Miracle-dz/UniFAR-FTUs huggingface dataset:
Repeatability of adaptation in experimental populations of different sizes

The degree to which evolutionary trajectories and outcomes are repeatable across independent populations depends on the relative contribution of selection, chance and history. Population size has been shown theoretically and empirically to affect the amount of variation that arises among independent populations adapting to the same environment. Here, we measure the contribution of selection, chance and history in different-sized experimental populations of the unicellular alga Chlamydomonas reinhardtii adapting to a high salt environment to determine which component of evolution is affected by population size. We find that adaptation to salt is repeatable at the fitness level in medium (Ne = 5 × 104) and large (Ne = 4 × 105) populations because of the large contribution of selection. Adaptation is not repeatable in small (Ne = 5 × 103) populations because of large constraints from history. The threshold between stochastic and deterministic evolution in this case is therefore between effective population sizes of 103 and 104. Our results indicate that diversity across populations is more likely to be maintained if they are small. Experimental outcomes in large populations are likely to be robust and can inform our predictions about outcomes in similar situations.
Novel Objective-Space-Dividing Multi-objectives evolutionary algorithm and its convergence property

To overcome the shortcomings of Multi-Objectives Evolutionary Algorithms (MOEAs) based on the notion of Objective-Space-Dividing (OSD) with high calculation complexity, this paper proposes an improved algorithm called OSD-MOEA. The proposed algorithm supports the following features: 1) transforming the Pareto relationship among individuals to the ranking relationship of the total value of indexes in divided space; 2) simple and efficient environment choosing method based on index ranking; 3) an individual crowding algorithm which rapidly chooses the nearest individual to the origin. Convergence analysis shows the convergence property of the proposed algorithm. Simulation results of the proposed algorithm OSD-MOEA are compared with NSGAII and PSFGA and high efficiency, low time complexity and good convergence are noticed.
A Dataset of Simplified Syntax Trees for C#

In this paper, we present a curated collection of 2833 C# solutions taken from Github. We encode the data in a new intermediate representation (IR) that facilitates further analysis by restricting the complexity of the syntax tree and by avoiding implicit information. The dataset is intended as a standardized input for research on recommendation systems for software engineering, but is also useful in many other areas that analyze source code.
Crude Oil Price Forecasting: A Transfer Learning Based Analog Complexing Model

Most of the existing models for oil price forecasting only use the data in the forecasted time series itself. This study proposes a transfer learning based analog complexing model (TLAC). It first transfers some related time series in source domain to assist in modeling the target time series by transfer learning technique, and then constructs the forecasting model by analog complexing method. Finally, genetic algorithm is introduced to find the optimal matching between the two important parameters in TLAC. Two main crude oil price series, West Texas Intermediate (WTI) crude oil spot price and Brent crude oil spot price are used for empirical analysis, and the results show the effectiveness of the proposed model.
Comparative Effectivenesses of Pulsed Radiofrequency and Transforaminal Steroid Injection for Radicular Pain due to Disc Herniation: a Prospective Randomized Trial

Transforaminal Epidural steroid injections (TFESI) have been widely adopted to alleviate and control radicular pain in accord with current guidelines. However, sometimes repeated steroid injections have adverse effects, and thus, this prospective randomized trial was undertaken to compare the effectivenesses of pulsed radiofrequency (PRF) administered to a targeted dorsal root ganglion (DRG) and TFESI for the treatment of radicular pain due to disc herniation. Subjects were recruited when first proved unsuccessful (defined as a score of > 4 on a visual analogue scale (VAS; 0-10 mm) and of > 30% according to the Oswestry Disability Index (ODI) or the Neck Disability Index (NDI)). Forty-four patients that met the inclusion criteria were enrolled. The 38 subjects were randomly assigned to receive either PRF (PRF group; n = 19) or additional TFESI (TFESI group; n = 19) and were then followed for 2, 4, 8, and 12 weeks. To evaluate pain intensity were assessed by VAS. ODI and NDI were applied to evaluate functional disability. Mean VAS scores for cervical and lumbar radicular pain were significantly lower 12 weeks after treatment in both study groups. NDI and ODI scores also declined after treatment. However, no statistically significant difference was observed between the PRF and TFESI groups in terms of VAS, ODI, or NDI scores at any time during follow-up. PRF administered to a DRG might be as effective as TFESI in terms of attenuating radicular pain caused by disc herniation, and its use would avoid the adverse effects of steroid.
A framework for histogram-induced 3D descriptors

We present a novel framework to describe 3D shapes, based on modeling the probability density of their shape functions. These functions are conceived to reflect the 3D geometrical properties of the shape surfaces. The densities are modeled as mixtures of Gaussians, each component being the distribution induced by a mesh triangle. A fast algorithm is developed exploiting both the special geometry of 3D triangles with numerical approximations as well as a transform technique. We test and compare the proposed descriptors to other histogram-based methods on two different 3D model databases. It is shown that 3D shape descriptors outperform all of its competitors except one in retrieval applications. Furthermore our methodology provides a fertile ground to introduce and test new descriptors.
Aspergillus Thyroiditis: A Complication of Respiratory Tract Infection in an Immunocompromised Patient

A 59-year-old male with past medical history significant for non-Hodgkin's lymphoma status after chemotherapy presented with acute onset of neck pain, odynophagia, and dysphagia associated with subjective fever, chills, and dyspnea. Physical findings included a temperature of 38.4°C, hypertension, and tachycardia. Patient was found to have anterior neck tenderness. Laboratory evaluation revealed neutropenia. The patient was started on empiric antibacterial and antiviral therapy and continued on home prophylactic antifungal treatment. Thyroid function tests revealed overt hyperthyroidism. A thyroid ultrasound showed heterogeneous echotexture without discrete nodules. Subacute thyroiditis was treated with methylprednisolone, metoprolol, and opiate analgesics. Patient's antibacterial, antifungal, and antiviral treatments were broadened. A fine needle aspiration was not conducted. The patient's condition deteriorated rapidly over his brief hospital course and he expired. Autopsy showed fungal thyroiditis secondary to disseminated invasive Aspergillus. This report describes the presentation of fungal thyroiditis secondary to disseminated invasive Aspergillus originating from the respiratory tract. The authors review the diagnostic challenges, pathophysiology, and treatment of this condition.
Mathematical models of the acute inflammatory response

Purpose of reviewTrauma and infection elicit an acute inflammatory response. In certain circumstances the degree of the acute inflammatory response may result in pathologic manifestations, namely, sepsis and multiple organ failure. Despite an extensive series of clinical trials designed to modulate inflammation in sepsis, only one compound, activated protein C, has emerged from more than 250 failed trials. There is a growing recognition that the complexity of the acute inflammatory response precludes the efficient development of therapies for sepsis and multiple organ failure until systems approaches are brought to bear on this problem. Recent findingsWork carried out by the authors’ groups suggests that mathematical modeling can provide a means by which in vitro and in vivo data can be synthesized into system-level analytic models of the acute inflammatory response. The authors have focused on agent-based modeling and modeling with ordinary differential equations. Some of the advantages and disadvantages of these modeling approaches are presented, and methods for calibration and validation of these models are discussed. Finally, the usefulness of mathematical models to evaluate the prospective therapeutic strategies in clinical trials of sepsis and trauma is examined. SummarySimulations using various methods can shed insight into the pathophysiology of the acute inflammatory response and may lead to better design of clinical trials in sepsis and trauma.
DMDSS: data mining based decision support system to integrate data mining and decision support

Modern organizations use several types of decision support systems to facilitate decision support. In many cases OLAP based tools are used in the business area, which enable multiple views on data and through that a deductive approach to data analysis. Data mining extends the possibilities for decision support by discovering patterns and relationships hidden in data and therefore enabling the inductive approach of data analysis. The paper introduces data mining based decision support system, which was designed for business users to enable them to use data mining models to facilitate decision support with only a basic level of knowledge of data mining
Motion analysis of lizard locomotion using motion capture

In this paper, we show the motion analysis of lizard locomotion as a part of a pre-study of surveillance and monitoring using an unmanned robot in a narrow area. The motion of a lizard was measured using 20 markers, adhered to the skin of the lizard joints, with an optical motion capture system. The lizard's gait was analyzed, and a kinematic model was proposed based on the measured data.
Multiple Object Tracking Using Particle Filters

MULTIPLE OBJECT TRACKING USING PARTICLE FILTERS Publication No. Hwangryol Ryu, MS The University of Texas at Arlington, 2006 Supervising Professor: Manfred Huber We describe a novel extension to the Particle Filter algorithm for tracking multiple objects. The recently proposed algorithms and the variants for multiple object tacking estimate multi-modal posterior distributions that potentially represent the multiple peaks (i.e., multiple tracked objects). However, the specific state representation does not demonstrate creation, deletion, and more importantly partial/complete occlusion of the objects. Furthermore, the weakness of the Particle Filter such that the representation may increasingly bias the posterior density estimates toward objects with dominant likelihood makes the multiple object tracking algorithms more difficult. To circumvent a sample depletion problem and maintain the computational complexity as good as the mixture Particle filters under certain assumptions (1) targets move independently, (2) targets are not transparent, (3) each pixel of the image can only come from one of the targets we proposed a new approach dealing with partial and complete occlusions of a fixed number of objects in an efficient manner that provides a robust means of tracking each object by projecting particles into the image space and back to a particle space. The projection procedure between the particle space and the image space represents an iv important probability density function not only to give more trust to a target being visible, but also to explain an occluded target. In addition, while joint Particle filters suffer from the curse of dimensionality in the number of the targets being tracked, the proposed algorithm only adds a constant factor to the computational cost of the standard Particle filters. To present qualitative results, experiments were performed using color-based tracking of multiple rectangular boxes of different colors. The experiments demonstrated that the Particle filters implemented using the proposed method effectively and precisely track multiple targets, whereas the standard Particle filters failed to track the multiple targets.
A comparison of joint/independent state particle filters for tracking closely spaced targets in clutter

In this paper, we present an overview of the literature for particle filtering under measurement origin uncertainty with an emphasize on single scan data association algorithms. We compare some of the existing and newly proposed joint state particle filtering algorithms for the closely spaced target tracking problem. Both maximum a posteriori (MAP) and minimum mean square error (MMSE) estimation outputs of four different algorithms are compared. We also include MMSE outputs of a non-joint (independent) state particle filter and Kalman filter in the comparison as a baseline.
Use of Number by Fish

Background Research on human infants, mammals, birds and fish has demonstrated that rudimentary numerical abilities pre-date the evolution of human language. Yet there is controversy as to whether animals represent numbers mentally or rather base their judgments on non-numerical perceptual variables that co-vary with numerosity. To date, mental representation of number has been convincingly documented only for a few mammals. Methodology/Principal Findings Here we used a training procedure to investigate whether mosquitofish could learn to discriminate between two and three objects even when denied access to non-numerical information. In the first experiment, fish were trained to discriminate between two sets of geometric figures. These varied in shape, size, brightness and distance, but no control for non-numerical variables was made. Subjects were then re-tested while controlling for one non-numerical variable at a time. Total luminance of the stimuli and the sum of perimeter of figures appeared irrelevant, but performance dropped to chance level when stimuli were matched for the cumulative surface area or for the overall space occupied by the arrays, indicating that these latter cues had been spontaneously used by the fish during the learning process. In a second experiment, where the task consisted of discriminating 2 vs 3 elements with all non-numerical variables simultaneously controlled for, all subjects proved able to learn the discrimination, and interestingly they did not make more errors than the fish in Experiment 1 that could access non-numerical information in order to accomplish the task. Conclusions/Significance Mosquitofish can learn to discriminate small quantities, even when non-numerical indicators of quantity are unavailable, hence providing the first evidence that fish, like primates, can use numbers. As in humans and non-human primates, genuine counting appears to be a ‘last resort’ strategy in fish, when no other perceptual mechanism may suggest the quantity of the elements. However, our data suggest that, at least in fish, the priority of perceptual over numerical information is not related to a greater cognitive load imposed by direct numerical computation.
Assessment of phylogenomic and orthology approaches for phylogenetic inference

MOTIVATION Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology. RESULTS Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content. CONCLUSIONS Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The Sunyaev Zel'dovich temperature of the intracluster medium

The relativistic Sunyaev–Zel’dovich (SZ) effect offers a method, independent of X-ray, for measuring the temperature of the intracluster medium (ICM) in the hottest systems. Here, using N-body/hydrodynamic simulations of three galaxy clusters, we compare the two quantities for a non-radiative ICM, and for one that is subject both to radiative cooling and to strong energy feedback from galaxies. Our study has yielded two interesting results. First, in all cases, the SZ temperature is hotter than the X-ray temperature and is within 10 per cent of the virial temperature of the cluster. Secondly, the mean SZ temperature is less affected by cooling and feedback than the X-ray temperature. Both these results can be explained by the SZ temperature being less sensitive to the distribution of cool gas associated with cluster substructure. A comparison of the SZ and X-ray temperatures (measured for a sample of hot clusters) would therefore yield interesting constraints on the thermodynamic structure of the intracluster gas.
Solutions to Australian Unemployment: Three Perspectives - What Do We Mean by an Unemployment Solution?

What unemployment level would be regarded as a solution to Australia’s unemployment problem? If the US is taken as a guide, a solution would be an unemployment level similar to that which prevailed here in the 1960s. This suggests an unemployment rate of around 2 per cent. Keeping the US as a guide, it also suggests an increase of perhaps 12–14 per cent in the number of jobs. Such a change, at current per capita income levels, would make a large difference to the Australian economy: tax revenue would be boosted, government expenditure reduced. There could be substantial personal tax cuts. It would be a completely new world. But I cannot see such an unemployment level in the near future. To achieve 2 per cent unemployment would require a combination of growth and labour productivity outcomes far outside the range of experience of the past two and a half decades. 1 I am not alone in this judgment and it illustrates, in a very clear way, that almost all of us believe that Australia cannot easily or quickly separate itself from its recent economic history.
Paracetamol (Acetaminophen): mechanisms of action

Paracetamol has a central analgesic effect that is mediated through activation of descending serotonergic pathways. Debate exists about its primary site of action, which may be inhibition of prostaglandin (PG) synthesis or through an active metabolite influencing cannabinoid receptors. Prostaglandin H2 synthetase (PGHS) is the enzyme responsible for metabolism of arachidonic acid to the unstable PGH2. The two major forms of this enzyme are the constitutive PGHS‐1 and the inducible PGHS‐2. PGHS comprises of two sites: a cyclooxygenase (COX) site and a peroxidase (POX) site. The conversion of arachidonic acid to PGG2 is dependent on a tyrosine‐385 radical at the COX site. Formation of a ferryl protoporphyrin IX radical cation from the reducing agent Fe3+ at the POX site is essential for conversion of tyrosine‐385 to its radical form. Paracetamol acts as a reducing cosubstrate on the POX site and lessens availability of the ferryl protoporphyrin IX radical cation. This effect can be reduced in the presence of hydroperoxide‐generating lipoxygenase enzymes within the cell (peroxide tone) or by swamping the POX site with substrate such as PGG2. Peroxide tone and swamping explain lack of peripheral analgesic effect, platelet effect, and anti‐inflammatory effect by paracetamol. Alternatively, paracetamol effects may be mediated by an active metabolite (p‐aminophenol). p‐Aminophenol is conjugated with arachidonic acid by fatty acid amide hydrolase to form AM404. AM404 exerts effect through cannabinoid receptors. It may also work through PGHS, particularly in areas of the brain with high concentrations of fatty acid amide hydrolase.
The action of Escherichia coli CRISPR–Cas system on lytic bacteriophages with different lifestyles and development strategies

Abstract CRISPR–Cas systems provide prokaryotes with adaptive defense against bacteriophage infections. Given an enormous variety of strategies used by phages to overcome their hosts, one can expect that the efficiency of protective action of CRISPR–Cas systems against different viruses should vary. Here, we created a collection of Escherichia coli strains with type I-E CRISPR–Cas system targeting various positions in the genomes of bacteriophages λ, T5, T7, T4 and R1-37 and investigated the ability of these strains to resist the infection and acquire additional CRISPR spacers from the infecting phage. We find that the efficiency of CRISPR–Cas targeting by the host is determined by phage life style, the positions of the targeted protospacer within the genome, and the state of phage DNA. The results also suggest that during infection by lytic phages that are susceptible to CRISPR interference, CRISPR–Cas does not act as a true immunity system that saves the infected cell but rather enforces an abortive infection pathway leading to infected cell death with no phage progeny release.
A morphometric study of foramen ovale.

AIM To note the morphological variations and morphometric details of foramina ovale in dry adult skulls of Indian origin. MATERIAL AND METHODS 82 dry adult human skulls of unknown sex and of Indian origin were obtained and variations in appearance and number of foramen ovale were noted. The length and width of the foramina ovale of both sides were determined using digital Vernier calipers and area (A) was also calculated and analyzed. RESULTS Out of 82 adult skulls, the values for the right side was 7.64 ± 1.194 mm, 5.128 ± 0.827 mm and 30.808 ± 7.545 mm2 and for the left side the values was 7.561 ± 1.123 mm, 5.244 ± 0.950 mm and 31.310 ± 8.262 mm2 respectively, for the mean length, width and area of the foramen ovale. The shape of foramen was typically ovale in most of the skulls (56.70%) with some bony variations such as spine, tubercles etc. CONCLUSION There was no statistically significant difference between the two sides in length, width and area of foramen ovale and there was a positive correlation between lengths and areas of both sides.