Modelling the spatial tuning of the Hermann grid illusion

PURPOSE: Does a physiologically plausible model of the retinal ganglion cell (RGC) receptive field (RF) predict the spatial tuning properties of the Hermann Grid Illusion (HGI)? METHODS: The spatial tuning of a single intersection HGI was measured psychophysically in normal observers using a nulling technique at different vertical grid line luminances. We used a model based upon a standard RGC RF, balanced to produce zero response under uniform illumination, to predict the response of the model cell to the equivalent range of stimulus conditions when placed in either the 'street' or the 'intersection' of a single element of a Hermann grid. We determined the equivalent of the nulling luminance required to balance these responses and minimise the HGI. RESULTS: The model and the psychophysical data demonstrated broad spatial tuning with similarly shaped tuning profiles and similar strengths of illusion. The line width at the peak of the model tuning function was around twice the model RGC RF centre size. Modelling the psychophysical functions gave RF centre sizes smaller than expected from human anatomical evidence but similar to that suggested by primate physiological evidence. In the model and psychophysically the strength of the illusion varied with the luminance of the vertical grid line when HGI strength was expressed as a Michelson nulling contrast, but this effect was smaller when HGI strength was expressed as a nulling luminance. CONCLUSIONS: The shape, width, height and position of the spatial tuning function of the HGI can be well modelled by a RGC RF based model. The broad tuning of these functions does not appear to require a broad range of different cell sizes either in the retina or later in the visual pathway.     

The effect of orientation on the clarity of Hermann grid illusory lines.

To test the hypothesis that Hermann grid illusory lines are most clear when the grid is presented at a 45 deg, each of 20 participants underwent 10 trials in each of two conditions ('make the lines least clear' and 'make the lines most clear') which were run using a method of adjustment. A matched-pairs t-test applied to the means of the two conditions was significant beyond the 0.01 level. One-group t-tests supported the claim that the illusory lines are least clear for a vertical/horizontal orientation of the grid and most clear when it is rotated 45 deg. The results substantiate, in a systematic manner, 70 years of claims about the effects of grid orientation on illusory line clarity.     

The use of PCR to help quantify the protection provided by impregnated bednets

Bednets impregnated with a pyrethroid insecticide are an important recent advance in malaria vector control. Here, Suzanne Gokool, Deborah Smith and Chris Curtis describe how a combination of field work with specially designed huts and DNA fingerprinting of mosquito bloodmeals can be used to help assess whether impregnated bednets would give sufficient protection to prevent infection in areas of intense malaria transmission.     

A technique to quantify skin displacement in the walking horse

A method is presented for quantitative determination of skin movement over the underlying skeletal structures during normal locomotion of the horse. The principle of the method is simultaneous visualization of the position of the skin and the underlying bony structures, by marking the bones with implanted light-emitting diodes (LEDs) and the skin with self adhesive spot labels. Recordings were made using photography.     

Use of the most probable number technique to quantify soil-borne plant pathogens

Bioassays using serial soil dilutions and most probable number (MPN) estimations have been used by various authors to quantify inoculum of soil-borne plant pathogens. The requirements of a reliable bioassay are discussed; they include a good choice of dilution series and reproducible growing conditions. Sources of computer programs for analysis of the data are listed. The importance of testing the fit to the mathematical model used is illustrated and emphasised. Factors affecting the size and stability of the standard errors and of the inherent bias of the most probable number estimate are discussed. Equations are presented for calculating the expected standard errors, approximate confidence limits and least significant differences for different dilution factors and numbers of replicates. The benefits of using uneven replication are illustrated. Mathematical considerations show that the technique should enable differences of an order of magnitude to be detected and MPNs should be quoted with a maximum of two significant figures. Dilution ratios as large as 10 should be avoided. Statistical and biological difficulties, especially in standardising growing conditions when soil moisture is critical, indicate that results should normally be regarded as relative, rather than absolute, measurements of inoculum.     

A reliable technique to quantify the individual variability of iridescent coloration in birds

The study of iridescent coloration in birds emerged only recently, mainly due to the difficulty inherent in quantifying its directionality. Directionality restrains color perception to a limited angle and thereby causes drastic changes in brightness when an animal is in motion. Although a versatile goniometer for quantifying iridescent coloration has been developed recently, so far, it has only been applied to measuring the highly directional iridescent coloration in a hummingbird species. Thus, the reliability of the goniometer for species displaying more common and less directional iridescent coloration has yet to be evaluated. Additionally, two important methodological aspects remain to be assessed before this apparatus can be used confidently: 1) whether directionality, which could be subject to sexual selection, can be quantified in a repeatable way; and 2) whether the apparatus gives more precise and accurate measurements than a less complex traditional method. Using feathers collected from 271 male tree swallows Tachycineta bicolor over two years, we found that the goniometer provided repeatable measurements of directionality across individuals and across three body regions, namely the crown, mantle and rump. The apparatus was also more repeatable than a traditional method involving a bifurcated probe and reduced a brightness bias associated with individual differences in barbule tilt. We strongly encourage researchers to invest in this methodological change considering the multiple advantages demonstrated and to quantify the directionality of iridescent coloration as to unveil its role in signaling and sexual selection.     

自适应干扰对消技术提取胎儿心电的可视化仿真实现

目的：用可视化编程技术实现胎儿心电信号提取和分析。方法：获取受试者仰卧位的腹部平行放置的两对电极的二道心电信号;在Windows系统下,用Delphi嵌入汇编技术实现对模/数采样卡的低层I/O操作;用自适应干扰对消技术提取胎儿心电信号。结果和结论：计算机仿真结果表明,该方法的能获取较清晰的胎儿心电信号。讨论：①基于Windows开发的系统具有较好的交互性和移植性,②获得胎儿心电后可用我们巳开发的成熟技术实现对胎儿心动周期信号的混沌特征分析,以估计胎儿自主神经系统功能。     

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

Most microorganisms remain uncultivated, and typically their ecological roles must be inferred from diversity and genomic studies. To directly measure functional roles of uncultivated microbes, we developed Chip-stable isotope probing (SIP), a high-sensitivity, high-throughput SIP method performed on a phylogenetic microarray (chip). This approach consists of microbial community incubations with isotopically labeled substrates, hybridization of the extracted community rRNA to a microarray and measurement of isotope incorporation—and therefore substrate use—by secondary ion mass spectrometer imaging (NanoSIMS). Laboratory experiments demonstrated that Chip-SIP can detect isotopic enrichment of 0.5 atom % ¹³C and 0.1 atom % ¹⁵N, thus permitting experiments with short incubation times and low substrate concentrations. We applied Chip-SIP analysis to a natural estuarine community and quantified amino acid, nucleic acid or fatty acid incorporation by 81 distinct microbial taxa, thus demonstrating that resource partitioning occurs with relatively simple organic substrates. The Chip-SIP approach expands the repertoire of stable isotope-enabled methods available to microbial ecologists and provides a means to test genomics-generated hypotheses about biogeochemical function in any natural environment.     

The use of digital image segmentation to quantify an aminoanthraquinone dye biotransformation by white-rot fungi

Summary Three methods are presented for the objective, digital evaluation of Remazol Brilliant Blue R dye biotransformation by the white rot fungi, Pycnoporus cinnabarinus and Phanerochaete chrysosporium. This screening technique uses computerized image analysis and a binary logical and function to provide a rapid (2 min per analysis), quantitative, digital densitometry interpretation of enzyme induced chromophore conversion by fungi. A kinetic measure of metabolic activity (enzyme activity coefficient, ) may also be determined. It is shown that chromophore conversion is more rapid and extensive by P. cinnabarinus.     

ESR technique for noninvasive way to quantify cyclodextrins effect on cell membranes

A new way to study the action of cyclodextrin was developed to quantify the damage caused on cell membrane and lipid bilayer. The Electron Spin Resonance (ESR) spectroscopy was used to study the action of Randomly methylated-beta-cyclodextrin (Rameb) on living cells (HCT-116). The relative anisotropy observed in ESR spectrum of nitroxide spin probe (5-DSA and cholestane) is directly related to the rotational mobility of the probe, which can be further correlated with the microviscosity. The use of ESR probes clearly shows a close correlation between cholesterol contained in cells and cellular membrane microviscosity. This study also demonstrates the Rameb ability to extract cholesterol and phospholipids in time- and dose-dependent ways. In addition, ESR spectra enabled to establish that cholesterol is extracted from lipid rafts to form stable aggregates. The present work supports that ESR is an easy, reproducible and noninvasive technique to study the effect of cyclodextrins on cell membranes.     

The use of intraoperative grid pattern markings in lipoplasty

Intraoperative grid pattern markings have been used in the performance of liposuction. Grid pattern markings include series of longitudinal and transverse lines to delineate various anatomical boundaries and landmarks, including the midline, lateral line, and medial line. The markings are superimposed on the customary preoperative markings and divide broad or circumferential body surfaces into smaller subunits for liposuction. Grid pattern markings are applied to areas such as the anterior thighs, medial thighs, entire abdomen, flanks, back, arms, buttocks, calves, and ankles; they are not applied to smaller, less curved areas. Eighty-two consecutive patients underwent lipoplasty in 562 areas of the body. The revision rate for postliposuction contour irregularities was 4.0 percent (nine of 224 areas) where grid pattern markings were used; one area had an indentation type of contour irregularity and required autologous fat grafting. The revision rate was 1.5 percent (five of 328 areas) where grid pattern markings were not used; two areas in one patient had indentation-type contour irregularities and required autologous fat grafting. All remaining areas requiring revision had protuberant-type contour irregularities and responded to additional liposuction only. The use of grid pattern markings is associated with a low incidence of serious contour-related complications.     

Adaptation of the polony technique to quantify Gokushovirinae,a diverse group of single-stranded DNA phage

Advances in metagenomics have revealed the ubiquity of single-stranded DNA (ssDNA) phage belonging to the subfamily Gokushovirinae in the oceans; however, the abundance and ecological roles of this group are unknown. Here, we quantify gokushoviruses through adaptation of the polony method, in which viral template DNA is immobilized in a gel, amplified by PCR, and subsequently detected by hybridization. Primers and probes for this assay were designed based on PCR amplicon diversity of gokushovirus major capsid protein gene sequences from a depth profile in the Gulf of Aqaba, Red Sea sampled in September 2015. At ≥95% identity, these 87 gokushovirus sequences formed 14 discrete clusters with the largest clades showing distinct depth distributions. The application of the polony method enabled the first quantification of gokushoviruses in any environment. The gokushoviruses were most abundant in the upper 40 m of the stratified water column, with a subsurface peak in abundance of 1.26 × 10⁵ viruses ml⁻¹. These findings suggest that discrete gokushovirus genotypes infect bacterial hosts that differentially partition in the water column. Since the designed primers and probe are conserved across marine ecosystems, this polony method can be applied broadly for the quantification of gokushoviruses throughout the global oceans.     

Limitations of the scrape-loading/dye transfer technique to quantify inhibition of gap junctional intercellular communication

Gap junctional intercellular communication (GJIC) is recognized as playing an important role in normal cell proliferation and development. Chemically induced alteration of GJIC has been proposed to be associated with abnormal cellular growth and/or tumor promotion. Several in vitro assays are currently used to determine the effects of chemicals on GJIC between cultured mammalian cells. One of these assays, the scrape-loading dye transfer (SLIDT) technique, is based on monitoring the transfer of the fluorescent dye Lucifer yellow from one cell into adjacent cells via functional gap junctions. The objective of our study was to evaluate and compare various approaches for quantifying results obtained with the SL/DT technique. Confluent cultures of either WB rat liver epithelial cells or LC-540 rat leydig cells were exposed to the animal tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA), solvent (0.1% ethanol), or culture medium for one hour at 37° C prior to analysis of GJIC. Inhibition of dye transfer was clearly evident following TPA exposure. Quantification of this dye transfer was assessed via four approaches: manually counting the number of labeled cells; measuring the distance of dye travel from the scrape line; quantifying the amount of cellular dye uptake; and determining the distribution of dye away from the scrape line. Our results suggest that while the SL/DT technique can be effectively used as a tool to determine the qualitative presence or absence of GJIC, its use in quantifying changes in GJIC following chemical exposure is limited. Since concentration-dependent responses are critical in chemical testing, application of the SLIDT method should be restricted to a screening assay for qualitatively assessing the presence or absence of GJIC. Another assay (e.g., electrical coupling, microinjection, metabolic cooperation, radioactive metabolite transfer, or fluorescence redistribution after photobleaching) should be considered to quantify changes in GJIC and construct chemical concentration-response curves.Abbreviations FBS, fetal bovine serum - GJIC, gap junctional intercellular communication - HBSS, Hank's balanced saline solution - SL/DT, scrape-loading/dye transfer - TPA, 12-O-tetradecanoylphorbol-13-acetate.     

The use of GIS techniques to quantify the hydrological regime of a karst wetland (Skealoghan turlough) in Ireland

Question: Can GIS and GPS technology be used to quantify the hydrological regime of different plant communities on turloughs (groundwater dependent calcareous wetlands)? Location: Skealoghan turlough, County Mayo, Ireland. Methods: Plant communities were mapped and digitised with GIS software and a digital elevation model of the site was constructed from differential GPS data. Together with records of water level fluctuations on the site from May 2001 to May 2004, these data were used to calculate hydrological variables for each plant community. Hierarchical cluster analysis was used to identify groups of plant communities with similar hydrological regimes. Results: 15 plant communities were mapped at Skea loghan, with the Cirsio‐Molinietum and Ranunculo‐Potentilletum anserinae being the dominant phytosociological associations. Skealoghan is subject to large temporal and spatial variation in its hydrological regime and fluctuations in water level are intrinsically linked to rainfall. The spatial variation in flooding can be linked to the vegetation zones. Conclusions: GIS and DGPS technology can be used to quantify the hydrological regime of different plant communities on turloughs. Since the hydrological regime is a major environmental factor controlling the vegetation composition of the site, the maintenance of natural flooding regimes is a vital component for the conservation and management of the diverse vegetation mosaic at Skealoghan turlough.     

The grid sectioning technique: a study of catalase platelets.

The grid sectioning technique has been used to obtain the two missing principal axis projections of orthorhombic catalase platelets and to measure directly the unit cell c-value. The negatively stained platelets have a unit cell c-dimension of half that proposed by Unwin (1975) from powder X-ray diffraction. The precision of the grid sectioning technique in positioning sections along a specimen axis shows that the growth fault lines usually observed on negatively stained catalase platelets are rows of missing molecules filled with stain. From these sections conclusions are drawn concerning the action of negative stain on a specimen, the microtomy process, and the specimen/supporting film interaction. Finally the value of microtomy for detailed structural analysis of biological objects is emphasized.     

The use of the fluorescence photobleaching recovery technique to study the self-assembly of tubulin

Fluorescently labeled microtubule-associated proteins or poly-L-lysine (13,000 MW) were prepared by reaction with fluorescein isothiocyanate. The labeled compounds were used as probes of the assembly of calf brain tubulin using fluorescence photobleaching recovery techniques which allow measurement of the diffusion coefficient and percentage mobility of the fluorescent probe. When unfractionated tubulin (defined as material containing tubulin and microtubule-associated proteins) was polymerized at room temperature or 37 degrees C, either probe could be incorporated into microtubules, since the observed diffusion coefficient (approximately 1.7 X 10(-8) cm2/s) was much slower than that for either probe free in solution. The microtubules formed in the presence of labeled microtubule-associated proteins were free to diffuse while those formed in the presence of labeled polylysine were partially immobilized. Thus the fluorescence photobleaching recovery technique can be used to measure crosslinking of microtubules as well as assembly or interactions with other structures. When unfractionated tubulin was incubated with labeled polylysine in the presence of Ca2+ at room temperature, the observed diffusion coefficient (approximately 5.1 X 10(-8) cm2/s) probably represents the formation of rings of tubulin. The effect of mild and vigorous shearing, of cholchicine, and of different Mg2+ concentrations on the properties of the system were examined.     

The use of proteolytic enzymes to improve immunoglobulin staining by the PAP technique

Synopsis Proteolytic enzymes, protease and trypsin have recently been introduced to reduce the inconsistency hitherto encountered in the unlabelled antibody-enzyme method using PAP. This study investigated factors determining the optimum conditions for use of such enzymes in order to establish which one is most suitable. Trypsin was the most effective enzyme; however, its activity decreased over 3 h, a feature paralleled immunocytochemically. Method and duration of fixation appears to influence the required time of exposure to trypsin in order that consistent immunostaining may be produced. Treatment of sections with trypsin prior to the use of the unlabelled antibody-enzyme method using PAP renders the technique reliable, provided the enzyme is used in a carefully controlled manner.     

The use of immunostaining to quantify x-ray and heat-induced multiple microtubule organizing centers in normal and transformed cells

Microtubule organizing centers (MTOC) in control, irradiated and heated C3H 10T1/2 mouse embryo cells and two radiation-transformed sublines, R1 and R25, were made visible by indirect immunofluorescence using antibody against tubulin. The MTOC were reformed by 5-min incubation in fresh medium after the microtubules were depolymerized with nocodazole. The R1 line had a different distribution of MTOC/cell than the parent 10T1/2 line or R25, which had similar distributions. After irradiation, multiple MTOC appeared in the normal and radiation-transformed cells irradiated to 10 Gy and incubated for 24 or 48 h. The multiple foci of microtubule reformation in the irradiated cells indicate that radiation damage is expressed in structural elements in the cytoplasm. After heat treatment of the three cell lines (43 degrees C for 93 min and 45 degrees C for 25 min), the MTOC were disrupted and many cells did not have visible organizing centers at 24 or 48 h, while others had a large number of small centers of microtubule reformation. The distribution of MTOC/cell seen in R25 cells after the treatment had similar patterns to those of the 10T1/2 line rather than to those of the other radiation-transformed line, R1. Thus, the radiation or heat response seen in the MTOC is not dependent upon cell transformation.