Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Evolutionary Methods to Study G-Protein Coupled Receptors

A novel method to analyze evolutionary change is presented and its application to the analysis of sequence data is discussed. The investigated method uses phylogenetic trees of related proteins with an evolutionary model in order to gain insight about protein structure and function. The evolutionary model, based on amino acid substitutions, contains adjustable parameters related to amino acid and sequence properties. A maximum likelihood approach is used with a phylogenetic tree to optimize these parameters. The model is applied to a set of Muscarinic receptors, members of the G-protein coupled receptor family. Here we show that the optimized parameters of the model are able to highlight the general structural features of these receptors.
Dynamics of self assembly of magnetized disks rotating at the liquid–air interface

This paper is a theoretical study of dynamic self assembly in a system of millimeter-sized magnetized disks floating at a liquid–air interface and spinning under the influence of a rotating magnetic field. Equations of motions are derived that account for the hydrodynamic and magnetic forces acting in the system. Numerical integration of these equations predicts formation of ordered structures of spinning disks; the simulated structures reproduce the patterns observed experimentally.
Cross-talk between Rho and Rac GTPases drives deterministic exploration of cellular shape space and morphological heterogeneity

One goal of cell biology is to understand how cells adopt different shapes in response to varying environmental and cellular conditions. Achieving a comprehensive understanding of the relationship between cell shape and environment requires a systems-level understanding of the signalling networks that respond to external cues and regulate the cytoskeleton. Classical biochemical and genetic approaches have identified thousands of individual components that contribute to cell shape, but it remains difficult to predict how cell shape is generated by the activity of these components using bottom-up approaches because of the complex nature of their interactions in space and time. Here, we describe the regulation of cellular shape by signalling systems using a top-down approach. We first exploit the shape diversity generated by systematic RNAi screening and comprehensively define the shape space a migratory cell explores. We suggest a simple Boolean model involving the activation of Rac and Rho GTPases in two compartments to explain the basis for all cell shapes in the dataset. Critically, we also generate a probabilistic graphical model to show how cells explore this space in a deterministic, rather than a stochastic, fashion. We validate the predictions made by our model using live-cell imaging. Our work explains how cross-talk between Rho and Rac can generate different cell shapes, and thus morphological heterogeneity, in genetically identical populations.
A clinical correlation between stature and posterior tooth length

Introduction Exploration and determination of the relationship between stature and length of tooth is essential in Paleontology, Forensic Odontology and Endodontology. This study aimed to determine any association between stature and posterior tooth length in a group of patients who required root canal treatment. Methods Age, sex and standing height of adults were considered for posterior tooth length measurement. Molars and Premolars of apparently normal males (n=115 for molars, n= 75 for premolars) and females (n=124 for molars, n=80 for premolars), aged 20-50 years with intact cuspal morphology, which required RCT were selected for this study. Females and males were divided into 2 groups each based on their heights females > 155 cm and ≤ 155 cm, males > 165.10 and ≤ 165.10cm. The tooth length of permanent molars and premolars in both groups were measured using RVG and Electronic apex locator. Measurements obtained were compared separately for males and females using descriptive statistics and Pearson correlation coefficient. Results In females MB, ML, D roots of molar showed significant association (P=0.021), (P=0.027), (P=0.010) and roots of premolars showed significant association (P=0.002), (P=0.006) between both the groups respectively In males MB, ML, D roots of molar showed significant association (P=0.009), (P=0.004), (P=0.015) and roots of premolars showed significant association (P=0.006), (P=0.020) between both the groups respectively. Conclusion The present clinical study reveals that there is a positive association between stature and posterior tooth length in both males and females.
Detecting Hunts in Wildlife Documentaries

We propose a multi-level video event detection methodology and apply it to animal hunt detection in wildlife documentaries. The proposed multi-level approach has three levels. The rst level extracts color, texture, and motion features, and detects moving object blobs. The mid-level employs a neural network to verify whether the moving object blobs belong to animals. This level also generates shot descriptors that combine features from the rst level and contain results of mid-level, domain speciic inferences made on the basis of shot features. The shot descriptors are then used by the domain-speciic inference process at the third level to detect the video segments that contain hunts. The proposed approach can be applied to diierent domains by adapting the mid and high-level inference processes. Event based video indexing, summarization and browsing are among the applications of the proposed approach.
Targeted Development of Registries of Biological Parts

Background The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea. Methods/Principal Findings By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. Conclusions/Significance Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.
APOE ε4 specific imbalance of arachidonic acid and docosahexaenoic acid in serum phospholipids identifies individuals with preclinical Mild Cognitive Impairment/Alzheimer's Disease

This study was designed to explore the influence of apolipoprotein E (APOE) on blood phospholipids (PL) in predicting preclinical Alzheimer's disease (AD). Lipidomic analyses were also performed on blood from an AD mouse model expressing human APOE isoforms (EFAD) and five AD mutations and from 195 cognitively normal participants, 23 of who converted to mild cognitive impairment (MCI)/AD within 3 years. APOE ε4-carriers converting to MCI/AD had high arachidonic acid (AA)/docosahexaenoic acid (DHA) ratios in PL compared to cognitively normal ε4 and non-ε4 carriers. Arachidonic acid and DHA containing PL species, ε4-status and Aβ42/Aβ40 ratios provided 91% accuracy in detecting MCI/AD. Fish oil/omega-3 fatty acid consumption was associated with lower AA/DHA ratios even among ε4 carriers. High plasma AA/DHA ratios were observed in E4FAD compared to EFAD mice with other isoforms. In particular, alterations in plasma AA and DHA containing PL species were also observed in the brains of E4FAD mice compared to E3FAD mice. Despite the small sample size and a short follow-up, these results suggest that blood PL could potentially serve as biomarkers of preclinical MCI/AD.
Evolution and chemical and dynamical effects of high-mass stars

Abstract We review general characteristics of massive stars, present the main observable constraints that stellar models should reproduce. We discuss the impact of massive star nucleosynthesis on the early phases of the chemical evolution of the Milky Way (MW). We show that rotating models can account for the important primary nitrogen production needed at low metallicity. Interestingly such rotating models can also better account for other features as the variation with the metallicity of the C/O ratio. Damped Lyman Alpha (DLA) systems present similar characteristics as the halo of the MW for what concern the N/O and C/O ratios. Although in DLAs, the star formation history might be quite different from that of the halo, in these systems also, rotating stars (both massive and intermediate) probably play an important role for explaining these features. The production of primary nitrogen is accompanied by an overproduction of other elements as 13C, 22Ne and s-process elements. We show also how the observed variation with the metallicity of the number ratio of type Ibc to type II supernovae may be a consequence of the metallicity dependence of the line-driven stellar winds.
Hyperspectral Image Classification Using Random Occlusion Data Augmentation

Convolutional neural networks (CNNs) have become a powerful tool for remotely sensed hyperspectral image (HSI) classification due to their great generalization ability and high accuracy. However, owing to the huge amount of parameters that need to be learned and to the complex nature of HSI data itself, these approaches must deal with the important problem of overfitting, which can lead to inadequate generalization and loss of accuracy. In order to mitigate this problem, in this letter, we adopt random occlusion, a recently developed data augmentation (DA) method for training CNNs, in which the pixels of different rectangular spatial regions in the HSI are randomly occluded, generating training images with various levels of occlusion and reducing the risk of overfitting. Our results with two well-known HSIs reveal that the proposed method helps to achieve better classification accuracy with low computational cost.
Premature Mortality from Cardiovascular Disease in the Americas – Will the Goal of a Decline of “25% by 2025” be Met?

Background Cardiovascular diseases (CVD) are the underlying cause 1.6 million deaths per year in the Americas, accounting for 30% of total mortality and 38% of by non-communicable deaths diseases (NCDs). A 25% reduction in premature mortality due four main NCDs was targeted by the 2011 High-level Meeting of the General Assembly on the Prevention and Control of NCDs. While overall CVD mortality fell in the Americas during the past decade, trends in premature CVD mortality during the same period have not been described, particularly in the countries of Latin America and the Caribbean. Methods This is a population-based trend-series study based on a total of 6,133,666 deaths to describe the trends and characteristics of premature mortality due to CVD and to estimates of the average annual percentage of change during the period 2000–2010 in the Americas. Findings Premature mortality due to CVD in the Americas fell by 21% in the period 2000–2010 with a -2.5% average annual rate of change in the last 5 year—a statistically significant reduction of mortality—. Mortality from ischemic diseases, declined by 25% - 24% among men and 26% among women. Cerebrovascular diseases declined by 27% -26% among men and 28% among women. Guyana, Trinidad and Tobago, the Dominican Republic, Bahamas, and Brazil had CVD premature mortality rates over 200 per 100,000 population, while the average for the Region was 132.7. US and Canada will meet the 25% reduction target before 2025. Mexico, Costa Rica, Venezuela, Dominican Republic, Panama, Guyana, and El Salvador did not significantly reduce premature mortality among men and Guyana, the Dominican Republic, and Panama did not achieve the required annual reduction in women. Conclusions Trends in premature mortality due to CVD observed in last decade in the Americas would indicate that if these trends continue, the Region as a whole and a majority of its countries will be able to reach the goal of a 25% relative reduction in premature mortality even before 2025.
The Effect of the Slope of the Psychometric Function on the Measurement of Speech Recognition Threshold Using a Female Talker

The Effect of the Slope of the Psychometric Function on the Measurement of Speech Recognition Threshold Using a Female Talker Jessica Lee Reese Department of Communication Disorders, BYU Master of Science Speech audiometry has long been a component of a thorough audiological examination. The speech recognition threshold (SRT) measurement is perhaps the most widely used measurement in speech audiometry. For decades, researchers and clinicians have worked to create and fine-tune word lists that for use in SRT testing; their aim being to improve the accuracy for classifying a client’s ability to hear and comprehend speech. Experts in the field have agreed to follow four tenets of speech audiometry when selecting word sets. This study examined whether improvement to stimulus lists for SRT measurement could be made in regards to the tenet of homogeneity with respect to audibility if the slope of the psychometric function were a selection consideration. The study was performed with the hypothesis that steeply sloping words would significantly reduce the number of words needed to obtain the SRT. Three word lists, all recorded by a female talker, comprising of steeply sloping words, medium sloping words, and shallow sloping words, were used in the study. Participants with normal hearing between the ages of 18 and 30 years provided data that was used to calculate SRT measurements for all three lists from each ear. The results showed a significant difference in the number of words needed to obtain the SRT when comparing the steep and shallow word sets and the shallow and medium word sets. Steeply sloping words required fewer words to obtain the SRT, M = 17.02. Shallow sloping words required the most words, M = 18.88, amounting to a difference of 1.86 words. While statistically different, a reduction by fewer than 2 words during the course of SRT testing will not equate to a substantial saving of time for the clinician. For clinical application, the slope of the psychometric function of the words used in SRT measurement need not be a primary consideration when developing stimulus lists.
Repetition Enhancement for Frequency-Modulated but Not Unmodulated Sounds: A Human MEG Study

Background Decoding of frequency-modulated (FM) sounds is essential for phoneme identification. This study investigates selectivity to FM direction in the human auditory system. Methodology/Principal Findings Magnetoencephalography was recorded in 10 adults during a two-tone adaptation paradigm with a 200-ms interstimulus-interval. Stimuli were pairs of either same or different frequency modulation direction. To control that FM repetition effects cannot be accounted for by their on- and offset properties, we additionally assessed responses to pairs of unmodulated tones with either same or different frequency composition. For the FM sweeps, N1m event-related magnetic field components were found at 103 and 130 ms after onset of the first (S1) and second stimulus (S2), respectively. This was followed by a sustained component starting at about 200 ms after S2. The sustained response was significantly stronger for stimulation with the same compared to different FM direction. This effect was not observed for the non-modulated control stimuli. Conclusions/Significance Low-level processing of FM sounds was characterized by repetition enhancement to stimulus pairs with same versus different FM directions. This effect was FM-specific; it did not occur for unmodulated tones. The present findings may reflect specific interactions between frequency separation and temporal distance in the processing of consecutive FM sweeps.
Grasp Planning for a Humanoid Hand

We focus on grasp planning for a humanoid multi-fingered hand attached at the tip of a humanoid robot’s arm. The hand has potential possibility to grasp various objects under several situations. Since the multi-fingered hand can use several grasp types such as fingertip grasp, and envelope grasp with taking the advantage of degrees of freedom. We develop grasp planner which selects a feasible grasp type based on the task, and determines contact positions for the fingers and the grasped object surface so that the fingers do not drop the object while staying with limited actuator capacity. To grasp an object, the robot first measures object position/orientation using vision sensor. Then, the planner plans the bodymotion to complete the grasping task based on vision sensor information. Even when the object’s location is not known beforehand, the robot should complete the grasping task as fast as possible. However, grasp planning with a humanoid robot is complex and often requires long calculation time. Hence, for the grasp planning, a heuristic but fast algorithm is preferred rather than precise but slow algorithms (Shimoga (1989)). Our planner calculates grasp motions within reasonable time by using predefined grasp types which are assigned with contacting finger links, desired sizes of the grasped object. Our planner selects a grasp type according to position/orientation of the grasped object similar to a human. As shown in Fig. 1 , a human grasps the side of the can with all fingers, grasps the top with fewer fingers. Failing to find feasible grasping posture using arm/hand kinematics alone, our planner attempts to do so using the full body kinematics. Using the degrees of freedom of full body, the planner has adaptable for reaching the object with the several motions such as twisting waist, bending waist, and squatting down. We demonstrate effectiveness of grasp planning through simulation and experimental results by using humanoid robot HRP-3P (Akachi et al. (2005)) shown in Fig. 2, which has a four-fingered hand HDH (Kaneko et al. (2007)) on its right-arm and a stereo camera system in its head. We has proposed the grasp planning which was executed within the reasonable time taking into account several constraints imposed on the system such as the feasible grasping style, the friction cone constraint at each contact point, the maximum contact force applied by the fingers, the inverse kinematics of the arm and the fingers (Harada et al. (2008); Tsuji et al. (2008; 2009)). The originality of our method is the following points; 4
Efficient HRTF Computation Using Adaptive Rectangular Decomposition

Accurate rendering of spatial audio over headphones requires the use of personalized head related transfer functions (HRTFs). These HRTFs are difficult to obtain due to the tedious and expensive measurement process requiring an anechoic chamber. An alternate approach uses accurate 3D meshes of human head and torso and numerical simulation techniques to compute personalized HRTFs. While these simulation techniques can compute accurate HRTFs, they require hours or days of computation on a desktop machine. We present an efficient technique to compute personalized HRTFs, combining a fast numerical solver, called adaptive rectangular decomposition, with the acoustic reciprocity principle and the Kirchhoff surface integral representation to reduce the overall computation. This technique requires only two numerical simulations and can compute the HRTF in 20 minutes on a desktop machine. We highlight the performance of our technique on the Fritz and KEMAR benchmarks and compare with measurements to test its accuracy.
A domain-specific language for enabling doctors to specify biomechanical protocols

New technologies are entering medical practice at an astounding pace. However, these technologies often cause to doctors learn and use difficulties. Then, doctors require assistance of a biomedical engineer. This is currently happening in a local hospital that has new technology to analyze biomechanical protocols in patients. Protocols are used to measure performances and identify changes in human body movements and muscles. Doctors are neither familiar with the concepts nor tools used, so biomedical engineers carry out descriptions of protocols rather than doctors. In this paper, we present the design of a domain-specific language that enables doctors to specify biomechanical protocols by addressing learning barriers (using design patterns). We also make doctors' descriptions compatible with the existing tools, and we also support legacy biomedical descriptions (combining meta-modeling and model transformations).
Avaliação de comportamentos em puericultura para identificação precoce do transtorno do espectro autista

Objetivou-se avaliar atendimentos de puericultura realizados nas Unidades Básicas de Saúde desde os primeiros dias de vida, os quais são possíveis contextos de diagnóstico de sinais de TEA. Participaram 13 crianças com até 18 meses, 7 auxiliares de enfermagem, 2 enfermeiras e 1 pediatra. Avaliaram-se, nas filmagens do atendimento de cada criança, os comportamentos dos profissionais de fazer perguntas às mães e de avaliar a criança, bem como a ocorrência de comportamentos de interação social, linguagem e padrões restritos e estereotipados das crianças. Questões médicas sobre sono e alimentação prevaleceram às questões sobre desenvolvimento neuropsicomotor, socialização e linguagem. Ocorreram mais comportamentos profissionais de avaliar o desenvolvimento neuropsicomotor do que a linguagem e a socialização. Nos atendimentos, observaram-se comportamentos das crianças de interação social e linguagem. Concluiu-se que, para a identificação precoce dos sinais do TEA, os atendimentos são contextos possíveis se houver reformulação do material utilizado e capacitação profissional.
A multi-parameter bio-electric ASIC sensor with integrated 2-wire data transmission protocol for wearable healthcare system

This paper presents a fully integrated application specific integrated circuit (ASIC) sensor for the recording of multiple bio-electric signals. It consists of an analog front-end circuit with tunable bandwidth and programmable gain, a 6-input 8-bit successive approximation register analog to digital converter (SAR ADC), and a reconfigurable digital core. The ASIC is fabricated in a 0.18-μm 1P6M CMOS technology, occupies an area of 1.5 × 3.0 mm2, and totally consumes a current of 16.7 μA from a 1.2 V supply. Incorporated with the ASIC, an Intelligent Electrode can be dynamically configured for on-site measurement of different bio-signals. A 2-wire data transmission protocol is also integrated on chip. It enables the serial connection over a group of Intelligent Electrodes, thus minimizes the number of connecting cables. A wearable healthcare system is built upon a printed Active Cable and a scalable number of Intelligent Electrodes. The system allows synchronous processing of maximum 14-channel bio-signals. The ASIC performance has been successfully verified in in-vivo bio-electric recording experiments.