ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization

BACKGROUND

Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions. Nevertheless, there is still an urgent need for sensitive, fast algorithms to maximise WES/WGS diagnostic yield in rare disease patients. Most tools devoted to this aim take advantage of patient phenotype information for prioritization of genomic data, although are often limited by incomplete gene-phenotype knowledge stored in biomedical databases and a lack of proper benchmarking on real-world patient cohorts.

METHODS

We developed ClinPrior, a novel method for the analysis of WES/WGS data that ranks candidate causal variants based on the patient's standardized phenotypic features (in Human Phenotype Ontology (HPO) terms). The algorithm propagates the data through an interactome network-based prioritization approach. This algorithm was thoroughly benchmarked using a synthetic patient cohort and was subsequently tested on a heterogeneous prospective, real-world series of 135 families affected by hereditary spastic paraplegia (HSP) and/or cerebellar ataxia (CA).

RESULTS

ClinPrior successfully identified causative variants achieving a final positive diagnostic yield of 70% in our real-world cohort. This includes 10 novel candidate genes not previously associated with disease, 7 of which were functionally validated within this project. We used the knowledge generated by ClinPrior to create a specific interactome for HSP/CA disorders thus enabling future diagnoses as well as the discovery of novel disease genes.

CONCLUSIONS

ClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses.

Dentate Gyrus Somatostatin Cells are Required for Contextual Discrimination During Episodic Memory Encoding

Memory systems ought to store and discriminate representations of similar experiences in order to efficiently guide future decisions. This problem is solved by pattern separation, implemented in the dentate gyrus (DG) by granule cells to support episodic memory formation. Pattern separation is enabled by tonic inhibitory bombardment generated by multiple GABAergic cell populations that strictly maintain low activity levels in granule cells. Somatostatin-expressing cells are one of those interneuron populations, selectively targeting the distal dendrites of granule cells, where cortical multimodal information reaches the DG. Nonetheless, somatostatin cells have very low connection probability and synaptic efficacy with both granule cells and other interneuron types. Hence, the role of somatostatin cells in DG circuitry, particularly in the context of pattern separation, remains uncertain. Here, by using optogenetic stimulation and behavioral tasks in mice, we demonstrate that somatostatin cells are required for the acquisition of both contextual and spatial overlapping memories.

Genetic testing among Spanish pediatric neurologists: Knowledge, attitudes and practices

Advances in genetic testing applied to child neurology have enabled the development of genetic tests with greater sensitivity in elucidating an etiologic diagnosis for common neurological conditions. The objective of the current study was to examine child neurologists' perspectives and insights into genetic testing. We surveyed 118 Spanish child neurologists, exploring their knowledge, attitudes, and practices concerning genetic tests. All of them had requested at least one genetic test in the past six months. Global developmental delay or intellectual disability in absence of a strong specific etiologic suspicion and autism spectrum disorders were the disorders for which genetic testing was most frequently requested. The most commonly requested genetic test was CGH-array. Overall, child neurologist perception of readiness for making genetic-related decisions was not bad, although many would like to have a greater support from geneticists and were interested in increasing the time dedicated to genetics within their continuing education program. These data have important implications for future practice, research, and education.

Association of ACACB polymorphisms with obesity and diabetes

Acetyl-CoA carboxylase beta, encoded by the ACAB gene, plays an important role in the oxidation of fatty acids. The aim of this study was to check the hypothesis that allelic variants of ACACB influence the risk of obesity and type 2 diabetes mellitus. Twenty five tagging single nucleotide polymorphisms (SNPs) capturing common variants of the ACACB gene were selected and analyzed in two cohorts including 1695 postmenopausal women of the general population and in 161 women with severe obesity (BMI>35). In vitro binding of transcription factors was explored by electrophoretic mobility shift assays (EMSA). T alleles at the rs2268388 locus were overrepresented in women with severe obesity (18% vs. 10% in controls; OR 1.74 [95% confidence interval 1.30-2.47]), which was statistically significant after multiple-test adjustment (p=0.0004). Likewise, T alleles at the rs2268388 locus and C alleles at the rs2239607 locus were associated with diabetes, in the discovery as well as in the replication cohorts, even after women with severe obesity were excluded (OR 3.6 and 2.8, for TT and CC homozygotes, respectively). Allelic differences in the binding affinity for nuclear proteins were revealed in vitro by EMSA and competition experiments were consistent with the binding of glucorticoid receptor and serum response factor. In conclusion, common polymorphisms of ACACB gene are associated with obesity and, independently, with type 2 diabetes in postmenopausal women, suggesting that the activity of acetyl-CoA carboxylase beta plays an important role in these disorders related to energy metabolism.

[Botulinum toxin type A for the treatment of primary hyperhidrosis: a prospective study of 52 patients]

BACKGROUND AND OBJECTIVES

Primary hyperhidrosis is characterized by excessive sweating in a defined region of the body. It should not be considered a purely cosmetic problem as it has a significant impact on the social and professional relationships of affected individuals. The aim of this study was to determine the clinical profile of patients with primary hyperhidrosis and assess the results obtained with the use of botulinum toxin type A (BTX-A) in clinical practice.

MATERIAL AND METHODS

The study included 52 patients (39 women and 13 men) with a diagnosis of primary hyperhidrosis treated for the first time with BTX-A. All patients completed a questionnaire that included the following information: age; sex; profession; age at onset, family history, and site of hyperhidrosis; accompanying signs and symptoms, and previous treatment; time to effect of BTX-A; local or systemic side effects; and severity of hyperhidrosis before and after BTX-A treatment.

RESULTS AND CONCLUSIONS

Primary hyperhidrosis began during puberty in 61.5% of the patients included in the study, 75% were women, and the mean age was 29.9 years. In 36.5% of patients, first-degree relatives also had primary hyperhidrosis. Hyperhidrosis was classified as palmar in 61.5% of cases, plantar in 53.8%, and axillary in 59.6%. Other sites were affected less frequently. The most common accompanying symptoms were facial erythema (32.7%), palpitations (30.7%), muscle tension (28.8%), shivering (23%), and headache (17.3%). Treatment with BTX-A was well tolerated and there was a highly significant reduction in the severity of hyperhidrosis 2 months after performing the treatment (P<0.001).

Progestogens reduce thromboxane production by cultured human endothelial cells

OBJECTIVES

Progestogens have been poorly studied concerning their roles in endothelial physiology. Prostanoids are vasoactive compounds, such as thromboxane A2, a potent vasoconstrictor, and prostacyclin, a vasodilator. We examined the effects of two progestogens used clinically, progesterone and medroxyprogesterone acetate, on thromboxane A2 production by cultured human umbilical vein endothelial cells (HUVEC) and investigated the role of progesterone receptors and the enzymes involved in production of thromboxane A2 and prostacyclin.

METHODS

Cells were exposed to 1-100  nmol/l of either progesterone or medroxyprogesterone acetate, and thromboxane A2 production was measured in culture medium by enzyme immunoassay. Gene expression of prostacyclin synthase and thromboxane synthase was analyzed by quantitative real-time polymerase chain reaction. Expression of prostacyclin synthase protein was analyzed by Western blot.

RESULTS

Both progestogens decreased thromboxane A2 release after 24 h. Protein and gene expression of prostacyclin synthase were increased after exposure to both progestogens, without changes in thromboxane synthase expression. These effects induced by progestogens were mediated through progesterone receptors, since they were decreased in the presence of the progesterone receptor antagonist RU486. The cyclo-oxygenase-1 selective inhibitor reduced thromboxane release.

CONCLUSION

Progesterone and medroxyprogesterone acetate decreased HUVEC thromboxane release in a progesterone receptor-dependent manner, without changes in thromboxane synthase expression and enhanced prostacyclin synthase gene and protein expression.

The new frontier of bone formation: a breakthrough in postmenopausal osteoporosis?

OBJECTIVE

Osteoporosis is a chronic disease that accelerates after menopause in many women. Most of the pharmacologic attempts to control the disease, such as hormone therapy, have emphasized the constraint of bone resorption. Since recent years have witnessed important advances in the field of bone formation, this review aims to update the present knowledge on the mechanisms affecting osteoblastogenesis and on the therapeutic results achieved by recently approved drugs.

METHOD

We sought peer-reviewed, full-length basic and clinical articles published between 1995 and May 2008 using a PubMed search strategy, with the terms osteoporosis and osteoblast, osteoporosis and strontium ranelate, and osteoporosis and parathyroid hormone (PTH). This search was further supplemented by a hand-search of reference lists of selected review papers. After crossing-cleaning the reference lists, some 800 articles were selected. Articles on regulators of osteoblast differentiation and function, together with well-designed clinical studies, were surveyed.

RESULTS

A complex network of systemic and local factors regulates osteoblastogenesis. Advances in fracture protection have been published in clinical studies with PTH. Some investigators claim an anabolic effect for strontium ranelate, which also confers protection against fracture.

CONCLUSION

The control of bone formation offers new clinical potential. Stimulation of bone formation by PTH has translated into fracture protection. The action of strontium ranelate has been claimed to be mediated by some level of bone formation, but this hypothesis still needs clarification.

A C >T polymorphism located at position -1 of the Kozak sequence of CD40 gene is associated with low bone mass in Spanish postmenopausal women

This study evaluated the association of a polymorphism in the CD40 gene with BMD and risk of osteopenia or osteoporosis in a population of 602 postmenopausal women. Results showed that women with the TT genotype had lower BMD at femoral neck and spine sites and increased risk of osteopenia or osteoporosis.

INTRODUCTION

Recent findings have demonstrated that the CD40/CD40L system, which is of main importance for the immune system, can also be implied in the regulation of bone metabolism. The main objective of the present work has been to clarify whether single nucleotide polymorphisms (SNPs) affecting genes of CD40/CD40L system could be linked with abnormalities in the level of bone mineral density (BMD) in menopausal women.

METHODS

We performed an association study of BMD values with a SNP located at position -1 of the Kozak consensus sequence of CD40 gene (rs1883832; C>T) in a population of 602 postmenopausal women.

RESULTS

Women with the TT genotype (8.6% of women) displayed a reduction in femoral neck BMD (FN BMD) and lumbar spine BMD (LS BMD) of 6.2% and of 6.3%, respectively, as compared to women with CC + CT genotype. Logistic regression analysis adjusted for age, weight, and height showed that women with the TT genotype had increased risk for FN (odds ratio: 2.34; 95% CI: 1.12-4.89) and LS (odds ratio: 2.49; 95% CI: 1.19-5.24) osteopenia or osteoporosis.

CONCLUSIONS

Women with the TT genotype in rs1883832 SNP affecting to Kozak consensus sequence of CD40 gene had lower BMD at FN and at LS sites and increased risk of osteopenia or osteoporosis.

Comparative effects of 17beta-estradiol, raloxifene and genistein on bone 3D microarchitecture and volumetric bone mineral density in the ovariectomized mice

This study assessed the effect of estradiol, raloxifene and genistein on the preservation of bone 3D-microarchitecture and volumetric bone mineral density (vBMD) in the ovariectomized mouse model. Our results indicated that raloxifene was more effective in preserving bone ovariectomized-induced changes, the advantage being concentrated in both bone microarchitecture and vBMD.

INTRODUCTION

This study assessed the effect of different estrogen receptor (ER) agonists on the preservation of bone 3D-microarchitecture and volumetric bone mineral density (vBMD) in the ovariectomized (OVX) mouse model.

METHODS

Twelve-week-old female C57BL/6 mice were randomly assigned to one of five groups: (1) SHAM-operated + vehicle; (2) OVX + vehicle; (3) OVX + 17beta-estradiol (5 microg/kg); (4) OVX + raloxifene (1 mg/kg); (5) OVX + genistein (25 mg/kg), during 4-weeks. Bone microarchitecture and trabecular, cortical and total vBMD of distal femur were imaged by ex vivo microcomputed tomography (micro-CT).

RESULTS

Ovariectomy produced a global deterioration involving both trabecular and cortical 3D-microarchitecture and vBMD. Raloxifene maintained both microarchitecture and vBMD, whereas estradiol prevented deterioration of some microstructural parameters, such as trabecular thickness (Tb.Th), trabecular bone pattern factor (Tb.Pf), and cortical periosteal perimeter (Ct.Pe.Pm), but did not completely block the loss in vBMD. Mice treated with genistein exhibited the less favourable profile in both vBMD and microstructural parameters preserving only cross-sectional bone area (B.Ar) and Ct.Pe.Pm in cortical bone.

CONCLUSION

Our data indicate that, at the selected doses, raloxifene was more effective in preserving bone OVX-induced changes than either estradiol or genistein, the advantage being concentrated in both bone microarchitecture and vBMD.

Estrogen receptor agonists and immune system in ovariectomized mice

Several data implicate the immune system in bone lost after estrogen deficiency, however, some of the effects on the immune system of estrogen deficiency or of estrogen receptor (ER) modulation are not well established. In this study, the effect of ER agonists on the immune system in ovariectomized mice is analyzed. Mice were ovariectomized and were administered 17beta-estradiol (E2), raloxifene (RAL) or genistein (GEN). The effect of a 4-week treatment on bone turnover and on several parameters that reflect the status of the immune system was studied. Results show that ovariectomy provoked both uterine atrophy and thymic hypertrophy. Although RAL corrected thymic hypertrophy, only E2 corrected both. Ovariectomized mice showed increased levels of serum calcium and cathepsin K gene expression and decreased levels of serum alkaline phosphatase (ALP) activity, which suggests that there is a persistent alteration in bone metabolism. Moreover, ovariectomy increased B-cells and CD25+ cells, and decreased the percentages of T-cells and Cbfa1 gene expression in bone marrow (BM). All ER agonists corrected, although to different degrees, changes induced by the ovariectomy. Furthermore, results showed that it is essential to adjust ER agonist doses to avoid immunosuppression, since all ER agonists decreased BM T-cell levels.

Alterations in the phenotype and function of immune cells in ovariectomy-induced osteopenic mice

BACKGROUND

Within the last few years, much evidence has been presented on the involvement of the immune system in certain types of bone loss, such as activated T cells in rheumatoid arthritis and in periodontitis. Estrogen deficiency induces bone loss; however, how this deficiency affects the immune system has not been sufficiently studied.

METHODS

To evaluate the effects of estrogen withdrawal on the status and functionality of the immune system, mice were ovariectomized or sham-operated, and 5 weeks after surgery, when osteopenia had developed, several parameters were analysed in spleen and in bone marrow. We analysed bone turnover, cell phenotype by flow cytometry, cell function by cell proliferation assays, and the expression of several genes related to the process.

RESULTS

Five weeks after ovariectomy, augmented osteoclastogenesis persisted in the bone marrow. In addition, the ovariectomized mice had more B-cells and CD3+ T-cells expressing the receptor activator of NF-kappaB ligand (CD3+/RANKL+). The ovariectomized mice had lower serum alkaline phosphatase activity, a normal amount of T cells, lower percentages of CD11b+ and CD51+ cells in the bone marrow, and a lower serum interferon-gamma level compared with sham-operated controls.

CONCLUSIONS

The data suggest that, 5 weeks after ovariectomy, bone turnover remains imbalanced, with increased osteoclastogenesis and a decreased rate of bone formation. Moreover, there is an increase in B-cell formation, with normal and decreased percentages of T cells and myelomonocytic cells (CD11b+), respectively, in the bone marrow. Decreased serum interferon-gamma levels could be involved in the increased osteoclastogenesis found in the present work.

[Control of arterial hypertension by means of a regimen of hemodialysis on alternate days (HDAA or EODD: "Every Other Day Dialysis") versus 2 conventional regiments of 4 and 5 hours per session 3 times a week with 72 hours without sessions during the weekends]

An increase in the frequency of hemodialysis sessions improves control of extracellular volume and blood hypertension and consequently reduces the mortality related to cardiovascular aetiology in hemodialysis patients.We report the evolution of the blood hypertension depending on the need for antihypertensive drugs in a group of 38 prevalent patients that were included in a every-other-day dialysis schedule (EODD), and compare it with the results in two other groups of prevalent patients that were dialyzed in conventional, previously employed schedules without week-end sessions 4 hours x 3 x week and 5 hours x 3 x week. All three groups received hemodialysis treatment for more than 6 months.A 68% (26/38) of the patients received antihypertensive treatment at the beginning the EODD schedule and, after 16 months, only 7.9% (3/38) of them required antihypertensive treatment (p < 0.001) with reduction in two of the three remanent patients; hypertension control in those 25 patients took an average of 100 +/- 15 days. The final frequency of hypertension in EODD was lower (p < 0.002) than the frequency registered in the 84 prevalent patients in 4h x 3 x week schedule, and also lower (p = 0.065) than the frequency of the 56 prevalent patients in 5h x 3 x week schedule. There is a significant difference (p < 0,05) between EODD and 4h x 3 x week schedule as regards average figures of: increase in weight, decrease in dry-weight, blood pressure levels and hypotension incidence. EODD also produced better results than 5h x 3 x week schedule in this regard although statistics did not reflect it. The results using the every-other-day hemodialysis schedule support previous experiences(Lecce, Columbia) which achieved a good control of the dry-weight by means of suppressing the volume overload gained during the weekend and consequently obtaining adequate ultrafiltration rates and high reduction both of the hypertension and of the symptoms of intolerance to hemodialysis, which are so frequent in conventional schedules with 72 hours without hemodialysis sessions.

Progestogens stimulate prostacyclin production by human endothelial cells

BACKGROUND

The effects of progestogens on endothelial physiology are poorly studied. Prostacyclin is a potent vasodilator synthesized by two isoforms of cyclooxygenase (COX) in endothelium. We examined the effects of two clinically used progestogens, progesterone and medroxyprogesterone acetate (MPA), on prostacyclin production by cultured human umbilical vein endothelial cells (HUVEC) and the possible role of progesterone receptors and both COX enzymes.

METHODS

Cells were exposed to 1-100 nmol/l of either progesterone or MPA and prostacyclin production was measured in culture medium.

RESULTS

Both progestogens significantly increased prostacyclin release in a time- and dose-dependent manner, being higher than control after 24 h. Progesterone and MPA, both at 10 nmol/l, increased mRNA expression and protein content of both COX. All these effects were mediated through progesterone receptor activation, since they were abolished by treatment of cells with the progesterone receptor antagonist RU-486. Selective inhibitors of COX-1 and -2 (SC-560 and NS-398 respectively) reduced basal prostacyclin release, and eliminated increased production in response to progestogens. In combination with estradiol, progestogens had an additive effect without eliminating estradiol-induced prostacyclin production.

CONCLUSIONS

Our results support the hypothesis that progesterone and MPA increased HUVEC prostacyclin production in a progesterone receptor-dependent manner, by enhancing COX-1 and COX-2 expression and activities.

Bone turnover markers and PTH levels in surgical versus natural menopause

In order to assess similarities and differences in women that suffer surgical versus natural menopause, a series of bone, clinical, and biochemical parameters was assayed in a clinical sample of 35 women with surgical menopause and 112 women with natural menopause. Biochemical parameters included hormones [parathyroid hormone (PTH) and the sex steroids estradiol and testosterone] and several markers of bone turnover measured in urine (N-telopeptide and calcium/creatinine ratio) or serum (osteocalcin, total alkaline phosphatase, total and ionic calcium, phosphate, and magnesium). In addition to type of menopause, women were divided by years since menopause (ysm </= 2 or >2). To detect differences and relationships between variables, ANOVA, ANCOVA, and linear regression analyses were used. Only N-telopeptide, one resorption marker, was significantly affected by the variable years since menopause </=2 or >2 ( P <0.01), but not by type of menopause. The age-corrected level of PTH was significantly decreased in the surgical menopause group ( P < 0.05). In conclusion, type of menopause did not impose significant differences in bone turnover markers. PTH, one powerful resorption hormone, was diminished in surgical menopause.

Effect of dietary supplementation with a mixture of Vitamins C and E on fertilization of tertiary butyl hydroperoxide-treated oocytes and parthenogenetic activation in the mouse

The present study aims to analyze the effect of dietary supplementation with a mixture of Vitamins C and E on fertilization and later development of tertiary butyl hydroperoxide (tBH)-treated mouse oocytes and on parthenogenetic activation of freshly ovulated mouse oocytes. We fed hybrid mice a standard diet supplemented or not supplemented with Vitamins C and E from the first day of weaning until the age of 12 weeks. We noted no significant effect of diet on fertilization rate, percentage of total and hatching blastocysts, total number of cells, mitotic index and percentage of apoptotic nuclei at 120 h post-insemination of oocytes incubated for 15 min in the presence of 0, 1, 5 and 10 microM tBH. Furthermore, diet did not affect the percentage of activated oocytes after treatment with Ca2+ ionophore, acid Tyrode's solution or ethanol. The percentage of parthenogenetically activated oocytes that progressed to the pronuclear stage was significantly higher in the antioxidant group. Oocytes from antioxidant females exhibited a significantly lower mitogen-activated protein kinase (MAPK) activity than oocytes from control females. We detected no significant differences between groups in M-phase-promoting factor (MPF) activity. These results show that oral administration of antioxidants decreases MAPK activity and increases the probability of reaching the pronuclear stage after parthenogenetic activation.

The decade 1989-1998 in Spanish psychology: an analysis of research in statistics, methodology, and psychometric theory

This paper presents an analysis of research published in the decade 1989-1998 by Spanish faculty members in the areas of statistical methods, research methodology, and psychometric theory. Database search and direct correspondence with faculty members in Departments of Methodology across Spain rendered a list of 193 papers published in these broad areas by 82 faculty members. These and other faculty members had actually published 931 papers over the decade of analysis, but 738 of them addressed topics not appropriate for description in this report. Classification and analysis of these 193 papers revealed topics that have attracted the most interest (psychophysics, item response theory, analysis of variance, sequential analysis, and meta-analysis) as well as other topics that have received less attention (scaling, factor analysis, time series, and structural models). A significant number of papers also dealt with various methodological issues (software, algorithms, instrumentation, and techniques). A substantial part of this report is devoted to describing the issues addressed across these 193 papers--most of which are written in the Spanish language and published in Spanish journals--and some representative references are given.

Intrasaccadic perception

Mammalian vision has a lowpass frequency characteristic that filters out fast temporal oscillations. Thus, fast-drifting gratings cannot be detected with static eyes, but the same gratings can easily be detected by executing saccades. Because these gratings are invisible under fixation, they are useful for isolating and studying intrasaccadic perception, which is normally masked by presaccadic and postsaccadic perception. We have conducted a number of psychophysical studies using these stimuli, and here we report that intrasaccadic visual processing allows for motion perception, that gratings drifting in the direction of a saccade are perceived as having more contrast than the same gratings drifting in the opposite direction, and that intrasaccadic contrast perception has sufficient grain to allow psychophysical matching of the perceived contrast of gratings drifting in opposite directions. The conditions in which these phenomena occur disprove a recent hypothesis that intrasaccadic motion perception occurs for stimuli processed by the magnocellular system, and our results can be explained by assuming that the temporal lowpass characteristic that accounts for flicker fusion phenomena under vision with static eyes is also operative during saccades.

Optimal setups for forced-choice staircases with fixed step sizes

Forced-choice staircases with fixed step sizes are used in a variety of formats whose relative merits have never been studied. This paper presents a comparative study aimed at determining their optimal format. Factors included in the study were the up/down rule, the length (number of reversals), and the size of the steps. The study also addressed the issue of whether a protocol involving three staircases running for N reversals each (with a subsequent average of the estimates provided by each individual staircase) has better statistical properties than an alternative protocol involving a single staircase running for 3N reversals. In all cases the size of a step up was different from that of a step down, in the appropriate ratio determined by García-Pérez (Vision Research, 1998, 38, 1861 - 1881). The results of a simulation study indicate that a) there are no conditions in which the 1-down/1-up rule is advisable; b) different combinations of up/down rule and number of reversals appear equivalent in terms of precision and cost: c) using a single long staircase with 3N reversals is more efficient than running three staircases with N reversals each: d) to avoid bias and attain sufficient accuracy, threshold estimates should be based on at least 30 reversals: and e) to avoid excessive cost and imprecision, the size of the step up should be between 2/3 and 3/3 the (known or presumed) spread of the psychometric function. An empirical study with human subjects confirmed the major characteristics revealed by the simulations.

Role of Nijmegen breakage syndrome protein in specific T-lymphocyte activation pathways

Nijmegen breakage syndrome (NBS) is a genetic disorder characterized by immunodeficiency, microcephaly, and "bird-like" facies. NBS shares some clinical features with ataxia telangiectasia (AT), including increased sensitivity to ionizing radiation, increased spontaneous and induced chromosome fragility, and strong predisposition to lymphoid cancers. The mutated gene that results in NBS codes for a novel double-stranded DNA break repair protein, named nibrin. In the present work, a Spanish NBS patient was extensively characterized at the immunological and the molecular DNA levels. He showed low CD3(+)-cell numbers and an abnormal low CD4(+) naive cell/CD4(+) memory cell ratio, previously described in AT patients and also described in the present report in the NBS patient. The proliferative response of peripheral blood lymphocytes in vitro to mitogens is deficient in NBS patients, but the possible link among NBS mutations and the abnormal immune response is still unknown.

Luminance artifacts of cathode-ray tube displays for vision research

Phosphor persistence, video bandwidth, DC restoration and high-voltage regulation affect the appearance of images presented on cathode-ray tubes (CRTs), potentially resulting in differences between nominal and actual stimuli. We illustrate these effects by measuring physical parameters of horizontal and vertical static and counter-phase flickering gratings, and we illustrate problems for vision research by measuring contrast sensitivity to these gratings. We also measured the extent to which calibration protocols actually result in the monitor being calibrated over its entire area regardless of image size. The results of our physical measurements indicate substantial differences between gratings that nominally differ only as to orientation. Consistent with these differences, our psychophysical measurements indicate different sensitivities when the bars of the gratings are parallel or orthogonal to raster lines, regardless of the retinal orientation of the gratings. The results of our calibration check show that only a small region around the target area of calibration can be regarded as effectively linearized, and only if the size of the test image used during the check is similar to the size of the calibration patch. Overall, our results indicate potentially severe problems with the use of CRTs in vision research, and we discuss some published results that are likely to have been affected by these problems.

Novel mutations and defective protein kinase C activation of T-lymphocytes in ataxia telangiectasia

Three ataxia telangiectasia (AT) patients have been characterized immunologically and molecularly. Patient 1 presents two nondescribed splicing mutations which affect exons 15 and 21 of the ATM gene. The maternal defect consists of a G > A transition in the first nucleotide of the intron 21 donor splicing site which results in a complete deletion of exon 21. The paternal mutation consists of an A > C transversion in the intron 14 acceptor splicing site which produces a partial skipping of exon 15. Two abnormal alternative transcripts were found, respectively, 17 and 41 nucleotides shorter. Patient 2 presents a homozygous genomic deletion of 28 nucleotides in the last exon of the gene. This deletion changes the normal reading frame after residue 3003 of the protein and introduces a premature stop codon at residue 3008 that could originate a truncated ATM protein. Patient 3, a compound heterozygote, presents a defect which consists of a G > A transition in the first nucleotide of intron 62 donor splicing site which results in a complete deletion of exon 62. The results obtained during a three year period in the proliferation assays show an impaired PMA (phorbol myristate acetate) activation in specific T lymphocyte activation pathways (CD69, CD26, CD28, CD3, PHA, PWM and Con A mediated) but not in others (CD2, ionomycin, and Ig surface receptor). The possible link among specific ATM mutations and abnormal immune responses is unknown.

Cathepsin C gene: First compound heterozygous patient with Papillon-Lefèvre syndrome and a novel symptomless mutation

Papillon-Lefèvre syndrome (PLS) has recently been shown to be caused by mutations in the cathepsin C gene resulting in periodontal disease and palmoplantar keratosis. Thirteen different homozygous mutations have been characterised in PLS patients of different ethnic origin. In the present paper, a PLS patient is described who carries two novel mutations (706G>T and 872G>A) in the paternal and maternal chromosomes, respectively. This is the first compound patient described so far. In addition, a novel symptomless mutation (458C>T) in the cathepsin C gene is described in three homozygous individuals. Thus, not all mutations should be considered as a cause of disease, whether case studies or general population screening is performed. Another already described mutation that provoked the Haim-Munk syndrome (HMS) in Indian Jews has also been found to give rise to PLS in a Spanish family from Madrid. On the other hand, PLS patients are ameliorated by retinoids, which indicates that retinoids may be used as therapeutic agents in this immune system deficiency.

Yes-no staircases with fixed step sizes: psychometric properties and optimal setup

Interest in the use of adaptive staircase methods in clinical practice is increasing, but time limitations require that they be based on yes-no trials. The psychometric properties of yes-no staircases with fixed step sizes (FSS staircases) in small-sample situations have never been studied in depth. As a result, information is lacking as to what is the optimal setup for an FSS staircase. To determine this optimal setup, we used simulation techniques to study the asymptotic and small-sample convergence of yes-no FSS staircases as a function of the up/down rule, the size of the steps up or down, the starting stimulus level, the spread of the psychometric function, and the lapsing rate. Our results indicate that yes-no FSS staircases with steps up and down of the same size are unstable because with these settings, the staircases yield different results across variations in irrelevant parameters such as the spread of the psychometric function or the starting level. Our study also identified settings with which the properties of estimates are unaffected by these factors. With these optimal settings, yes-no FSS staircases can provide very quick and accurate estimates in 7 to 8 trials. Practical recommendations are given to get the best out of yes-no FSS staircases.

A point mutation in a domain of gamma interferon receptor 1 provokes severe immunodeficiency

Gamma interferon (IFN-gamma) and the cellular responses induced by it are essential for controlling mycobacterial infections. Most patients bearing an IFN-gamma receptor ligand-binding chain (IFN-gammaR1) deficiency present gross mutations that truncate the protein and prevent its expression, giving rise to severe mycobacterial infections and, frequently, a fatal outcome. In this report a new mutation that affects the IFN-gammaR1 ligand-binding domain in a Spanish patient with mycobacterial disseminated infection and multifocal osteomyelitis is characterized. The mutation generates an amino acid change that does not abrogate protein expression on the cellular surface but that severely impairs responses after the binding of IFN-gamma (CD64 and HLA class II induction and tumor necrosis factor alpha and interleukin-12 production). A patient's younger brother, who was also probably homozygous for the mutation, died from meningitis due to Mycobacterium bovis. These findings suggest that a point mutation may be fatal when it affects functionally important domains of the receptor and that the severity is not directly related to a lack of IFN-gamma receptor expression. Future research on these nontruncating mutations will make it possible to develop new therapeutical alternatives in this group of patients.

Exact finite-sample significance and confidence regions for goodness-of-fit statistics in one-way multinomials

As multinomial processing tree models become more popular in psychology, appropriate methods for statistical inference also become more necessary. Conventional methods are all based on the asymptotic chi-square approximation to the exact multinomial test, but the accuracy of this approximation has been shown to be poor in the usual small-sample situation. This paper describes an efficient algorithm that allows the exact multinomial test to be applied without incurring prohibitive computational costs. The algorithm is well suited to addressing three different aspects of statistical inference in one-way multinomials: (i) evaluating the exact significance of a multinomial test; (ii) determining significance at a given preset level; and (iii) enumerating exact confidence regions. Examples are given that illustrate how this algorithm accomplishes each of these tasks, and an analysis of its computational cost in some small-sample situations is also provided.

A novel CD18 genomic deletion in a patient with severe leucocyte adhesion deficiency: a possible CD2/lymphocyte function-associated antigen-1 functional association in humans

Leucocyte adhesion deficiency (LAD) is an autosomal-recessive genetic disease that is characterized clinically by severe bacterial infections and caused by mutations in the CD18 gene that codes for the beta2 integrin subunit. A patient with a severe LAD phenotype was studied and the molecular basis of the disease was identified as a single homozygous defect in a Herpes virus saimiri (HVS)-transformed T-cell line. The defect identified involves a deletion of 171 bp in the cDNA that encodes part of the proteic extracellular domain. This genetic abnormality was further studied at the genomic DNA level and found to consist of a deletion of 169 bp (from -37 of intron 4 to +132 of exon 5), which abolishes the normal splicing and results in the total skipping of exon 5. The 171-bp shortened 'in-frame' mRNA not only resulted in the absence of CD18 expression on the cell surface but also in its absence in the cytoplasm of HVS T-cell lines. Functionally, the LAD-derived HVS T-cell lines showed a severe, selective T-cell activation impairment in the CD2 (but not in the CD3) pathway. This defect was not reversible when exogenous interleukin-2 (IL-2) was added, suggesting that there is also a functional interaction of the lymphocyte function-associated antigen-1 (LFA-1) protein in the CD2 signal transduction pathway in human T cells, as has been previously reported in mice and in the human Papillon-Lefèvre syndrome. Thus, HVS transformation is not only a suitable model for T-cell immunodeficiency studies and characterization, but is also a good system for investigating the immune system in pathological conditions. It may also be used in the future in cellular models for in vitro gene-therapy trials.

Complex cells as linear mechanisms receiving sequential afferents

Complex cells in mammalian visual cortex appear to be non-linear mechanisms lacking a structured receptive field, and different complex cells display mutually inconsistent behaviors. Current models postulate nonlinear interactions among multiple simultaneous afferents, but none explains the diversity of complex cell behaviors. We propose that complex cell inputs are sequential and cyclic. Cells receiving such input behave as if their spatial receptive field changes shape over time. Different putative time-varying receptive fields arise when the number of afferents, their characteristics and/or the sequence of their inputs vary, and simulations show that they exhibit all reported varieties of complex cell behavior. Our results suggest a common functional description for simple and complex cells. Additional non-linearities are unnecessary to explain complex cell behavior.

MPROB: computation of multinomial probabilities

An algorithm for computing exact multinomial probabilities is presented that uses the fewest number of operations that are possible without symbolic simplification of the multinomial coefficient and performs them in a sequence that minimizes the potential for overflow or underflow errors. Multinomial probabilities computed with this algorithm are accurate to machine precision, unlike those based on logarithmic transformations and/or the evaluation of factorials, using Stirling's approximation.

Identification of a cytogenetic deletion and of four novel mutations (Q69X, I172F, G188V, G197R) affecting the gene for ornithine transcarbamylase (OTC) in Spanish patients with OTC deficiency

A deletion of at least 11.5 cM in the paternal X chromosome mapping between microsatellites DXS989 and DXS1003 and encompassing the genes for ornithine transcarbamylase (OTC), retinitis pigmentosa GTPase regulator (RPGR) and dystrophin, was associated with the loss of band Xp21 in a female patient with OTC deficiency. Another four female patients were heterozygous for point mutations in the OTC gene: the nonsense mutation Q69X or the missense mutations I172F, G188V and G197R. In the OTC amino acid sequence, I172 and G197 are proximate to residues involved in catalysis, and G188 is within a loop joining helix 5 and strand 6 in the core of the ornithine-bindingdomain. Therefore, the mutations of these residues may cause structural changes affecting catalysis and/or the architecture of the ornithine domain. The mutation appeared "de novo" in the patients or, in one case, in the mother of the patient, in agreement with the predominance of "de novo" mutations in female patients of OTC deficiency. There was full agreement between the results of mutational analysis and of allopurinol testing in the patients and their female relatives, supporting the value of the allopurinol test in the detection of carriers of OTC deficiency. This deficiency is a genetically heterogeneous X-linked condition.

Direction selectivity and spatiotemporal separability in simple cortical cells

Simple cells in mammalian visual cortex are quasi-linear mechanisms whose behavior departs from true linearity in a very consistent manner. Empirical research on direction selectivity (DS) clearly illustrates these characteristics. A linear DS cell will be DS for all stimuli, whereas a linear non-DS cell will not be DS for any stimuli. However, many simple cells have opposite preferred directions for stimuli of reversed polarity, and some cells are DS for some stimuli (e.g., moving bars) but not for others (e.g., drifting gratings). Also, linear non-DS cells must have separable spatiotemporal receptive fields (RFs), and linear DS cells must have inseparable RFs. Yet many actual DS cells have separable RFs. Here we present a nonlinear model of simple-cell behavior that reproduces all of these empirical behaviors. The model is a variant of the current linear model, amended to include an interleaved nonlinearity (half-wave rectification) that allows it to mimic the (im)balance of push-pull mechanisms. We present simulation results showing that balanced push-pull mechanisms result in linear behavior, while imbalanced push-pull arrangements produce all of the incongruent DS-related behaviors that have been reported for simple cells.

Fitting logistic IRT models: small wonder

State-of-the-art item response theory (IRT) models use logistic functions exclusively as their item response functions (IRFs). Logistic functions meet the requirements that their range is the unit interval and that they are monotonically increasing, but they impose a parameter space whose dimensions can only be assigned a metaphorical interpretation in the context of testing. Applications of IRT models require obtaining the set of values for logistic function parameters that best fit an empirical data set. However, success in obtaining such set of values does not guarantee that the constructs they represent actually exist, for the adequacy of a model is not sustained by the possibility of estimating parameters. This article illustrates how mechanical adoption of off-the-shelf logistic functions as IRFs for IRT models can result in off-the-shelf parameter estimates and fits to data. The results of a simulation study are presented, which show that logistic IRT models can fit a set of data generated by IRFs other than logistic functions just as well as they fit logistic data, even though the response processes and parameter spaces involved in each case are substantially different. An explanation of why logistic functions work as they do is offered, the theoretical and practical consequences of their behavior are discussed, and a testable alternative to logistic IRFs is commented upon.

Lack of covariation of the effects of luminance and eccentricity on contrast sensitivity

BACKGROUND AND PURPOSE

Qualitative individual differences in visual processing along various stimulus dimensions have been previously documented. For instance, as compared to the foveal contrast sensitivity function (CSF), the peripheral CSF of some subjects shifts toward lower frequencies, but it scales down for others; also, sensitivity to low spatial frequencies increases monotonically with luminance in some subjects, but it displays a decline at high luminances in others. Although these qualitatively distinct eccentricity- and luminance-related patterns have been thoroughly described separately, their joint occurrence has never been studied. This study aimed at determining whether there is covariation between the effects of luminance and eccentricity on contrast sensitivity, i.e., whether each eccentricity-related pattern occurs with one and only one of the luminance-related patterns.

METHODS

We have measured contrast sensitivity to sine-wave grating patches as a function of luminance and eccentricity in a sample of 18 subjects.

RESULTS

We found positive evidence of lack of covariation between the effects of eccentricity and luminance: we found subjects who show the same eccentricity-related pattern but differ as to their luminance-related patterns, and we have also found a subject who, unlike the rest, shows qualitatively distinct luminance-related patterns at different eccentricities.

CONCLUSION

The dependence of contrast sensitivity on eccentricity and luminance is subject to qualitative variations both across and within individuals, suggesting that meaningful conclusions on the effects of luminance and eccentricity on contrast sensitivity cannot be drawn when the data from all available subjects are aggregated.

Immunodeficiency associated with anorexia nervosa is secondary and improves after refeeding

Several studies have addressed the question of starvation effects on immune function by means of changes in lymphocyte subsets, cytokine induction or lymphocyte activation. Anorexia nervosa (AN) patients are severely malnourished and contradictory results have been obtained regarding the accompanying immunodeficiency, including its assignation as a part of the primary nervous disorder. In the present work, an extensive immunological function examination was carried out on 40 AN patients who were compared with a control group of 14 healthy girls. The AN patients were also classified according to their nutritional status (by the Body Mass Index: BMI), this being critical for a better understanding of these secondary immunodeficiency bases. Moreover, another immune system study was performed on five patients after refeeding. Lymphocyte subsets and function, cytokine induction and peripheral blood concentrations, and innate as well as humoral immunity were evaluated. Deregulation in the cytokine network, owing to the interaction of the central nervous (CNS) and immune systems, seems to be the initial immune alteration in AN immunodeficiency but it has not been disproved that the immunodeficiency is a direct consequence of the original psychiatric perturbation. Spontaneous high levels of circulating interleukin-1beta (IL-1beta) and tumour necrosis factor-alpha (TNF-alpha) have been observed; this is probably one of the causes of the anomalies found in the T-cell subpopulations (mainly the naive CD4+CD45RA+ reduction and the cytotoxic CD8+ increase) and T-cell activation status (mainly the down-regulation of the CD2 and CD69 activation pathways). This finally leads to an impairment, not only in T-cell function but also in T-cell to B-cell co-operation. The AN specificity of these results is confirmed by the fact that these immune alterations improve after refeeding and when nutritional status becomes less critical, which also suggests that AN immunodeficiency is indeed secondary to malnutrition.

Forced-choice staircases with fixed step sizes: asymptotic and small-sample properties

Visual detection and discrimination thresholds are often measured using adaptive staircases, and most studies use transformed (or weighted) up/down methods with fixed step sizes--in the spirit of Wetherill and Levitt (Br J Mathemat Statist Psychol 1965;18:1-10) or Kaernbach (Percept Psychophys 1991;49:227-229)--instead of changing step size at each trial in accordance with best-placement rules--in the spirit of Watson and Pelli (Percept Psychophys 1983;47:87-91). It is generally assumed that a fixed-step-size (FSS) staircase converges on the stimulus level at which a correct response occurs with the probabilities derived by Wetherill and Levitt or Kaernbach, but this has never been proved rigorously. This work used simulation techniques to determine the asymptotic and small-sample convergence of FSS staircases as a function of such parameters as the up/down rule, the size of the steps up or down, the starting stimulus level, or the spread of the psychometric function. The results showed that the asymptotic convergence of FSS staircases depends much more on the sizes of the steps than it does on the up/down rule. Yet, if the size delta+ of a step up differs from the size delta- of a step down in a way that the ratio delta-/delta+ is constant at a specific value that changes with up/down rule, then convergence percent-correct is unaffected by the absolute sizes of the steps. For use with the popular one-, two-, three- and four-down/one-up rules, these ratios must respectively be set at 0.2845, 0.5488, 0.7393 and 0.8415, rendering staircases that converge on the 77.85%-, 80.35%-, 83.15%- and 85.84%-correct points. Wetherill and Levitt's transformed up/down rules--which require delta-/delta+ = 1--and the general version of Kaernbach's weighted up/down rule--which allows any delta-/delta+ ratio--fail to reach their presumed targets. The small-sample study showed that, even with the optimal settings, short FSS staircases (up to 20 reversals in length) are subject to some bias, and their precision is less than reasonable, but their characteristics improve when the size delta+ of a step up is larger than half the spread of the psychometric function. Practical recommendations are given for the design of efficient and trustworthy FSS staircases.

The optimal motion stimulus: comments on Watson and Turano (1995)

Watson and Turano (Vision Research 1995;35:325-336) described experimental research aimed at determining the motion stimulus that the visual system detects best. They reported conflicting results in the determination of the optimal spatial size and they interpreted them as an effect of probability summation. They also reported disagreement with earlier results of Watson et al. (Nature 1983;302:419-422). This study shows (i) that probability summation is not responsible for those results and (ii) that they can be explained as a consequence of the method that was used to search for the optimal stimulus.

Missense mutations in codon 225 of ornithine transcarbamylase (OTC) result in decreased amounts of OTC protein: a hypothesis on the molecular mechanism of the OTC deficiency

Mutations P225L and P225R were identified in codon 225 of the gene for ornithine transcarbamylase (OTC) in two patients with the neonatal form of OTC deficiency. The mutations occur at a CpG dinucleotide and eliminate a unique MspI restriction site in exon 7 of the OTC gene. They do not alter existing splice sites or create new sites, as judged from the nucleotide sequence. Both mutations are associated with undetectable levels of OTC antigen in liver homogenates, and with either complete lack of OTC activity (P225R mutation) or very small residual activity (0.15% of normal in the P225L mutation). The residual activity observed with P225L exhibits normal pH dependence, little or no increases in the Km values for ornithine and carbamoyl phosphate and normal stability at either 37 degrees C or, in the presence of 0.66 mol/L urea, at 0 degree C. The latter conditions were used to examine whether the P225L mutation favours dissociation of the active OTC trimer. Given the normal stability and lack of tendency to dissociation of the mutant enzyme, it appears likely that the dramatic reduction in the level of OTC protein is due to inefficient conversion of the mutant OTC precursor polypeptide (pOTC) into the correctly localized, appropriately folded, mature enzyme trimer, suggesting degradation of pOTC in transit to the mitochondria.

The transition from DeVries-Rose to Weber's laws: comments on Rovamo, Mustonen and Näsänen (1995)

Rovamo et al. [Vision Research (1995), 35, 767-774] measured contrast sensitivity at several frequencies in the fovea and periphery as a function of retinal illuminance, concluding that the critical illuminance for the transition from DeVries-Rose to Weber's laws is proportional to squared frequency at all retinal locations. Yet, inspection of their data clearly reveals that the DeVries-Rose range was hardly ever followed by a Weber range: either no sign of any second range was apparent or the transition was to a qualitatively different range in which sensitivity decreased with increasing illuminance. The validity of their conclusions is questioned, and the status of the "DeVries-Rose to Weber transition" as a description of the relationship between sensitivity and illuminance is discussed in the light of mounting empirical evidence of a decreasing range in this relationship.

Do channels shift their tuning towards lower spatial frequencies in the periphery?

Space-variant multichannel spatial vision models include either anchored channels whose units (sensors) share their tuning frequency, or shifting channels whose sensors shift their tuning towards lower frequencies in the periphery. Each type of model embodies a different type of structural organization across eccentricity. Anchored- and shifting-channel models are tested in this paper against empirical data from five types of relevant detection experiment: measurements of the local sine-wave contrast sensitivity function (CSF) at several eccentricities using (a) fixed apertures, (b) apertures scaled with eccentricity or (c) fixed number of cycles, (d) measurements of foveal sensitivity as a function of aperture size, and (e) measurements of the contrast sensitivity gradient across the visual field. Each type of model is shown to predict a different outcome in each type of experiment. A review of empirical research reveals that three of the five experiment types have yielded two distinct sets of results, each of which is consistent with the predictions from one of the types of model, while the two other types of experiment have always yielded similar results which support anchored-channel models. Further scrutiny of the models reveals that the distinction between anchored and shifting channels is more apparent than real, as model predictions are only determined by how sensor gain is assumed to change with eccentricity and tuning frequency. Two alternative sensor gain functions are identified and interpreted in terms of two versions of the cortical magnification theory of spatial vision. Altogether, these two functions account for all extant data on the five types of experiment, suggesting individual differences in the functional organization of the human visual system across eccentricity.

A splicing mutation, a nonsense mutation (Y167X) and two missense mutations (I159T and A209V) in Spanish patients with ornithine transcarbamylase deficiency

Four novel mutations are identified in the ornithine transcarbamylase (OTC) gene, in four patients with OTC deficiency (an X-linked disorder). The mutations represent three different categories: missense (Ile159Thr and Ala209Val), nonsense (Tyr167Stop), and causing inefficient splicing (G-->A in the first intronic base) with associated aberrant splicing. They are located in exons 5, and 6, and in intron 3. Two of the mutations arose de novo in the patients, and only one mutation occurs at a CpG site. The nonsense and the splicing mutation cause, respectively, lethal early onset and non-lethal, delayed early onset clinical presentations in males. Our results confirm for Spain the high genotypic heterogeneity of OTC deficiency.

Demonstration of the spf-ash mutation in Spanish patients with ornithine transcarbamylase deficiency of moderate severity

We have found in patients with ornithine transcarbamylase (OTC) deficiency from two Spanish families (A and B), replacement by A of G at the 3'-end of exon 4 of the OTC gene. The same mutation is found in the spf-ash mouse, a rodent model of mild OTC deficiency, causing a neutral R129H mutation and inefficient splicing at the 5' donor site of the exon 4-intron 4 junction, with resultant 4%-7% residual OTC activity. The mutation, detected in our patients using polymerase chain reaction (PCR) amplification of the ten OTC exons, single strand conformation polymorphism (SSCP) analysis and direct sequencing of PCR-amplified exon 4, results in the loss of a unique MspI restriction site which can be used for rapid diagnosis. The mutation was transmitted by the mother in family A and arose de novo in the patient in family B. Residual OTC activity, determined in a male and a female patient, was 1.3% and 3.5% of normal, respectively. Despite this low activity, the surviving patients have developed normally.

Deriving channel gains from large-area sine-wave contrast sensitivity data

A wealth of detection data can be accounted for by a spatial-vision model including a finite number of space-variant, spatial-frequency and orientation-selective channels of varying gains coupled with a detection rule involving probability summation over space and among channels. This paper shows that the detection of large-area, foveally fixated sine-wave gratings can be understood as if it occurred merely as a result of the activity of the subset of channels whose orientation matches that of the gratings, and operating under a peak-detection rule. This simplification makes it possible to show the theoretical relationship between the large-area sine-wave contrast sensitivity function, the channel gain function, and the channel modulation-transfer functions. It is also shown that the human visual system must have many more channels than are normally assumed in spatial-vision models, for otherwise the contrast sensitivity function would show significant bumps. An unlimited-channel model with a given mathematical form for the channels' modulation transfer functions is used to derive a mathematical expression for the (foveal) channel gain function from the large-area psychophysical sine-wave contrast sensitivity function.

N-acetyl-L-glutamate in brain: assay, levels, and regional and subcellular distribution

N-Acetyl-L-glutamate (NAG), the activator of mitochondrial carbamoyl phosphate synthetase (CPS), is demonstrated by several methods, including a new HPLC assay, in the brain of mammals and of chicken. The brain levels of NAG are 200-300 times lower than the levels of N-acetyl-L-aspartate (NAA), and are similar to the levels of NAG in rat liver. The NAG levels in chicken liver are very low. Although NAG is mitochondrial in the liver, it is cytosolic in brain. Using enzyme activity and immuno assays we did not detect CPS in brain (detection limit, 12.5 micrograms/g brain), excluding that brain NAG is involved in citrullinogenesis. The regional distribution of brain NAG differs from that of NAA and resembles that of N-acetyl-L-aspartyl-L-glutamate (NAAG), suggesting that NAG and NAAG are related. NAG might be involved in the modulation of NAAG degradation.

Visual phenomena without low spatial frequencies: a closer look

Two studies in which visual grouping and visual illusions were claimed to occur in the absence of low-spatial-frequency information are analyzed in detail. It is shown that this claim was not justified given the characteristics of the stimuli that were used in the demonstrations. It is concluded that visual grouping of unconnected elements without low spatial frequencies cannot be studied, and more work should be done before the role of low spatial frequencies in producing visual illusions is ruled out.