Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunomodulation with Glatiramer Acetate Prevents Long-Term Inflammatory Pain

The potential application of glatiramer acetate (GA) therapy as a safe pharmacological treatment for the attenuation or prevention of long-term inflammatory pain in a rat model was explored. Peripheral inflammatory pain was induced by an injection of Complete Freund's Adjuvant (CFA) into the plantar surface of the hind paw. Genome-wide DNA microarray studies were used to survey molecular mechanisms involved in long-term GA analgesic responses. Administration of a single or double subcutaneous injection of GA before, or immediately after, intraplantar injection of pro-inflammatory CFA significantly attenuated allodynia and hyperalgesic pain responses up to ∼3 weeks after CFA treatment. These beneficial effects of GA immunization therapy coincided with the attenuation of expression of the chemotactic fractalkine chemokine (CX3CL1) in the dorsal horn of the lumbar spinal cord (L4-L5) in response to CFA treatment, assessed by DNA microarray and confirmed immunocytochemically (ICC). This study is consistent with the hypothesis that a novel mechanism through which GA immunization therapy may beneficially influence long-term allodynia and hyperalgesia is through central regulation of fractalkine-mediated responses.
Chimerism analysis in clinical practice and its relevance for the detection of graft rejection and malignant relapse in pediatric hematopoietic stem cell transplant patients

Chimerism and clinical outcome data from 244 hematopoietic stem cell transplants in 218 children were retrospectively analyzed to assess their relevance for the detection of graft rejection and malignant relapse. Patients transplanted for a non‐malignant disease had significantly higher proportions of residual recipient T cells in peripheral blood at one, three, and six months compared with patients transplanted for malignant disease. Recipient T‐cell levels were below 50% at one month after transplantation in most patients (129 of 152 transplants). Graft rejection occurred more frequently in the group of patients with high levels of recipient cells at one month (10 graft rejections in the 23 patients with recipient T cells >50% at one month as compared to seven graft rejections occurred in 129 patients with recipient T cells <50% (p < 0.001). Multilineage chimerism data in 87 children with leukemia at one, three, and six months after transplantation were not correlated with subsequent relapse of malignant disease. In conclusion, early analysis of lineage‐specific chimerism in peripheral blood can be used to identify patients who are at high risk of graft rejection. However, the efficacy of early chimerism analysis for predicting leukemia relapse was limited.
Multilevel Modeling in Personality and Social Psychology

An integrated personality and social psychology needs to take into account different levels of analysis by definition. In both disciplines, it is widely accepted that personality and the social context affect social behavior and that social behavior, in turn, also informs us about personality. The challenge for an integrated personality and social psychology is to simultaneously analyze the complex relations between the different levels of analysis for both theoretical and statistical reasons. Innovations in statistical analysis have made it possible to simultaneously take into account different levels of analysis This chapter reviews the basics and recent advances in multilevel modeling to develop a framework of multilevel analyses for an integrated personality and social psychology and to illustrate the importance of multilevel modeling for theory development and testing using examples from research on personality and social behavior.
Mental and physical health-related quality of life in obese patients before and after bariatric surgery: A meta-analysis

In this meta-analysis, we review studies that compare mental and physical health-related quality of life measured with the Short-Form 36 of obese patients before and after bariatric surgery with a follow-up measure until one year. Twenty-one studies were selected to conduct the meta-analysis about the relationship between quality of life in obesity before (2680 subjects) and after (2251 subjects) bariatric surgery. Results reveal that obese patients scored less in the mental health component of the Short-Form 36 before bariatric surgery than after (d = −9.00). The same pattern could be observed in the case of the physical health component of the Short-Form 36 (d = −22.84). The results show the strong improvement that obese patients experience in both mental and physical components of the Short-Form 36 after receiving bariatric surgery.
Clostridium difficile Testing Algorithms Using Glutamate Dehydrogenase Antigen and C. difficile Toxin Enzyme Immunoassays with C. difficile Nucleic Acid Amplification Testing Increase Diagnostic Yield in a Tertiary Pediatric Population

ABSTRACT We evaluated the performance of the rapid C. diff Quik Chek Complete's glutamate dehydrogenase antigen (GDH) and toxin A/B (CDT) tests in two algorithmic approaches for a tertiary pediatric population: algorithm 1 entailed initial testing with GDH/CDT followed by loop-mediated isothermal amplification (LAMP), and algorithm 2 entailed GDH/CDT followed by cytotoxicity neutralization assay (CCNA) for adjudication of discrepant GDH-positive/CDT-negative results. A true positive (TP) was defined as positivity by CCNA or positivity by LAMP plus another test (GDH, CDT, or the Premier C. difficile toxin A and B enzyme immunoassay [P-EIA]). A total of 141 specimens from 141 patients yielded 27 TPs and 19% prevalence. Sensitivity, specificity, positive predictive value, and negative predictive value were 56%, 100%, 100%, and 90% for P-EIA and 81%, 100%, 100%, and 96% for both algorithm 1 and algorithm 2. In summary, GDH-based algorithms detected C. difficile infections with superior sensitivity compared to P-EIA. The algorithms allowed immediate reporting of half of all TPs, but LAMP or CCNA was required to confirm the presence or absence of toxigenic C. difficile in GDH-positive/CDT-negative specimens.
Biological Physics: Energy, Information, Life

PART I: MYSTERIES, METAPHORS, MODELS - What the Ancients Knew - What's Inside Cells - PART II: DIFFUSION, DISSIPATION, DRIVE - The Molecular Dance - Random Walks, Friction, and Diffusion - Life in the Slow Lane: The Low Reynolds-Number World - Entropy, Temperature, and Free Energy - Entropic Forces at Work - Chemical Forces and Self-Assembly - PART III: MOLECULES, MACHINES, MECHANISMS - Cooperative Transitions in Macromolecules - Enzymes and Molecular Machines - Machines in Membranes - Nerve Impulses - Global List of Symbols and Units - Numerical Values - Index
On Simulated Likelihood of Discretely Observed Diffusion Processes and Comparison to Closed-Form Approximation

This article focuses on two methods to approximate the log-likelihood of discretely observed univariate diffusions: (1) the simulation approach using a modified Brownian bridge as the importance sampler, and (2) the closed-form approximation approach. For the case of constant volatility, we give a theoretical justification of the modified Brownian bridge sampler by showing that it is exactly a Brownian bridge. We also discuss computational issues in the simulation approach such as accelerating the numerical variance stabilizing transformation, computing derivatives of the simulated log-likelihood, and choosing initial values of parameter estimates. The two approaches are compared in the context of financial applications under a benchmark model which has an unknown transition density and has no analytical variance stabilizing transformation. The closed-form approximation, particularly the second-order closed-form, is found to be computationally efficient and very accurate when the observation frequency is monthly or higher. It is more accurate in the center than in the tails of the transition density. The simulation approach combined with the variance stabilizing transformation is found to be more reliable than the closed-form approximation when the observation frequency is lower. Both methods perform better when the volatility level is lower, but the simulation method is more robust to the volatility level. When applied to two well-known datasets of daily observations, the two methods yield similar parameter estimates in both datasets but slightly different log-likelihoods in the case of higher volatility.
Comparative Mycotoxin Profiles of Gibberella zeae Populations from Barley, Wheat, Potatoes, and Sugar Beets

ABSTRACT Gibberella zeae is one of the most devastating pathogens of barley and wheat in the United States. The fungus also infects noncereal crops, such as potatoes and sugar beets, and the genetic relationships among barley, wheat, potato, and sugar beet isolates indicate high levels of similarity. However, little is known about the toxigenic potential of G. zeae isolates from potatoes and sugar beets. A total of 336 isolates of G. zeae from barley, wheat, potatoes, and sugar beets were collected and analyzed by TRI (trichothecene biosynthesis gene)-based PCR assays. To verify the TRI-based PCR detection of genetic markers by chemical analysis, 45 representative isolates were grown in rice cultures for 28 days and 15 trichothecenes and 2 zearalenone (ZEA) analogs were quantified using gas chromatography-mass spectrometry. TRI-based PCR assays revealed that all isolates had the deoxynivalenol (DON) marker. The frequencies of isolates with the 15-acetyl-deoxynivalenol (15-ADON) marker were higher than those of isolates with the 3-acetyl-deoxynivalenol (3-ADON) marker among isolates from all four crops. Fusarium head blight (FHB)-resistant wheat cultivars had little or no influence on the diversity of isolates associated with the 3-ADON and 15-ADON markers. However, the frequency of isolates with the 3-ADON marker among isolates from the Langdon, ND, sampling site was higher than those among isolates from the Carrington and Minot, ND, sites. In chemical analyses, DON, 3-ADON, 15-ADON, b-ZEA, and ZEA were detected. All isolates produced DON (1 to 782 μg/g) and ZEA (1 to 623 μg/g). These findings may be useful for monitoring mycotoxin contamination and for formulating FHB management strategies for these crops.
Generalized Method of Moments

1. Introduction 2. The Instrumental Variable Estimator in the Linear Regression Model 3. GMM Estimation in Correctly Specified Models 4. GMM Estimation in Misspecified Models 5. Hypothesis Testing 6. Asymptotic Theory and Finite Sample Behaviour 7. Moment Selection in Theory and in Practice 8. Alternative Approximations in Finite Sample Behaviour 9. Empirical Examples 10. Related Methods of Estimation Appendix: Mixing processes and Nonstationarity
On Your Mark, Get Set, Go: Levels of Physical Activity in the Kingdom of Saudi Arabia, 2013.

BACKGROUND With the lack of appropriate data, we conducted a large household survey in 2013 to determine current rates of physical activity in the Kingdom of Saudi Arabia (KSA). METHODS The Saudi Health Interview Survey is a national multistage survey of individuals aged 15 years or older. We used a multivariate logistic regression model to measure association between sociodemographic and selected characteristics and meeting the recommended levels of moderate and vigorous weekly physical activity. RESULTS Of a total of 12,000 households contacted, 10,735 (89.4%) participants completed Saudi Health Interview Survey. An estimated 4.5 million (34.5%) Saudis aged 15 years or older reported no weekly physical activity, while only 1.7 million (12.9%) meet the recommended levels of moderate physical activity (MPA). The likelihood of meeting MPA decreased with age, education, among women, those with a history of diagnosis of select chronic conditions, including diabetes. Similar results were found for the likelihood of meeting the recommended levels of vigorous weekly physical activity. CONCLUSIONS We found very low levels of physical activity in KSA. Perhaps, KSA can challenge communities or employers to devise solutions and reward those with the best results. These solutions would be of great value to other Gulf countries, as well.
Shiga toxin-converting phages and the emergence of new pathogenic Escherichia coli: a world in motion

Shiga toxin (Stx)-producing Escherichia coli (STEC) are pathogenic E. coli causing diarrhea, hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). STEC are characterized by a constellation of virulence factors additional to Stx and have long been regarded as capable to cause HC and HUS when possessing the ability of inducing the attaching and effacing (A/E) lesion to the enterocyte, although strains isolated from such severe infections sometimes lack this virulence feature. Interestingly, the capability to cause the A/E lesion is shared with another E. coli pathogroup, the Enteropathogenic E. coli (EPEC). In the very recent times, a different type of STEC broke the scene causing a shift in the paradigm for HUS-associated STEC. In 2011, a STEC O104:H4 caused a large outbreak with more than 800 HUS and 50 deaths. Such a strain presented the adhesion determinants of Enteroaggregative E. coli (EAggEC). We investigated the possibility that, besides STEC and EAggEC, other pathogenic E. coli could be susceptible to infection with stx-phages. A panel of stx2-phages obtained from STEC isolated from human disease was used to infect experimentally E. coli strains representing all the known pathogenic types, including both diarrheagenic E. coli (DEC) and extra-intestinal pathogenic E. coli (ExPEC). We observed that all the E. coli pathogroups used in the infection experiments were susceptible to the infection. Our results suggest that the stx2-phages used may not have specificity for E. coli adapted to the intestinal environment, at least in the conditions used. Additionally, we could only observe transient lysogens suggesting that the event of stable stx2-phage acquisition occurs rarely.
Comparison of Diet versus Exercise on Metabolic Function and Gut Microbiota in Obese Rats.

UNLABELLED Cardiometabolic impairments that begin early in life are particularly critical, because they often predict metabolic dysfunction in adulthood. Obesity, high-fat diet (HFD), and inactivity are all associated with adipose tissue (AT) inflammation and insulin resistance (IR), major predictors of metabolic dysfunction. Recent evidence has also associated the gut microbiome with cardiometabolic health. PURPOSE The objective of this study is to compare equal energy deficits induced by exercise and caloric reduction on cardiometabolic disease risk parameters including AT inflammation, IR, and gut microbiota changes during HFD consumption. METHODS Obesity-prone rats fed HFD were exercise trained (Ex, n = 10) or weight matched to Ex via caloric reduction although kept sedentary (WM, n = 10), and compared with ad libitum HFD-fed (Sed, n = 10) rats for IR, systemic energetics and spontaneous physical activity (SPA), adiposity, and fasting metabolic parameters. Visceral, subcutaneous, periaortic, and brown AT (BAT), liver, aorta, and cecal digesta were examined. RESULTS Despite identical reductions in adiposity, Ex, but not WM, improved IR, increased SPA by approximately 26% (P < 0.05 compared with WM and Sed), and reduced LDL cholesterol (P < 0.05 compared with Sed). WM and Ex both reduced inflammatory markers in all AT depots and aorta, whereas only Ex increased indicators of mitochondrial function in BAT. Ex significantly increased the relative abundance of cecal Streptococcaceae and decreased S24-7 and one undefined genus in Rikenellaceae; WM induced similar changes but did not reach statistical significance. CONCLUSIONS Both Ex and WM reduced AT inflammation across depots, whereas Ex caused more robust changes to gut microbial communities, improved IR, increased fat oxidation, increased SPA, and increased indices of BAT mitochondrial function. Our findings add to the growing body of literature indicating that there are weight-loss-independent metabolic benefits of exercise.
The emergence of coordinative structures during offensive movement for goal-scoring in soccer

This study examined how offensive movements leading to goal-scoring opportunities emerge through coordinative actions between players in professional soccer. Twenty soccer clubs in the English Premier League were observed and analysed for 12 successive competitive Premier League matches each during the 2011-12 season. A coordinative structure was defined as the partnership between the player who delivered the assist pass and the goal scoring player. According to conditions of two players in the last action before a goal being scored four coordinative states were defined: Passer Standing-Receiver Standing; Passer Standing-Receiver Moving; Passer Moving-Receiver Standing; Passer Moving-Receiver Moving. The result of repeated-measures Analysis of Variance (F3, 57=1.94, p>0.05) showed that there was no significant difference between the occurrence of different coordinative states. The Markov chain model was used to examine the predictability of coordinative structure states in successive matches. We found a low transition probability and small transitional rate in each coordinative state. The results showed that the emergence of coordinative structure during offensive movements varies between EPL soccer clubs and it follows a stochastic process in successive matches. One implication of these findings for coaches is the need for varied tactics in attack through using different states of coordinative actions between players in order to increase goal-scoring opportunities.
Single Nucleotide Changes in the Human Iγ1 and Ιγ4 Promoters Underlie Different Transcriptional Responses to CD401

Analysis of subclass-specific germline transcription in activated peripheral B cells revealed a highly biased expression pattern of the four Iγ transcripts to signals through CD40 and IL-4. This difference was most pronounced when comparing the profile of Iγ1 and Iγ4 transcripts and was not expected given the very high degree of sequence conservation between promoters. In this report, the influence of sequence differences on the regulation of the Iγ1 and Iγ4 promoters has been investigated given the highly muted transcriptional activity of the Iγ4 promoter. Two regions were analyzed where single nucleotide differences corresponded to major changes in transcriptional activity. These regions were the previously defined CD40 response region containing three putative NF-κB-binding sites and the downstream 36-bp region containing CREB/activating transcription factor and κB6 sites. Mutation of a single nucleotide at position 6 within the Iγ4 κB6 site increased promoter activity to ∼50% of the activity of the Iγ1 promoter. Furthermore, elevated promoter strength corresponded with increased binding of p50, p65, c-Rel, RelB, and p300 proteins to a level comparable with that of Iγ1. Minor nucleotide changes to both the Iγ4 CD40 response region and the 36-bp element resulted in a response undistinguishable from an Iγ1 response, suggesting cooperation between the two regulatory regions for optimal transcriptional activity. Collectively, these mutational analyses suggest that minor sequence differences contribute to the composition and affinity of transcriptional protein complexes regulating subclass-specific germline transcription, which in part impacts the overall level of class switch recombination to targeted CH regions.
Language Identification of Short Text Segments with N-gram Models

There are many accurate methods for language identification of long text samples, but identification of very short strings still presents a challenge. This paper studies a language identification task, in which the test samples have only 5-21 characters. We compare two distinct methods that are well suited for this task: a naive Bayes classifier based on character n-gram models, and the ranking method by Cavnar and Trenkle (1994). For the n-gram models, we test several standard smoothing techniques, including the current state-of-the-art, the modified Kneser-Ney interpolation. Experiments are conducted with 281 languages using the Universal Declaration of Human Rights. Advanced language model smoothing techniques improve the identification accuracy and the respective classifiers outperform the ranking method. The higher accuracy is obtained at the cost of larger models and slower classification speed. However, there are several methods to reduce the size of an n-gram model, and our experiments with model pruning show that it provides an easy way to balance the size and the identification accuracy. We also compare the results to the language identifier in Google AJAX Language API, using a subset of 50 languages.
Fusogenicity of Jaagsiekte Sheep Retrovirus Envelope Protein Is Dependent on Low pH and Is Enhanced by Cytoplasmic Tail Truncations

ABSTRACT Jaagsiekte sheep retrovirus (JSRV) envelope (Env) is an active oncogene responsible for neoplastic transformation in animals and cultured cells. In this study, we used syncytium induction and fluorescence-based cell fusion assays to investigate JSRV Env fusion and its modulation by the cytoplasmic tail (CT). We found that JSRV Env induced syncytia in cells overexpressing the receptor for JSRV and that a low pH was required for this process to occur. Fusion kinetics studies revealed that cell-cell fusion by JSRV Env at neutral pH was poor, taking up to a day, in sharp contrast to fusion at low pH, which peaked within 2 min following a low-pH trigger. Deletion of the C-terminal 7 or 16 amino acids of the JSRV Env CT had no or little effect on fusion, yet additional truncation toward the membrane-spanning domain, resulting in mutants retaining as little as 1 amino acid of the CT, led to progressively increased syncytium formation at neutral pH that was further enhanced by low-pH treatment. Notably, the severely truncated mutants showed elevated levels of surface subunits in culture medium, suggesting that the CT truncations resulted in conformational changes in the ectodomain of Env that impaired surface subunit associations. Taken together, this study reveals for the first time that the fusion activity of the JSRV Env protein is dependent on a low pH and is modulated by the CT, whose truncation overcomes, at least partially, the low-pH requirement for fusion and enhances Env fusion activity and kinetics.
Magnetic Resonance Imaging Findings in the Evaluation of Traumatic Anosmia

Objectives: Head trauma is a common cause of anosmia, but diagnosis is typically late, owing to more life-threatening sequelae of the injury. Herein, we describe our workup for a case of traumatic anosmia and the magnetic resonance imaging (MRI) findings both at the time of injury and at the 18-month follow-up. Methods: We present a case report and a review of the literature. Results: A 33-year-old woman presented to our institution with a chief complaint of loss of smell and taste following an occipital blow to her head that occurred when she was hit by a car while riding a bicycle. We present the findings of MRI performed at the time of the injury and at the 18-month follow-up. We describe the clinical progression of her disease, from symptoms of parosmic and phantosmic episodes accompanied by dysgeusia to total anosmia at the 18-month follow-up. Conclusions: We advocate the use of MRI, coupled with otolaryngology consultation and formal olfactory testing, in the diagnosis, management, and counseling of patients with anosmia sustained from head injury.