Miracle-dz/UniFAR-FTUs huggingface dataset:
Maximum likelihood on four taxa phylogenetic trees: analytic solutions

Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees (Felsenstein, 1981), but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM), are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only for the simplest model - three taxa, two state characters, under a molecular clock (MC). Quoting Ziheng Yang (2000), who initiated the analytic approach, "this seems to be the simplest case, but has many of the conceptual and statistical complexities involved in phylogenetic estimation". In this work, we give analytic solutions for four taxa, two state characters under a molecular clock. The change from three to four taxa incurs a major increase in the complexity of the underlying algebraic system, and requires novel techniques and approaches. We start by presenting the general maximum likelihood problem on phylogenetic trees as a constrained optimization problem, and the resulting system of polynomial equations. In full generality, it is infeasible to solve this system, therefore specialized tools for the MC case are developed.Four taxa rooted trees have two topologies -- the fork (two subtrees with two leaves each) and the comb (one subtree with three leaves, the other with a single leaf). We combine the ultrametric properties of MC trees with the Hadamard conjugation (Hendy and Penny, 1993) to derive a number of topology dependent identities. Employing these identities, we substantially simplify the system of polynomial equations. We finally use tools from algebraic geometry (e.g. Grobner bases, ideal saturation, resultants) and employ symbolic algebra software to obtain closed form analytic solutions (expressed parametrically in the input data) for the fork topology, and analytic solutions for the comb. We show that in contrast to the fork, the comb has no closed form solutions (expressed by radicals in the input data). In general, four taxa trees can have multiple ML points (Steel, 1994, Chor et. al., 2001). In contrast, we can now prove that under the MC assumption, both the fork and the comb topologies have a unique (local and global) ML point.
COFFE: Fully-automated transistor sizing for FPGAs

In this paper, we present COFFE (Circuit Optimization For FPGA Exploration), a new fully-automated transistor sizing tool for FPGAs. Automated transistor-level CAD tools are an important part of the architecture exploration flow because they provide accurate area and delay estimates of low-level FPGA circuitry, which must be obtained for each architecture. We show that modeling transistors as linear resistances and capacitances as has been done in previous FPGA transistor sizing tools is highly inaccurate for fine-grained transistor-level design in advanced process nodes. Therefore, COFFE's transistor sizing algorithm maintains circuit non-linearities by relying exclusively on HSPICE simulations to measure delay. Area is estimated with a transistor size-based model that incorporates a number of improvements to enhance its accuracy in advanced process technologies versus prior methods. In addition to more accurate area and delay estimation, COFFE considers more layout effects than prior published work by automatically accounting for transistor and wire loads, which are computed based on architectural parameters and layout area. This new FPGA transistor sizing tool requires only several hours to produce high-quality transistor sizing results for an entire FPGA tile; a task that would normally take months of manual effort. We demonstrate COFFE's utility in FPGA architecture studies by investigating an important new architectural question at the logic-to-routing interface.
STEATOSIS IN CHRONIC HEPATITIS C: WHY DOES IT REALLY MATTER?

Hepatic steatosis is a common histological feature of chronic hepatitis C. Various factors are associated with hepatic steatosis, including obesity, high alcohol consumption, diabetes type II, and hyperlipidaemia. These factors may contribute to steatosis in patients with chronic hepatitis C. In humans, hepatitis C virus (HCV) genotype 3 is more commonly associated with steatosis. In vitro studies and the transgenic mouse model have suggested that the HCV core protein (genotype 1) can induce lipid accumulation within hepatocytes. However, what is the relevance of steatosis in chronic hepatitis C? It seems that in certain populations, steatosis may be associated with fibrosis progression and this may be genotype specific. The mechanisms underlying this association are unknown; neither is it clear whether this holds true for all patients or only a subgroup. Indeed, after antiviral treatment, virus related steatosis disappears whereas the host associated steatosis remains unaffected. This review describes and discusses the basic and clinical aspects of the relationship between steatosis and progression of fibrosis, and response to treatment in patients with chronic hepatitis C.
The N-terminal domain of TWINKLE contributes to single-stranded DNA binding and DNA helicase activities

The TWINKLE protein is a hexameric DNA helicase required for replication of mitochondrial DNA. TWINKLE displays striking sequence similarity to the bacteriophage T7 gene 4 protein (gp4), which is a bi-functional primase-helicase required at the phage DNA replication fork. The N-terminal domain of human TWINKLE contains some of the characteristic sequence motifs found in the N-terminal primase domain of the T7 gp4, but other important motifs are missing. TWINKLE is not an active primase in vitro and the functional role of the N-terminal region has remained elusive. In this report, we demonstrate that the N-terminal part of TWINKLE is required for efficient binding to single-stranded DNA. Truncations of this region reduce DNA helicase activity and mitochondrial DNA replisome processivity. We also find that the gp4 and TWINKLE are functionally distinct. In contrast to the phage protein, TWINKLE binds to double-stranded DNA. Moreover, TWINKLE forms stable hexamers even in the absence of Mg2+ or NTPs, which suggests that an accessory protein, a helicase loader, is needed for loading of TWINKLE onto the circular mtDNA genome.
DETECTION OF TT VIRUS AMONG CHIMPANZEES IN THE WILD USING A NONINVASIVE TECHNIQUE

Zoonotic transmission and emergence of pathogens are serious threats to endangered populations of free-ranging primate species. Recent discovery of a nonpathogenic yet highly prevalent virus in human populations, TT virus (TTV), has prompted studies into the presence of this virus among captive individuals of other species of nonhuman primates. In this study, we screened captive primate species for TTV. In addition, we provide the first data on TTV infection in free-ranging primates by noninvasive screening of three chimpanzee (Pan troglodytes sweinfurthii) communities. Phylogenetic relationships between virus isolates and those previously reported from human populations, captive primates, and domesticated species are inferred. Our findings are discussed with respect to potential zoonotic events that may result from increased levels of human encroachment into wild habitats.
Cerebral palsy in southern Sweden II. Gross motor function and disabilities

The gross motor function and disabilities in children with cerebral palsy in southern Sweden were investigated and related to clinical features. The study covered the birth year period 1990‐1993 and comprised 167 children, 145 of them born in Sweden and 22 born abroad. The clinical features and gross motor function were analysed at a mean age of 6.8 y. Clinical features were obtained from a continuing healthcare follow‐up programme. Gross motor function was classified according to the Gross Motor Function Classification System (GMFCS). Walking independently was possible for 86% of the hemiplegic, 63% of the pure ataxic, 61% of the diplegic and 21% of the dyskinetic children. None of the tetraplegic children was able to walk. The classification of gross motor function revealed that 59% of the children were categorized into levels I and II (mildly disabled), 14% into level III (moderately disabled) and 27% into levels IV and V (severely disabled). Children born abroad were more severely disabled.
Brain tumor imaging using small-angle x-ray scattering tomography

We demonstrate high-resolution small-angle x-ray scattering computed tomography (SAXS-CT) of soft matter and soft tissue samples. Complete SAXS patterns over extended ranges of momentum transfer are reconstructed spatially resolved from volumes inside an extended sample. Several SAXS standard samples are used to quantitatively validate the method and demonstrate its performance. Further results on biomedical tissue samples (rat brains) are presented that demonstrate the advantages of the method compared to existing biomedical x-ray imaging approaches. Functional areas of the brains as well as tumor morphology are imaged. By providing insights into the structural organization at the nano-level, SAXS-CT complements and extends results obtainable with standard methods such as x-ray absorption tomography and histology.
Template‐based and free modeling of I‐TASSER and QUARK pipelines using predicted contact maps in CASP12

We develop two complementary pipelines, “Zhang‐Server” and “QUARK”, based on I‐TASSER and QUARK pipelines for template‐based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I‐TASSER and QUARK successfully folds three medium‐size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence‐based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines. The inclusion of NeBcon predicted contacts as restraints in the QUARK simulations results in an average TM‐score of 0.41 for the best in top five predicted models, which is 37% higher than that by the QUARK simulations without contacts. In particular, there are seven targets that are converted from non‐foldable to foldable (TM‐score >0.5) due to the use of contact restraints in the simulations. Another additional feature in the current pipelines is the local structure quality prediction by ResQ, which provides a robust residue‐level modeling error estimation. Despite the success, significant challenges still remain in ab initio modeling of multi‐domain proteins and folding of β‐proteins with complicated topologies bound by long‐range strand‐strand interactions. Improvements on domain boundary and long‐range contact prediction, as well as optimal use of the predicted contacts and multiple threading alignments, are critical to address these issues seen in the CASP12 experiment.
Walking Speed Feature Extraction Based on Wavelet Packet Decomposition

Sufficient sensor information is needed in the control of intelligent lower limb prosthesis. Sensor system includes MEMS Accelerometer and MEMS Gyroscope. The sensor system is installed in prosthetic socket. Walking information is obtained using this system. Hip joint and knee joint motion is measured by Vicon MX system. the angle, velocity and acceleration of Hip joint and knee joint is analyzed. The signal of sensor system is collected by Quarc system. Using the wavelet analysis method, characteristic values is extracted from the measurement signal after errors separation process. The results of experiment indicate that the sensor system has advantages of small size, sensitive response,quick examine,convinence to take with and use and so on. The system is very suitable for the information acquisition.
Optimal Rhode Island Hold'em Poker

Rhode Island Hold'em is a poker card game that has been proposed as a testbed for AI research. This game, with a tree size larger than 3.1 billion nodes, features many characteristics present in full-scale poker (e.g., Texas Hold'em). Our research advances in equilibrium computation have enabled us to solve for the optimal (equilibrium) strategies for this game. Some features of the equilibrium include poker techniques such as bluffing, slow-playing, check-raising, and semi-bluffing. In this demonstration, participants will compete with our optimal opponent and will experience these strategies firsthand.
A High Performance Video Transform Engine by Using Space-Time Scheduling Strategy

In this paper, a spatial and time scheduling strategy, called the space-time scheduling (STS) strategy, that achieves high image resolutions in real-time systems is proposed. The proposed spatial scheduling strategy includes the ability to choose the distributed arithmetic (DA)-precision bit length, a hardware sharing architecture that reduces the hardware cost, and the proposed time scheduling strategy arranges different dimensional computations in that it can calculate first-dimensional and second-dimensional transformations simultaneously in single 1-D discrete cosine transform (DCT) core to reach a hardware utilization of 100%. The DA-precision bit length is chosen as 9 bits instead of the traditional 12 bits based on test image simulations. In addition, the proposed hardware sharing architecture employs a binary signed-digit DA architecture that enables the arithmetic resources to be shared during the four time slots. For this reason, the proposed 2-D DCT core achieves high accuracy with a small area and a high throughput rate and is verified using a TSMC 0.18-μm 1P6M CMOS process chip implementation. Measurement results show that the core has a latency of 84 clock cycles with a 52 dB peak-signal-to-noise-ratio and is operated at 167 MHz with 15.8 K gate counts.
A queueing model with time-varying QoS and call dropping for evaluating the performance of CDMA cellular systems

In this paper, we present a queueing model to evaluate the performance of CDMA reverse link in a multiple cell environment. Since CDMA capacity is interference limited, both the communication quality of ongoing calls and the admission condition of new arriving calls for each cell depend on the time-varying signal-to-interference ratio (SIR). We use a quasi-birth-and-death process to capture the variation of traffic loads in cells. After obtaining the stationary distribution of the system, we study some important performance indices such as the outage probability of existing calls, the blocking probability of new calls, the average carried traffic in a cell and the dropping frequency of ongoing calls. Numerical results reveal the effects of system parameters on its performance. Copyright © 2004 John Wiley & Sons, Ltd.
Swarm assignment and trajectory optimization using variable-swarm, distributed auction assignment and sequential convex programming

This paper presents a distributed, guidance and control algorithm for reconfiguring swarms composed of hundreds to thousands of agents with limited communication and computation capabilities. This algorithm solves both the optimal assignment and collision-free trajectory generation for robotic swarms, in an integrated manner, when given the desired shape of the swarm (without pre-assigned terminal positions). The optimal assignment problem is solved using a distributed auction assignment that can vary the number of target positions in the assignment, and the collision-free trajectories are generated using sequential convex programming. Finally, model predictive control is used to solve the assignment and trajectory generation in real time using a receding horizon. The model predictive control formulation uses current state measurements to resolve for the optimal assignment and trajectory. The implementation of the distributed auction algorithm and sequential convex programming using model predictive control produces the swarm assignment and trajectory optimization (SATO) algorithm that transfers a swarm of robots or vehicles to a desired shape in a distributed fashion. Once the desired shape is uploaded to the swarm, the algorithm determines where each robot goes and how it should get there in a fuel-efficient, collision-free manner. Results of flight experiments using multiple quadcopters show the effectiveness of the proposed SATO algorithm.
Multi-Vehicle Tracking Based Traffic Illegal Parking Detection

Vehicle detection and tracking are the foundations of traffic violation punishment. The current methods have more parameters to be adjusted and can not adapt to the complex traffic scenes. For the purpose of practice application, we propose an illegal parking detection algorithm based on vehicle tracking theory. In order to filter the dynamic interferences such as vehicles parking for a long time, moving vehicles overlapping, and the vehicle losing momentarily from the video, a Gaussian mixture model is combined with the correlations among adjacent pixels to update background and eliminate noises. In allusion to complex traffic scenes, a fast multi-object tracking algorithm is presented to track occluded vehicles effectively. This method predicts vehicle trajectory by Kalman filter and achieves real-time object tracking state judgment by using the feature matching matrix. The experimental results show that this method can track multiple moving vehicles effectively and has high detection precision for illegal parking incidents.
Molecular candidates for cardiac stretch-activated ion channels

The heart is a mechanically-active organ that dynamically senses its own mechanical environment. This environment is constantly changing, on a beat-by-beat basis, with additional modulation by respiratory activity and changes in posture or physical activity, and further overlaid with more slowly occurring physiological (e.g. pregnancy, endurance training) or pathological challenges (e.g. pressure or volume overload). Far from being a simple pump, the heart detects changes in mechanical demand and adjusts its performance accordingly, both via heart rate and stroke volume alteration. Many of the underlying regulatory processes are encoded intracardially, and are thus maintained even in heart transplant recipients. Over the last three decades, molecular substrates of cardiac mechanosensitivity have gained increasing recognition in the scientific and clinical communities. Nonetheless, the processes underlying this phenomenon are still poorly understood. Stretch-activated ion channels (SAC) have been identified as one contributor to mechanosensitive autoregulation of the heartbeat. They also appear to play important roles in the development of cardiac pathologies – most notably stretch-induced arrhythmias. As recently discovered, some established cardiac drugs act, in part at least, via mechanotransduction pathways suggesting SAC as potential therapeutic targets. Clearly, identification of the molecular substrate of cardiac SAC is of clinical importance and a number of candidate proteins have been identified. At the same time, experimental studies have revealed variable–and at times contrasting–results regarding their function. Further complication arises from the fact that many ion channels that are not classically defined as SAC, including voltage and ligand-gated ion channels, can respond to mechanical stimulation. Here, we summarise what is known about the molecular substrate of the main candidates for cardiac SAC, before identifying potential further developments in this area of translational research.
Architectural framework for immersive web based virtual environments

The development of 3D web based applications has been possible with the establishment of a number of 3D web technologies. Such applications have been utilized in different disciplines such as surgery planning, architectural design and games. However, most of these applications are trapped to the desktop setting provided by default in 3D technologies. Very few attempts have been made to present 3D immersive web based applications and to evaluate the usability of the technologies used and the interaction techniques. In this paper, we will attempt to address these questions by examining different ways of providing an immersive virtual environment on the web.
Classification of the Excitation Location of Snore Sounds in the Upper Airway by Acoustic Multifeature Analysis

Objective: Obstructive sleep apnea (OSA) is a serious chronic disease and a risk factor for cardiovascular diseases. Snoring is a typical symptom of OSA patients. Knowledge of the origin of obstruction and vibration within the upper airways is essential for a targeted surgical approach. Aim of this paper is to systematically compare different acoustic features, and classifiers for their performance in the classification of the excitation location of snore sounds. Methods: Snore sounds from 40 male patients have been recorded during drug-induced sleep endoscopy, and categorized by Ear, Nose & Throat (ENT) experts. Crest Factor, fundamental frequency, spectral frequency features, subband energy ratio, mel-scale frequency cepstral coefficients, empirical mode decomposition-based features, and wavelet energy features have been extracted and fed into several classifiers. Using the ReliefF algorithm, features have been ranked and the selected feature subsets have been tested with the same classifiers. Results: A fusion of all features after a ReliefF feature selection step in combination with a random forests classifier showed the best classification results of 78% unweighted average recall by subject independent validation. Conclusion: Multifeature analysis is a promising means to help identify the anatomical mechanisms of snore sound generation in individual subjects. Significance: This paper describes a novel approach for the machine-based multifeature classification of the excitation location of snore sounds in the upper airway.
Low Prevalence of Vitamin D Insufficiency among Nepalese Infants Despite High Prevalence of Vitamin D Insufficiency among Their Mothers

Background: Describing vitamin D status and its predictors in various populations is important in order to target public health measures. Objectives: To describe the status and predictors of vitamin D status in healthy Nepalese mothers and infants. Methods: 500 randomly selected Nepalese mother and infant pairs were included in a cross-sectional study. Plasma 25(OH)D concentrations were measured by LC-MS/MS and multiple linear regression analyses were used to identify predictors of vitamin D status. Results: Among the infants, the prevalence of vitamin D insufficiency (25(OH)D <50 nmol/L) and deficiency (<30 nmol/L) were 3.6% and 0.6%, respectively, in contrast to 59.8% and 14.0% among their mothers. Infant 25(OH)D concentrations were negatively associated with infant age and positively associated with maternal vitamin D status and body mass index (BMI), explaining 22% of the variability in 25(OH)D concentration. Global solar radiation, maternal age and BMI predicted maternal 25(OH)D concentration, explaining 9.7% of its variability. Conclusion: Age and maternal vitamin D status are the main predictors of vitamin D status in infants in Bhaktapur, Nepal, who have adequate vitamin D status despite poor vitamin D status in their mothers.