Miracle-dz/UniFAR-FTUs huggingface dataset:
Seroepidemiological study of Toxoplasma gondii infection in a population of Iranian epileptic patients

Epilepsy is one of the most common neurologic disorders. Underlying cause of epilepsy is unknown in 60 % of the patients. Toxoplasma gondii is an intracellular parasite which is capable of forming tissue cysts in brain of chronically infected hosts including humans. Some epidemiological studies suggested an association between toxoplasmosis and acquisition of epilepsy. In this study we determined seroprevalence of latent Toxoplasma infection in a population of Iranian epileptic patients. Participants were classified in three groups as Iranian epileptic patients (IEP, n = 414), non-epileptic patients who had other neurologic disorders (NEP, n = 150), and healthy people without any neurologic disorders (HP, n = 63). The presence of anti-Toxoplasma IgG antibodies and IgG titer in the sera were determined by ELISA method. Anti-T. gondii IgG seroprevalence obtained 35.3 %, 34.7 % and 38.1 % in IEP, NEP and HP, respectively. The seroprevalence rate was not significantly different among the three groups (P = 0.88). Anti-T. gondii IgG titer was 55.7 ± 78, 52.4 ± 74 and 69.7 ± 92 IU/ml in IEP, NEP and HP, respectively. There was not any statistically significant difference in the antibody titer between the study groups (P = 0.32). The rate of T. gondii infection in epileptic patients was not higher than non-epileptic patients and healthy people in the Iranian population.
Penalized classification using Fisher's linear discriminant

Summary. We consider the supervised classification setting, in which the data consist of p features measured on n observations, each of which belongs to one of K classes. Linear discriminant analysis (LDA) is a classical method for this problem. However, in the high dimensional setting where p≫n, LDA is not appropriate for two reasons. First, the standard estimate for the within‐class covariance matrix is singular, and so the usual discriminant rule cannot be applied. Second, when p is large, it is difficult to interpret the classification rule that is obtained from LDA, since it involves all p features. We propose penalized LDA, which is a general approach for penalizing the discriminant vectors in Fisher's discriminant problem in a way that leads to greater interpretability. The discriminant problem is not convex, so we use a minorization–maximization approach to optimize it efficiently when convex penalties are applied to the discriminant vectors. In particular, we consider the use of L1 and fused lasso penalties. Our proposal is equivalent to recasting Fisher's discriminant problem as a biconvex problem. We evaluate the performances of the resulting methods on a simulation study, and on three gene expression data sets. We also survey past methods for extending LDA to the high dimensional setting and explore their relationships with our proposal.
Application of the phase extension method in virus crystallography

The procedure for phase extension (PX) involves gradually extending the initial phases from low resolution (e.g. ∼8 Å) to the high-resolution limit of a diffraction data set. Structural redundancy present in the viral capsids that display icosahedral symmetry results in a high degree of non-crystallographic symmetry (NCS), which in turn translates into higher phasing power and is critical for improving and extending phases to higher resolution. Greater completeness of the diffraction data and determination of a molecular replacement solution, which entails accurately identifying the virus particle orientation(s) and position(s), are important for the smooth progression of the PX procedure. In addition, proper definition of a molecular mask (envelope) around the NCS-asymmetric unit has been found to be important for the success of density modification procedures, such as density averaging and solvent flattening. Regardless of the degree of NCS, the PX method appears to work well in all space groups, provided an accurate molecular mask is used along with reasonable initial phases. However, in the cases with space group P1, in addition to requiring a molecular mask, starting the PX at a higher resolution (e.g. 6 Å) overcame the previously reported problems due to Babinet phases and phase flipping errors.
Memory and Markets

In many environments, including credit and online markets, records about participants are collected, published, and erased after some time. We study the effects of erasing past records in a dynamic market where the quality of sellers follows a Markov process, and buyers leave feedback about sellers to an information intermediary. When the average quality of sellers is low, unlimited records lead to a market breakdown in the long run. We consider the information design problem and characterize information policies that can sustain trade and that maximize social welfare. These policies hide some information from the market in order to foster socially desirable experimentation. We show that these outcomes can be implemented by appropriately deleting past records. Crucially, positive and negative records play opposite roles with different intensities and must have different lengths: negative records must be deleted sufficiently late, and positive ones sufficiently early.
Synaptic transmission in the auditory brainstem of normal and congenitally deaf mice

The deafness (dn/dn) mutant mouse provides a valuable model of human congenital deafness. We investigated the properties of synaptic transmission in the anteroventral cochlear nucleus (AVCN) of normal and congenitally deaf dn/dn mice. Excitatory postsynaptic currents (EPSCs) were evoked by focal stimulation of single auditory nerve fibres, and measured by whole‐cell recordings from neurones in AVCN slices (mean postnatal age = P13). Absolute amplitudes of both AMPA‐ and NMDA‐mediated components of evoked EPSCs were greater (170 %) in deaf versus control animals. Enhanced transmission in deaf mice was due to a presynaptic mechanism. Variance‐mean analysis revealed that the probability of transmitter release was significantly greater in deaf (Pr= 0.8) versus control animals (Pr= 0.5). Following high frequency stimulation, deaf mice showed a greater depression of evoked EPSCs, and a significant increase in the frequency of delayed‐release (asynchronous) miniature EPSCs (aEPSCs) (deaf 100 Hz vs. control 7 Hz). The acetoxymethyl ester of EGTA (EGTA‐AM) blocked the increase in miniature aEPSCs and returned tetanic depression to control values. In deaf mice, reduction of mean Pr using cadmium caused an expected increase in paired‐pulse ratio (PPR). However, in the same cells, a similar reduction in release by EGTA‐AM did not result in a change in PPR, demonstrating that a change may occur in Pr without a concomitant change in PPR. In many respects, transmission in deaf mice was found to be remarkably similar to control mice, implying that many parameters of synaptic transmission develop normally in these animals. The two significant differences (higher Pr and asynchronous release in deaf mice) could both be reversed by the addition of EGTA‐AM, suggesting that endogenous calcium buffering may be impaired or undeveloped in the presynaptic terminals of the auditory nerve in deaf mice.
The Importance of Supertagging for Wide-Coverage CCG Parsing

This paper describes the role of supertagging in a wide-coverage CCG parser which uses a log-linear model to select an analysis. The supertagger reduces the derivation space over which model estimation is performed, reducing the space required for discriminative training. It also dramatically increases the speed of the parser. We show that large increases in speed can be obtained by tightly integrating the supertagger with the CCG grammar and parser. This is the first work we are aware of to successfully integrate a supertagger with a full parser which uses an automatically extracted grammar. We also further reduce the derivation space using constraints on category combination. The result is an accurate wide-coverage CCG parser which is an order of magnitude faster than comparable systems for other linguistically motivated formalisms.
A Switching Regime Model for the EMG-Based Control of a Robot Arm

Human-robot control interfaces have received increased attention during the last decades. These interfaces increasingly use signals coming directly from humans since there is a strong necessity for simple and natural control interfaces. In this paper, electromyographic (EMG) signals from the muscles of the human upper limb are used as the control interface between the user and a robot arm. A switching regime model is used to decode the EMG activity of 11 muscles to a continuous representation of arm motion in the 3-D space. The switching regime model is used to overcome the main difficulties of the EMG-based control systems, i.e., the nonlinearity of the relationship between the EMG recordings and the arm motion, as well as the nonstationarity of EMG signals with respect to time. The proposed interface allows the user to control in real time an anthropomorphic robot arm in the 3-D space. The efficiency of the method is assessed through real-time experiments of four persons performing random arm motions.
Prevalence of Metabolic Syndrome among Hypertensive Patients Attending a Primary Care Clinic in Kuwait

Objective: To determine the prevalence of metabolic syndrome among hypertensive patients using the criteria of the National Cholesterol Education Program’s Adult Treatment Panel III in a primary care health center in Kuwait. Subjects and Methods: A population of 250 Kuwaiti hypertensive patients (129 males and 121 females) over the age of 40 were screened for metabolic syndrome by determining body mass index (BMI), waist circumference, levels of fasting plasma glucose and fasting plasma lipids (serum triglycerides, total cholesterol and high-density lipoprotein cholesterol). The study was carried out in the Mishref Family Practice Health Center, Kuwait, from January to July 2001. Results: The total number of patients who met the criteria for metabolic syndrome was 85 (34%), 55% of them were males and 45% females. Prevalence of the syndrome was 28.2% among 40- to 55-year-olds and 41.9% in those above the age of 55 years. Among the 250 hypertensive patients, type II diabetes mellitus was found in 52.8% (54% males and 46% females), impaired fasting glucose in 8% (70% males and 30% females), high plasma triglycerides in 44.8% (53% males and 47% females) and low high-density lipoprotein cholesterol in 63.2% (54% males and 46% females). Obesity measured as BMI = 30 kg/m2 was noted in 46% (43% males and 57% females) and increased waist circumference in 58% (44% males and 56% females). Conclusion: The prevalence of metabolic syndrome is high among hypertensives attending primary health care centers in Kuwait.
Gender Issues in Recovery from Alcoholism

Female recovering alcoholics were compared with female non-problem drinkers and male recovering alcoholics on 2 locus of control measures and family dynamics. A significant difference was found between groups of recovering females and males regarding the measure of spousal fusion. Significant differences were found between the AA females and the non-problem drinking females on drinking related locus of control measures and family dynamics regarding spousal fusion and intimacy with parents.
Comparison of Sisomicin and Gentamicin in Bacteriuric Patients with Underlying Diseases of the Urinary Tract

Sisomicin and gentamicin (2 mg/kg) were administered in a random fashion to patients with bacteriuria superimposed on abnormalities of the urinary tract. Cure was achieved in a similar number of patients in both groups, but superinfection and reinfection with resistant microorganisms was more frequent in patients receiving gentamicin. Untoward side effects were not frequent in this series, especially if the serious underlying urological disease of most patients is taken into consideration. The susceptibility of the causative pathogens to the antibiotic administered and the severity of the underlying disease were the most important factors in the outcome.
Fiber optic bronchoscopy-assisted percutaneous tracheostomy: a decade of experience at a university hospital

Objective To evaluate the efficacy and safety of percutaneous tracheostomy by means of single-step dilation with fiber optic bronchoscopy assistance in critical care patients under mechanical ventilation. Methods Between the years 2004 and 2014, 512 patients with indication of tracheostomy according to clinical criteria, were prospectively and consecutively included in our study. One-third of them were high-risk patients. Demographic variables, APACHE II score, and days on mechanical ventilation prior to percutaneous tracheostomy were recorded. The efficacy of the procedure was evaluated according to an execution success rate and based on the necessity of switching to an open surgical technique. Safety was evaluated according to post-operative and operative complication rates. Results The mean age of the group was 64 ± 18 years (203 women and 309 males). The mean APACHE II score was 21 ± 3. Patients remained an average of 11 ± 3 days on mechanical ventilation before percutaneous tracheostomy was performed. All procedures were successfully completed without the need to switch to an open surgical technique. Eighteen patients (3.5%) presented procedure complications. Five patients experienced transient desaturation, 4 presented low blood pressure related to sedation, and 9 presented minor bleeding, but none required a transfusion. No serious complications or deaths associated with the procedure were recorded. Eleven patients (2.1%) presented post-operative complications. Seven presented minor and transitory bleeding of the percutaneous tracheostomy stoma, 2 suffered displacement of the tracheostomy cannula, and 2 developed a superficial infection of the stoma. Conclusion Percutaneous tracheostomy using the single-step dilation technique with fiber optic bronchoscopy assistance seems to be effective and safe in critically ill patients under mechanical ventilation when performed by experienced intensive care specialists using a standardized procedure.
DDX3 as a strongest prognosis marker and its downregulation promotes metastasis in colorectal cancer

Background Conflicting results regarding the role of DEAD-box polypeptide 3 (DDX3) are seen not only between cancer types but also within the same type of cancer. In this study, we aimed at clarifying the prognostic significance of DDX3 in patients of major cancer types through large cohort survival analysis and further investigated its effects on cancer progression. Methods Large cohort survival analysis of 7 cancer types, including colorectal cancer, breast cancer, lung cancer, head and neck cancer, liver cancer, glioblastoma, and ovarian cancer, was performed using public database at RNA level and was further confirmed by IHC analysis at protein level. Phenotype parameters of DDX3 knockdown colon cancer cells and the mechanism of DDX3 regulated cancer progression were investigated in vitro and in vivo. Results In large cohort survival analysis, DDX3 had a significant prognostic predictive power in colorectal cancer at both RNA and protein level. Patients with low DDX3 expression had poor prognosis and frequent distant metastasis. Knockdown of DDX3 enhanced the migration and invasion abilities of colon cancer cells and promoted tumor metastasis in vivo. Snail upregulation with decreased membranous E-cadherin expression and reduced cell aggregation were found after DDX3 downregulation. Conclusions Our study revealed the strong prognostic effect of DDX3 on colorectal cancer among seven major cancer types through larger cohort survival analysis at RNA and protein level. Low DDX3 expression promotes Snail/E-cadherin pathway mediated cancer metastasis and poor clinical outcome in colorectal cancer patients.
Modeling Change in Student Attitude Toward and Beliefs About Mathematics

Abstract The authors used data from the Longitudinal Study of American Youth to investigate variables related to change in students' attitude toward and beliefs about mathematics in middle school and high school. Using hierarchical linear modeling techniques, the authors modeled variation in students' rate of change with variables associated with student characteristics, instructional experiences, and environment. They also identified variables that differentially affect change at different levels of secondary school (i.e., middle school vs. high school) and for different affective dimensions (i.e., attitude toward mathematics, beliefs about the social importance of mathematics, and beliefs about the nature of mathematics). Results showed a substantial negative change in students' attitudes toward and beliefs about the social importance of mathematics throughout secondary school. However, students' notions of the nature of mathematics did not change throughout secondary school. The authors identified variables related to change and found that they differed according to the level of secondary school and affective dimensions.
Genetic and Environmental Control of Variation in Retinal Ganglion Cell Number in Mice

How much of the remarkable variation in neuron number within a species is generated by genetic differences, and how much is generated by environmental factors? We address this problem for a single population of neurons in the mouse CNS. Retinal ganglion cells of inbred and outbred strains, wild species and subspecies, andF1 hybrids were studied using an unbiased electron microscopic method with known technical reliability. Ganglion cell numbers among diverse types of mice are highly variable, ranging from 32,000 to 87,000. The distribution of all cases (n = 252) is close to normal, with a mean of 58,500 and an SD of 7800. Genetic factors are most important in controlling this variation; 76% of the variance is heritable and up to 90% is attributable to genetic factors in a broad sense. Strain averages have an unanticipated bimodal distribution, with distinct peaks at 55,500 and 63,500 cells. Three pairs of closely related strains have ganglion cell populations that differ by >20% (10,000 cells). These findings indicate that different alleles at one or two genes have major effects on normal variation in ganglion cell number. Nongenetic factors are still appreciable and account for a coefficient of variation that averages ∼3.6% within inbred strains and isogenicF1 hybrids. Age- and sex-related differences in neuron number are negligible. Variation within isogenic strains appears to be generated mainly by developmental noise.
Correlation of bony ingrowth to the distribution of stress and strain parameters surrounding a porous‐coated implant

The ability of shear strains to inhibit bony ingrowth was investigated by use of a transcortical porouscoated cylindrical plug implant in a functionally isolated turkey ulna model in which the mechanical loading environment could be accurately controlled and rigorously defined. The distribution of ingrowth at the bone‐implant interface was quantified following 8 weeks of in vivo loading consisting of 100 seconds per day of a 20 Hz sinusoidal stimulus sufficient to cause a local peak strain of approximately 100 microstrain in the cortex at the bone‐implant interface in four turkeys. A nonuniform but repeatable pattern of bony ingrowth, from 33 ± 6 to 72 ± 6% (mean ± SE), was observed. The mechanical environment in the vicinity of the bone‐implant interface was calculated using a three‐dimensional elastic orthotropic finite element model. The general stress‐strain state of the bone as predicted by the finite element model was validated in two additional turkeys using four three‐element rosette strain gauges, while high resolution moiré interferometry was used to determine the mechanical state of the region immediately adjacent to the implant itself. Shear strains and stresses were evaluated at the interface and correlated to the pattern of bony ingrowth circumscribing the implant interface. Linear regressions between ingrowth and both shear strain and shear stress were negative, with the values of R = −0.75 and R = −0.78 (p < 0.001), respectively, indicating significant inhibition of ingrowth where shear components were maximal. These results suggest that the minimization of shear stress and strain components is a major determinant in achieving successful ingrowth of bone into a prosthesis.
Approximation algorithms for finding low‐degree subgraphs

We give quasipolynomial‐time approximation algorithms for designing networks with a minimum degree. Using our methods, one can design networks whose connectivity is specified by “proper” functions, a class of 0–1 functions indicating the number of edges crossing each cut. We also provide quasipolynomial‐time approximation algorithms for finding two‐edge‐connected spanning subgraphs of approximately minimum degree of a given two‐edge‐connected graph, and a spanning tree (branching) of approximately minimum degree of a directed graph. The degree of the output network in all cases is guaranteed to be at most (1 + ϵ) times the optimal degree, plus an additive O(log1+ϵn) for any ϵ > 0. Our analysis indicates that the degree of an optimal subgraph for each of the problems above is well estimated by certain polynomially solvable linear programs. This suggests that the linear programs we describe could be useful in obtaining optimal solutions via branch and bound. © 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 44(3), 203–215 2004
Modelling and predicting a Web page accesses using Markov processes

The significance of modelling and measuring various attributes of the Web in part or as a whole is undeniable. Although Web related metrics have become increasingly sophisticated, few employ models to explain their measurements. In this paper, we discuss metrics for usage characterization. We considered the application of patterns in browsing behavior of users for predicting access to Web documents. We proposed two models based on Markov processes for addressing our specification of the access prediction problem. The first adapts a stochastic model for library circulations, i.e., Morse's model in the context of accessing Web documents. The second approach can be used for determining access probabilities of Web pages within a site by modelling the browsing process as an ergodic Markov chain.