Temporal Properties of Liquid Crystal Displays: Implications for Vision Science Experiments

Liquid crystal displays (LCD) are currently replacing the previously dominant cathode ray tubes (CRT) in most vision science applications. While the properties of the CRT technology are widely known among vision scientists, the photometric and temporal properties of LCDs are unfamiliar to many practitioners. We provide the essential theory, present measurements to assess the temporal properties of different LCD panel types, and identify the main determinants of the photometric output. Our measurements demonstrate that the specifications of the manufacturers are insufficient for proper display selection and control for most purposes. Furthermore, we show how several novel display technologies developed to improve fast transitions or the appearance of moving objects may be accompanied by side–effects in some areas of vision research. Finally, we unveil a number of surprising technical deficiencies. The use of LCDs may cause problems in several areas in vision science. Aside from the well–known issue of motion blur, the main problems are the lack of reliable and precise onsets and offsets of displayed stimuli, several undesirable and uncontrolled components of the photometric output, and input lags which make LCDs problematic for real–time applications. As a result, LCDs require extensive individual measurements prior to applications in vision science.     

The ‘sparkle’ in fake eyes – the protective effect of mimic eyespots in lepidoptera

Many species of lepidoptera bear conspicuous circular patterns on their wings, known as eyespots, that are hypothesised to protect their bearers against predatory birds. In this study, we focus on a small but ubiquitous feature occurring naturally in lepidopteran eyespots, namely the so‐called ‘sparkle’. The ‘pupil’ in an eyespot is often highlighted by a ‘sparkle’, which is hypothesised to mimic a natural corneal total light reflection evident as a highlight, twinkle, or sparkle in the vertebrate eye. In a study exploring the presence of such sparkles, we found that 53% of lepidopteran eyespots exceeding 1 mm in diameter have a central, pinpoint‐like ‘sparkle’, 12% have a marginal, crescent‐shaped ‘sparkle’, 13% have a semi‐circular ‘sparkle’, and 22% have an intermediate semi‐circular to crescent‐shaped ‘sparkle’. In the lepidopterans’ natural resting position, the marginal ‘sparkles’ are positioned in the upper part of the eyespots’‘pupil’ and thus may create the illusion of a spherical eyeball. The ‘sparkles’ in lepidopteran eyespots do not only appear white to humans, but also reflect ultraviolet light. White and UV‐reflecting ‘sparkles’ also appear ‘white’ for UV‐sensitive viewers such as birds, and thus may effectively mimic the natural highlight in vertebrate eyes as an area of total light reflection. In field experiments using lepidopteran dummies baited with a mealworm, we show that the ‘sparkle’ is one of several components of eyespots eliciting a deterrent effect and that eyespots with a ‘sparkle’ in a natural position have a stronger deterrent effect than those with a ‘sparkle’ in an unnatural position. These findings support the eye mimicry hypothesis that better vertebrate eye mimicry improves the deterrent effect of eyespots.     

Expanding the versatility of phage display I: efficient display of peptide-tags on protein VII of the filamentous phage

Background

Phage display is a platform for selection of specific binding molecules and this is a clear-cut motivation for increasing its performance. Polypeptides are normally displayed as fusions to the major coat protein VIII (pVIII), or the minor coat protein III (pIII). Display on other coat proteins such as pVII allows for display of heterologous peptide sequences on the virions in addition to those displayed on pIII and pVIII. In addition, pVII display is an alternative to pIII or pVIII display.

Methodology/Principal Findings

Here we demonstrate how standard pIII or pVIII display phagemids are complemented with a helper phage which supports production of virions that are tagged with octa FLAG, HIS₆ or AviTag on pVII. The periplasmic signal sequence required for pIII and pVIII display, and which has been added to pVII in earlier studies, is omitted altogether.

Conclusions/Significance

Tagging on pVII is an important and very useful add-on feature to standard pIII and pVII display. Any phagemid bearing a protein of interest on either pIII or pVIII can be tagged with any of the tags depending simply on choice of helper phage. We show in this paper how such tags may be utilized for immobilization and separation as well as purification and detection of monoclonal and polyclonal phage populations.     

Expanding the versatility of phage display II: improved affinity selection of folded domains on protein VII and IX of the filamentous phage

Background

Phage display is a leading technology for selection of binders with affinity for specific target molecules. Polypeptides are normally displayed as fusions to the major coat protein VIII (pVIII) or the minor coat protein III (pIII). Whereas pVIII display suffers from drawbacks such as heterogeneity in display levels and polypeptide fusion size limitations, toxicity and infection interference effects have been described for pIII display. Thus, display on other coat proteins such as pVII or pIX might be more attractive. Neither pVII nor pIX display have gained widespread use or been characterized in detail like pIII and pVIII display.

Methodology/Principal Findings

Here we present a side-by-side comparison of display on pIII with display on pVII and pIX. Polypeptides of interest (POIs) are fused to pVII or pIX. The N-terminal periplasmic signal sequence, which is required for phage integration of pIII and pVIII and that has been added to pVII and pIX in earlier studies, is omitted altogether. Although the POI display level on pIII is higher than on pVII and pIX, affinity selection with pVII and pIX display libraries is shown to be particularly efficient.

Conclusions/Significance

Display through pVII and/or pIX represent platforms with characteristics that differ from those of the pIII platform. We have explored this to increase the performance and expand the use of phage display. In the paper, we describe effective affinity selection of folded domains displayed on pVII or pIX. This makes both platforms more attractive alternatives to conventional pIII and pVIII display than they were before.     

A Depth-Based Head-Mounted Visual Display to Aid Navigation in Partially Sighted Individuals

Independent navigation for blind individuals can be extremely difficult due to the inability to recognise and avoid obstacles. Assistive techniques such as white canes, guide dogs, and sensory substitution provide a degree of situational awareness by relying on touch or hearing but as yet there are no techniques that attempt to make use of any residual vision that the individual is likely to retain. Residual vision can restricted to the awareness of the orientation of a light source, and hence any information presented on a wearable display would have to limited and unambiguous. For improved situational awareness, i.e. for the detection of obstacles, displaying the size and position of nearby objects, rather than including finer surface details may be sufficient. To test whether a depth-based display could be used to navigate a small obstacle course, we built a real-time head-mounted display with a depth camera and software to detect the distance to nearby objects. Distance was represented as brightness on a low-resolution display positioned close to the eyes without the benefit focussing optics. A set of sighted participants were monitored as they learned to use this display to navigate the course. All were able to do so, and time and velocity rapidly improved with practise with no increase in the number of collisions. In a second experiment a cohort of severely sight-impaired individuals of varying aetiologies performed a search task using a similar low-resolution head-mounted display. The majority of participants were able to use the display to respond to objects in their central and peripheral fields at a similar rate to sighted controls. We conclude that the skill to use a depth-based display for obstacle avoidance can be rapidly acquired and the simplified nature of the display may appropriate for the development of an aid for sight-impaired individuals.     

Photocleavable linkage between genotype and phenotype for rapid and efficient recovery of nucleic acids encoding affinity-selected proteins

In vitro display technologies, such as mRNA display and DNA display are powerful tools to screen peptides and proteins with desired functions from combinatorial libraries in the fields of directed protein evolution and proteomics. When screening combinatorial libraries of polypeptides (phenotype), each of which is displayed on its gene (genotype), the problem remains, how best to recover the genotype moiety whose phenotype moiety has bound to the desired target. Here, we describe the use of a photocleavable 2-nitrobenzyl linker between genotype (DNA or mRNA) and phenotype (protein) in our DNA and mRNA display systems. This technique allows rapid and efficient recovery of selected nucleic acids by simple UV irradiation at 4 degrees C for 15 min. Further, we confirmed that the photocleavable DNA display and mRNA display systems are useful for in vitro selection of epitope peptides, recombinant antibodies, and drug-receptor interactions. Thus, these improved methods should be useful in therapeutics and diagnostics, e.g., for screening high-affinity binders, such as enzyme inhibitors and recombinant antibodies from random peptide and antibody libraries, as well as for screening drug-protein interactions from cDNA libraries.     

无眼动条件下中文阅读的研究

设计了计算机控制的中文阅读材料的不同显示方式,并对各种阅读过程中的徙动波形进行记录和分析。实验结果表明,无眼动的阅读速度较正常有眼动高,分别为853字/分和640字/分。通过固定窗口显示方式和知动窗口显示方式条件下中文阅读的比较,排除了强迫阅读的因素,说明有无眼动是产生阅读速度差异的主要原因;根据以上实验结果,可得出结论,在有眼动的情况下,除了saccade抑制影响阅读和识别外,主要的因素在于高级中枢对位置信号的处理,眼动的驱动控制及运动过程影响了高级中枢对阅读内容和识别内容的解码速率。无眼动阅读的速度主要受到高级中枢解码速率和记忆的影响,而不是周边视觉系统的限制。实验结果还表明,在无眼动的情况下,周边信息对阅读不仅不起帮助作用,反而起到干扰作用。     

The kinemage: a tool for scientific communication.

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared and specified by the author(s) of a journal article, in order to better communicate ideas that depend on three-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program, such as the one described here (called MAGE), which presently runs on Macintosh computers. A utility (called PREKIN) helps authors prepare the kinemages. Kinemages are being implemented under the auspices of the Innovative Technology Fund.     

Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL

Autotransporters have been employed as the anchoring scaffold for cell surface display by replacing their passenger domains with heterologous proteins to be displayed. We adopted an autotransporter (YfaL) of Escherichia coli for the cell surface display system. The critical regions in YfaL for surface display were identified for the construction of a ligation-independent cloning (LIC)-based display system. The designed system showed no detrimental effect on either the growth of the host cell or overexpressing heterologous proteins on the cell surface. We functionally displayed monomeric red fluorescent protein (mRFP1) as a reporter protein and diverse agarolytic enzymes from Saccharophagus degradans 2-40, including Aga86C and Aga86E, which previously had failed to be functional expressed. The system could display different sizes of proteins ranging from 25.3 to 143 kDa. We also attempted controlled release of the displayed proteins by incorporating a tobacco etch virus protease cleavage site into the C termini of the displayed proteins. The maximum level of the displayed protein was 6.1 × 10(4) molecules per a single cell, which corresponds to 5.6% of the entire cell surface of actively growing E. coli.     

Modeling Lanthanide Complexes: Towards the Theoretical Design of Light Conversion Molecular Devices

Theoretical techniques have been developed and/or improved to predict the molecular structure of lanthanide complexes which were used to calculate their electronic properties, in particular, their electronic spectra and energy levels necessary to calculate the rates of energy transfer from the ligands to the metal ion. The molecular structure has been obtained by the SMLC/AM1 (Sparkle Model for the Calculation of Lanthanide Complexes – Austin Model 1) model where the lanthanide ion is simulated by a sparkle implemented into the AM1 Hamiltonian used to perform a HF-SCF (Hartree-Fock Self-Consistent Field) calculation. The previous implementation of the SMLC/AM1 model (sparkle/1) involving only two parameters has been generalized to be consistent with the AM1 Hamiltonian and the new model (sparkle/2) significantly improved the prediction of molecular structures of Eu(III) complexes. For the electronic spectra and energy level calculations of the lanthanide complexes the model replaces the metal ion by a point charge with the ligands held in their positions as determined by the SMLC/AM1 model, and uses a INDO/S-CI (intermediate neglect of differential overlap/spectroscopic-configuration interaction) model. A preliminary study of the solvent effects on the absorption spectra of the free ligand is also presented. For the ligand-lanthanide ion energy transfer Fermi's golden rule is used with the multipolar and exchange mechanisms being implemented and tested for several complexes. These theoretical techniques have been applied to several complexes yielding very good results when compared to experimental data as well as predictions for the molecular and electronic structures and the relative contributions of the mechanisms for the energy transfer rates. This revised version was published online in June 2006 with corrections to the Cover Date.     

Employing phage display to study the mode of action of Bacillus thuringiensis Cry toxins

Phage display is an in vitro method for selecting polypeptides with desired properties from a large collection of variants. The insecticidal Cry toxins produced by Bacillus thuringiensis are highly specific to different insects. Various proteins such as cadherin, aminopeptidase-N (APN) and alkaline phosphatase (ALP) have been characterized as potential Cry-receptors. We used phage display to characterize the Cry toxin-receptor interaction(s). By employing phage-libraries that display single-chain antibodies (scFv) from humans or from immunized rabbits with Cry1Ab toxin or random 12-residues peptides, we have identified the epitopes that mediate binding of lepidopteran Cry1Ab toxin with cadherin and APN receptors from Manduca sexta and the interaction of dipteran Cry11Aa toxin with the ALP receptor from Aedes aegypti. Finally we displayed in phages the Cry1Ac toxin and discuss the potential for selecting Cry variants with improved toxicity or different specificity.     

Biochemical and pharmacological aspects of two bradykinin-potentiating peptides obtained from tryptic hydrolysis of casein

Peptides that display bradykinin-potentiating activity have been obtained from a number of distinct sources, such as snake venoms, fibrinogen, and casein. This paper describes the characterization of two new peptides generated by tryptic hydrolysis of casein. No homology was found with other known vasoactive or vasopotentiating peptides, especially by the lack of Ile-Pro-Pro motif. The peptides EMPFPK and YPVEPFTE, corresponding to the gamma casein sequence (108-113 and 114-121, respectively), displayed a selective potentiating activity on isolated guinea pig ileum for bradykinin. Besides, the octapeptide YPVEPFTE showed an in vitro competitive inhibitor effect on angiotensin-converting enzyme and thimet oligopeptidase and presented an opiate-like activity, increasing two times the latence time in the hot-plate assay. The results suggest that the isolated bioactive peptides act on conversion and/or inactivation of endogenous peptides by enzymes such as angiotensin-converting enzyme and thimet oligopeptidase by modifying several systemic responses such as blood-pressure regulation and in pain response.     

PCA2GO: a new multivariate statistics based method to identify highly expressed GO-Terms

Background  

Several tools have been developed to explore and search Gene Ontology (GO) databases allowing efficient GO enrichment analysis and GO tree visualization. Nevertheless, identification of highly specific GO-terms in complex data sets is relatively complicated and the display of GO term assignments and GO enrichment analysis by simple tables or pie charts is not optimal. Valuable information such as the hierarchical position of a single GO term within the GO tree (topological ordering), or enrichment within a complex set of biological experiments is not displayed. Pie charts based on GO tree levels are, themselves, one-dimensional graphs, which cannot properly or efficiently represent the hierarchical specificity for the biological system being studied.     

Production of glucoamylase in pyruvate decarboxylase deletion mutants of the yeast Kluyveromyces lactis

We have developed a novel Escherichia coli cell surface display system by employing PgsA as an anchoring motif. In our display system, C-terminal fusion to PgsA anchor protein from Bacillus subtilis was used. The enzymes selected for display were α-amylase (AmyA) from Streptococcus bovis 148 and lipase B (CALB) from Candida antarctica. The molecular mass values of AmyA and CALB are approximately 77 and 34 kDa, respectively. The enzymes were displayed on the surface as a fusion protein with a FLAG peptide tag at the C terminus. Both the PgsA-AmyA-FLAG and PgsA-CALB-FLAG fusion proteins were shown to be displayed by immunofluorescence labeling using anti-FLAG antibody. The displayed enzymes were active forms, and AmyA and CALB activities reached 990 U/g (dry cell weight) and 4.6 U/g (dry cell weight), respectively. AmyA-displaying E. coli cells grew utilizing cornstarch as the sole carbon source, while CALB-displaying E. coli cells catalyzed enantioselective transesterification, indicating that they are effective whole-cell biocatalysts. Since a target enzyme with a size of 77 kDa and an industrially useful lipase have been successfully displayed on the cell surface of E. coli for the first time, PgsA protein is probably a useful anchoring motif to display various enzymes.     

Decoupled Visually-Guided Reaching in Optic Ataxia: Differences in Motor Control between Canonical and Non-Canonical Orientations in Space

Guiding a limb often involves situations in which the spatial location of the target for gaze and limb movement are not congruent (i.e. have been decoupled). Such decoupled situations involve both the implementation of a cognitive rule (i.e. strategic control) and the online monitoring of the limb position relative to gaze and target (i.e. sensorimotor recalibration). To further understand the neural mechanisms underlying these different types of visuomotor control, we tested patient IG who has bilateral caudal superior parietal lobule (SPL) damage resulting in optic ataxia (OA), and compared her performance with six age-matched controls on a series of center-out reaching tasks. The tasks comprised 1) directing a cursor that had been rotated (180° or 90°) within the same spatial plane as the visual display, or 2) moving the hand along a different spatial plane than the visual display (horizontal or para-sagittal). Importantly, all conditions were performed towards visual targets located along either the horizontal axis (left and right; which can be guided from strategic control) or the diagonal axes (top-left and top-right; which require on-line trajectory elaboration and updating by sensorimotor recalibration). The bilateral OA patient performed much better in decoupled visuomotor control towards the horizontal targets, a canonical situation in which well-categorized allocentric cues could be utilized (i.e. guiding cursor direction perpendicular to computer monitor border). Relative to neurologically intact adults, IG''s performance suffered towards diagonal targets, a non-canonical situation in which only less-categorized allocentric cues were available (i.e. guiding cursor direction at an off-axis angle to computer monitor border), and she was therefore required to rely on sensorimotor recalibration of her decoupled limb. We propose that an intact caudal SPL is crucial for any decoupled visuomotor control, particularly when relying on the realignment between vision and proprioception without reliable allocentric cues towards non-canonical orientations in space.     

Integration across Time Determines Path Deviation Discrimination for Moving Objects

Background

Human vision is vital in determining our interaction with the outside world. In this study we characterize our ability to judge changes in the direction of motion of objects–a common task which can allow us either to intercept moving objects, or else avoid them if they pose a threat.

Methodology/Principal Findings

Observers were presented with objects which moved across a computer monitor on a linear path until the midline, at which point they changed their direction of motion, and observers were required to judge the direction of change. In keeping with the variety of objects we encounter in the real world, we varied characteristics of the moving stimuli such as velocity, extent of motion path and the object size. Furthermore, we compared performance for moving objects with the ability of observers to detect a deviation in a line which formed the static trace of the motion path, since it has been suggested that a form of static memory trace may form the basis for these types of judgment. The static line judgments were well described by a ‘scale invariant’ model in which any two stimuli which possess the same two-dimensional geometry (length/width) result in the same level of performance. Performance for the moving objects was entirely different. Irrespective of the path length, object size or velocity of motion, path deviation thresholds depended simply upon the duration of the motion path in seconds.

Conclusions/Significance

Human vision has long been known to integrate information across space in order to solve spatial tasks such as judgment of orientation or position. Here we demonstrate an intriguing mechanism which integrates direction information across time in order to optimize the judgment of path deviation for moving objects.     

A Wireless Lingual Feedback Device to Reduce Overpressures in Seated Posture: A Feasibility Study

Background

Pressure sores are localized injuries to the skin and underlying tissues and are mainly resulting from overpressure. Paraplegic peoples are particularly subjects to pressure sores because of long-time seated postures and sensory deprivation at the lower limbs.

Methodology/Principal Findings

Here we report outcomes of a feasibility trial involving a biofeedback system aimed at reducing buttock overpressure whilst an individual is seated. The system consists of (1) pressure sensors, (2) a laptop coupling sensors and actuator (3) a wireless Tongue Display Unit (TDU) consisting of a circuit embedded in a dental retainer with electrodes put in contact with the tongue. The principle consists in (1) detecting overpressures in people who are seated over long periods of time, (2) estimating a postural change that could reduce these overpressures and (3) communicating this change through directional information transmitted by the TDU.Twenty-four healthy subjects voluntarily participated in this study. Twelve healthy subjects initially formed the experimental group (EG) and were seated on a chair with the wireless TDU inside their mouth. They were asked to follow TDU orders that were randomly spread throughout the session. They were evaluated during two experimental sessions during which 20 electro-stimulations were sent. Twelve other subjects, added retrospectively, formed the control group (CG). These subjects participated in one session of the same experiment without any biofeedback.Three dependent variables were computed: (1) the ability of subjects to reach target posture (EG versus CG), (2) high pressure reductions after a biofeedback (EG versus CG) and (3) the level of these reductions relative to their initial values (EG only). Results show (1) that EG reached target postures in 90.2% of the trials, against 5,3% in the CG, (2) a significant reduction in overpressures in the EG compared to the CG and (3), for the EG, that the higher the initial pressures were, the more they were decreased.

Conclusions/Significance

The findings suggest that, in this trial, subjects were able to use a tongue tactile feedback system to reduce buttock overpressure while seated. Further evaluation of this system on paraplegic subjects remains to be done.     

Increased expression of the nicotinic acetylcholine receptor in stimulated muscle

Chronic low-frequency stimulation has been used as a model for investigating responses of skeletal muscle fibres to enhanced neuromuscular activity under conditions of maximum activation. Fast-to-slow isoform shifting of markers of the sarcoplasmic reticulum and the contractile apparatus demonstrated successful fibre transitions prior to studying the effect of chronic electro-stimulation on the expression of the nicotinic acetylcholine receptor. Comparative immunoblotting revealed that the alpha- and delta-subunits of the receptor were increased in 10-78 day stimulated specimens, while an associated component of the surface utrophin-glycoprotein complex, beta-dystroglycan, was not drastically changed in stimulated fast skeletal muscle. Previous studies have shown that electro-stimulation induces degeneration of fast glycolytic fibres, trans-differentiation leading to fast-to-slow fibre transitions and activation of muscle precursor cells. In analogy, our results indicate a molecular modification of the central functional unit of the post-synaptic muscle surface within existing neuromuscular junctions and/or during remodelling of nerve-muscle contacts.     

Electro-stimulation of tofu wastewater for the production of single cell protein from various microorganisms

Tofu wastewater can be utilized as a substrate for microorganisms that produce single-cell proteins (SCPs). Because different microorganisms have different cellular components, the composition of SCPs varies. Electro-stimulation has the potential to speed up fermentation and increase product yield. The goal of this study was to find the best way to produce SCPs from Aspergillus awamori, Rhizopus oryzae, and Saccharomyces cerevisiae in the tofu wastewater substrate using electro-stimulation. The experimental method was used in the study, the data were analyzed using independent t-test statistical analysis, and the best treatment was identified using the effective index method. This treatment consisted of producing SCP with electro-stimulation of −1.5 V and without electro-stimulation for 72 h for the yeast and 96 h for the mold at 25 °C in tofu wastewater that had already been conditioned to a pH of 5. The parameters measured included measurement of population of microorganism, change in pH, dry biomass weight, carbohydrate content, and protein content. Electro-stimulation reduced the optimum fermentation time of A. awamori SCP from 56 to 32 h, resulting in 0.0406 g/50 mL of dry biomass, 30.09% carbohydrate content, and 6.86% protein content. Meanwhile, the optimal fermentation time on R. oryzae and S. cerevisiae were not accelerated by electro-stimulation. The best treatment was A. awamori without electro-stimulation, which produced 0.0931 g/50 mL of dry biomass, 20.29% carbohydrate, and 7.55% protein.