Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of polyamines on the inhibition of peptidyltransferase by antibiotics: revisiting the mechanism of chloramphenicol action.

Chloramphenicol is thought to interfere competitively with the binding of the aminoacyl-tRNA 3'-terminus to ribosomal A-site. However, noncompetitive or mixed-noncompetitive inhibition, often observed to be dependent on chloramphenicol concentration and ionic conditions, leaves some doubt about the precise mode of action. Here, we examine further the inhibition effect of chloramphenicol, using a model system derived from Escherichia coli in which a peptide bond is formed between puromycin and AcPhe-tRNA bound at the P-site of poly(U)-programmed ribosomes, under ionic conditions (6 mM Mg2+, 100 mM NH4+, 100 microM spermine) more closely resembling the physiological status. Kinetics reveal that chloramphenicol (I) reacts rapidly with AcPhe-tRNA.poly(U). 70S ribosomal complex (C) to form the encounter complex CI which is then isomerized slowly to a more tight complex, C*I. A similar inhibition pattern is observed, if complex C modified by a photoreactive analogue of spermine, reacts in buffer free of spermine. Spermine, either reversibly interacting with or covalently attached to ribosomes, enhances the peptidyltransferase activity and increases the chloramphenicol potency, without affecting the isomerization step. As indicated by photoaffinity labeling, the peptidyltransferase center at which chloramphenicol binds, is one of the preferred cross-linking sites for polyamines. This fact may explain the effect of spermine on chloramphenicol binding to ribosomes.
DNA Diversification in Two Sinorhizobium Species

ABSTRACT The comparative analysis of genomic characteristics and single-nucleotide polymorphism patterns from large fragments borne on different replicons of Sinorhizobium spp. genomes clearly demonstrate that DNA recombination among closely related bacteria is a major event in the diversification of this genome, especially in pSymA, resulting in mosaic structure.
Antioxidant enzymes in intramolluscan Schistosoma mansoni and ROS-induced changes in expression

Killing of intramolluscan schistosomes by host haemocytes is mediated by reactive oxygen metabolites. Hence, defence against oxidative damage is essential for the parasite to survive. In this study, expression of three key antioxidant enzymes, superoxide dismutase (EC 1.15.1.1), glutathione peroxidase (EC 1.11.1.9) and glutathione-S-transferase (EC 2.5.1.18) was determined in Schistosoma mansoni miracidia, sporocysts and cercariae. Stage-dependent expression of these enzymes was shown to be regulated at the transcriptional level. Second, the influence on enzyme expression of reactive oxygen species (ROS) and of haemocytes from schistosome-resistant and -susceptible host snails was determined. Generation of ROS by xanthine/xanthine oxidase resulted in increased transcript levels for all three enzymes. Addition of hydrogen peroxide induced a significantly increased expression of GPx and SOD but not GST. Snail haemocytes induced an up-regulation of SOD and GPx at 12 and 18 h post-exposure, respectively. Susceptible haemocytes elicited a stronger induction of transcript expression than resistant haemocytes. After 36–48 h, SOD remained up-regulated in sporocysts encapsulated by haemocytes from susceptible hosts, whereas a down-regulation of SOD and GPx occurred in schistosomes encapsulated by haemocytes from resistant snails. These observations indicate that schistosomes express elevated levels of antioxidant enzymes in interaction with haemocytes from susceptible snail hosts in which they survive. On the other hand, haemocytes of resistant snails may interfere with reactive oxygen detoxification via down-regulation of schistosome antioxidant enzymes, thus shifting the balance towards parasite killing.
Performance evaluation of fingerprint verification systems

This paper is concerned with the performance evaluation of fingerprint verification systems. After an initial classification of biometric testing initiatives, we explore both the theoretical and practical issues related to performance evaluation by presenting the outcome of the recent fingerprint verification competition (FVC2004). FVC2004 was organized by the authors of this work for the purpose of assessing the state-of-the-art in this challenging pattern recognition application and making available a new common benchmark for an unambiguous comparison of fingerprint-based biometric systems. FVC2004 is an independent, strongly supervised evaluation performed at the evaluators' site on evaluators' hardware. This allowed the test to be completely controlled and the computation times of different algorithms to be fairly compared. The experience and feedback received from previous, similar competitions (FVC2000 and FVC2002) allowed us to improve the organization and methodology of FVC2004 and to capture the attention of a significantly higher number of academic and commercial organizations (67 algorithms were submitted for FVC2004). A new, "light" competition category was included to estimate the loss of matching performance caused by imposing computational constraints. This paper discusses data collection and testing protocols, and includes a detailed analysis of the results. We introduce a simple but effective method for comparing algorithms at the score level, allowing us to isolate difficult cases (images) and to study error correlations and algorithm "fusion. " The huge amount of information obtained, including a structured classification of the submitted algorithms on the basis of their features, makes it possible to better understand how current fingerprint recognition systems work and to delineate useful research directions for the future.
A model of tutoring: facilitating knowledge integration using multiple models of the domain

This thesis describes a model of tutoring. This model is intended for CIRCSIM-Tutor (v.3)--an Intelligent Tutoring System (ITS)--that teaches the functioning of the baroreceptor reflex to the first year medical students. This model is based on the behavior of human tutors in the keyboard-to-keyboard sessions. The major theme of this model is that, in a problem-solving environment, it helps the student integrate his/her knowledge into a coherent qualitative causal model of the domain and solve problems in the domain. The key feature of this model is that it uses multiple qualitative models of the domain in the process of facilitating knowledge integration. The development of this model of tutoring has been approached by using an ITS development framework that views the development of an ITS as a modeling activity. There are three major phases of this methodology. These are the conceptual phase, the system phase, and physical phase. At each phase a different model of an ITS results. The conceptual model, resulting out of the conceptual phase, deals in this research only with the domain and the pedagogy aspects of tutoring. The domain knowledge here consists of multiple qualitative models that are used to support decision making. This decision making process considers three major functions: what to teach, when to teach, and how to teach. The system model, resulting out of the system phase, provides a generic framework to represent three different types of knowledge. These are the planning knowledge, the curriculum knowledge, and the domain knowledge. The system model can also be viewed as consisting of a set of tutoring spaces. Each space is responsible for performing one type of major decision of the tutor while interacting with the student. The second model resulting out of the system phase is the architecture of the system. Here an object-oriented methodology is used to develop some of the major components of this architecture. These architectural components are coded using the Common Lisp Object System on the Apple Macintosh.
Magnetic helicity fluxes in an α 2 dynamo embedded in a halo

We present the results of simulations of forced turbulence in a slab where the mean kinetic helicity has a maximum near the mid-plane, generating gradients of magnetic helicity of both large and small-scale fields. We also study systems that have poorly conducting buffer zones away from the midplane in order to assess the effects of boundaries. The dynamical α quenching phenomenology requires that the magnetic helicity in the small-scale fields approaches a nearly static, gauge independent state. To stress-test this steady state condition we choose a system with a uniform sign of kinetic helicity, so that the total magnetic helicity can reach a steady state value only through fluxes through the boundary, which are themselves suppressed by the velocity boundary conditions. Even with such a set up, the small-scale magnetic helicity is found to reach a steady state. In agreement with the earlier work, the magnetic helicity fluxes of small-scale fields are found to be turbulently diffusive. By comparing results with and without halos, we show that artificial constraints on magnetic helicity at the boundary do not have a significant impact on the evolution of the magnetic helicity, except that “softer” (halo) boundary conditions give a lower energy of the saturated mean magnetic field.
Intratumoral CD3+ T-Lymphocytes Immunoexpression and Its Association with c-Kit, Angiogenesis, and Overall Survival in Malignant Canine Mammary Tumors

In this study 80 malignant CMT were submitted to immunohistochemical detection of CD3, c-kit, VEGF, and CD31, together with clinicopathological parameters of tumor aggressiveness. CD3+ T-cells and c-kit overexpression revealed a positive correlation with VEGF (r = 0.503, P < 0.0001; r = 0.284, P = 0.023 for CD3 and c-kit, resp.) and CD31 (r = 0.654, P < 0.0001; r = 0.365, P = 0.003 for CD3 and c-kit, resp.). A significant association (P = 0.039) and a positive correlation (r = 0.263, P = 0.039) between CD3 and c-kit were also observed. High CD3/VEGF, c-kit/VEGF, and CD3/c-kit tumors were associated with elevated grade of malignancy (P < 0.0001 for all groups), presence of intravascular emboli (P < 0.0001 for CD3/VEGF and CD3/c-kit; P = 0.002 for c-kit/VEGF), and presence of lymph node metastasis (P < 0.0001 for all groups). Tumors with high CD3/VEGF (P = 0.006), c-kit/VEGF (P < 0.0001), and CD3/c-kit (P = 0.002) were associated with poor prognosis. Interestingly high c-kit/VEGF tumors retained their significance by multivariate analysis arising as independent prognostic factor.
Quantitative thyroglobulin response to radioactive iodine treatment in predicting radioactive iodine-refractory thyroid cancer with pulmonary metastasis

Objective Current diagnosis of radioactive iodine (RAI)-refractory (RAIR) differentiated thyroid cancer (DTC) is based on the imaging technique, which is of a high cost. Serum thyroglobulin (Tg) is a sensitive and easily obtained biomarker. Hence, we aimed to assess the predicting value of quantitative response of Tg in earlier identifying the RAIR-DTC with pulmonary metastasis. Patients and methods Pulmonary metastatic DTC patients who underwent total or near-total thyroidectomy and at least two times of RAI therapy were included in this study. The pre-ablative stimulated Tg at the first and second RAI therapy were defined as pstim-Tg1 and pstim-Tg2, while the suppressed Tg before and after the second RAI therapy were designated sup-Tg1 and sup-Tg2. The predicted value of pstim-Tg2/Tg1 and sup-Tg2/Tg1 ratio were detected using the receiver operating characteristic (ROC) curve and logistic regression analyses. Results Totally 115 patients were involved in this study. ROC curves showed a cut-off value of 0.544 for pstim-Tg2/ pstim-Tg1 in detecting RAIR, with a sensitivity of 0.9 and specificity of 0.477, and an area under the curve (AUC) of 0.744. Similarly, the cut-off of sup-Tg2/ sup-Tg1 was 0.972, with a sensitivity of 0.733 and specificity of 0.935, and AUC of 0.898. Univariate analysis illustrated that age, tumor size, pstim-Tg2/Tg1, sup-Tg2/ sup-Tg1 and BRAFV600E mutation were eligible to predict RAIR. While from multivariate analysis, only age, pstim-Tg2/Tg1, sup-Tg2/ sup-Tg1 and BRAFV600E mutation were verified to be the independent predictive factors. Conclusion The quantitative Tg response was encouraging in identifying RAIR-DTC with pulmonary metastasis. Age, BRAFV600E mutation and Tg response were independent predictors in predicting RAIR-DTC.
The molecular basis of myelodysplastic syndromes.

BACKGROUND AND OBJECTIVE The myelodysplastic syndromes comprise a heterogeneous group of neoplastic disorders characterized by ineffective hematopoiesis with an increased tendency to evolve to acute leukemia. Clinically, the common manifestations include peripheral blood cytopenias of one or more lineages and a normal to hyperplastic marrow. MDS has been defined on the basis of morphological criteria, namely the percentage of blast cells in the bone marrow, by the French-American-British study group. Scoring systems have been developed to include such factors as hemoglobin, leukocyte count and age in the evaluation of MDS prognosis. Although useful in the prediction of clinical course and design of therapy regimens, our understanding of the basis of MDS has come from recent advances in molecular analysis of these disorders. This review describes some of the established and recent contributions to our understanding of the molecular basis of the myelodysplastic syndromes. EVIDENCE AND INFORMATION SOURCES The authors of the present review have been working in the field of myelodysplastic syndromes for several years and have contributed original papers on the molecular pathogenesis of these disorders. In addition, in the present review they have critically examined articles and abstracts published in journals covered by the Science Citation Index and Medline. STATE OF ART AND PERSPECTIVES Cytogenetic anomalies and proto-oncogene abnormalities point to new understanding of the pathogenesis of MDS as a sequence of DNA lesions leading to the evolution of the pre-malignant clone. The prognostic significance of these factors in predicting leukemic transformation and survival remains controversial. Characterization of MDS cells in vitro in response to combinations of exogenous growth factors have not only provided valuable information regarding ineffective hematopoiesis in MDS but have provided a new insight into treatment of MDS. One major development in our understanding of MDS is the possible explanation for the apparent paradox of a cellular marrow in combination with peripheral cytopenias. Extensive premature programmed cell death or apoptosis has been reported to be at least partly responsible. It will remain to be seen whether this fundamental characteristic of myelodysplastic hematopoiesis will play a central role in the drug or genetic based therapy in the myelodysplastic syndromes.
Anti-inflammatory effect of prophylactic macrolides on children with chronic lung disease: a protocol for a double-blinded randomised controlled trial

Introduction Recent studies suggest that the high mortality rate of respiratory viral infections is a result of an overactive neutrophilic inflammatory response. Macrolides have anti-inflammatory properties, including the ability to downregulate the inflammatory cascade, attenuate excessive cytokine production in viral infections, and may reduce virus-related exacerbations. In this study, we will test the hypothesis that prophylactic macrolides will reduce the severity of respiratory viral illness in children with chronic lung disease by preventing the full activation of the inflammatory cascade. Methods and analysis A randomised double-blind placebo-controlled trial that will enrol 92 children to receive either azithromycin or placebo for a period of 3–6 months during two respiratory syncytial virus (RSV) seasons (2015–2016 and 2016–2017). We expect a reduction of at least 20% in the total number of days of unscheduled face-to-face encounters in the treatment group as compared with placebo group. Standard frequentist and Bayesian analyses will be performed using an intent-to-treat approach. Discussion We predict that the prophylactic use of azithromycin will reduce the morbidity associated with respiratory viral infections during the winter season in patients with chronic lung disease as evidenced by a reduction in the total number of days with unscheduled face-to-face provider encounters. Ethics and dissemination This research study was approved by the Institutional Review Board of the University of Texas Health Science Center in Houston on 9 October 2014. On completion, the results will be published. Trial registration number NCT02544984.
Higher Toda Mechanics and Spectral Curves

For each of the Lie algebras and , we construct a family of integrable generalizations of the Toda chains characterized by two integers and . The Lax matrices and the equations of motion are given explicitly, and the integrals of motion can be calculated in terms of the trace of powers of the Lax matrix L. For the case of , we find a symmetric reduction for each generalized Toda chain we found, and the solution to the initial value problems of the reduced systems is outlined. We also studied the spectral curves of the periodic -Toda chains, which turns out to be very different for different pairs of and . Finally we also obtain the nonabelian generalizations of the -Toda chains in an explicit form.
Drug eluting coronary stent: in vitro evaluation of magnet resonance safety at 3 Tesla.

PURPOSE To evaluate MR safety at 3 Tesla for a drug eluting coronary stent. METHODS A drug eluting coronary stent (Endeavor, cobalt alloy, Medtronic Vascular, Santa Rosa, CA) was evaluated for magnetic field interactions, heating, and artifacts at 3 Tesla. MRI-related heating was assessed with the stent in a gelled saline-filled phantom using a transmit/received RF body coil with a whole body averaged SAR of 2.0 W/kg. Artifacts were characterized using T1-weighted, spin echo, and gradient echo pulse sequences. RESULTS The stent exhibited minor magnetic field interactions that will not cause migration. Heating was not substantial (+0.5 degrees C). Artifacts may create a problem if the area of interest is in the same area or close to the stent (e.g., for a T1-weighted, spin echo pulse sequence, within approximately 16 mm; for a gradient echo pulse sequence, within approximately 23 mm). Conclusion. The findings indicated that it would be safe for a patient with this cobalt alloy-based, drug-eluting coronary stent to undergo MRI at 3 Tesla or less. Importantly, because of the relative lack of magnetic field interactions, MRI may be performed immediately after implantation.
Error Rates of the Maximum-Likelihood Detector for Arbitrary Constellations: Convex/Concave Behavior and Applications

Motivated by a recent surge of interest in convex optimization techniques, convexity/concavity properties of error rates of the maximum likelihood detector operating in the AWGN channel are studied and extended to frequency-flat slow-fading channels. Generic conditions are identified under which the symbol error rate (SER) is convex/concave for arbitrary multidimensional constellations. In particular, the SER is convex in SNR for any one- and two-dimensional constellation, and also in higher dimensions at high SNR. Pairwise error probability and bit error rate are shown to be convex at high SNR, for arbitrary constellations and bit mapping. Universal bounds for the SER first and second derivatives are obtained, which hold for arbitrary constellations and are tight for some of them. Applications of the results are discussed, which include optimum power allocation in spatial multiplexing systems, optimum power/time sharing to decrease or increase (jamming problem) error rate, an implication for fading channels (¿fading is never good in low dimensions¿) and optimization of a unitary-precoded OFDM system. For example, the error rate bounds of a unitary-precoded OFDM system with QPSK modulation, which reveal the best and worst precoding, are extended to arbitrary constellations, which may also include coding. The reported results also apply to the interference channel under Gaussian approximation, to the bit error rate when it can be expressed or approximated as a nonnegative linear combination of individual symbol error rates, and to coded systems.
Testing the generality of above‐ground biomass allometry across plant functional types at the continent scale

Accurate ground‐based estimation of the carbon stored in terrestrial ecosystems is critical to quantifying the global carbon budget. Allometric models provide cost‐effective methods for biomass prediction. But do such models vary with ecoregion or plant functional type? We compiled 15 054 measurements of individual tree or shrub biomass from across Australia to examine the generality of allometric models for above‐ground biomass prediction. This provided a robust case study because Australia includes ecoregions ranging from arid shrublands to tropical rainforests, and has a rich history of biomass research, particularly in planted forests. Regardless of ecoregion, for five broad categories of plant functional type (shrubs; multistemmed trees; trees of the genus Eucalyptus and closely related genera; other trees of high wood density; and other trees of low wood density), relationships between biomass and stem diameter were generic. Simple power‐law models explained 84–95% of the variation in biomass, with little improvement in model performance when other plant variables (height, bole wood density), or site characteristics (climate, age, management) were included. Predictions of stand‐based biomass from allometric models of varying levels of generalization (species‐specific, plant functional type) were validated using whole‐plot harvest data from 17 contrasting stands (range: 9–356 Mg ha−1). Losses in efficiency of prediction were <1% if generalized models were used in place of species‐specific models. Furthermore, application of generalized multispecies models did not introduce significant bias in biomass prediction in 92% of the 53 species tested. Further, overall efficiency of stand‐level biomass prediction was 99%, with a mean absolute prediction error of only 13%. Hence, for cost‐effective prediction of biomass across a wide range of stands, we recommend use of generic allometric models based on plant functional types. Development of new species‐specific models is only warranted when gains in accuracy of stand‐based predictions are relatively high (e.g. high‐value monocultures).
Food for thought: an analysis of power and identity in prison food narratives

The consumption of food is one of the principal concerns within institutional environments such as prisons. This is because it is necessary to feed people, but also because, as humans, we have a symbolic relationship to food. Therefore, inside of prison, food is an excellent means through which expressions of power can be made. The aim of this article is to examine prisoners' stories about how food and food-related rituals were used by institutional authorities to manage and control the lives of prisoners. This analysis of prisoners' food narratives provides insight into how, in a total institution, the loss of control over the consumptive process is a key aspect of transforming individuals into inmates by creating a sense of estrangement between one's self and one's body.