leads to premature deaths, leaves survivors with ongoing disabilities, and has a major financial impact on the individual, their families, and the community. Reliable, high-quality evidence is needed on stroke risk factors, incidence, and outcomes to provide information on how best to reduce this burden. Population-based studies are regarded as the ‘gold-standard’ of measuring disease burden but are not common due to the logistical and financial challenges they present. The Auckland Regional Community Stroke Studies are among a few in the world that have been carried out at a population level and at regular intervals. Aim The aim of the fourth Auckland Regional Community Stroke Studies IV is to examine the current measures of stroke incidence, prevalence, and outcomes as well the trends over four decades. This article describes the methodology of the Auckland Regional Community Stroke Studies IV with stroke and transient ischemic attacks cases registered over a 12-month period from March 1, 2011 to February 29, 2012. Conclusions The methodology described may be used as a guide in order to design similar population-based stroke incidence and outcome studies in other countries and populations, thus facilitating the collection of most consistent and accurate stroke epidemiological data.
Metagenome sequence clustering with hash-based canopies

Metagenomics is the collective sequencing of co-existing microbial communities which are ubiquitous across various clinical and ecological environments. Due to the large volume and random short sequences (reads) obtained from community sequences, analysis of diversity, abundance and functions of different organisms within these communities are challenging tasks. We present a fast and scalable clustering algorithm for analyzing large-scale metagenome sequence data. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using hashing. These canopies are then refined by using state-of-the-art sequence clustering algorithms. This canopy-clustering (CC) algorithm can be used as a pre-processing phase for computationally expensive clustering algorithms. We use and compare three hashing schemes for canopy construction with five popular and state-of-the-art sequence clustering methods. We evaluate our clustering algorithm on synthetic and real-world 16S and whole metagenome benchmarks. We demonstrate the ability of our proposed approach to determine meaningful Operational Taxonomic Units (OTU) and observe significant speedup with regards to run time when compared to different clustering algorithms. We also make our source code publicly available on Github. a.
Adaptive segmentation technique for automatic object region and boundary extraction for activity recognition

An unsupervised adaptive segmentation technique based on active contour model for automatic object region and boundary extraction in video sequences is proposed. The active contour model identies each region using certain region descriptors that guide the motion of the initial contour towards the actual region of interest. The region descriptors depend on the statistical information inside and outside the initial contour, which control the growth or contraction of the contour. A process of selective binary and Gaussian ltering regularization level set smooths the level-set function in order to maintain the level of expansion of the active contour. The adaptivity of the proposed method comes from automatic selection of an optimal Gaussian lter parameter which depends on the characteristics of the input video frames. More precisely, the algorithm utilizes the statistical information of each video frame to identify the optimal value of the Gaussian parameter which should be large enough to cover most of the level-set function, but not too large to overlap multiple neighbouring objects. The optimal value of Gaussian parameter aects the segmentation performance of the entire activity video sequence. The performance of the proposed method was tested and evaluated on Weizmann database and KTH database which represent object regions in dierent illuminations and scenarios. The performance of the proposed method is also compared to several state-of-the-art image segmentation methods and observed improved performance in terms of accuracy and eciency. The study demonstrates the robustness of the method to non-uniform illuminations and background noises.
Optimization-Based Whole-Body Control of a Series Elastic Humanoid Robot

As whole-body control approaches begin to enter the mainstream of humanoid robotics research, there is a real need to address the challenges and pitfalls encountered in hardware implementations. This paper presents an optimization-based whole-body control framework enabling compliant locomotion on THOR, a 34 degree of freedom humanoid featuring force-controllable series elastic actuators (SEAs). Given desired momentum rates of change, end-effector accelerations, and joint accelerations from a high-level locomotion controller, joint torque setpoints are computed using an efficient quadratic program (QP) formulation designed to solve the floating-base inverse dynamics (ID). Constraints on the centroidal dynamics, frictional contact forces, and joint position/torque limits ensure admissibility of the optimized joint setpoints. The control approach is supported by an electromechanical design that relies on custom linear SEAs and embedded joint controllers to accurately regulate the internal and external force.
Comparative Toxicity of Different Crude Oils on the Cardiac Function of Marine Medaka (Oryzias melastigma) Embryo

The acute toxic effect of different crude oils (heavy crude oil and bonny light crude oil) on embryos of marine medaka Oryzias melastigma was measured and evaluated by exposure to the water-accommodated fraction (WAF) in the present study. The cardiac function of medaka embryos was used as target organ of ecotoxicological effect induced by oil exposure. Results showed that the developing marine medaka heart was a sensitive target organ to crude oil exposure the heavy crude oil WAF was more toxic to cardiac function of medaka embryos than bonny light cured oil one. Cardiac function of medaka embryos was clearly affected by exposure to heavy crude oil WAF after 24 hours exposure and showed a dose-dependent slowing of heart rate. Furthermore, swelled and enlarged heart morphology, lowered blood circulation and accumulation of blood cells around the heart area were found. However, the toxic effect of bonny light crude oil on cardiac function of medaka embryos was comparatively low. Statistical results showed that the cardiac function was only affected by highest bonny light crude oil WAF (9.8 mg/L) exposure treatment. These findings indicated that cardiac function of marine medaka embryo was a good toxicity model for oil pollution and could be used to compare and evaluate the toxicity of different crude oils. The heart rate was an appropriate endpoint in the acute toxicity test.
Examining the Construct Validity of the Elemental Psychopathy Assessment

Lynam and colleagues recently developed a new self-report inventory for the assessment of psychopathy, the Elemental Psychopathy Assessment (EPA). Using a sample of undergraduates (N = 227), the authors examined the construct validity of the EPA by examining its correlations with self and stranger ratings on the Five-Factor Model, as well as self-reported ratings of personality disorders, social cognition, and love styles. The EPA psychopathy scores manifested expected correlations with both self and stranger ratings of the Five-Factor Model, particularly with the domains of Agreeableness and Conscientiousness, and were significantly related to various forms of personality pathology such as narcissism and antisocial personality disorders. The EPA also manifested expected relations with aggressive social cognitions. Finally, the EPA psychopathy scores were correlated with romantic love styles indicative of game playing and infidelity. The current results provide further evidence of the construct validity of the EPA as it manifests relations consistent with the nomological network of psychopathy.
Legislativo brasileiro em perspectiva comparada

El libro ofrece a lo largo de sus casi 500 paginas un panorama de la produccion de estudios sobre el Poder legislativo en Brasil. Producto de diferentes trabajos presentados en el seminario Legislativo Brasileiro em Perspectiva Comparada, realizado en mayo de 2008 en la capital de aquel pais, este volumen cuenta con la colaboracion de renombrados academicos de universidades brasilenas y extranjeras.
Demand side management of electric boilers

In this paper a control strategy for demand side management of electric storage water heaters is presented. The proposed algorithm reduces load variations, during any given optimization period, taken into account the base load. The algorithm uses the energy consumption model of the water heater as an input. The strategy can be applied to optimize present control strategies based on the existing ripple control technology, in order to improve the performance of the power system.
Performance of DCO-OFDM in Optical Wireless Communication System

-OFDM scheme is widely adopted as it has high data rate and good performance under various channel conditions. In this paper, a number of unipolar optical OFDM scheme has been used for IM/DD system using simulink. To develop such a complex system, this paper proposes MATLAB as the platform for its implementation. The modeling of block diagram is done using Fast Fourier Transform and Hermitian symmetry. The concept of Optical OFDM uses LED at the transmitter and Photodiode at the receiver to demonstrate the optical characteristics of the system. The model has been implemented using different modulation techniques and under various channels. The paper suggests that using QPSK modulation in white Gaussian noise with 5dB SNR gives best result in terms of BER. Similarly, DBPSK modulation technique performs better with the increase in fading frequency. Thus, the complete model description suggests novelty in the modulation schemes that can be accepted for channels applicable in optical OFDM communication
Gerbil brain-stem auditory-evoked responses to maximum length sequences.

This study evaluated the feasibility of obtaining brain-stem auditory-evoked responses (BAERs) to trains of clicks with average rates of up to 500 clicks per second in the gerbil, in order to evaluate BAER behavior at rates higher than those possible in conventional averaging, and to evaluate whether these higher rates allow obtaining BAERs more efficiently. Gerbils were anesthetized with Nembutal, and normothermia was maintained with a homeothermic blanket system. Pseudorandom pulse trains, called maximum length sequences (MLSs), were generated by an Ariel DSP-16 board housed in an IBM-AT. Electrical activity was recorded with Grass needle electrodes placed subdermally. This activity was amplified and filtered by a Nicolet Compact Four, and digitized by the A/D of the Ariel DSP-16. Clicks were presented at levels of 50, 60, 70, 80, and 90 dB pSPL. Conventional BAERs were obtained at a rate of 30 Hz. MLS BAERs were obtained by presenting MLS pulse trains which were comprised of 64 pulses. Following collection of the response to MLS pulse trains, the MLS BAER was obtained by cross correlating the response with a recovery sequence. The minimum time between pulses is called the minimum pulse interval (MPI). MLS BAERs were obtained for MPIs of 6, 4, 2, and 1 ms. BAERs were obtained in ten young adult gerbils for all rate by click-level conditions. BAERs were observed in all animals for all click levels and rates. Generally, with increasing click level there were decreases in peak latencies and increases in peak amplitudes. With increasing rate (decreasing MPI), there were increases in peak latencies, increases in the i-iv interval, and decreases in peak amplitudes. Computations suggested the the most efficient rate (i.e., the rate producing a constant signal-to-noise ratio response in the least amount of time) is not necessarily the fastest rate, but depends on the BAER peak and click level.
Publication Bias in the Organizational Sciences

Publication bias poses multiple threats to the accuracy of meta-analytically derived effect sizes and related statistics. Unfortunately, a review of the literature indicates that unlike meta-analytic reviews in medicine, research in the organizational sciences tends to pay little attention to this issue. In this article, the authors introduce advances in meta-analytic techniques from the medical and related sciences for a comprehensive assessment and evaluation of publication bias. The authors illustrate their use on a data set on employment interview validities. Using multiple methods, including contour-enhanced funnel plots, trim and fill, Egger’s test of the intercept, Begg and Mazumdar’s rank correlation, meta-regression, cumulative meta-analysis, and selection models, the authors find limited evidence of publication bias in the studied data.
Change in Rigidity in the Activated Form of the Glucose / Galactose Receptor from E . coli : A Phenomenon

Recently a periplasmic glucose/galactose binding protein, GGRQ26C, immobilized on gold surface has been used as an active part of a glucose biosensor based on quartz microbalance technique (QCM). However the nature of the glucose detection was not clear. Here we have found that the receptor protein film immobilized on the gold surface increases its rigidity when glucose is added, which explains the unexpected detection signal. To study the rigidity change, we developed a new fast and simple method based on using atomic force microscopy (AFM) in tapping mode. The method was verified by explicit measurements of the Young’s modulus of the protein film by conventional AFM methods. Since there are a host of receptors that undergo structural change when activated by ligand, AFM can play a key role in the development and/or optimization of biosensors based on rigidity changes in biomolecules.
State estimation for gene networks with intrinsic and extrinsic noise: A case study on E.coli arabinose uptake dynamics

We address state estimation for gene regulatory networks at the level of single cells. We consider models that include both intrinsic noise, in terms of stochastic dynamics, and extrinsic noise, in terms of random parameter values. We take the Chemical Master Equation (CME) with random parameters as a reference modeling approach, and investigate the use of stochastic differential model approximations for the construction of practical real-time filters. To this aim we consider a Square-Root Unscented Kalman Filter (SRUKF) built on a Chemical Langevin Equation (CLE) approximation of the CME. Using arabinose uptake regulation in Escherichia coli bacteria as a case study, we show that performance is comparable to that of a (computationally heavier) particle filter built directly on the CME, and that the use of information about parameter uncertainty allows one to improve state estimation performance.
Gaussian linear frequency modulation signal SAR processing

High resolution of targets, fine quality of image, reduction the computation and the power consumption of transmitter signal are four elements of radar systems attracted considerable interest at the number searchers of SAR focusing systems. To get this need, different modulation have been developed and used to perfect the quality of image like Linear Frequency Modulation (LFM). In this paper, we investigate new radar waveforms that are used to improve the resolution of targets named Gaussian linear frequency modulation (GLFM). Preliminary simulations are performed and discussed.
Snoezelen: an overview of research with people with developmental disabilities and dementia

Purpose : This paper was to provide an overview of the research studies on snoezelen with people with developmental disabilities and dementia. Method : Computerized and manual searches were carried out to identify the aforementioned studies. Within-session, post-session, and longer-term effects of snoezelen were examined. Results and Conclusion : Twenty-one research studies were identified, 14 concerning people with developmental disabilities and seven people with dementia. Of those studies: 14 reported positive within-session effects; four positive post-session effects; and two positive longer-term effects. These findings were discussed in relation to: (1) methodological aspects (weaknesses) of the studies; (2) the cost of arranging a snoezelen programme and possibilities of reducing the range of stimuli available in the programme; and (3) some research issues for advancing the understanding and effectiveness of intervention programmes with people with developmental disabilities and dementia.
Hybrid Assistive Systems for Rehabilitation: Lessons Learned from Functional Electrical Therapy in Hemiplegics

This paper suggests that the optimal method for promoting of the recovery of upper extremity function in hemiplegic individuals is the use of hybrid assistive systems (HAS). The suggested HAS is a combination of stimulation of paralyzed distal segments (hand) in synchrony with robot controlled movements of proximal segments (upper arm and forearm). The use of HAS is envisioned as part of voluntary activation of preserved sensory-motor systems during task related exercise. This HAS design follows our results from functional electrical therapy, constraint induced movement therapy, intensive exercise therapy, and use of robots for rehabilitation. The suggestion is also based on strong evidences that cortical plasticity is best promoted by task related exercise and patterned electrical stimulation
Accelerated Type III Secretion System 2-Dependent Enteropathogenesis by a Salmonella enterica Serovar Enteritidis PT4/6 Strain

ABSTRACT Salmonella enterica subsp. I serovars Typhimurium and Enteritidis are major causes of enteric disease. The pathomechanism of enteric infection by serovar Typhimurium has been studied in detail. Serovar Typhimurium employs two pathways in parallel for triggering disease, i.e., the “classical” pathway, triggered by type III secretion system 1 (TTSS-1), and the “alternative” pathway, mediated by TTSS-2. It had remained unclear whether these two pathways would also explain the enteropathogenesis of strains from other serovars. We chose the isolate P125109 of the epidemic serovar Enteritidis PT4/6, generated isogenic mutants, and studied their virulence. Using in vitro and in vivo infection experiments, a dendritic cell depletion strategy, and MyD88−/− knockout mice, we found that P125109 employs both the “classical” and “alternative” pathways for triggering mucosal inflammation. The “classical” pathway was phenotypically similar in serovar Typhimurium strain SL1344 and in P125109. However, the kinetics of the “alternative” pathway differed significantly. Via TTSS-2, P125109 colonized the gut tissue more efficiently and triggered mucosal inflammation approximately 1 day faster than SL1344 did. In conclusion, our data demonstrate that different Salmonella spp. can differ in their capacity to trigger mucosal inflammation via the “alternative” pathway in vivo.
Microarray analysis of port wine stains before and after pulsed dye laser treatment

Neither the pathogenesis of port wine stain (PWS) birthmarks nor tissue effects of pulsed dye laser (PDL) treatment of these lesions is fully understood. There are few published reports utilizing gene expression analysis in human PWS skin. We aim to compare gene expression in PWS before and after PDL, using DNA microarrays that represent most, if not all, human genes to obtain comprehensive molecular profiles of PWS lesions and PDL‐associated tissue effects.
Isolamento e seleção de fungos filamentosos produtores de lipases.

Os estudos sobre a producao de substâncias de origem microbiana sao realizados a partir de cepas adquiridas de colecoes de cultura ou cepas isoladas de nichos naturais. No presente estudo foi avaliada a capacidade de producao de lipase por 73 cepas fungicas, 14 obtidas de colecoes de cultura e 59 isoladas de amostras do solo do cerrado de Minas Gerais, com o emprego de tecnicas de enriquecimento seletivo. O isolamento e selecao primaria foram realizados em meio de cultura contendo agar, emulsao de oleo de oliva, sais biliares e nutrientes. As colonias lipoliticas foram detectadas pela presenca no meio opaco de uma zona clara ao redor delas. Vinte e uma cepas foram avaliadas como produtoras em potencial e a capacidade de producao determinada em condicoes de cultivo submerso e cultivo em estado solido (selecao secundaria). Apenas 7 delas foram selecionadas como boas produtoras. A cepa melhor produtora, identificada como Colletotrichum gloesporioides, produziu 27.700 U/L de lipase, empregando-se inoculo vegetativo, com cultivo submerso em frascos agitados a 150 rpm e 30 oC, durante 96 h, em meio de cultura basal contendo peptona bacteriologica (20,0 g/L), oleo de oliva (8,0 mL/L) e sais inorgânicos, no pH 7,0. A preparacao bruta da enzima foi capaz de hidrolisar amplo espectro de substratos incluindo gordura de porco (banha), oleos vegetais e tributirina. Foram realizados estudos visando a determinacao das melhores condicoes para a producao da lipase pelo C. gloesporioides. Inicialmente foram identificados os fatores (variaveis) mais importantes, tendo sido, em seguida, selecionados como significativos a peptona bacteriologica, o oleo de oliva e o pH inicial do meio de cultura. Os estudos para a determinacao das condicoes otimizadas para a producao da lipase foram realizados aplicando-se a metodologia de superficies de respostas, com o emprego de um planejamento fatorial 23 com cinco pontos centrais. Foi demonstrado que o modelo estatistico linear que indicou a variacao da producao da enzima em funcao da concentracao da peptona (na faixa de 10 a 30 g/L), do oleo de oliva (na faixa de 4-16 mL/L) e do pH (na faixa de 6-7) foi representado pela equacao ajustada ~ = 27,2 3,4 x1 4,1 x2 + 0,7 x3 1,8 x1 x2 + 0,6 x1 x3 + 0,7 x2 x3 2,1 x1 x2 x3, sendo simplificada para ~ = 27,2 3,4 x1 4,1 x2, devido ao efeito do pH e das possiveis interacoes entre os efeitos nao serem significativos. Desse modo, foi verificado que a representacao bidimensional da superficie de resposta do referido modelo foi um plano inclinado obliquamente em relacao aos eixos cartesianos com direcao descendente indo da direita para a esquerda. Concluiu-se que, para serem conseguidos maiores rendimentos de producao, devia-se deslocar a regiao experimental para menores valores de x1 (peptona) e de x2 (oleo de oliva). Seguindo essa orientacao conseguiu-se que a cepa fungica produzisse cerca de 36.000 U/L de lipase extracelular que se mostrou bastante ativa em pH alcalino.