Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes. (C) 2004 Elsevier Inc. All rights reserved.

Snakes and kittens in the grass: No evidence for preferential processing of fear-relevant animals in visual search

Ohman and colleagues provided evidence for preferential processing of pictures depicting fear-relevant animals by showing that pictures of snakes and spiders are found faster among pictures of fiowers and mushrooms than vice versa and that the speed of detecting fear-relevant animals was not affected by set size whereas the speed of detecting fiowers/mushrooms was. Experiment 1 replicated this finding. Experiment 2, however, found similar search advantages when pictures of cats and horses or of wolves and big cats were to be found among pictures of flowers and mushrooms. Moreover, Experiment 3, in a within subject comparison, failed to find faster identification of snakes and spiders than of cats and horses among flowers and mushrooms. The present findings seem to indicate that previous reports of preferential processing of pictures of snakes and spiders in a visual search task may reflect a processing advantage for animal pictures in general rather than fear-relevance.

HPLC-FLD methods to quantify chloroaluminum phthalocyanine in nanoparticles, plasma and tissue: application in pharmacokinetic and biodistribution studies

Analytical and bioanalytical methods of high-performance liquid chromatography with fluorescence detection (HPLC-FLD) were developed and validated for the determination of chloroaluminum phthalocyanine in different formulations of polymeric nanocapsules, plasma and livers of mice. Plasma and homogenized liver samples were extracted with ethyl acetate, and zinc phthalocyanine was used as internal standard. The results indicated that the methods were linear and selective for all matrices studied. Analysis of accuracy and precision showed adequate values, with variations lower than 10% in biological samples and lower than 2% in analytical samples. The recoveries were as high as 96% and 99% in the plasma and livers, respectively. The quantification limit of the analytical method was 1.12 ng/ml, and the limits of quantification of the bioanalytical method were 15 ng/ml and 75 ng/g for plasma and liver samples, respectively. The bioanalytical method developed was sensitive in the ranges of 15-100 ng/ml in plasma and 75-500 ng/g in liver samples and was applied to studies of biodistribution and pharmacokinetics of AlClPc. (C) 2011 Elsevier B.V. All rights reserved.

Activation of visual areas during the attentional blink

When two targets are presented in rapid succession, identification of the first target is nearly perfect while identification of the second is severely impaired at shorter inter-target lags, and then gradually improves as lag increases. This second-target deficit is known as the attentional blink (AB). Numerous studies have implicated competition for access to higher-order processing mechanisms as the primary cause of the AB. However, relatively few studies have directly examined how the AB modulates activity in specific brain areas. To this end, we used fMRI to measure activation in the occipital and parietal cortices (including V1, V2, and area MT) during an AB task. Participants were presented with an initial target of oriented line segments embedded in a central stream of letter distractors. This central target was followed 100 - 700 ms later by a peripheral ‘X’ presented at one of four locations along with three ‘+’ distractors. All peripheral items were presented in the centre of a small field of moving dots. Participants made non-speeded judgments about line-segment orientation and the location of the second target at the end of a trial and to ignore all other stimuli. The results showed a robust AB characterised by a linear improvement in second-target accuracy as lag increased. This pattern of behavioural results was mirrored by changes in activation patterns across a number of visual areas indicating robust modulation of brain activity by the AB.

Comparative Study of Analgesic Effectiveness Using Three Different Anesthetic Techniques for Intravitreal Injection of Bevacizumab

BACKGROUND AND OBJECTIVE: To compare the analgesic effectiveness and aesthetic appearance associated with topical, subconjunctival, and peribulbar anesthesia for intravitreal bevacizumab injection. PATIENTS AND METHODS: Sixty consecutive patients undergoing their first intravitreal bevacizumab injection were randomized to receive one of three forms of anesthesia: proxymetacaine eye drops, subconjunctival injection of 2% xylocaine, and peribulbar injection of 2% xylocaine. Pain associated with the intravitreal injection and with the entire procedure (including anesthesia administration) was recorded using a Visual Analog Scale 15 minutes after intravitreal injection. Anterior segment evaluation was performed 24 hours after injection to measure the number of clock hours of subconjunctival hemorrhage. RESULTS: Median injection-related pain score was significantly lower in the peribulbar group compared with the topical and subconjunctival groups (P < .05). Median entire procedure pain score was significantly higher In the peribulbar group compared with the topical and subconjunctival groups (P < .05). The median extent of subconjunctival hemorrhage was significantly lower in the topical group compared with the other groups (P < .05). CONCLUSION: Among the three anesthetic techniques, peribulbar anesthesia was associated with greater effectiveness in controlling injection-related pain but was least effective in controlling entire procedure pain. There was no significant difference in pain scores between the topical and subconjunctival groups, and topical anesthesia was associated with less subconjunctival hemorrhage.

Validated spectrophotometric and spectrofluorimetric methods for determination of chloroaluminum phthalocyanine in nanocarriers

UV-VIS-Spectrophotometric and spectrofluorimetric methods have been developed and validated allowing the quantification of chloroaluminum phthalocyanine (CIAIPc) in nanocarriers. In order to validate the methods, the linearity, limit of detection (LOD), limit of quantification (LOQ), precision, accuracy, and selectivity were examined according to USP 30 and ICH guidelines. Linearities range were found between 0.50-3.00 mu g.mL(-1) (Y=0.3829 X [CIAIPc, mu g.mL(-1)] + 0.0126; r=0.9992) for spectrophotometry, and 0.05-1.00 mu g.mL(-1) (Y=2.24 x 10(6) X [CIAIPc, mu g.L(-1)] + 9.74 x 10(4); r=0.9978) for spectrofluorimetry. In addition, ANOVA and Lack-of-fit tests demonstrated that the regression equations were statistically significant (p<0.05), and the resulting linear model is fully adequate for both analytical methods. The LOD values were 0.09 and 0.01 mu g.mL(-1), while the LOCI were 0.27 and 0.04 mu g.mL(-1) for spectrophotometric and spectrofluorimetric methods, respectively. Repeatability and intermediate precision for proposed methods showed relative standard deviation (RSD) between 0.58% to 4.80%. The percent recovery ranged from 98.9% to 102.7% for spectrophotometric analyses and from 94.2% to 101.2% for spectrofluorimetry. No interferences from common excipients were detected and both methods were considered specific. Therefore, the methods are accurate, precise, specific, and reproducible and hence can be applied for quantification of CIAIPc in nanoemulsions (NE) and nanocapsules (NC).

The fMRI response of the LGN and V1 to cardinal red-green, blue-yellow, and achromatic visual stimuli

We compared the responsiveness of the LGN and the early retinotopic cortical areas to stimulation of the two cone-opponent systems (red - green and blue - yellow) and the achromatic system. This was done at two contrast levels to control for any effect of contrast. MR images were acquired on seven subjects with a 4T Bruker MedSpec scanner. The early visual cortical areas were localised by phase encoded retinotopic mapping with a volumetric analysis (Dumoulin et al, 2003 NeuroImage 18 576 - 587). We initially located the LGN in four subjects by using flickering stimuli in a separate scanning session, but subsequently identified it using the experimental stimuli. Experimental stimuli were sine-wave counterphasing rings (2 Hz, 0.5 cycle deg-1), cardinal for the selective activation of the L/M cone-opponent (RG), S cone-opponent (BY), and achromatic (Ach) systems. A region of interest analysis was performed. When presented at equivalent absolute contrasts (cone contrast = 5% - 6%), the BOLD response of the LGN is strongest to isoluminant red - green stimuli and weakest to blue - yellow stimuli, with the achromatic response falling in between. Area V1, on the other hand, responds best to both chromatic stimuli, with the achromatic response falling below. The key change from the LGN to V1 is a dramatic boost in the relative blue - yellow response, which occurred at both contrast levels used. This greatly enhanced cortical response to blue - yellow relative to the red - green and achromatic responses may be due to an increase in cell number and/or cell response between the LGN and V1. We speculate that the effect might reflect the operation of contrast constancy across colour mechanisms at the cortical level.

Trigeminal pain and quantitative sensory testing in painful peripheral diabetic neuropathy

Objective: To evaluate patients with Diabetes Mellitus type 2 and painful peripheral neuropathy in order to investigate oral complaints and facial somatosensory findings. Research design and methods: Case-control study; 29 patients (12 women, mean age 57.86 yo) with Diabetes Mellitus type 2 and 31 age-gender-matched controls were evaluated with a standardized protocol for general characteristics, orofacial pain, research diagnostic criteria for temporomandibular disorders, visual analogue scale and McGill Pain questionnaire, and a systematic protocol of quantitative sensory testing for bilateral facial sensitivity at the areas innervated by the trigeminal branches, which included the thermal detection by ThermoSensi 2, tactile evaluation with vonFrey filaments, and superficial pain thresholds with a superficial algometer (Micromar). Statistical analysis was performed with Wilcoxon, chi-square, confidence intervals and Spearman (p < 0.05). Results: Orofacial pain was reported by 55.2% of patients, and the most common descriptor was fatigue (50%); 17.2% had burning mouth. Myofascial temporomandibular disorders were diagnosed in 9(31%) patients. The study group showed higher sensory thresholds of pain at the right maxillary branch (p = 0.017) but sensorial differences were not associated with pain (p = 0.608). Glycemia and HbA(1c) were positively correlated with the quantitative sensory testing results of pain (p < 0.05) and cold (p = 0.044) perceptions. Higher pain thresholds were correlated with higher glycemia and glycated hemoglobin (p = 0.027 and p = 0.026). Conclusions: There was a high prevalence of orofacial pain and burning mouth was the most common complaint. The association of loss of pain sensation and higher glycemia and glycated hemoglobin can be of clinical use for the follow-up of DM complications. (C) 2010 Elsevier Ltd. All rights reserved.

Wavefront analysis and modulation transfer function of three multifocal intraocular lenses

Purpose: To evaluate wavefront performance and modulation transfer function (MTF) in the human eye aft er the implantation of diffractive or refractive multifocal intraocular lenses (IOLs). Materials and Methods: This was a prospective, interventional, comparative, nonrandomized clinical study. Uncorrected distance and near visual acuity, and wavefront analysis including MTF curves (iTrace aberrometer, Tracey Technologies, Houston, TX, USA) were measured in 60 patients aft er bilateral IOL implantation with 6 months of follow-up. Forty eyes received the diffractive ReSTOR (Alcon), 40 eyes received the refractive ReZoom (Advanced Medical Optics) and 40 eyes, the Tecnis ZM900 (Advanced Medical Optics). The comparison of MTF and aberration between the intraocular lenses was performed using analysis of variance (ANOVA), followed by the Dunn test when necessary. Results: The mean uncorrected distance visual acuity was similar in all three groups of multifocal IOLs. The ReSTOR group provided better uncorrected near visual acuity than the ReZoom group (P < 0.001), but similar to the Tecnis group. Spherical aberration was significantly higher in the ReZoom group (P = 0.007). Similar MTF curves were found for the aspheric multifocal IOL Tecnis and the spheric multifocal IOL ReSTOR, and both performed better than the multifocal IOL ReZoom in a 5 mm pupil (P < 0.001 at all spatial frequencies). Conclusions: Diffractive IOLs studied presented similar MTF curves for a 5 mm pupil diameter. Both diffractive IOLs showed similar spherical aberration, which was significantly better with the full-diffractive IOL Tecnis than with the refractive IOL ReZoom.

Wavefront Analysis, Contrast Sensitivity, and Depth of Focus After Cataract Surgery With Aspherical Intraocular Lens Implantation

PURPOSE: To determine whether implantation of an aspherical intraocular lens (IOL) results in reduced ocular aberrations and improved contrast sensitivity after cataract surgery without critical reduction of depth of focus. DESIGN: Double-blinded, randomized, prospective study. METHODS: In an intraindividual study of 25 patients with bilateral cataract, an aspherical IOL (Akreos Advanced Optic [AO]; Bausch & Lomb, Inc., Rochester, New York, USA) was implanted in one eye and a spherical IOL (Akreos Fit; Bausch & Lomb, Inc) in the fellow eye. Higher-order aberrations with a 5- and 6-mm pupil were measured with a dynamic retinoscopy aberrometer at 1 and 3 months after surgery. Uncorrected and best-corrected visual acuity and contrast sensitivity under mesopic and photopic conditions also were measured. Distance-corrected near and intermediate visual acuity were studied as a measurement of depth of focus. RESULTS: There was no statistically significant difference between eyes in uncorrected and best-corrected visual acuity at I and 3 months after surgery. There was a statistically significant between-group difference in contrast sensitivity under photopic conditions at 12 cycles per degree and under mesopic conditions at all spatial frequencies. The Akreos AO group obtained statistically significant lower values of higher-order aberrations and spherical aberration with 5- and 6-mm pupils compared with the Akreos Fit group (P < .05). There was no significant difference in distance-corrected near and intermediate visual acuity between both groups. CONCLUSIONS: Aspherical aberration-free Akreos AO IOL induced significantly less higher-order aberrations and spherical aberration than the Akreos Fit. Contrast sensitivity was better under mesopic conditions with the Akreos AO with similar results of depth of focus. (Am J Ophthalmol 2010;149:383-389. (C) 2010 by Elsevier Inc. All rights reserved.)

EEG-based Brain-Computer Interfaces: An Overview of Basic Concepts and Clinical Applications in Neurorehabilitation

Some patients are no longer able to communicate effectively or even interact with the outside world in ways that most of us take for granted. In the most severe cases, tetraplegic or post-stroke patients are literally `locked in` their bodies, unable to exert any motor control after, for example, a spinal cord injury or a brainstem stroke, requiring alternative methods of communication and control. But we suggest that, in the near future, their brains may offer them a way out. Non-invasive electroencephalogram (EEG)-based brain-computer interfaces (BCD can be characterized by the technique used to measure brain activity and by the way that different brain signals are translated into commands that control an effector (e.g., controlling a computer cursor for word processing and accessing the internet). This review focuses on the basic concepts of EEG-based BC!, the main advances in communication, motor control restoration and the down-regulation of cortical activity, and the mirror neuron system (MNS) in the context of BCI. The latter appears to be relevant for clinical applications in the coming years, particularly for severely limited patients. Hypothetically, MNS could provide a robust way to map neural activity to behavior, representing the high-level information about goals and intentions of these patients. Non-invasive EEG-based BCIs allow brain-derived communication in patients with amyotrophic lateral sclerosis and motor control restoration in patients after spinal cord injury and stroke. Epilepsy and attention deficit and hyperactive disorder patients were able to down-regulate their cortical activity. Given the rapid progression of EEG-based BCI research over the last few years and the swift ascent of computer processing speeds and signal analysis techniques, we suggest that emerging ideas (e.g., MNS in the context of BC!) related to clinical neuro-rehabilitation of severely limited patients will generate viable clinical applications in the near future.

Attentional modulation of visual cortex activity following right parietal damage in humans

Pathological inattention following parietal damage causes perceptual impairments for visual stimuli in the contralesional hemifield. Here we used functional magnetic resonance imaging (fMRI) to examine visual cortex activity in parietal patients as they performed a spatial attention task. Righthemisphere patients and healthy controls viewed counterphasing checkerboards in which coloured targets appeared briefly within the contralesional and ipsilesional hemifields. In separate fMRI runs participants focused their attention covertiy on the left or right hemifield, or on both hemifields concurrentiy. They were required to detect coloured targets that appeared briefly within the attended hemifield(s), and to withhold responses to distractor stimuli. Neural activit}' was significantly attenuated in early visual areas within the damaged hemisphere. Crucially, although attention significantiy modulated early visual activit}' within the intact (left) hemisphere, there was relatively littie modulation of activity within the affected hemisphere. Our findings suggest that parietal lesions alter early cortical responses to contralesional visual inputs.

Anemia screening in potential female blood donors: comparison of two different quantitative methods

Anemia screening before blood donation requires an accurate, quick, practical, and easy method with minimal discomfort for the donors. The aim of this study was to compare the accuracy of two quantitative methods of anemia screening: the HemoCue 201(+) (Aktiebolaget Leo Diagnostics) hemoglobin (Hb) and microhematocrit (micro-Hct) tests. Two blood samples of a single fingerstick were obtained from 969 unselected potential female donors to determine the Hb by HemoCue 201(+) and micro-Hct using HemataSTAT II (Separation Technology, Inc.), in alternating order. From each participant, a venous blood sample was drawn and run in an automatic hematology analyzer (ABX Pentra 60, ABX Diagnostics). Considering results of ABX Pentra 60 as true values, the sensitivity and specificity of HemoCue 201(+) and micro-Hct as screening methods were compared, using a venous Hb level of 12.0 g per dL as cutoff for anemia. The sensitivities of the HemoCue 201(+) and HemataSTAT II in detecting anemia were 56 percent (95% confidence interval [CI], 46.1%-65.5%) and 39.5 percent (95% CI, 30.2%-49.3%), respectively (p < 0.001). Analyzing only candidates with a venous Hb level lower than 11.0 g per dL, the deferral rate was 100 percent by HemoCue 201(+) and 77 percent by HemataSTAT II. The specificities of the methods were 93.5 and 93.2 percent, respectively. The HemoCue 201(+) showed greater discriminating power for detecting anemia in prospective blood donors than the micro-Hct method. Both presented equivalent deferral error rates of nonanemic potential donors. Compared to the micro-Hct, HemoCue 201(+) reduces the risk of anemic female donors giving blood, specially for those with lower Hb levels, without increasing the deferral of nonanemic potential donors.