Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids

Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.

Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks

Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing high-quality nutritional value. Alfalfa breeding is usually carried out by phenotypic recurrent selection and is commonly done at the family level. The application of GS in alfalfa could be simplified and less costly by genotyping and phenotyping families in bulks. For this study, an alfalfa reference population composed of 142 full-sib and 35 half-sib families was bulk-genotyped using target enrichment sequencing and phenotyped for dry matter yield (DMY) and canopy height (CH) in Florida, USA. Genotyping of the family bulks with 17,707 targeted probes resulted in 114,945 single-nucleotide polymorphisms. The markers revealed a population structure that matched the mating design, and the linkage disequilibrium slowly decayed in this breeding population. After exploring multiple prediction scenarios, a strategy was proposed including data from multiple harvests and accounting for the G×E in the training population, which led to a higher predictive ability of up to 38 and 24% for DMY and CH, respectively. Although this study focused on the implementation of GS in alfalfa families, the bulk methodology and the prediction schemes used herein could guide future studies in alfalfa and other crops bred in bulks.

Genome-Wide Association Study of Healthful Flavonoids among Diverse Mandarin Accessions

Mandarins have many unique flavonoids with documented health benefits and that help to prevent chronic human diseases. Flavonoids are difficult to measure and cannot be phenotyped without the use of specialized equipment; consequently, citrus breeders have not used flavonoid contents as selection criteria to develop cultivars with increased benefits for human health or increased tolerance to diseases. In this study, peel, pulp, and seed samples collected from many mandarin accessions and their hybrids were analyzed for the presence of selected flavonoids with documented human health benefits. A genome-wide association study (GWAS) was used to identify SNPs associated with biosynthesis of flavonoids in these mandarin accessions, and there were 420 significant SNPs were found to be associated with 28 compounds in peel, pulp, or seed samples. Four candidate genes involved in flavonoid biosynthesis were identified by enrichment analysis. SNPs that were found to be associated with compounds in pulp samples have the potential to be used as markers to select mandarins with improved phytonutrient content to benefit human health. Mandarin cultivars bred with increased flavonoid content may provide value to growers and consumers.

Genomic prediction in family bulks using different traits and cross-validations in pine

Genomic prediction integrates statistical, genomic, and computational tools to improve the estimation of breeding values and increase genetic gain. Due to the broad diversity in mating systems, breeding schemes, propagation methods, and unit of selection, no universal genomic prediction approach can be applied in all crops. In a genome-wide family prediction (GWFP) approach, the family is the basic unit of selection. We tested GWFP in two loblolly pine (Pinus taeda L.) datasets: a breeding population composed of 63 full-sib families (5–20 individuals per family), and a simulated population with the same pedigree structure. In both populations, phenotypic and genomic data was pooled at the family level in silico. Marker effects were estimated to compute genomic estimated breeding values (GEBV) at the individual and family (GWFP) levels. Less than six individuals per family produced inaccurate estimates of family phenotypic performance and allele frequency. Tested across different scenarios, GWFP predictive ability was higher than those for GEBV in both populations. Validation sets composed of families with similar phenotypic mean and variance as the training population yielded predictions consistently higher and more accurate than other validation sets. Results revealed potential for applying GWFP in breeding programs whose selection unit are family, and for systems where family can serve as training sets. The GWFP approach is well suited for crops that are routinely genotyped and phenotyped at the plot-level, but it can be extended to other breeding programs. Higher predictive ability obtained with GWFP would motivate the application of genomic prediction in these situations.

Phenomics-Assisted Selection for Herbage Accumulation in Alfalfa (Medicago sativa L.)

The application of remote sensing in plant breeding is becoming a routine method for fast and non-destructive high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) equipped with sensors. Alfalfa (Medicago sativa L.) is a perennial forage legume grown in more than 30 million hectares worldwide. Breeding alfalfa for herbage accumulation (HA) requires frequent and multiple phenotyping efforts, which is laborious and costly. The objective of this study was to assess the efficiency of UAV-based imagery and spatial analysis in the selection of alfalfa for HA. The alfalfa breeding population was composed of 145 full-sib and 34 half-sib families, and the experimental design was a row-column with augmented representation of controls. The experiment was established in November 2017, and HA was harvested four times between August 2018 and January 2019. A UAV equipped with a multispectral camera was used for HTP before each harvest. Four vegetation indices (VIs) were calculated from the UAV-based images: NDVI, NDRE, GNDVI, and GRVI. All VIs showed a high correlation with HA, and VIs predicted HA with moderate accuracy. HA and NDVI were used for further analyses to calculate the genetic parameters using linear mixed models. The spatial analysis had a significant effect in both dimensions (rows and columns) for HA and NDVI, resulting in improvements in the estimation of genetic parameters. Univariate models for NDVI and HA, and bivariate models, were fit to predict family performance for scenarios with various levels of HA data (simulated in silico by assigning missing values to full dataset). The bivariate models provided higher correlation among predicted values, higher coincidence for selection, and higher genetic gain even for scenarios with only 30% of HA data. Hence, HTP is a reliable and efficient method to aid alfalfa phenotyping to improve HA. Additionally, the use of spatial analysis can also improve the accuracy of selection in breeding trials.

How can a high-quality genome assembly help plant breeders?

The decreasing costs of next-generation sequencing and the improvements in de novo sequence assemblers have made it possible to obtain reference genomes for most eukaryotes, including minor crops such as the blueberry (Vaccinium corymbosum). Nevertheless, these genomes are at various levels of completeness and few have been anchored to chromosome scale and/or are haplotype-phased. We highlight the impact of a high-quality genome assembly for plant breeding and genetic research by showing how it affects our understanding of the genetic architecture of important traits and aids marker selection and candidate gene detection. We compared the results of genome-wide association studies and genomic selection that were already published using a blueberry draft genome as reference with the results using the recent released chromosome-scale and haplotype-phased blueberry genome. We believe that the benefits shown herein reinforce the importance of genome assembly projects for other non-model species.

High-Resolution Linkage Map and QTL Analyses of Fruit Firmness in Autotetraploid Blueberry

Blueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits related to machine harvestability through Quantitative Trait Loci (QTL) mapping is the first step toward implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses in 2-year field trials for a trait crucial to machine harvesting: fruit firmness. Preliminary insights were also sought for single evaluations of firmness retention after cold storage, and fruit detachment force traits. Significant QTL peaks were identified for all the traits and overlapping QTL intervals were detected for firmness across the years. We found low-to-moderate QTL effects explaining the phenotypic variance, which suggest a quantitative nature of these traits. The QTL intervals were further speculated for putative gene repertoire. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.

Understanding the Complexity of Cold Tolerance in White Clover using Temperature Gradient Locations and a GWAS Approach

White clover ( L.) is the most important grazing perennial forage legume in temperate climates. However, its limited capacity to survive and restore growth after low temperatures during winter constrains the productivity and wide adoption of the crop. Despite the importance of cold tolerance for white clover cultivar development, the genetic basis of this trait remains largely unknown. Hence, in this study, we performed the first genome-wide association study (GWAS) analyses in white clover to identify quantitative trait loci (QTL) for cold-tolerance-related traits. Seeds from 192 divergent genotypes from six populations in the Patagonia region of South America were collected and seed-derived plants were further clonally propagated. Clonal trials were established in three locations representing temperature gradient associated with elevation. Given the allotetraploid nature of the white clover genome, distinct genetic models (diploid and tetraploid) were tested. Only the tetraploid parameterization was able to detect the 53 loci associated with cold-tolerance traits. Out of the 53 single nucleotide polymorphism (SNP) trait associations, 17 controlled more than one trait or were stable across multiple sites. This work represents the first report of QTL for cold-tolerance-related traits, providing insights into its genetic basis and candidate genomic regions for further functional validation studies.

Diagnosis and management of Aspergillus diseases: executive summary of the 2017 ESCMID-ECMM-ERS guideline

The European Society for Clinical Microbiology and Infectious Diseases, the European Confederation of Medical Mycology and the European Respiratory Society Joint Clinical Guidelines focus on diagnosis and management of aspergillosis. Of the numerous recommendations, a few are summarized here. Chest computed tomography as well as bronchoscopy with bronchoalveolar lavage (BAL) in patients with suspicion of pulmonary invasive aspergillosis (IA) are strongly recommended. For diagnosis, direct microscopy, preferably using optical brighteners, histopathology and culture are strongly recommended. Serum and BAL galactomannan measures are recommended as markers for the diagnosis of IA. PCR should be considered in conjunction with other diagnostic tests. Pathogen identification to species complex level is strongly recommended for all clinically relevant Aspergillus isolates; antifungal susceptibility testing should be performed in patients with invasive disease in regions with resistance found in contemporary surveillance programmes. Isavuconazole and voriconazole are the preferred agents for first-line treatment of pulmonary IA, whereas liposomal amphotericin B is moderately supported. Combinations of antifungals as primary treatment options are not recommended. Therapeutic drug monitoring is strongly recommended for patients receiving posaconazole suspension or any form of voriconazole for IA treatment, and in refractory disease, where a personalized approach considering reversal of predisposing factors, switching drug class and surgical intervention is also strongly recommended. Primary prophylaxis with posaconazole is strongly recommended in patients with acute myelogenous leukaemia or myelodysplastic syndrome receiving induction chemotherapy. Secondary prophylaxis is strongly recommended in high-risk patients. We strongly recommend treatment duration based on clinical improvement, degree of immunosuppression and response on imaging.

QTLs Associated with Crown Root Angle, Stomatal Conductance, and Maturity in Sorghum

Three factors that directly affect the water inputs in cropping systems are root architecture, length of the growing season, and stomatal conductance to water vapor (). Deeper-rooted cultivars will perform better under water-limited conditions because they can access water stored deeper in the soil profile. Reduced limits transpiration rate () and thus throughout the vegetative phase conserves water that may be used during grain filling in water-limited environments. Additionally, growing early-maturing varieties in regions that rely on soil-stored water is a key water management strategy. To further our understanding of the genetic basis underlying root depth, growing season length, and we conducted a quantitative trait locus (QTL) study. A QTL for crown root angle (a proxy for root depth) new to sorghum was identified in chromosome 3. For , a QTL in chromosome seven was identified. In a follow-up field study it was determined that the QTL for was associated with reduced but not with net carbon assimilation rate () or shoot biomass. No differences in guard-cell length or stomatal density were observed among the lines, leading to the conclusion that the observed differences in must be explained by partial stomatal closure. The well-studied maturity gene was identified in the QTL for maturity. The transgressive segregation of the population was explained by the possible interaction of with other loci. Finally, the most probable position of the genes underlying the QTLs and candidate genes were proposed.

The misleading effect of serum galactomannan testing in high-risk haematology patients receiving prophylaxis with micafungin

OBJECTIVES

To investigate the performance of the routine serum galactomannan (sGM) assay in the diagnosis of invasive aspergillosis (IA) in high-risk haematology patients receiving prophylaxis with micafungin.

METHODS

Retrospective study including all haematological patients who received prophylaxis with micafungin during high-risk IA episodes (neutropenic patients after chemotherapy for acute myeloid leukaemia/myelodysplastic syndrome; allogeneic haematopoietic stem-cell transplantation during early neutropenic phase or graft-versus-host disease requiring high prednisone doses) and for whom at least one sGM result was available. Episodes were classified as follows: true-positive (positive GM in the context of IA), false-positive (positive GM result in patients who had no evidence of IA), true-negative (negative GM test results and no IA), or false-negative (negative GM test in the context of IA). Non-evaluable patients were excluded.

RESULTS

Among 146 evaluable episodes, four were true-positive in the context of probable breakthrough IA (incidence of breakthrough IA, 2.7%); 111/146 high-risk episodes (76%) were considered true-negative and 31/146 (21.2%) were considered false-positive. No false-negative episodes were detected. All but one of the false-positive episodes were detected in surveillance GM tests, leading to high-resolution CT scans in eight cases (8/31; 25.8%), all of which were negative. The positive predictive and negative predictive values of sGM for surveillance and diagnostic approaches were 3.2% (1/31) and 100% (110/110) and 75% (3/4) and 100% (1/1), respectively.

CONCLUSIONS

Surveillance of asymptomatic patients receiving prophylaxis with micafungin using sGM is unnecessary, because the results are either negative or false-positive. However, sGM remains useful in the diagnosis of breakthrough IA in symptomatic patients during prophylaxis.

Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations

Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial resin canal number (RCN), single nucleotide polymorphisms (SNPs) in 4027 genes were tested for association with RCN in two growth rings and three environments in a complex pedigree of 520 Pinus taeda individuals (CCLONES). The map locations of associated genes were compared with RCN quantitative trait loci (QTLs) in a (P. taeda × Pinus elliottii) × P. elliottii pseudo-backcross of 345 full-sibs (BC1). Resin canal number was heritable (h(2) ˜ 0.12-0.21) and positively genetically correlated with xylem growth (rg ˜ 0.32-0.72) and oleoresin flow (rg ˜ 0.15-0.51). Sixteen well-supported candidate regulators of RCN were discovered in CCLONES, including genes associated across sites and ages, unidirectionally associated with oleoresin flow and xylem growth, and mapped to RCN QTLs in BC1. Breeding is predicted to increase RCN 11% in one generation and could be accelerated with genomic selection at accuracies of 0.45-0.52 across environments. There is significant genetic variation for RCN in loblolly pine, which can be exploited in breeding for elevated terpene content.

ESCMID and ECMM joint guidelines on diagnosis and management of hyalohyphomycosis: Fusarium spp., Scedosporium spp. and others

Mycoses summarized in the hyalohyphomycosis group are heterogeneous, defined by the presence of hyaline (non-dematiaceous) hyphae. The number of organisms implicated in hyalohyphomycosis is increasing and the most clinically important species belong to the genera Fusarium, Scedosporium, Acremonium, Scopulariopsis, Purpureocillium and Paecilomyces. Severely immunocompromised patients are particularly vulnerable to infection, and clinical manifestations range from colonization to chronic localized lesions to acute invasive and/or disseminated diseases. Diagnosis usually requires isolation and identification of the infecting pathogen. A poor prognosis is associated with fusariosis and early therapy of localized disease is important to prevent progression to a more aggressive or disseminated infection. Therapy should include voriconazole and surgical debridement where possible or posaconazole as salvage treatment. Voriconazole represents the first-line treatment of infections due to members of the genus Scedosporium. For Acremonium spp., Scopulariopsis spp., Purpureocillium spp. and Paecilomyces spp. the optimal antifungal treatment has not been established. Management usually consists of surgery and antifungal treatment, depending on the clinical presentation.

Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential

Rapidly enhancing oleoresin production in conifer stems through genomic selection and genetic engineering may increase resistance to bark beetles and terpenoid yield for liquid biofuels. We integrated association genetic and genomic prediction analyses of oleoresin flow (g 24 h(-1)) using 4854 single nucleotide polymorphisms (SNPs) in expressed genes within a pedigreed population of loblolly pine (Pinus taeda) that was clonally replicated at three sites in the southeastern United States. Additive genetic variation in oleoresin flow (h(2) ≈ 0.12-0.30) was strongly correlated between years in which precipitation varied (r(a) ≈ 0.95), while the genetic correlation between sites declined from 0.8 to 0.37 with increasing differences in soil and climate among sites. A total of 231 SNPs were significantly associated with oleoresin flow, of which 81% were specific to individual sites. SNPs in sequences similar to ethylene signaling proteins, ABC transporters, and diterpenoid hydroxylases were associated with oleoresin flow across sites. Despite this complex genetic architecture, we developed a genomic prediction model to accelerate breeding for enhanced oleoresin flow that is robust to environmental variation. Results imply that breeding could increase oleoresin flow 1.5- to 2.4-fold in one generation.

Interoperable and standard e-Health solution over Bluetooth

The new paradigm of e-Health demands open sensors and middleware components that permit transparent integration and end-to-end interoperability of new personal health devices. The use of standards seems to be the internationally adopted way to solve these problems. This paper presents the implementation of an end-to-end standards-based e-Health solution. This includes ISO/IEEE11073 standard for the interoperability of the medical devices in the patient environment and EN13606 standard for the interoperable exchange of the Electronic Healthcare Record. The design strictly fulfills all the technical features of the most recent versions of both standards. The implemented prototype has been tested in a laboratory environment to demonstrate its feasibility for its further transfer to the healthcare system.

Impaired cognition, sensorimotor gating, and hippocampal long-term depression in mice lacking the prostaglandin E2 EP2 receptor

Cyclooxygenase-2 (COX-2) is a neuronal immediate early gene that is regulated by N-methyl d aspartate (NMDA) receptor activity. COX-2 enzymatic activity catalyzes the first committed step in prostaglandin synthesis. Recent studies demonstrate an emerging role for the downstream PGE(2) EP2 receptor in diverse models of activity-dependent synaptic plasticity and a significant function in models of neurological disease including cerebral ischemia, Familial Alzheimer's disease, and Familial amyotrophic lateral sclerosis. Little is known, however, about the normal function of the EP2 receptor in behavior and cognition. Here we report that deletion of the EP2 receptor leads to significant cognitive deficits in standard tests of fear and social memory. EP2-/- mice also demonstrated impaired prepulse inhibition (PPI) and heightened anxiety, but normal startle reactivity, exploratory behavior, and spatial reference memory. This complex behavioral phenotype of EP2-/- mice was associated with a deficit in long-term depression (LTD) in hippocampus. Our findings suggest that PGE(2) signaling via the EP2 receptors plays an important role in cognitive and emotional behaviors that recapitulate some aspects of human psychopathology related to schizophrenia.

Risk factors for invasive aspergillosis in solid-organ transplant recipients: a case-control study

BACKGROUND

To facilitate the design of strategies for prevention of invasive aspergillosis in solid-organ transplant recipients, this study investigates whether the development of early-onset and late-onset aspergillosis are related to different risk factors, thereby distinguishing 2 risk populations for this serious complication.

METHODS

A retrospective case-control study was performed, including 156 cases of proven or probable invasive aspergillosis in patients recruited from 11 Spanish centers since the start of the centers' transplantation programs.

RESULTS

Among all patients, 57% had early-onset IA (i.e., occurred during the first 3 months after transplantation). Risk factor analysis in this group identified as significantly associated risk factors a more complicated postoperative period, repeated bacterial infections or cytomegalovirus disease, and renal failure or the need for dialysis. Among patients with late-onset infections (i.e., occurred > 3 months after transplantation), who comprised 43% of cases, the patients at risk were older, were in an overimmunosuppressed state because of chronic transplant rejection or allograft dysfunction, and had posttransplantation renal failure.

CONCLUSIONS

Risk factors in patients with early-onset cases and patients with late-onset cases of posttransplantation invasive aspergillosis are not the same, a fact that could have implications for the preventive approaches used for this infection.

Semiquantitative Culture of Open Surgical Wounds for Diagnosis of Surgical Site Infection

The aim of this study was to assess the performance of a semiquantitative culture method and traditional qualitative culture for the diagnosis of surgical site infections resulting in an open wound. Results were correlated with the definitions for the diagnosis of SSI proposed by the Centers for Disease Control and Prevention, Atlanta, Ga., USA. The sensitivity, specificity, positive and negative predictive values of the qualitative culture method were 96%, 61%, 84% and 89%, respectively. For the semiquantitative technique with a breakpoint of 15 colony forming units/plate these values were 91%, 96%, 98% and 83%, respectively. Analysis of the receiver operating characteristic curve revealed an area under the curve of 94.44% (95% confidence interval, 88.5%-99%) for the semiquantitative method. This result indicates that our easy-to-perform semiquantitative culture technique for open surgical wounds correlates better with the diagnosis of SSI than the traditional qualitative method.

Analysis and design of arrayed waveguide gratings with MMI couplers

We present an extension of the AWG model and design procedure described in [1] to incorporate multimode interference, MMI, couplers. For the first time to our knowledge, a closed formula for the passing bands bandwidth and crosstalk estimation plots are derived.

Effects of prediction on timing and dynamics of vergence eye movements

Periodic square waves were used to generate predictable vergence eye movement responses. The timing and dynamic characteristics of vergence eye movement responses to predictable and non-predictable stimuli were compared. Results showed significant changes in timing characteristics along with a highly characteristic anticipatory movement in the early part of predictable vergence responses. This phenomenon is similar to that seen in saccadic eye movements and appears to influence the timing and dynamics of the subsequent vergence response. A model-based analysis of dynamics showed that the pulse width, pulse gain, and step gain of the motor command signal did not show major differences between predictable and non-predictable response. However, other model parameters related to the acceleration of the response showed a substantial decrease when the movements were predictive.

Disparity vergence double responses processed by internal error

Disparity vergence eye movements occasionally exhibit two high-velocity components to a single step stimulus (Alvarez, T. L., Semmlow, J. L. & Yuan, W. (1998). Journal of Neurophysiology, 79, 37-44). This research investigates the neural strategy used to trigger the second component of double high-velocity vergence eye movements. Vergence doubles evoked by an experimental protocol that induces post-movement visual error were compared to doubles that occur normally. The second component of a visually evoked response double occurred later, and with slower dynamics, than that of a naturally occurring double. These differences in timing and dynamics indicate that natural double responses are mediated, at least in part, by a mechanism other than visual feedback. The faster dynamics and timing of natural doubles suggest that an internal monitoring process triggers these movements.

Dynamics of the disparity vergence step response: a model-based analysis

A new method to analyze the dynamics of vergence eye movements was developed based on a reconstruction of the presumed motor command signal. A model was used to construct equivalent motor command signals and transform an associated vergence transient response into an equivalent set of motor commands. This model represented only the motor components of the vergence system and consisted of signal generators representing the neural burst and tonic cells and a plant representing the ocular musculature and dynamics of the orbit. Through highly accurate simulations, dynamic vergence responses could be reduced to a set of five model parameters, each relating to a specific feature of the internal motor command. This dynamic analysis tool was applied to the analysis of inter-movement variability in vergence step responses. Model parameters obtained from a large number of response simulations showed that the width of the command pulse was tightly controlled while its amplitude, rising slope, and falling slope were less tightly regulated. Variation in the latter three parameters accounted for the most of the movement-to-movement variability seen in vergence step responses. Unlike version movements, pulse width did not increase with increased stimulus amplitude, although the other command signal parameters were substantially influenced by stimulus amplitude.

Short term modification of disparity vergence eye movements

Dynamics of disparity vergence eye movements can be modified by adaptive stimuli that generate large transient disparities. These modifications were observed for convergence as well as divergence eye movements. After modification, the peak velocities of the step responses for convergence and divergence were substantially higher than in normal baseline responses, a change observed in all four subjects studied. The change in peak velocity of a step response occurred very rapidly after presentation of the adaptive stimuli. Main sequence plots showed that first-order dynamic characteristics increased for post-adaptive responses with respect to normal step responses. Hence, response modification could be quantified as a change in gain accompanied with an increase in the effective response time constant. The adaptive responses to convergent and divergent 'disappearing' step stimuli revealed that the adaptation process modifies the high-velocity component of both disparity convergence and divergence eye movements. Moreover, a gain change in this component alone could account for both the gain and the time constant modifications seen in the overall response. A process of recovery or de-adaptation was also observed for both convergence and divergence eye movements. This observed short-term modification demonstrates a unique control mechanism for vergence eye movements that is effective in either direction.

Age-related changes in human ciliary muscle and lens: a magnetic resonance imaging study

PURPOSE

To use high-resolution magnetic resonance (MR) images of the eye to directly measure the relationship between ciliary muscle contraction and lens response with advancing age.

METHODS

A General Electric, 1.5-Tesla MR imager and a custom-designed eye imaging coil were used to collect high-resolution MR images from 25 subjects, 22 through 83 years of age. A nonmagnetic binocular stimulus apparatus was used to induce both relaxed accommodation (0.1 diopter [D]) and strong accommodative effort (8.0 D). Measurements of the ciliary muscle ring diameter (based on the inner apex), lens equatorial diameter, and lens thickness were derived from the MR images.

RESULTS

Muscle contraction is present in all subjects and reduces only slightly with advancing age. A decrease in the diameter of the unaccommodated ciliary muscle ring was highly correlated with advancing age. Lens equatorial diameter does not correlate with age for either accommodative state. Although unaccommodated lens thickness (i.e., lens minor axis length) increases with age, the thickness of the lens under accommodative effort is only modestly age-dependent.

CONCLUSIONS

Ciliary muscle contractile activity remains active in all subjects. A decrease in the unaccommodated ciliary muscle diameter, along with the previously noted increase in lens thickness (the "lens paradox"), demonstrates the greatest correlation with advancing age. These results support the theory that presbyopia is actually the loss in ability to disaccommodate due to increases in lens thickness, the inward movement of the ciliary ring, or both.

Dynamic details of disparity convergence eye movements

Classically, the primary tool for quantifying the dynamics of vergence and other eye movements has been the main sequence. The main sequence is a plot of peak velocity versus response amplitude and is particularly useful for comparing the dynamics of a large number of eye movements over a range of response amplitudes. However, the main sequence represents only the equivalent first-order behavior of a response and does not describe its dynamics in detail. Since the main sequence is based on only two points on the dynamic trajectory, it is sensitive to measurement artifacts and noise. A new methodology is presented which quantifies the equivalent second-order dynamics of eye movements using a larger region of the transient response. These new indexes were applied to vergence eye movements and were found to differentiate between subtle, but important differences in movement dynamics.

The role of radiotherapy in the conservative treatment of rectal carcinoma--the Lyon experience

The purpose of this study was to present the Lyon experience using radiotherapy alone or with surgery, with intent to cure rectal cancer and to avoid rectal amputation. Two groups of patients were treated between 1980 and 1996: Group I with radiotherapy alone with contact x-ray for T1 N0 (101 patients) or with a combination of external beam radiation therapy (EBRT), contact x-ray and 192 iridium implant in inoperable T2-3 N0-1 patients (43 patients); Group II with preoperative EBRT either as a pilot study (158 patients) or in a randomized trial (210 patients). With contact x-ray alone it was possible to control T1 N0 in 90% of cases, and with the combined approach 70% of the inoperable patients were controlled. In Group II, anterior resection was performed in 60% to 70% of the patients. Local recurrence was seen in 11% of cases. Surgery is the basic treatment used for rectal cancer but radiotherapy is playing an increasing role in the conservative treatment of this cancer.

Evidence for K+ channels involvement in capillary sensing and for bidirectionality in capillary communication

Although the capillary sensing and communication phenomenon has been characterized, its mechanism is not clear. It has been hypothesized that capillary sensing involves a membrane potential change in the capillary endothelium and/or pericyte and that communication represents an electrotonic spread of this change along the capillary. The goal of the present study was to address this hypothesis by examining the presence of K+ channels on the capillary and by determining bidirectionality of communication. Using intravital microscopy, we locally applied K+ (100 mM), acetylcholine (ACh; 3 mM), and norepinephrine (NE; 0.3 mM) on capillaries, 400-500 microns downstream from the arteriole, at the surface of the sartorius muscle in anesthetized frogs. Responses were measured in terms of red blood cell velocity (VRBC) changes in the stimulated capillary (control prestimulation VRBC ranged from 110 to 770 microns/sec). K+ and ACh caused significant 19 and 38% increases in VRBC, while NE caused a -46% decrease, respectively. The K+ response was blocked by local pretreatment with K+ channel blocker BaCl2 (1 microM) and by pretreatment with tetraethyl ammonium chloride (TEA; 5 mM). Responses to ACh and NE were attenuated by pretreatment with 1 microM BaCl2 (to 1%) and with 50 mM TEA (to -25%), respectively. In a separate experiment, NE (3 mM) application on the capillary 500 microns away from the draining venule (capillary occluded) caused a 19% venular constriction (i.e., similar to a reported 21% arteriolar constriction caused by the NE stimulus). We concluded that (i) K+ channels were present on the capillary and (ii) capillary communication was bidirectional. We interpreted these results to be consistent with the above hypothesis of membrane potential change and electrotonic spread.