Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variant calling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources

Assessing the (a)symmetry of concentration-effect curves: empirical versus mechanistic models.

Modeling the shape of concentration-effect curves is of prime importance in pharmacology. Geometric descriptors characterizing these curves (the upper and lower asymptotes, the mid-point, the mid-point slope, and the point of inflection) are used for drug comparison or for assessing the change in agonist function after a system modification. The symmetry or asymmetry around the mid-point of a concentration-effect curve is a fundamental property that, regretfully, is often overlooked because, generally, models yielding exclusively symmetric curves are used. In the present review, empirical and mechanistic models are examined in their ability to fit experimental data. The geometric parameters of a survey of empirical models, the Hill equation, a logistic variant that we call the modified Hill equation, the Richards function, and the Gompertz model are determined. To analyze the relationship between asymmetry and mechanism, some examples from the ionic channel field, in an increasing degree of complexity, are used. It is shown that asymmetry arises from ionic channels with multiple binding sites that are partly occupied. The operational model of agonism is discussed both in its empirical general formulation and including the signal transduction mechanisms through G-protein-coupled receptors. It is shown that asymmetry results from systems where receptor distribution is allowed. Developed mathematical models are compared for describing experimental data on alpha-adrenoceptors. The existence or not of a relationship between the shape of the curves and receptor reserve is discussed.

Animals↗

Structure/function analysis of the domains required for the multimerisation of phenylalanine hydroxylase.

Phenylalanine hydroxylase (PAH) exists as an equilibrium of dimers and tetramers. However, there is little information concerning the inter- or intra-molecular interactions required for enzyme quaternary structure. It is predicted that the formation of a PAH tetramer will require at least two points of contact per enzyme subunit. Sequence analysis has suggested the existence of a C-terminal domain with characteristics of a leucine zipper or a variant of this called a coiled-coil. By deletion of 24 amino acids from the C-terminus or conversion of leucine 448 to an alanine residue, we have shown that this putative leucine zipper/coiled-coil domain is involved in the assembly of an active enzyme tetramer from dimers. The removal of this C-terminal domain of PAH reduces enzyme activity but does not abolish it. Furthermore, we report that an alanine 447 to aspartate mutation associated with phenylketonuria may affect subunit assembly which suggests the formation of enzyme tetramers is physiologically relevant. Our analysis of subunit interactions in vivo, show that in the absence of the C-terminal coiled-coil domain, dimers can form and this is only possible when the N-terminal domain is present. This provides the first evidence that N-terminal domain is required for multimerisation. We propose that the N-terminal regulatory domain in conjunction with the C-terminal coiled-coil domain, mediates the formation of fully active enzyme tetramers.

Amino Acid Sequence↗

When inclusion costs and ostracism pays, ostracism still hurts.

Recent research indicates that ostracism is painful even in the face of mitigating circumstances. However, in all previous experiments, there have been no costs to inclusion or benefits for ostracism. If being included meant losing money and being ostracized meant retaining money, would individuals still be distressed when ostracized? In 2 studies, the authors attempted to "load the dice" against inclusion in favor of ostracism. Participants played a variant of Cyberball called euroyberball (pronounced Euroball), in which ostracism and inclusion were crossed with whether the participants earned or lost money for each ball toss they received. In 2 experiments, the authors found that even when being ostracized meant retaining more money than the other players, it was painful. In Study 2, the authors also introduced conditions in which participants were overincluded. In these conditions, participants were sensitive to financial incentives. However, even then participants felt worse when given no positive attention than when given punitive attention.

Adult↗

Two distinct mechanisms of fibroblast adhesion.

The adhesion of cells to the connective tissue matrix is commonly thought to be governed by fibronectin, a pericellular glycoprotein with binding sites for cell surfaces, collagen and glycosaminoglycans. Here we report evidence that Chinese hamster ovary (CHO) cells possess an alternative mechanism for adhesion which is independent of fibronectin. Cells of a variant CHO clone called ADvF11 are defective in their ability to adhere to fibronectin-coated substrata, but can adhere to a substratum coated with SAM (substrate-attached material), a pericellular material produced by fibroblasts. The adhesion of wild-type CHO cells to fibronectin-coated substrate and adhesion of ADvF11 cells to SAM-coated substrata are differentially sensitive to proteolytic treatment. This suggests that there are two distinct adhesion mechanisms for CHO cells, only one of which is dependent on fibronectin.

Animals↗

Mutation of BSND causes Bartter syndrome with sensorineural deafness and kidney failure.

Antenatal Bartter syndrome (aBS) comprises a heterogeneous group of autosomal recessive salt-losing nephropathies. Identification of three genes that code for renal transporters and channels as responsible for aBS has resulted in new insights into renal salt handling, diuretic action and blood-pressure regulation. A gene locus of a fourth variant of aBS called BSND, which in contrast to the other forms is associated with sensorineural deafness (SND) and renal failure, has been mapped to chromosome 1p. We report here the identification by positional cloning, in a region not covered by the human genome sequencing projects, of a new gene, BSND, as the cause of BSND. We examined ten families with BSND and detected seven different mutations in BSND that probably result in loss of function. In accordance with the phenotype, BSND is expressed in the thin limb and the thick ascending limb of the loop of Henle in the kidney and in the dark cells of the inner ear. The gene encodes a hitherto unknown protein with two putative transmembrane alpha-helices and thus might function as a regulator for ion-transport proteins involved in aBS, or else as a new transporter or channel itself.

Animals↗

Urinary free cortisone and the assessment of 11 beta-hydroxysteroid dehydrogenase activity in man.

OBJECTIVE: Two isoforms of 11 beta-hydroxysteroid dehydrogenase (11 beta-HSD) catalyse the interconversion of cortisol to hormonally inactive cortisone; defects in the 11 beta-HSD2 isoform result in hypertension. The kidney, expressing high levels of 11 beta-HSD2, is the principal source of cortisone in man. We have validated the measurement of urinary free cortisone (UFE) excretion in normals and in patients with disorders of the pitultary-adrenal axis in an attempt to more accurately measure the activity of 11 beta-HSD2 in vivo. SUBJECTS: Forty-one normal adults, 12 normal children < 12 years of age, 15 patients with Cushing's syndrome, 12 with hypopitultarism on replacement hydrocortisone, 12 with the syndrome of apparent mineralocorticoid excess (AME) and 7 volunteers consuming liquorice. MEASUREMENTS: A complete 24-hour urine collection was analysed by gas chromatography/mass spectrometry for "A-ring' reduced cortisol and cortisone metabolites, i.e. tetrahydrocortisols (THF and allo-THF) and tetrahydrocortisone (THE). In addition, urinary free cortisol (UFF) and urinary free cortisone were quantified using deuterium-labelled internal standards. RESULTS: In normal adults and children, UFE excretion exceeded that of UFF (UFF 30.4 +/- 2.4 micrograms/24h (mean +/- SE), UFE 54.6 +/- 4.1 micrograms/24h, adults) (for conversion to nmol/24h multiply E by 2.78 and F by 2.76 respectively). Thus the normal UFF/UFE ratio was 0.54 +/- 0.05 in contrast to the (THF + allo-THF)/THE ratio of 1.21 +/- 0.06. UFE excretion was normal in hypopituitary patients on replacement hydrocortisone. Although UFE was elevated in all forms of Cushing's syndrome, the UFF/UFE ratio was grossly elevated in patients with the ectopic ACTH syndrome (14.0 +/- 6.7, n = 6). UFE was below the lower limit of the assay (< 1 microgram/24h) in most patients with the so-called type 1 variant of AME and significantly reduced in 4 patients described as having the type 2 variant of AME (10.5 +/- 3.5 micrograms/h, P < 0.05) and in 7 volunteers consuming liquorice (26.8 +/- 10.0 micrograms/24h, P < 0.01). In ectopic ACTH syndrome, AME, and liquorice ingestion the UFF/UFE ratio was more deranged than the (THF + allo-THF)/THE ratio. CONCLUSION: In normals the discrepant THF + allo-THF/ THE and UFF/UFE ratio suggests that much more of the UFE is derived from the kidney. Reduction in UFE excretion is seen following liquorice ingestion and in both variants of AME, though it is more profound in AME1. The high UFF/UFE ratio in the mineralocorticoid excess state seen in the ectopic ACTH syndrome is compatible with substrate-saturation of renal 11 beta-HSD2. The measurement of UFE and the UFF/UFE ratio is a significant advance in the analysis of human 11 beta-HSD activity in vivo; in particular, the UFF/UFE ratio appears to be a more sensitive index than the (THF + allo-THF)/THE ratio of renal 11 beta-HSD2 activity.

11-beta-Hydroxysteroid Dehydrogenases↗

Leiomyosarcoma of the heart and its pulmonary metastasis, both with prominent osteoclast-like multinucleated giant cells expressing tartrate-resistant acid phosphatase activity.

An autopsy case of cardiac leiomyosarcoma and its pulmonary metastasis, both with osteoclast-like multinucleated giant cells (OMGC) mimicking the so-called giant cell variant of malignant fibrous histiocytoma (MFH), is reported. The patient, a 70-year-old male, was admitted for sudden dyspnea. Extensive work-up established only a left atrial tumor mass. Three months after admission, the patient developed multiple intracranial and pulmonary metastases, followed by a worsening clinical course characterized by semicoma and dyspnea, and subsequently died 6 months after the onset of his symptoms. At subsequent autopsy, the left atrial polypoid tumor was found to have invaded destructively to the left half of the cardiac wall. Histology of the cardiac tumor revealed a bimorphic sarcoma in which a poorly differentiated leiomyosarcoma comfirmed by histologic and immunohistochemical findings was juxtaposed to a small nodule with features closely mimicking giant cell MFH. The pulmonary metastatic nodules exhibited features that were entirely indistinguishable from giant cell MFH except for the fact that a minority of polymorphic cells manifested myogenic differentiation. We believe that such a MFH-like pattern represents a pleomorphic form of leiomyosarcoma rather than a dedifferentiated one. The OMGC within the MFH-like component coexpressed CD68 and tartrate-resistant acid phosphatase activity.

Acid Phosphatase↗

Pituitary adenylate cyclase-activating polypeptide triggers dual transduction signaling in CATH.a cells and transcriptionally activates tyrosine hydroxylase and c-fos expression.

We used a catecholaminergic neuron-like cell line (CATH.a cells) as a model system to investigate the likelihood that pituitary adenylate cyclase-activating polypeptide (PACAP) may participate in the regulation of specific gene expression in catecholaminergic neurons. Analysis by reverse transcriptase-PCR amplification revealed the presence in these cells of type I PACAP receptors, with a short isoform, together with a heavier so-called Hop splice variant. PACAP38 and PACAP27 enhanced, in a dose-dependent manner, both cyclic AMP formation and phosphoinositide breakdown, with EC50 values of, respectively, 0.6 x 10(-10) and 2 x 10(-9) M. These peptides, in addition, also elevated [Ca2+]i by mobilizing intracellular calcium pools. Vasoactive intestinal peptide (VIP) was approximately 1,000-fold less potent in stimulating cyclic AMP (with EC50 = 2 x 10(-7) M) and failed to change the turnover of phosphoinositides and to alter [Ca2+]i. Both forms of PACAP, as well as forskolin, stimulated transcriptional induction of tyrosine hydroxylase (TH) and c-fos promoters fused to a chloramphenicol acetyltransferase (CAT) reporter gene in transiently transfected cells (p < 0.01 vs. controls). Induction of CAT activity linked to both TH and c-fos promoters was obliterated upon coexpression of a dominant inhibitory mutant (Mt-RAB) of cyclic AMP-dependent protein kinase. We conclude that CATH.a cells do express functional PACAP type I receptors, the activation of which impinges on TH and c-fos transcription according to a process that is primarily dependent on the cyclic AMP-PKA pathway.

Adenylyl Cyclases↗

Gitelman's syndrome revisited: an evaluation of symptoms and health-related quality of life.

BACKGROUND: Gitelman's syndrome (GS), also called Gitelman's variant of Bartter's syndrome, is an autosomal recessive renal disorder characterized by hypokalemia, hypomagnesemia, metabolic alkalosis, and hypocalciuria. GS is caused by inactivating mutations in the thiazide-sensitive sodium chloride cotransporter gene (NCCT). It is also known as the "milder" form of Bartter's syndrome, as patients with GS are usually diagnosed in adulthood during routine investigation. Symptoms reported in the literature range from asymptomatic, to mild symptoms of cramps and fatigue, to severe manifestations such as tetany, paralysis, and rhabdomyolysis. This is the first systematic evaluation of a large group of patients with genetically defined GS. METHODS: We evaluated the symptoms and quality of life (QOL) in 50 adult GS patients with confirmed mutations in NCCT, using a standardized questionnaire. This cohort was compared with 25 age- and sex-matched controls. RESULTS: GS patients were significantly more symptomatic than controls. The most common symptoms were salt craving, with musculoskeletal symptoms such as cramps, muscle weakness, and aches and constitutional symptoms such as fatigue, generalized weakness and dizziness, and nocturia and polydipsia. Forty-five percent of GS patients consider their symptoms a moderate to big problem. Measures of health-related QOL were significantly lower in GS patients compared with controls, particularly in terms of role limitations caused by physical health, emotion, level of energy, and general health perception. CONCLUSIONS: This descriptive study indicates that GS is not an asymptomatic disease and adversely affects QOL in these patients. Further studies are needed to assess the impact of therapy on symptoms and QOL.

Adolescent↗

[Significance of intermittent slow waves with right posterior accentuation in the EEG's of psychiatric patients].

The study was based on the frequent occurrence of intermittent slow waves right-posterior accentuation (IRP) in the EEGs of psychiatric patients. With regard to the EEG-phenomenon we present a detailed morphological and functional description as well as an evaluation from a developmental point of view. According to case histories a clinico-psychopathological characterization of the patients with IRP is given. The IRP-phenomenon can be interpreted electrogenetically against the background of and in connection with the so-called slow alpha variant rhythms as well as the posterior slow waves characteristic of children and adolescents. These patterns have in common a certain tendency to right-sided accentuation. In accord with a hypothesis (which has been derived from other observations and considerations) of a "maturation gradient" which favours the left hemisphere, we try to explain the IRP-phenomenon as an expression of a maturation deficit. Whereas the slow alpha variant rhythms and the posterior slow waves characteristic of children and adolescents appear bilaterally for the most part, IRP by definition, limited to the right hemisphere, may be considered as a less pronounced form in comparison. Deriving from clinico-psychopathological assessment the relationships are as follows: Patients with IRP account for about 5% of the in-patients in our psychiatric hospital. The IRP phenomenon seems to be closely linked to the male sex. Although a clear relationship with nosological categories (ICD) could not be proved, it seems that patients suffering from schizophrenic psychoses (ICD No. 295) are more frequently represented among the patients with the IRP-phenomenon than others. For the group of schizophrenic patients with IRP we found in contrast to a control group of schizophrenics without IRP a tendency to earlier onset of their disease. Compared with the control group it is found that the IRP groups consists of younger patients at the time of conducting this study. The two comparative groups of schizophrenics with and without IRP can be characterized by differences in the more or less pronounced manifestation of a fairly large number of AMDP items. Whereas for the IRP group a symptom pattern emerges with a hypermotoric -expansive accentuation, the control group seems to tend more towards a syndrome with depressive shading. The slight tendencies towards increased hereditary disposition as well as towards increased perinatal complications among the schizophrenic IRP patients necessitate further studies.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗

Third-order multireference perturbation theory: the n-electron valence state perturbation-theory approach.

A formulation of the n-electron valence state perturbation theory (NEVPT) at the third order of perturbation is presented. The present implementation concerns the so-called strongly contracted variant of NEVPT, where only a subspace of the first-order interacting space is taken into account. The resulting strongly contracted NEVPT3 approach is discussed in three test cases: (a) the energy difference between the 3B1 and 1A1 states of the methylene molecule, (b) the potential-energy curve of the N2 molecule ground state, and (c) the chromium dimer (Cr2) ground-state potential-energy profile. Particular attention is devoted to the last case where large basis sets comprising also h orbitals are adopted and where remarkable differences between the second- and third-order results show up.

Journal Article↗

Human hypoxanthine (guanine) phosphoribosyltransferase: an amino acid substitution in a mutant form of the enzyme isolated from a patient with gout.

We have investigated the molecular basis for a deficiency of the enzyme hypoxanthine (guanine) phosphoribosyltransferase (HPRT; IMP:pyrophosphate phosphoribosyltransferase, EC 2.4.2.8) in a patient with a severe form of gout. We reported in previous studies the isolation of a unique structural variant of HPRT from this patient's erythrocytes and cultured lymphoblasts. This enzyme variant, which is called HPRTLondon, is characterized by a decreased concentration of HPRT protein in erythrocytes and lymphoblasts, a normal Vmax, a 5-fold increased Km for hypoxanthine, a normal isoelectric point, and an apparently smaller subunit molecular weight. Comparative peptide mapping experiments revealed a single abnormal tryptic peptide in HPRTLondon. Edman degradation of the aberrant peptide from HPRTLondon identified a serine-to-leucine amino acid substitution at position 109. This substitution can be explained by a single nucleotide change in the codon for serine-109 (UCA leads to UUA). Thus a mutation at the HPRT locus has now been defined at the molecular level.

Amino Acid Sequence↗

The N-terminal end of Bax contains a mitochondrial-targeting signal.

The translocation of Bax alpha, a pro-apoptotic member of the BCL-2 family from the cytosol to mitochondria, is a central event of the apoptotic program. We report here that the N-terminal (NT) end of Bax alpha, which contains its first alpha helix (Eta alpha 1), is a functional mitochondrial-addressing signal both in mammals and in yeast. Similar results were obtained with a newly described variant of Bax called Bax psi, which lacks the first 20 amino acids of Bax alpha and is constitutively associated with mitochondria. Deletion of Eta alpha 1 impairs the binding of Bax psi to mitochondria, whereas a fusion of the N terminus of Bax alpha, which contains Eta alpha 1 with a cytosolic protein, results in the binding of the chimeric proteins to mitochondria both in a cell-free assay and in vitro. More importantly, the mitochondria-bound chimeric proteins inhibit the interaction of Bax psi with mitochondria as well as Bax-apoptogenic properties. The mutations of the Eta alpha 1, which inhibit Bax alpha and Bax psi translocation to mitochondria, also block the subsequent activation of the execution phase of apoptosis. Conversely, a deletion of the C terminus does not appear to influence Bax alpha and Bax psi mitochondrial addressing. Taken together, our results suggest that Bax is targeted to mitochondria by its NT and thus through a pathway that is unique for a member of the BCL-2 family.

Amino Acid Sequence↗

Impaired functioning of thermolabile methylenetetrahydrofolate reductase is dependent on riboflavin status: implications for riboflavin requirements.

BACKGROUND: Methylenetetrahydrofolate reductase (MTHFR; EC 1.7.99.5) supplies the folate needed for the metabolism of homocysteine. A reduction in MTHFR activity, as occurs in the homozygous state for the 677C-->T (so-called thermolabile) enzyme variant (TT genotype), is associated with an increase in plasma total homocysteine (tHcy). OBJECTIVE: In vitro studies suggest that the reduced activity of thermolabile MTHFR is due to the inappropriate loss of its riboflavin cofactor. We investigated the hypothesis that MTHFR activity in the TT genotype group is particularly sensitive to riboflavin status. DESIGN: We studied tHcy and relevant B-vitamin status by MTHFR genotype in a cross-sectional study of 286 healthy subjects aged 19-63 y (median: 27 y). The effect of riboflavin status was examined by dividing the sample into tertiles of erythrocyte glutathionine reductase activation coefficient, a functional index of riboflavin status. RESULTS: Lower red blood cell folate (P = 0.0001) and higher tHcy (P = 0.0082) concentrations were found in the TT group than in the heterozygous (CT) or wild-type (CC) groups. However, these expected relations in the total sample were driven by the TT group with the lowest riboflavin status, whose mean tHcy concentration (18.09 micromol/L) was almost twice that of the CC or CT group. By contrast, adequate riboflavin status rendered the TT group neutral with respect to tHcy metabolism. CONCLUSIONS: The high tHcy concentration typically associated with homozygosity for the 677C-->T variant of MTHFR occurs only with poor riboflavin status. This may have important implications for governments considering new fortification policies aimed at the prevention of diseases for which this genotype is associated with increased risk.

Adult↗

Marfan's disease and Erdheim's cystic medionecrosis. A study of their pathology.

Differentiation between Marfan's disease, or its forme fruste counterpart and Erdheim's cystic medionecrosis can be made in cases of aortic dilatation or dissection. This study examined the morphological features at light microscopy of aortic tissue, removed at surgery in 10 patients with Marfan's disease. A separate group consisted of 24 patients who did not express the complete Marfan phenotype but had family members who displayed the full and typical features of the disease. This group represented the so-called 'forme fruste' variant. These two groups were compared with 12 patients in whom a histopathological diagnosis of Erdheim's cystic medionecrosis had been made. Finally normal aortic tissue from post-mortem subjects were made available representing controls. In each case the degree of elastic fragmentation and cystic change of the aortic media was assessed and tabulated. The results indicate that severe fragmentation of elastic is similarly identifiable in both Marfan and Marfan forme fruste groups and that differentiation is easy pathologically from subjects with the comparatively modest fragmentation seen in Erdheim's cystic medionecrosis. Although cystic change was encountered in all groups, its severity tended to parallel the age of the subject, and we consider from our study that Erdheim's cystic medionecrosis represents no more than an exaggerated age-related change.

Adolescent↗

Encephalomyocarditis virus and diabetes mellitus: studies on virus mutants in susceptible and non-susceptible mice.

The so-called M-variant (especially subtype D) of encephalomyocarditis virus (EMCV) induces a diabetes-like syndrome in certain mouse strains which may serve as a model of insulin-dependent diabetes mellitus (IDDM) in man. The development and course of diabetes was influenced by a number of virus and host factors, among these being virus strain, virus dose, mouse strain, age, sex, and the host's immunological status. In a D-variant stock of EMCV, we found a virus plaque variant (PV 2) diabetogenic for DBA/2 mice, and at least one variant (PV 7) that did not affect carbohydrate metabolism. Although the diabetogenicity of PV 2 proved to be a genetically stable characteristic after further passages in vivo and in vitro, the incidence of diabetes varied somewhat (mean value 65% in 10-week-old DBA/2 mice infected with 10(5) p.f.u.). Both lower (10(1) or 10(3) p.f.u.) and higher (10(7) or 10(8) p.f.u.) virus doses led to a diminished incidence and severity of diabetes. In younger animals (5 weeks) transient hyperglycaemia often appeared, whereas in older animals (20 weeks) there was a higher rate of mortality. Histological examination of the islets of Langerhans in diabetes-susceptible (DBA/2) and resistant (C57BL/6) mice revealed that EMCV-induced hyperglycaemia appeared to develop in parallel to islet cell damage. Even in diabetic animals, some unaffected islets were regularly found. This study demonstrates that EMCV mutants may have completely different biological effects and produce diabetes only in special circumstances. Host factors play a significant role in the development of diabetes.

Age Factors↗

Efficient dynamic Monte Carlo algorithm for time-dependent catalytic surface chemistry.

Several numerical algorithms for dynamic Monte Carlo simulations of surface chemistry have been proposed in the past. The variable step size method (VSSM) is commonly used for systems where the rate coefficients are constant in time, owing to its good efficiency. If rate coefficients vary in time, the first reaction method (FRM) has been shown to be more efficient. However, the cost of this algorithm to execute a reaction step depends on the considered lattice size, which can make this method inefficient for systems involving surface phenomena on different scales. Here we propose a general and efficient algorithm, the fast first reaction method (fFRM), which has the advantages of being applicable to systems with constant and time-varying rate coefficients, and of having a computational cost per reaction step that is independent of the lattice size. An additional feature of fFRM is that it is rejection-free, which means that once a reaction class is selected, a reaction of that type will be executed. A rejection-free variant of VSSM, called rVSSM, is also presented, which leads to an approximately 15% speedup compared with the VSSM algorithm for the considered example.

Journal Article↗

The staircasing effect in neighborhood filters and its solution.

Many classical image denoising methods are based on a local averaging of the color, which increases the signal/noise ratio. One of the most used algorithms is the neighborhood filter by Yaroslavsky or sigma filter by Lee, also called in a variant "SUSAN" by Smith and Brady or "Bilateral filter" by Tomasi and Manduchi. These filters replace the actual value of the color at a point by an average of all values of points which are simultaneously close in space and in color. Unfortunately, these filters show a "staircase effect," that is, the creation in the image of flat regions separated by artifact boundaries. In this paper, we first explain the staircase effect by finding the subjacent partial differntial equation (PDE) of the filter. We show that this ill-posed PDE is a variant of another famous image processing model, the Perona-Malik equation, which suffers the same artifacts. As we prove, a simple variant of the neighborhood filter solves the problem. We find the subjacent stable PDE of this variant. Finally, we apply the same correction to the recently introduced NL-means algorithm which had the same staircase effect, for the same reason.

Algorithms↗