Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Transport of IgG across the blood-luminal barrier of the male reproductive tract of the rat and the effect of estradiol administration on reabsorption of fluid and IgG by the epididymal ducts

In rats immunized systemically with tetanus toxoid the concentration of specific anti-tetanus-toxoid-specific IgG in fluid from the rete testis and cauda epididymidis were respectively 0.6% and 1.4% the concentration in blood serum. The extratesticular duct system reabsorbed 97% of the IgG and 99% of the fluid leaving the rete, but estradiol administration affected the site of reabsorption. In untreated rats, the ductuli efferentes reabsorbed 94% of the IgG and 96% of the fluid leaving the rete, whereas estradiol-treated rats reabsorbed 83% of the IgG and 86% of the fluid, and the ductus epididymidis fully compensated for these different effects of estradiol on the ductuli efferentes. The concentrations of IgG in secretions of the seminal vesicles and prostate gland were lower (0.1% and 0.3% respectively of the titers in blood serum) than in fluids from the extratesticular ducts, and were not affected by the administration of estradiol. RT-PCR showed that Fcgrt (neonatal Fc receptor, also known as FcRn) is expressed in the reproductive ducts, where IgG is probably transported across epithelium, being particularly strong in the ductuli efferentes (where most IgG was reabsorbed) and distal caput epididymidis. It is concluded that IgG enters the rete testis and is concentrated only 2.5-fold along the extratesticular duct system, unlike spermatozoa, which are concentrated 95-fold. Further, the ductus epididymidis can recognize and compensate for changes in function of the ductuli efferentes.

Comparison of intraocular pressure measurement between rebound, non-contact and Goldmann applanation tonometry in treated glaucoma patients

Background: To compare the intraocular pressure readings obtained with the iCare rebound tonometer and the 7CR non-contact tonometer with those measured by Goldmann applanation tonometry in treated glaucoma patients. Design: A prospective, cross sectional study was conducted in a private tertiary glaucoma clinic. Participants: 109 (54M:55F) patients including only eyes under medical treatment for glaucoma. Methods: Measurement by Goldmann applanation tonometry, iCare rebound tonometry and 7CR non-contact tonometry. Main Outcome Measures: Intraocular pressure. Results: There were strong correlations between the intraocular pressure measurements obtained with Goldmann and both the rebound and non-contact tonometers (Spearman r values ≥ 0.79, p < 0.001). However, there were small, statistically significant differences between the average readings for each tonometer. For the rebound tonometer, the mean intraocular pressure was slightly higher compared to the Goldmann applanation tonometer in the right eyes (p = 0.02), and similar in the left eyes (p = 0.93) however these differences did not reach statistical significance. The Goldmann correlated measurements from the noncontact tonometer were lower than the average Goldmann reading for both right (p < 0.001) and left (p > 0.01) eyes. The corneal compensated measurements from the non-contact tonometer were significantly higher compared to the other tonometers (p ≤ 0.001). Conclusions: The iCare rebound tonometer and the 7CR non-contact tonometer measure IOP in fundamentally different ways to the Goldmann applanation tonometer. The resulting IOP values vary between the instruments and will need to be considered when comparing clinical versus home acquired measurements.

Predictive factors of contact lens case contamination

PURPOSE: To examine the relationship between contact lens (CL) case contamination and various potential predictive factors. METHODS: 74 subjects were fitted with lotrafilcon B (CIBA Vision) CLs on a daily wear basis for 1 month. Subjects were randomly assigned one of two polyhexamethylene biguanide (PHMB) preserved disinfecting solutions with the corresponding regular lens case. Clinical evaluations were conducted at lens delivery and after 1 month, when cases were collected for microbial culture. A CL care non-compliance score was determined through administration of a questionnaire and the volume of solution used was calculated for each subject. Data was examined using backward stepwise binary logistic regression. RESULTS: 68% of cases were contaminated. 35% were moderately or heavily contaminated and 36% contained gram-negative bacteria. Case contamination was significantly associated with subjective dryness symptoms (OR 4.22, CI 1.37–13.01) (P<0.05). There was no association between contamination and subject age, ethnicity, gender, average wearing time, amount of solution used, non-compliance score, CL power and subjective redness (P>0.05). The effect of lens care system on case contamination approached significance (P=0.07). Failure to rinse the case with disinfecting solution following CL insertion (OR 2.51, CI 0.52–12.09) and not air drying the case (OR 2.31, CI 0.39–13.35) were positively correlated with contamination; however, did not reach statistical significance. CONCLUSIONS: Our results suggest that case contamination may influence subjective comfort. It is difficult to predict the development of case contamination from a variety of clinical factors. The efficacy of CL solutions, bacterial resistance to disinfection and biofilm formation are likely to play a role. Further evaluation of these factors will improve our understanding of the development of case contamination and its clinical impact.

From barrier elimination to barrier negotiation : a qualitative study of parents' attitudes about active travel for elementary school trips

This paper examines parents' responses to key factors associated with mode choices for school trips. The research was conducted with parents of elementary school students in Denver Colorado as part of a larger investigation of school travel. School-based active travel programs aim to encourage students to walk or bike to school more frequently. To that end, planning research has identified an array of factors associated with parents' decisions to drive children to school. Many findings are interpreted as ‘barriers’ to active travel, implying that parents have similar objectives with respect to travel mode choices and that parents respond similarly and consistently to external conditions. While the conclusions are appropriate in forecasting demand and mode share with large populations, they are generally too coarse for programs that aim to influence travel behavior with individuals and small groups. This research uses content analysis of interview transcripts to examine the contexts of factors associated with parents' mode choices for trips to and from elementary school. Short, semi-structured interviews were conducted with 65 parents from 12 Denver Public Elementary Schools that had been selected to receive 2007–08 Safe Routes to School non-infrastructure grants. Transcripts were analyzed using Nvivo 8.0 to find out how parents respond to selected factors that are often described in planning literature as ‘barriers’ to active travel. Two contrasting themes emerged from the analysis: barrier elimination and barrier negotiation. Regular active travel appears to diminish parents' perceptions of barriers so that negotiation becomes second nature. Findings from this study suggest that intervention should build capacity and inclination in order to increase rates of active travel.

The effect of hydrogel and silicone hydrogel contact lenses on the measurement of intraocular pressure with rebound tonometry

Purpose: To assess the accuracy of intraocular pressure(IOP) measurements using rebound tonometry over disposable hydrogel (etafilcon A) and silicone hydrogel (senofilcon A) contact lenses (CLs) of different powers. Methods: The experimental group comprised 36 subjects (19 male, 17 female). IOP measurements were undertaken on the subject’s right eyes in random order using a rebound tonometer (ICare). The CLs had powers of +2.00D, −2.00D and−6.00D. Six measurements were taken over each contact lens and also before and after the CLs had been worn. Results: A good correlation was found between IOP measurements with and without CLs (all r≥0.80; p < 0.05). Bland Altman plots did not show any significant trend in the difference in IOP readings with and without CLs as a function of IOP value. A two-way ANOVA revealed a significant effect of material and power (p < 0.01) but no interaction. All the comparisons between the measurements without CLs and with hydrogel CLs were significant (p < 0.01). The comparisons with silicone hydrogel CLs were not significant. Conclusions: Rebound tonometry can be reliably performed over silicone hydrogel CLs. With hydrogel CLs, the measurements were lower than those without CLs. However, despite the fact that these differences were statistically significant, their clinical significance was minimal.

Noninvasive in vivo assessment of soft contact lens type on tear film surface quality

To evaluate the effect of soft contact lens type on the in vivo tear film surface quality (TFSQ) on daily disposable lenses and to establish whether two recently developed techniques for noninvasive measurement of TFSQ can distinguish between different contact lens types.

Grading scales for contact lens complications

Purpose. To devise and validate artist-rendered grading scales for contact lens complications Methods. Each of eight tissue complications of contact lens wear (listed under 'Results') was painted by a skilled ophthalmic artist (Terry R. Tarrant) in five grades of severity: 0 (normal), 1 (trace), 2 (mild), 3 (moderate) and 4 (severe). A representative slit lamp photograph of a tissue response of each of the eight complications was shown to 404 contact lens practitioners who had never before used clinical grading scales. The practitioners were asked to grade each tissue response to the nearest 0.1 grade unit by interpolation. Results. The standard deviation (± s.d.) of the 404 responses for each tissue complication is tabulated below:_ing_ 0.5 Endothelial pplymegethisjij-4 0.7 Epithelial microcysts 0.5 Endothelial blebs_ 0.4 Stromal edema_onjunctiva! hyperemia 0.4 Stromal neovascularization 0.4 Papillary conjunctivitis 0.5 The frequency distributions and best-fit normal curves were also plotted. The precision of grading (s.d. x 2) ranged from 0.8 to 1.4, with a mean precision of 1.0. Conclusions. Grading scales afford contact lens practitioners with a method of quantifying the severity of adverse tissue responses to contact lens wear. It is noteworthy that the statistically verified precision of grading (1.0 scale unit) concurs precisely with the essential design feature of the grading scales that each grading step of 1.0 corresponds to clinically significant difference in severity. Thus, as a general rule, a difference or change in grade of > 1.0 can be taken to be both clinically and statistically significant when using these grading scales. Trained observers are likely to achieve even greater grading precision. Supported by Hydron Limited.

Ocular surface changes with short-term contact lens wear

Contact lenses are a common method for the correction of refractive errors of the eye. While there have been significant advancements in contact lens designs and materials over the past few decades, the lenses still represent a foreign object in the ocular environment and may lead to physiological as well as mechanical effects on the eye. When contact lenses are placed in the eye, the ocular anatomical structures behind and in front of the lenses are directly affected. This thesis presents a series of experiments that investigate the mechanical and physiological effects of the short-term use of contact lenses on anterior and posterior corneal topography, corneal thickness, the eyelids, tarsal conjunctiva and tear film surface quality. The experimental paradigm used in these studies was a repeated measures, cross-over study design where subjects wore various types of contact lenses on different days and the lenses were varied in one or more key parameters (e.g. material or design). Both, old and newer lens materials were investigated, soft and rigid lenses were used, high and low oxygen permeability materials were tested, toric and spherical lens designs were examined, high and low powers and small and large diameter lenses were used in the studies. To establish the natural variability in the ocular measurements used in the studies, each experiment also contained at least one “baseline” day where an identical measurement protocol was followed, with no contact lenses worn. In this way, changes associated with contact lens wear were considered in relation to those changes that occurred naturally during the 8 hour period of the experiment. In the first study, the regional distribution and magnitude of change in corneal thickness and topography was investigated in the anterior and posterior cornea after short-term use of soft contact lenses in 12 young adults using the Pentacam. Four different types of contact lenses (Silicone hydrogel/ Spherical/–3D, Silicone Hydrogel/Spherical/–7D, Silicone Hydrogel/Toric/–3D and HEMA/Toric/–3D) of different materials, designs and powers were worn for 8 hours each, on 4 different days. The natural diurnal changes in corneal thickness and curvature were measured on two separate days before any contact lens wear. Significant diurnal changes in corneal thickness and curvature within the duration of the study were observed and these were taken into consideration for calculating the contact lens induced corneal changes. Corneal thickness changed significantly with lens wear and the greatest corneal swelling was seen with the hydrogel (HEMA) toric lens with a noticeable regional swelling of the cornea beneath the stabilization zones, the thickest regions of the lenses. The anterior corneal surface generally showed a slight flattening with lens wear. All contact lenses resulted in central posterior corneal steepening, which correlated with the relative degree of corneal swelling. The corneal swelling induced by the silicone hydrogel contact lenses was typically less than the natural diurnal thinning of the cornea over this same period (i.e. net thinning). This highlights why it is important to consider the natural diurnal variations in corneal thickness observed from morning to afternoon to accurately interpret contact lens induced corneal swelling. In the second experiment, the relative influence of lenses of different rigidity (polymethyl methacrylate – PMMA, rigid gas permeable – RGP and silicone hydrogel – SiHy) and diameters (9.5, 10.5 and 14.0) on corneal thickness, topography, refractive power and wavefront error were investigated. Four different types of contact lenses (PMMA/9.5, RGP/9.5, RGP/10.5, SiHy/14.0), were worn by 14 young healthy adults for a period of 8 hours on 4 different days. There was a clear association between fluorescein fitting pattern characteristics (i.e. regions of minimum clearance in the fluorescein pattern) and the resulting corneal shape changes. PMMA lenses resulted in significant corneal swelling (more in the centre than periphery) along with anterior corneal steepening and posterior flattening. RGP lenses, on the other hand, caused less corneal swelling (more in the periphery than centre) along with opposite effects on corneal curvature, anterior corneal flattening and posterior steepening. RGP lenses also resulted in a clinically and statistically significant decrease in corneal refractive power (ranging from 0.99 to 0.01 D), large enough to affect vision and require adjustment in the lens power. Wavefront analysis also showed a significant increase in higher order aberrations after PMMA lens wear, which may partly explain previous reports of "spectacle blur" following PMMA lens wear. We further explored corneal curvature, thickness and refractive changes with back surface toric and spherical RGP lenses in a group of 6 subjects with toric corneas. The lenses were worn for 8 hours and measurements were taken before and after lens wear, as in previous experiments. Both lens types caused anterior corneal flattening and a decrease in corneal refractive power but the changes were greater with the spherical lens. The spherical lens also caused a significant decrease in WTR astigmatism (WRT astigmatism defined as major axis within 30 degrees of horizontal). Both the lenses caused slight posterior corneal steepening and corneal swelling, with a greater effect in the periphery compared to the central cornea. Eyelid position, lid-wiper and tarsal conjunctival staining were also measured in Experiment 2 after short-term use of the rigid and SiHy contact lenses. Digital photos of the external eyes were captured for lid position analysis. The lid-wiper region of the marginal conjunctiva was stained using fluorescein and lissamine green dyes and digital photos were graded by an independent masked observer. A grading scale was developed in order to describe the tarsal conjunctival staining. A significant decrease in the palpebral aperture height (blepharoptosis) was found after wearing of PMMA/9.5 and RGP/10.5 lenses. All three rigid contact lenses caused a significant increase in lid-wiper and tarsal staining after 8 hours of lens wear. There was also a significant diurnal increase in tarsal staining, even without contact lens wear. These findings highlight the need for better contact lens edge design to minimise the interactions between the lid and contact lens edge during blinking and more lubricious contact lens surfaces to reduce ocular surface micro-trauma due to friction and for. Tear film surface quality (TFSQ) was measured using a high-speed videokeratoscopy technique in Experiment 2. TFSQ was worse with all the lenses compared to baseline (PMMA/9.5, RGP/9.5, RGP/10.5, and SiHy/14) in the afternoon (after 8 hours) during normal and suppressed blinking conditions. The reduction in TFSQ was similar with all the contact lenses used, irrespective of their material and diameter. An unusual pattern of change in TFSQ in suppressed blinking conditions was also found. The TFSQ with contact lens was found to decrease until a certain time after which it improved to a value even better than the bare eye. This is likely to be due to the tear film drying completely over the surface of the contact lenses. The findings of this study also show that there is still a scope for improvement in contact lens materials in terms of better wettability and hydrophilicity in order to improve TFSQ and patient comfort. These experiments showed that a variety of changes can occur in the anterior eye as a result of the short-term use of a range of commonly used contact lens types. The greatest corneal changes occurred with lenses manufactured from older HEMA and PMMA lens materials, whereas modern SiHy and rigid gas permeable materials caused more subtle changes in corneal shape and thickness. All lenses caused signs of micro-trauma to the eyelid wiper and palpebral conjunctiva, although rigid lenses appeared to cause more significant changes. Tear film surface quality was also significantly reduced with all types of contact lenses. These short-term changes in the anterior eye are potential markers for further long term changes and the relative differences between lens types that we have identified provide an indication of areas of contact lens design and manufacture that warrant further development.