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Agmatine, 1-Amino-4-guanidinobutane, is a ubiquitous naturally occurring molecule present in low amounts in a wide variety of foodstuff. Clinical trials have demonstrated the safety of oral agmatine sulfate and have led to its development as an effective dietary ingredient for promoting resilient nerve functions. Although clearly required, the mutagenic and genotoxic effects of agmatine have not been previously reported. The present study, therefore, undertook to assess the safety profile of agmatine using currently accepted in vitro and in vivo mutagenicity and genotoxicity tests. The test item was G-Agmatine®, a proprietary brand of agmatine sulfate. Using the bacterial reverse mutation assay (Ames test), the study found that G-Agmatine® has no mutagenic effects. It had no clastogenic effects as observed by the in vitro chromosomal aberration test using Chinese Hamster lung cells. And it lacked genotoxic effects as evidenced by the lack of increased frequency of micronucleated polychromatic immature erythrocytes following oral administration in the mouse micronucleus test. Taken together with previously published data, results of the present study further support the safety of agmatine sulfate as a dietary ingredient.
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Ecological and environmental problems resulting from fossil fuels are due to the harmful emissions released into the atmosphere. The rising interest in searching for alternative fuels like biodiesel is growing to solve these problems. Waste cooking oil (WCO) is transformed into methyl ester and combined with biodiesel in percentages of 25, 50, 75, and 100%. Research is done on the impacts of methyl ester blends on engine performance and emissions. Compared to diesel, the methyl ester combination showed 25% lower brake power and 24% loss in thermal efficiency at maximum load and 1500 rpm. However, diesel fuel showed 23% lower specific fuel consumption increase than biodiesel. Compared to diesel, methyl ester exhibits 15% lower air-fuel ratio and 4% volumetric efficiency. Biodiesel lowers CO, HC, and smoke concentrations by 12, 44, and 48%, respectively, compared to diesel. Biodiesel emits 23% higher NOx at 1500 rpm and 100% engine load. To predict the emissions and performance of different percentages of biodiesel at engine speed variation, an artificial neural network (ANN) model is presented. ANN modeling minimizes labor, time, and finances and uses nonlinear data. Predictions were produced about the brake output power, specific fuel consumption, thermal efficiency, air-fuel ratio, volumetric efficiency, and emissions of smoke, CO, HC, and NOx as a function of engine speed and blend ratio. All correlation coefficients (r) over 0.99 and R 2 values were beyond 0.98 for all variables. There were low values of MSE, MAPE, and MSLE with significant predictive ability. WCO's biodiesel is a viable diesel engine replacement fuel.
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The use of nano additives to improve the cold properties of biodiesel is encouraged by its drawbacks and incompatibility in cold climate. Waste cooking oil (WCO) was transesterified to create biodiesel. A 20% by volume was used for combination of diesel and methyl ester. Current study aims to evaluate diesel engine emissions and performance. TiO2, alumina, and hybrid TiO2 + Al2O3 nanoparticles are added to WCO biodiesel mixture at 25 mg/liter. When B20 combined with nano materials such as TiO2, Al2O3, and hybrid nano, the highest declines in brake specific fuel consumption were 4, 6, and 11%, respectively. As compared to biodiesel blend, the largest gains in thermal efficiency were 4.5, 6.5, and 12.5%, respectively, at maximum engine output power. Introduction of TiO2, Al2O3, and hybrid nano particles to B20 at 100% load resulted in the highest decreases in HC concentrations up to 7, 13, and 20%, and the biggest reductions in CO emissions, up to 6, 12, and 16%. Largest increases in NOx concentrations at full load were about 7, 15, and 23% for B20 + 25TiO2, B20 + 25 Al2O3, and B20 + 25TiO2 + 25 Al2O3, respectively. Up to 8, 15, and 21% less smoke was released, correspondingly, which were the largest reductions. Recommended dosage of 25 ppm alumina and 25 ppm TiO2 achieved noticeable improvements in diesel engine performance, combustion and emissions about B20.
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INTRODUCTION: Prosthetic complications that occur to some implant prosthetics may require removal of the prosthesis for replacement or repair. Therefore, the presence of a technique to identify the type of dental implant is mandatory to provide the suitable components. Hence, the aim of the current study was to evaluate the accuracy of YOLOv8 object detection algorithm in automatic identification of the type of dental implant from digital periapical radiographs. METHODS: YOLOv8m-seg object detection algorithm was used to build a model to automatically identify the type of dental implant. A set of 2573 digital periapical radiographs for six distinct dental implants manufacturers were used to train the model. The outcomes were evaluated using precision, recall, F1 score and mAP. RESULTS: The overall accuracy of the YOLOv8m-seg model in terms of precision, recall, F1 score and mAP revealed values of 0.919, 0.98, 0.95 and 0.972 respectively. The average detection speed of the images was 1.3 seconds. The model was able to detect and identify multiple implants simultaneously on the same image. CONCLUSIONS: YOLOv8m-seg object detection algorithm is promising in identification of dental implants from periapical radiographs with high detection accuracy (97.2%), fast detection results and multi-implant detection from the same image. CLINICAL SIGNIFICANCE: This AI system can accurately identify the type of osseointegrated dental implants enabling dentists to provide the appropriate prosthetic components even if different implant systems are used within the same patient. This can save tremendous amounts of time, effort and cost for both the dentist and the patient.
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Increasing of energy consumption, depletion of petroleum fuels and harmful emissions have triggered the interest to find substitute fuels for diesel engines. Palm ethyl ester was synthesized from palm oil through transesterification process. The physicochemical properties of palm biodiesel have been measured and confirmed in accordance with ASTM standards. The aim of the paper is to show the effect of different diesel-palm biodiesel blends on performance, combustion and emissions in diesel engine at engine load variation. Artificial Neural Network was used for the prediction of engine performance, exhaust emission and combustion characteristics parameters. Palm ethyl ester and diesel oil were blended in 5, 10, 15 and 20 by volume percentage. The maximum decreases in thermal efficiency, fuel-air equivalence ratio for B20 were 1.5, 3.5, 6 and 8% but the maximum increases in BSFC, exhaust gas temperature and NOx emission for B20 at full load about diesel fuel were 9, 8 and 10%, respectively. The highest decreases in CO, HC and smoke emissions of B20 about diesel oil at full load were 2, 35 and 18.5% at full load, respectively. Biodiesel blend B20 achieved the maximum declines in peak HRR, cylinder temperature and combustion duration about diesel fuel. The results of ANN were compared with experimental results and showed that ANN is effective modeling method with high accuracy. Palm biodiesel blends up to 20% showed the highest enhancements in engine performance, combustion and emission reductions compared to diesel fuel.
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Biocombustíveis , Gasolina , Ésteres , Redes Neurais de Computação , Emissões de VeículosRESUMO
Peripheral neuropathies associated with painful small fiber neuropathy (SFN) are complex conditions, resistant to treatment with conventional medications. Previous clinical studies strongly support the use of dietary agmatine as a safe and effective treatment for neuropathic pain. Based on this evidence, we conducted an open-label consecutive case series study to evaluate the effectiveness of agmatine in neuropathies associated with painful SFN (Study Registry: ClinicalTrials.gov, System Identifier: NCT01524666). Participants diagnosed with painful SFN and autonomic dysfunctions were treated with 2.67 g/day agmatine sulfate (AgmaSet® capsules containing G-Agmatine® brand of agmatine sulfate) for a period of 2 months. Before the beginning (baseline) and at the end of the treatment period, participants answered the established 12-item neuropathic pain questionnaire specifically developed to distinguish symptoms associated with neuropathy and to quantify their severity. Secondary outcomes included other treatment options and a safety assessment. Twelve patients were recruited, and 11 patients-8 diagnosed with diabetic neuropathy, two with idiopathic neuropathy and one with inflammatory neuropathy-completed the study. All patients showed improvement in neuropathic pain to a varied extent. The average decrease in pain intensity was 26.0 rating points, corresponding to a 46.4% reduction in overall pain (p < 0.00001). The results suggest that dietary agmatine sulfate has a significant effect in reducing neuropathic pain intensity associated with painful SFN resistant to treatment with conventional neuropathic pain medications. Larger randomized placebo-controlled studies are expected to establish agmatine sulfate as a preferred treatment.
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Agmatina/uso terapêutico , Dieta , Neuralgia/tratamento farmacológico , Neuropatia de Pequenas Fibras/tratamento farmacológico , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Medição da Dor , Projetos Piloto , Inquéritos e QuestionáriosRESUMO
With the rise of e-cigarette use, teen nicotine exposure is becoming more widespread. Findings from clinical and preclinical studies show that the adolescent brain is particularly sensitive to nicotine. Animal studies have demonstrated that adolescent nicotine exposure increases reinforcement for cocaine and other drugs. However, the mechanisms that underlie these behaviors are poorly understood. Here, we report reactive microglia are critical regulators of nicotine-induced increases in adolescent cocaine self-administration. Nicotine has dichotomous, age-dependent effects on microglial morphology and immune transcript profiles. A multistep signaling mechanism involving D2 receptors and CX3CL1 mediates nicotine-induced increases in cocaine self-administration and microglial activation. Moreover, nicotine depletes presynaptic markers in a manner that is microglia-, D2- and CX3CL1-dependent. Taken together, we demonstrate that adolescent microglia are uniquely susceptible to perturbations by nicotine, necessary for nicotine-induced increases in cocaine-seeking, and that D2 receptors and CX3CL1 play a mechanistic role in these phenomena.
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Cocaína/farmacologia , Comportamento de Procura de Droga/efeitos dos fármacos , Microglia/efeitos dos fármacos , Microglia/metabolismo , Nicotina/farmacologia , Aminopiridinas/farmacologia , Animais , Quimiocina CX3CL1/metabolismo , Modelos Animais de Doenças , Sistemas Eletrônicos de Liberação de Nicotina , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Masculino , Minociclina/farmacologia , Fenótipo , Pirróis/farmacologia , Ratos , Ratos Sprague-Dawley , Receptores de Dopamina D2/efeitos dos fármacos , Reforço Psicológico , Recompensa , Autoadministração , SinaptofisinaRESUMO
Despite historically known as "junk" DNA, nowadays non-coding RNA transcripts (ncRNAs) are considered as fundamental players in various physiological and pathological conditions. Nonetheless, any alteration in their expression level has been reported to be directly associated with the incidence and aggressiveness of several diseases. MicroRNAs (miRNAs) are the well-studied members of the ncRNAs family. Several reports have highlighted their crucial roles in the post-transcriptional manipulation of several signaling pathways in different pathological conditions. In this review, our main focus is the multifaceted microRNA-486 (miR-486). miR-486-5p and miR-486-3p have been reported to have central roles in several types oncological and non-oncological conditions such as lung, liver, breast cancers and autism, intervertebral disc degeneration and metabolic syndrome, respectively. Moreover, we spotted the light onto the pleiotropic role of miR-486-5p in acting as competing endogenous RNA with other members of ncRNAs family such as long non-coding RNAs.
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Major hemodynamic changes are frequently noted during liver transplantation (LT). We evaluated the performance of electrical velocimetry (EV) as compared to that of TEE in SV optimization during liver transplantation. This was an observational study in 32 patients undergoing LT. We compared SV values measured simultaneously by EV (SVEV) and TEE (SVTEE) at baseline 30 min after induction, at the end of dissection phase, 30 min after anhepatic phase, 30 min after reperfusion. We also evaluated the reliability of EV to track changes In SV before and after 49 fluid challenges. Finally, the SV variation (SVV) and pulse pressure variation (PPV) were tested as predictors for volume responsiveness, defined as an increase in SV ≥ 10% after 250 ml of colloid. For 112 paired SV data, the overall correlation was 0.76 and bias (limits of agreement) 0.3 (- 29 to 29) ml percentage error 62%. The EV was able to track changes in SV with a concordance rate of 97%, and a sensitivity and specificity of 93% to detect a positive fluid challenge. The AUC values (with 95% confidence intervals) for SVV and PPV were 0.68 (0.52-0.83) and 0.72 (0.57-0.86), respectively, indicating low predictive capacity in these setting. The absolute values of SV derived from EV did not agree with SV derived from TEE. However, EV was able to track the direction of changes in SV during hemodynamic management of patients undergoing liver transplantation.Clinical trial registration: Clinicaltrials.gov Identifier: NCT03228329 prospectively Registered on 13-July-2017.
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Monitorização Hemodinâmica/métodos , Transplante de Fígado , Monitorização Intraoperatória/métodos , Ressuscitação , Reologia/métodos , Adulto , Cardiografia de Impedância/métodos , Cardiografia de Impedância/estatística & dados numéricos , Ecocardiografia Transesofagiana , Feminino , Hidratação , Monitorização Hemodinâmica/estatística & dados numéricos , Humanos , Masculino , Pessoa de Meia-Idade , Monitorização Intraoperatória/estatística & dados numéricos , Estudos Prospectivos , Reologia/estatística & dados numéricos , Volume SistólicoRESUMO
OBJECTIVES: Quantitative assessment of 3-dimensional progressive changes of the maxillary geometry in unilateral cleft lip palate (UCLP) with and without nasoalveolar molding (NAM). METHODS: The study was designed as a prospective 2-arm randomized controlled clinical trial conducted in parallel. Forty infants with nonsyndromic UCLP were randomly assigned into a NAM-treated group (n = 20) and non-NAM treated group (n = 20). A total of 120 laser-scanned maxillary casts were collected and blindly analyzed via a modified algorithm at T0 (initial visit; baseline), T1 (after 3 wk; first interval), and T2 (after 6 wk; second interval). The main outcome measures were the amount and rate of cleft gap changes, the midline position, and the transverse, sagittal, and vertical growth through intervals. RESULTS: More than 50% of the cleft gap (56.42%; P < 0.001) was reduced in the first 3 wk of alveolar molding (AM). The end point of the AM was obtained in 6 wk (86.25%; P < 0.001); then, the kinks of the greater segment were noticed. The AM effect decreased as far as posterior; the anterior arch width reduced slightly (1.23%; P < 0.001), while the middle and posterior arches increased slightly (P > 0.999 and P = 0.288, respectively). The posterior arch width was the least changing and was considered a baseline, while the anterior was the pivot of the segment rotation. Both groups showed different patterns of segment rotation and sagittal growth. The non-NAM treated group showed a slight increase in cleft gap length, arch width, and midline position. CONCLUSION: Based on this study, it was concluded that the NAM treatment is effective in minimizing cleft severity and realigning maxillary segments without the deterioration of the transverse and vertical arch growth. Near follow-up visits are recommended to monitor the rapid gap reduction within the first 3 wk. Further trials are recommended to compare the outcomes regarding the sagittal growth to reference values (ClinicalTrials.gov NCT03029195). KNOWLEDGE TRANSFER STATEMENT: The results of this study will help clinicians understand nasoalveolar molding biomechanics that may improve the treatment outcomes for patients with unilateral cleft lip and palate. The trial data can be a valuable guide to the qualitative and quantitative predictive virtual molding in computer aided design-simulated nasoalveolar molding therapy. The modified algorithm can be used by researchers to quantify the rate, the sequence, and the direction of the maxillary segments movement in unilateral cleft lip and palate.
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Fenda Labial , Fissura Palatina , Processo Alveolar , Fenda Labial/terapia , Fissura Palatina/terapia , Humanos , Moldagem Nasoalveolar , Nariz , Estudos ProspectivosRESUMO
Background: Pain from coxofemoral joint (CFJ) osteoarthritis (OA) characteristic of canine hip dysplasia (CHD) afflicts many dogs. Intervertebral disc (IVD) degeneration is a common CFJ OA comorbidity. Non-steroidal anti-inflammatory drug (NSAID) administration is standard for treatment of pain from degenerative joint disease. Potential side effects and tolerance from prolonged administration drive efforts to identify compounds that may be alternatives to or combined with NSAIDs. Agmatine, decarboxylated arginine, reportedly alleviates neuropathic pain, a likely component of OA pain. The objective of this study was to compare treatment response to agmatine and carprofen in dogs with varying degrees of CFJ OA with or without IVD degeneration and to test the hypothesis that agmatine improves hindlimb use comparably to carprofen and more than placebo. Methods: Nine hound-type dogs received oral carprofen (4.4 mg/kg, sid) for 7 days. Six months later, oral agmatine sulfate (25 mg/kg, bid) or placebo (hydroxypropyl methylcellulose, bid) was administered to the same dogs for 28 days with a 2 week washout period between treatments. Validated pain assessment scores were measured before treatment and every seven days throughout the treatment periods. Serum chemistry levels and ground reaction forces (GRF) were quantified before and after each treatment period. A board-certified radiologist quantified radiographic CFJ OA based on Orthopedic Foundation for Animals criteria and IVD degeneration on magnetic resonance images. GRFs were compared among treatments at each time point and among time points for each treatment. Results: There were no detectable adverse effects with any treatment. Significant results included improved GRFs in dogs with mild CFJ OA (N = 3) following agmatine administration compared to carprofen or placebo and a trend for improved GRFs in dogs with moderate CFJ OA (N = 2) following carprofen vs. agmatine or placebo. Neither agmatine nor carprofen improved GRFs in dogs with severe CFJ OA (N = 4). The GRFs improved in dogs with IVD degeneration (N = 3) following carprofen treatment compared to agmatine or placebo regardless of CFJ OA score, but no effect was observed in dogs with normal lumbar spines (N = 6). Conclusions: Results support agmatine over carprofen treatment to improve limb use in dogs with early or mild CFJ OA, while carprofen may be the better choice for dogs with moderate CFJ OA or IVD degeneration regardless of CFJ OA severity.
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Regulatory CD4+ T cells (Tregs) are pivotal for prevention of autoimmunity. The use of Tregs is therefore of increasing interest in in vitro drug screening assays as well as for a cytotherapy per se against autoimmune disorders. For both purposes, in vitro expansion of peripheral blood Tregs is necessary and there is an increasing need to identify novel markers that can discriminate natural thymic-derived Tregs (tTregs) from other T cell subsets, and ideally, such markers should be stably expressed during in vitro expansion procedures. We screened for novel miRNAs differentially expressed in tTregs and identified miR-146a and 142-3p as possible candidates. We analysed freshly isolated naïve and activated tTregs and non-Treg subsets after or prior to in vitro expansion. We observed a tTreg-specific profile of these miRNAs together with FOXP3 and Helios in freshly isolated tTregs, but observed a decline in the same markers in activated tTregs as opposed to naïve tTregs. In vitro-expanded Tregs could be identified based on FOXP3 expression, but with loss of a discriminate profile for miRNA candidates and a decline in FOXP3 when activated tTregs were expanded. Our data demonstrate miR-146a and 142-3p as potential miRNA markers for discrimination between non-Treg cells and tTregs, but these miRNAs are not stable markers for in vitro-expanded Treg cells. In addition, the loss of FOXP3 in expansion of activated tTregs has implication for in vitro use of this cell subset in immunopharmacological assays and cytotherapy as FOXP3 is pivotal for suppressive function.
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Proliferação de Células/genética , MicroRNAs/genética , Linfócitos T Reguladores/metabolismo , Biomarcadores/metabolismo , Células Cultivadas , Citometria de Fluxo , Fatores de Transcrição Forkhead/genética , Fatores de Transcrição Forkhead/metabolismo , Perfilação da Expressão Gênica/métodos , Humanos , Fator de Transcrição Ikaros/genética , Fator de Transcrição Ikaros/metabolismo , Ativação Linfocitária/genética , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Linfócitos T Reguladores/citologiaRESUMO
The purpose of this study was to investigate the influence of a 6-week proprioceptive neuromuscular facilitation (PNF) stretching training program on the various parameters of the human gastrocnemius medialis muscle and the Achilles tendon. Therefore, 49 volunteers were randomly assigned into PNF stretching and control groups. Before and after the stretching intervention, we determined the maximum dorsiflexion range of motion (RoM) with the corresponding fascicle length and pennation angle. Passive resistive torque (PRT) and maximum voluntary contraction (MVC) of the musculo-articular complex were measured with a dynamometer. Muscle-tendon junction (MTJ) displacement allowed us to determine the length changes in tendon and muscle, and hence to calculate stiffness. Mean RoM increased from 31.1 ± 7.2° to 33.1 ± 7.2° (P = 0.02), stiffness of the tendon decreased significantly in both active (from 21.1 ± 8.0 to 18.1 ± 5.5 N/mm) and passive (from 12.1 ± 4.9 to 9.6 ± 3.2 N/mm) conditions, and the pennation angle increased from 18.5 ± 1.8° to 19.5 ± 2.1° (P = 0.01) at the neutral ankle position (90°), only in the intervention group, whereas MVC and PRT values remained unchanged. We conclude that a 6-week PNF stretching training program increases RoM and decreases tendon stiffness, despite no change in PRT.
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Tendão do Calcâneo/fisiologia , Articulação do Tornozelo/fisiologia , Exercícios de Alongamento Muscular/métodos , Músculo Esquelético/fisiologia , Amplitude de Movimento Articular/fisiologia , Adulto , Feminino , Humanos , Masculino , Contração Muscular/fisiologia , Força Muscular/fisiologia , Dinamômetro de Força Muscular , Torque , Adulto JovemRESUMO
There is presently a great interest in the therapeutic potential of agmatine, decarboxylated arginine, for various diseases. Recent clinical studies have already shown that oral agmatine sulfate given for up to 3 weeks provides a safe and, as compared with current therapeutics, more effective treatment for neuropathic pain. These studies have ushered in the use of dietary agmatine as a nutraceutical. However, in view of information paucity, assessment of long-term safety of oral agmatine treatment is now clearly required. The authors of this report undertook to assess their own health status during ongoing consumption of a high daily dosage of oral agmatine over a period of 4-5 years. A daily dose of 2.67 g agmatine sulfate was encapsulated in gelatin capsules; the regimen consists of six capsules daily, each containing 445 mg, three in the morning and three in the evening after meals. Clinical follow-up consists of periodic physical examinations and laboratory blood and urine analyses. All measurements thus far remain within normal values and good general health status is sustained throughout the study period, up to 5 years. This case study shows for the first time that the recommended high dosage of agmatine may be consumed for at least 5 years without evidence of any adverse effects. These initial findings are highly important as they provide significant evidence for the extended long-term safety of a high daily dosage of dietary agmatine--a cardinal advantage for its utility as a nutraceutical.
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Agmatina/efeitos adversos , Suplementos Nutricionais/efeitos adversos , Segurança , Administração Oral , Agmatina/administração & dosagem , Agmatina/uso terapêutico , Dieta , Feminino , Nível de Saúde , Humanos , Masculino , Pessoa de Meia-Idade , Neuralgia/tratamento farmacológico , Fatores de TempoRESUMO
In this paper, we provide an O(n log(2) n log log n log* n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. The motivation of this problem stems from computational biology, in particular, from analysis of complex gene clusters. The problem is also related to computing edit distance with block operations, but, in our scenario, the start of the history is not fixed, but chosen to minimize the distance measure.
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BACKGROUND: Identifying sequence-structure motifs common to two RNAs can speed up the comparison of structural RNAs substantially. The core algorithm of the existent approach ExpaRNA solves this problem for a priori known input structures. However, such structures are rarely known; moreover, predicting them computationally is no rescue, since single sequence structure prediction is highly unreliable. RESULTS: The novel algorithm ExpaRNA-P computes exactly matching sequence-structure motifs in entire Boltzmann-distributed structure ensembles of two RNAs; thereby we match and fold RNAs simultaneously, analogous to the well-known "simultaneous alignment and folding" of RNAs. While this implies much higher flexibility compared to ExpaRNA, ExpaRNA-P has the same very low complexity (quadratic in time and space), which is enabled by its novel structure ensemble-based sparsification. Furthermore, we devise a generalized chaining algorithm to compute compatible subsets of ExpaRNA-P's sequence-structure motifs. Resulting in the very fast RNA alignment approach ExpLoc-P, we utilize the best chain as anchor constraints for the sequence-structure alignment tool LocARNA. ExpLoc-P is benchmarked in several variants and versus state-of-the-art approaches. In particular, we formally introduce and evaluate strict and relaxed variants of the problem; the latter makes the approach sensitive to compensatory mutations. Across a benchmark set of typical non-coding RNAs, ExpLoc-P has similar accuracy to LocARNA but is four times faster (in both variants), while it achieves a speed-up over 30-fold for the longest benchmark sequences (≈400nt). Finally, different ExpLoc-P variants enable tailoring of the method to specific application scenarios. ExpaRNA-P and ExpLoc-P are distributed as part of the LocARNA package. The source code is freely available at http://www.bioinf.uni-freiburg.de/Software/ExpaRNA-P . CONCLUSIONS: ExpaRNA-P's novel ensemble-based sparsification reduces its complexity to quadratic time and space. Thereby, ExpaRNA-P significantly speeds up sequence-structure alignment while maintaining the alignment quality. Different ExpaRNA-P variants support a wide range of applications.
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Algoritmos , Dobramento de RNA , Homologia de Sequência do Ácido Nucleico , RNA/química , Análise de Sequência de RNA , SoftwareRESUMO
Detecting local common sequence-structure regions of RNAs is a biologically important problem. Detecting such regions allows biologists to identify functionally relevant similarities between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work on local pattern matching of RNAs, we support the breaking of arcs. This allows us to add flexibility over matching only fixed structures; potentially matching only a similar subset of specified base pairs. We present an O(n(3)) algorithm for local exact pattern matching between two nested RNAs, and an O(n(3) log n) algorithm for one nested RNA and one bounded-unlimited RNA. In addition, an algorithm for approximate pattern matching is introduced that for two given nested RNAs and a number k, finds the maximal local pattern matching score between the two RNAs with at most k mismatches in O(n(3)k(2)) time. Finally, we present an O(n(3)) algorithm for finding the most similar subforest between two nested RNAs.
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Biologia Computacional/métodos , Reconhecimento Automatizado de Padrão/métodos , RNA/química , Análise de Sequência de RNA/métodos , Algoritmos , Conformação de Ácido NucleicoRESUMO
A subset of Shiga toxin-producing Escherichia coli strains, termed enterohemorrhagic E. coli (EHEC), is defined in part by the ability to produce attaching and effacing (A/E) lesions on intestinal epithelia. Such lesions are characterized by intimate bacterial attachment to the apical surface of enterocytes, cytoskeletal rearrangements beneath adherent bacteria, and destruction of proximal microvilli. A/E lesion formation requires the locus of enterocyte effacement (LEE), which encodes a Type III secretion system that injects bacterial proteins into host cells. The translocated proteins, termed effectors, subvert a plethora of cellular pathways to the benefit of the pathogen, for example, by recruiting cytoskeletal proteins, disrupting epithelial barrier integrity, and interfering with the induction of inflammation, phagocytosis, and apoptosis. The LEE and selected effectors play pivotal roles in intestinal persistence and virulence of EHEC, and it is becoming clear that effectors may act in redundant, synergistic, and antagonistic ways during infection. Vaccines that target the function of the Type III secretion system limit colonization of reservoir hosts by EHEC and may thus aid control of zoonotic infections. Here we review the features and functions of the LEE-encoded Type III secretion system and associated effectors of E. coli O157:H7 and other Shiga toxin-producing E. coli strains.
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Aderência Bacteriana , Enterócitos/microbiologia , Escherichia coli Êntero-Hemorrágica/genética , Escherichia coli Êntero-Hemorrágica/fisiologia , Proteínas de Escherichia coli/genética , Fosfoproteínas/genética , Fatores de Virulência/genética , Interações Hospedeiro-Patógeno , HumanosRESUMO
Agmatine, decarboxylated arginine, exerts beneficial effects in various experimental disease models. Clinical trials indicate the safety and effectiveness of short-term (up to 21 days) high dose regimens of oral agmatine sulfate, but longer term studies are lacking. This pilot study undertook to assess the safety of a longer term high dosage oral agmatine sulfate in laboratory rats. Adult Wistar rats consumed 5.3 g/l agmatine sulfate in their drinking water for 95 days, a regimen estimated to result in a daily dosage of absorbed agmatine of about 100mg/kg. Animals' body weight, water consumption and blood pressure were periodically measured, and general cage behavior, fur appearance, urination and feces appearance monitored. These parameters were also determined at 20 days after treatment cessation (day 115). On days 95 and 115, animals were euthanized for gross necropsy assessment. Agmatine-treated rats showed slight, but significant reductions in body weight and blood pressure, and reduced water consumption during treatment, which recovered completely within 20 days after treatment cessation. Otherwise, no abnormal behaviors or organ pathologies were observed. These findings are first to suggest apparent safety of sub-chronic high dosage dietary agmatine sulfate in laboratory rats, thus lending further support to the therapeutic applications of agmatine.