Miracle-dz/UniFAR-FTUs huggingface dataset:
Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method

Abstract I analyzed various site pattern combinations in a 4-OTU case to identify sources of starless bias and parameter-estimation bias in likelihood-based phylogenetic methods, and reported three significant contributions. First, the likelihood method is counterintuitive in that it may not generate a star tree with sequences that are equidistant from each other. This behaviour, dubbed starless bias, happens in a 4-OTU tree when there is an excess (i.e., more than expected from a star tree and a substitution model) of conflicting phylogenetic signals supporting the three resolved topologies equally. Special site pattern combinations leading to rejection of a star tree, when sequences are equidistant from each other, were identified. Second, fitting gamma distribution to model rate heterogeneity over sites is strongly confounded with tree topology, especially in conjunction with the starless bias. I present examples to show dramatic differences in the estimated shape parameter Α between a star tree and a resolved tree. There may be no rate heterogeneity over sites (with the estimated Α > 10000) when a star tree is imposed, but Α < 1 (suggesting strong rate heterogeneity over sites) when an (incorrect) resolved tree is imposed. Thus, the dependence of “rate heterogeneity” on tree topology implies that “rate heterogeneity” is not a sequence-specific feature, cautioning against interpreting a small Α to mean that some sites are under strong purifying selection and others not. Thirdly, because there is no existing (and working) likelihood method for evaluating a star tree with continuous gamma-distributed rate, I have implemented the method for JC69 in a self-contained R script for a four-OTU tree (star or resolved), in addition to another R script assuming a constant rate over sites. These R scripts should be useful for teaching and exploring likelihood methods in phylogenetics.
Weight Gain in Epileptic Patients During Treatment with Valproic Acid: a Retrospective Study

ABSTRACT: Background: Weight gain has been recognized as a common adverse effect of valproic acid (VPA) that leads to discontinuation in some patients but its incidence and correlates have been rarely studied. Methods: We have analyzed the records retrospectively and interviewed 70 adult patients attending an epilepsy clinic on VPA mono- or polytherapy followed over a median of 27 months (range 3-189), as well as 20 patients on carbamazepine (CBZ) monotherapy. Patients were divided into non-weight gainers (< 5% baseline body weight), mild-moderate weight gainers (5-10% body weight) and marked weight gainers (> 10% body weight). The following variables were statistically analyzed to determine their relationship to weight gain: gender, age, body mass index, drug dose, personal or family history of obesity and monotherapy versus polytherapy. Results: Seventy-one percent of the VPA group were weight gainers versus 43% in the CBZ group. A weight gain of more than 4 kg in 70% of the VPA group was observed. The weight gain was often sustained and frequently socially significant to the patients. Patients below or within normal range body mass index prior to the start of VPA experienced the most severe percentage weight gain. From the structured patient interviews, patients with no personal history of weight problems experienced the greatest initial weight increase. Conclusion: Strategies should be devised to help patients avoid weight gain when starting on VPA, especially if they are not already overweight.
Geodesic Flows in Manifolds of Nonpositive Curvature

I. Introduction-a quick historical survey of geodesic flows on negatively curved spaces. II. Preliminaries on Riemannian manifolds A. Riemannian metric and Riemannian volume element B. Levi Civita connection and covariant differentiation along curves C. Parallel translation of vectors along curves D. Curvature E. Geodesics and geodesic flow F. Riemannian exponential map and Jacobi vector fields G. Isometries and local isometries H. Geometry of the tangent bundle with the Sasaki metric III. Manifolds of nonpositive sectional curvature A. Definition of nonpositive curvature by triangle comparisons B. Growth of Jacobi vector fields C. The Riemannian exponential map is a covering map. Theorem of Cartan-Hadamard. D. Examples : Riemannian symmetric spaces E. Convexity properties and the Cartan Fixed Point Theorem F. Fundamental group of a nonpositively curved manifold. G. Rank of a nonpositively curved manifold IV. Sphere at infinity of a simply connected manifold of nonpositive sectional curvature A. Asymptotic geodesics and cone topology for M ~ (∞)
Non-linear distance based large scale data classifications

Linear subspace projections are an important technique to reduce the dimensionality of data for automatic classification. Especially for large-scale and on-line systems, e.g. gesture recognition applications, this is important to guarantee near real-time processing. The linear subspace projections, however, fail if the classes are not linearly separable. Kernel methods, in contrast, have been widely applied to linear classification algorithms to solve problems of non-linearly separable classes. This technique, however, increases the computational complexity by introducing the evaluation of a possibly non-linear function. Here, we extend a linear subspace projection that has been applied to large-scale systems using a kernel function. The method is evaluated on Fisher's Iris dataset and a recorded gesture dataset. The results indicate that the proposed method yields an increased accuracy at a subspace of lower dimension while achieving a similar runtime at a subspace of the same dimension. The proposed method is thus expected to work well with online systems.
A Novel Induction Motor Speed Estimation Using Neuro - Fuzzy

Speed control performance of induction motors are affected by parameter variations and non linearity in the induction motor. This paper introduces a novel adaptive speed control of induction motor drives using Neuro-Fuzzy. Speed estimation method for control of induction machine drive has gained increasing interest among the research communities. The supremacy of an induction machine drive depends on the speed estimation accuracy. To ensure accurate speed estimation over a wide range, from zero to high levels exceeding the rated speed, accurate values of the machine's parameters, the aim of the simulation proposed control is to improve the performance and robustness of the induction motor drives under non linear loads and parameter variations. Both the design of the fuzzy controller and its integration with neural network in a global control system are discussed. Simulation results shown excellent tracking performance of the proposed control system, and have convincingly demonstrated the usefulness of the neuro-fuzzy controller in high performance drives with uncertainly. Keyword: Neuro- fuzzy, speed control, induction motor
Modulation of aflatoxin metabolism, aflatoxin-N7-guanine formation, and hepatic tumorigenesis in rats fed ethoxyquin: role of induction of glutathione S-transferases.

The effects of dietary administration of ethoxyquin (EQ) on aflatoxin B1 (AFB1) metabolism, DNA adduct formation and removal, and hepatic tumorigenesis were examined in male Fischer rats. Rats were fed a semipurified diet containing 0.4% EQ for 1 wk, gavaged with 250 micrograms of AFB1 per kg 5 times a wk during the next 2 wk, and, finally, restored to the control diet 1 wk after cessation of dosing. At 4 mo, focal areas of hepatocellular alteration were identified and quantitated by staining sections of liver for gamma-glutamyl transpeptidase. Treatment with EQ reduced by greater than 95% both area and volume of liver occupied by gamma-glutamyl transpeptidase-positive foci. Utilizing the same multiple dosing protocol, patterns of covalent modifications of DNA by AFB1 were determined. EQ produced a dramatic reduction in the binding of AFB1 to hepatic DNA: 18-fold initially and 3-fold at the end of the dosing period. Although binding was detectable at 3 and 4 mo postdosing, no effect of EQ was observed, suggesting that these persistent adducts are not of primary relevance to AFB1 carcinogenesis. Analysis of nucleic acid bases by high-performance liquid chromatography revealed no qualitative differences in adduct species between treatment groups. The inhibitory effect of EQ on AFB1 binding to DNA and tumorigenesis appears related to induction of detoxication enzymes. Rats fed 0.4% EQ for 7 days showed a 5-fold increase in hepatic cytosolic glutathione S-transferase (GST)-specific activities. Multiple molecular forms of GST were induced, and concomitant elevations in messenger RNA levels coding for the synthesis of GST subunits were observed. Correspondingly, biliary elimination of AFB1-glutathione conjugate was increased 4.5-fold in animals on the EQ diet during the first 2 h following p.o. administration of 250 micrograms of AFB1 per kg. Thus, induction by EQ of enzymes important to AFB1 detoxication, such as GST, can lead to enhanced carcinogen elimination, as well as reductions of AFB1-DNA adduct formation and subsequent expression of preneoplastic lesions, and, ultimately, neoplasia.
Lack of Understanding , Misunderstanding and Language Acquisition

It is hardly an exaggeration to say that lack of understanding and mis-understanding are the main difficulties that anyone encounters who must communicate in a language, while at the same time learning it. In this paper we investigate what types of comprehension difficulties occur in this situation and what the mechanisms are that lead to the difficulties arising. Further, we want to initiate a discussion of the effects that lack of understanding and mis-understanding could have on linguistic interaction and on language acquisition.
T cells from fully H-2 allogeneic (A replaced by B) radiation bone marrow chimeras are functionally competent and host restricted but are alloreactive against hybrid Ia determinants expressed on (A x B)F1 cells

In this communication it is demonstrated that T cells from fully allogeneic A replaced by B radiation bone marrow chimeras are alloreactive against the hybrid Ia molecules expressed on the surface of heterozygous A X B cells. These results suggested that previous failures to generate cytotoxic T lymphocyte (CTL) responses from fully allogeneic chimeras by sensitizing the chimeric T cells to antigen in an (A X B)F1-priming environment might have been confounded by an ongoing alloreaction against determinants created by hybrid Ia molecules expressed on F1 cells. Consequently, the ability to generate CTL responses from fully allogeneic chimeras was re-examined by sensitizing the chimeric T cells to antigen presented by homozygous rather that F1 stimulator cells. It was found that T cells of donor bone marrow origin that mediate cytotoxic responses to trinitrophenyl- modified self determinants do differentiate into functional competence in an H-2-incompatible host environment and are restricted to the host H-2 haplotype.
**volume Title** Asp Conference Series, Vol. **volume Number** **author** Astronomical Data Processing Using Sciql, an Sql Based Query Language for Array Data

Data-intensive scientific research, such as in astronomy, calls for functional enhancements to DBMS technologies. In this paper we introduce SciQL (pronounced as 'cycle'), a novel SQL-based array query language for scientific applications with both tables and arrays as first class citizens. SciQL lowers the entrance fee of adopting relational DBMS in scientific domains, because it includes functionality often only found in mathematics software packages. We demonstrate SciQL using examples taken from a real-life astronomical data processing system, e.g. the Transient Key Project (TKP) of the LOFAR radio telescope. In particular, we show how a a full Stokes spectral light-curve database of all detected sources can be constructed, by cross-correlation over multiple catalogues can be constructed. By exposing the properties of array data to the relational DBMS, SciQL also opens up many opportunities to enhance the data mining possibilities for real-time transient and variability searches.
Enumerative covert channel audit model in MLS networks

A network covert channel is a mechanism that can be used to leak information across a network in violation of a security policy. In this paper, we first describe an enumerative covert channel existing in MSL networks, and then we propose a model for detecting it. This model caches a certain percentage of static enumerative dataset in advance and a certain percentage of dynamic dataset on the fly to audit the channel, it also inserts bogus packets and disorders query sequence to obscure a Trojan in high security network from identifying partners in low security network. We conclude that the model can audit enumerative channel effectively according to calculation and some experiments.
Photocorrosion Inhibition of Semiconductor-Based Photocatalysts: Basic Principle, Current Development, and Future Perspective

Heterogeneous photocatalysis is a promising strategy for addressing the worldwide environmental pollution and energy shortage issues. However, unlike TiO2 with good photostability, the intrinsic drawback of photoinduced decomposition, i.e., photocorrosion, of semiconductors significantly challenges durable photocatalysis. In this review, the photocorrosion mechanisms of typical semiconductors and different characterization methods proposed for monitoring the photocorrosion process of semiconductor-based composite photocatalysts are elaborated. Dedicated emphasis is put on the strategies for improving the anti-photocorrosion property of semiconductor-based photocatalysts, including modifying the crystal structure or morphology of semiconductors, doping with heteroatoms, hybridizing with various semiconductors and/or cocatalysts, and regulating the photocatalytic reaction conditions. Finally, we cast a personal prospect on the future development of the rational design of corrosion-controlled semiconductor-b.
Pituitary adenylate cyclase-activating polypeptide is a sympathoadrenal neurotransmitter involved in catecholamine regulation and glucohomeostasis

The adrenal gland is important for homeostatic responses to metabolic stress: hypoglycemia stimulates the splanchnic nerve, epinephrine is released from adrenomedullary chromaffin cells, and compensatory glucogenesis ensues. Acetylcholine is the primary neurotransmitter mediating catecholamine secretion from the adrenal medulla. Accumulating evidence suggests that a secretin-related neuropeptide also may function as a transmitter at the adrenomedullary synapse. Costaining with highly specific antibodies against the secretin-related neuropeptide pituitary adenylate cyclase-activating peptide (PACAP) and the vesicular acetylcholine transporter (VAChT) revealed that PACAP is found in nerve terminals at all mouse adrenomedullary cholinergic synapses. Mice with a targeted deletion of the PACAP gene had otherwise normal cholinergic innervation and morphology of the adrenal medulla, normal adrenal catecholamine and blood glucose levels, and an intact initial catecholamine secretory response to insulin-induced hypoglycemia. However, insulin-induced hypoglycemia was more profound and longer-lasting in PACAP knock-outs, and was associated with a dose-related lethality absent in wild-type mice. Failure of PACAP-deficient mice to adequately counterregulate plasma glucose levels could be accounted for by impaired long-term secretion of epinephrine, secondary to a lack of induction of tyrosine hydroxylase, normally occurring after insulin hypoglycemia in wild-type mice, and a consequent depletion of adrenomedullary epinephrine stores. Thus, PACAP is needed to couple epinephrine biosynthesis to secretion during metabolic stress. PACAP appears to function as an “emergency response” cotransmitter in the sympathoadrenal axis, where the primary secretory response is controlled by a classical neurotransmitter but sustained under paraphysiological conditions by a neuropeptide.
Contrôle d'un bioréacteur à perfusion pour la régénération du tissu vasculaire

The limited availability of autologous blood vessels for bypass surgeries (coronary or peripheral) and the poor patency rate of vascular prosthesis for the replacement of small diameter vessels (Ø < 6 mm) motivate researches in the domain of vascular tissue engineering. One of the possible strategies named functional tissue engineering aims to regenerate a blood vessel in vitro in a controlled environment. The objective of this thesis is to design a perfusion bioreactor and develop a control system able to dynamically interact with a growing blood vessel in order to guide and stimulate the maturation of the vascular construct. The principal question addressed in this work is: How to choose culture conditions in a bioreactor in the most efficient way? Two main challenges have been identified: first, the need to develop a better comprehension of the physical and biological phenomenon occurring in bioreactors; second, the need to influence and optimize vascular tissue maturation. A controller based on the concept of genetic programming was developed for real-time modeling of vascular tissue regeneration. Using the produced models, the controller searches an optimal culture strategy (circumferential strain, longitudinal shear stress and frequency of the pulsed pressure signal) by the mean of a Markov decision process solved by dynamic programming. Numerical simulations showed that the method has the potential to improve growth, safety of the process, and information gathering. The controller is able to work with common nonlinearities in tissue growth. Experimental results show that the controller is able to identify important culture parameters for the growth and remodelling of tissue engineered blood vessels. Furthermore, this bioreactor represents an interesting tool to study the evolution of the mechanical properties of a vascular construct during maturation.
Hepatitis C Virus Infection in Chicago Women With or at Risk for HIV Infection: Evidence for Sexual Transmission

Background and Objectives: The importance of sexual transmission of hepatitis C virus (HCV) infection is unclear. We attempted to define its role in women with or at risk for HIV infection. Goal of this Study: To ascertain if high‐risk sexual behavior was independently associated with HCV infection. Study Design: Risk factors were assessed cross‐sectionally in Chicago women newly enrolled in the Women's Interagency HIV Study. Women who had (n = 243) or were at risk for HIV infection (n = 53) were tested for HCV antibodies (Ab). Results: Of 296 women, 123 (42%) were HCV Ab positive; prevalence was 90% in women who injected drugs (IDU) compared with 12% in noninjectors (odds ratio [OR], 64.0, 95% confidence interval [CI], 29.9 to 137.0). A multivariate model showed associations with IDU (OR, 110.3, 95% CI, 33.3 to 365.8), prior gonorrhea (OR, 3.6, 95% CI, 1.4 to 8.9), and sex with a male IDU (OR, 2.7, 95% CI, 1.1 to 7.0). Conclusion: Injection drug use is the strongest predictor of HCV infection, but sexual risk factors are also independently associated.
A Negative Result Concerning Explicit Matrices With The Restricted Isometry Property

In this note, we prove that matrices whose entries are all 0 or 1 cannot achieve good performance with respect to the Restricted Isometry Property (RIP). Most currently known deterministic constructions of matrices satisfying the RIP fall into this category, and hence these constructions suffer inherent limitations. In particular, we show that DeVore’s construction of matrices satisfying the RIP is close to optimal once we add the constraint that all entries of the matrix are 0 or 1.
An intelligent categorization engine for bilingual web content filtering

It is important to protect children and unsuspecting adults from the harmful effects of objectionable materials, such as pornography, violence, and hate messages, which are now prevalent on the World-Wide Web. This calls for effective tools for web content analysis and filtering of objectionable contents. Our study of existing web content filtering systems has identified a number of deficiencies in these systems. Using the analysis of pornographic web pages as a case study, we present an intelligent bilingual web page categorization engine that can determine if an English or Chinese language web page contains pornographic materials. We have implemented the categorization engine to perform offline web page analysis and near-instantaneous online filtering. Performance evaluation of our system has verified its effectiveness.
Mouse Cursor Control System Based on Facial Electromyogram and Mechanomyogram

This paper reports the development of a mouse cursor control system as an assistive technology for upper arm amputees. The control is based on facial electromyogram (fEMG) and mechanomyogram (MMG) signals. The fEMG and MMG signals are collected for six words from eight subjects. A reference signal has been simulated based on the mean values of the signals representing the six words. The Euclidian distance between the Cepstral coefficients of the six words from that of the reference signal comprised the feature vector. Classification is through a probabilistic neural network. Six mouse cursor operations: up, down, left, right, left click and right click are reproduced. We have achieved an average classification rate of 91.5% using fEMG and 89.5% using MMG signal. The classification result is mapped into cursor operations through a switch based linear control.
Histopathological and molecular characterization of encephalitic listeriosis in small ruminants from northern Paraná, Brazil

Listeriosis is a disease primarily of ruminants caused by the Gram-positive bacterium Listeria monocytogenes. Ruminants either demonstrate manifestations of the encephalitic, septicemic, or reproductive form of listeriosis. The pathological and molecular findings with encephalitic listeriosis in a 5.5-month-old, male, mixed-breed goat and a 3-year-old Texel-crossed sheep from northern Paraná, Brazil are described. Clinically, the kid demonstrated circling, lateral protrusion of the tongue, head tilt, and convulsions; the ewe presented ataxia, motor incoordination, and lateral decumbency. Brainstem dysfunctions were diagnosed clinically and listeriosis was suspected. Necropsy performed on both animals did not reveal remarkable gross lesions; significant histopathological alterations were restricted to the brainstem (medulla oblongata; rhombencephalitis) and were characterized as meningoencephalitis that consisted of extensive mononuclear perivascular cuffings, neutrophilic and macrophagic microabscesses, and neuroparenchymal necrosis. PCR assay and direct sequencing, using genomic bacterial DNA derived from the brainstem of both animals, amplified the desired 174 base pairs length amplicon of the listeriolysin O gene of L. monocytogenes. Phylogenetic analyses demonstrated that the strains associated with rhombencephalitis during this study clustered with known strains of L. monocytogenes lineage I from diverse geographical locations and from cattle of the state of Paraná with encephalitic listeriosis. Consequently, these strains should be classified as L. monocytogenes lineage I. These results confirm the active participation of lineage I strains of L. monocytogenes in the etiopathogenesis of the brainstem dysfunctions observed during this study, probably represent the first characterization of small ruminant listeriosis by molecular techniques in Latin America, and suggest that ruminants within the state of Paraná were infected by the strains of the same lineage of L. monocytogenes.