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PubMed1995

Unbalanced translocation t(5;17) in an typical acute promyelocytic leukemia.

Acute promyelocytic leukemia (APL; M3 in the FAB classification) is specifically associated with the t(15;17)(q23;q12) and the consequent formation of a PML/RARA fusion gene. A few cases of APL with a t(11;17)(q23;q12) and a PLZF/RARA fusion gene have recently been reported. In addition, a new variant, t(5;17)(q32;q12), with a RARA rearrangement was described in a child with atypical APL. We report an unbalanced der(5)t(5;17) in an atypical APL case showing unusual dysgranulopoiesis and some M2 features. The breakpoints were difficult to localize precisely on chromosome 5, because the translocation may have occurred on a previous del(5q). The karyotype also showed del(8q) and multiple double-minutes (dmin). Molecular studies evidenced RARA rearrangement but showed neither PML rearrangement nor PML/RARA fusion. Fluorescence in situ hybridization revealed that the dmin were of chromosome 8 origin and that they accounted for the MYC amplification observed in Southern blots. The patient did very poorly despite chemotherapy and all-trans retinoic acid (ATRA) treatment. Thus, the t(5;17) could represent a second type of variant translocation in APL that, like the disease associated with t(11;17), does not seem to respond to ATRA therapy. Whereas RARA rearrangement appears sufficient for an APL-like phenotype, it seems that the presence of a classical PML/RARA is required for typical APL with response to ATRA.

Aged↗
PubMed2000

An algebraic/graphical tool to compare ecosystems with respect to their pollution V: cluster analysis and Hasse diagrams.

In case of large data matrices comparative evaluations of objects/regions with the technique of Hasse diagrams may be troublesome due to a messy system of lines in the graphical representation. Here fuzzy clustering leads to useful simplifications because regions with slightly different pollution pattern are grouped together. However, fuzzy clustering implies to introduce a threshold value for the membership of an object to a cluster and to select the best number of clusters. Therefore many arbitrarities evolve. Within the systematic study presented here we found that some objects are very stable against variations of the threshold value and the number of cluster whereas other objects behaves different. According to their behaviour we investigated a classification of the objects. Formal Concept Analysis shows that in some cases specific pollution pattern imply the membership to one of these classes. For example objects which are characterized by high Pb-, Zn-concentration and moderate S-concentration imply a high stability against variants of the clustering process. Further implications are described in the paper.

Cadmium↗
PubMed2004

Genome wide identification and classification of alternative splicing based on EST data.

MOTIVATION: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon-intron boundaries, gene structure and alternative splicing events. However, the alternative splicing events are obscured by a large number of putatively artificial exon boundaries arising due to genomic contamination or alignment errors. The current work describes a methodology to associate quality values to the predicted exon-intron boundaries. High quality exon-intron boundaries are used to predict constitutive and alternative splicing ranked by confidence values, aiming to facilitate large-scale analysis of alternative splicing and splicing in general. RESULTS: Applying the current methodology, constitutive splicing is observed in 33,270 EST clusters, out of which 45% are alternatively spliced. The classification derived from the computed confidence values for 17 of these splice events frequently correlate (15/17) with RT-PCR experiments performed for 40 different tissue samples. As an application of the confidence measure, an evaluation of distribution of alternative splicing revealed that majority of variants correspond to the coding regions of the genes. However, still a significant fraction maps to non-coding regions, thereby indicating a functional relevance of alternative splicing in untranslated regions. AVAILABILITY: The predicted alternative splice variants are visualized in the SpliceNest database at http://splicenest.molgen.mpg.de

Algorithms↗
PubMed1998

Pharmacodynamic evaluation of factors associated with the development of bacterial resistance in acutely ill patients during therapy.

The selection of bacterial resistance was examined in relationship to antibiotic pharmacokinetics (PK) and organism MICs in the patients from four nosocomial lower respiratory tract infection clinical trials. The evaluable database included 107 acutely ill patients, 128 pathogens, and five antimicrobial regimens. Antimicrobial pharmacokinetics were characterized by using serum concentrations, and culture and sensitivity tests were performed daily on tracheal aspirates to examine resistance. Pharmacodynamic (PD) models were developed to identify factors associated with the probability of developing bacterial resistance. Overall, in 32 of 128 (25%) initially susceptible cases resistance developed during therapy. An initial univariate screen and a classification and regression tree analysis identified the ratio of the area under the concentration-time curve from 0 to 24 h to the MIC (AUC[0-24]/MIC) as a significant predictor of the development of resistance (P < 0.001). The final PK/PD model, a variant of the Hill equation, demonstrated that the probability of developing resistance during therapy increased significantly when antimicrobial exposure was at an AUC[0-24]/MIC ratio of less than 100. This relationship was observed across all treatments and within all organism groupings, with the exception of beta-lactamase-producing gram-negative organisms (consistent with type I beta-lactamase producers) treated with beta-lactam monotherapy. Combination therapy resulted in much lower rates of resistance than monotherapy, probably because all of the combination regimens examined had an AUC[0-24]/MIC ratio in excess of 100. In summary, the selection of antimicrobial resistance appears to be strongly associated with suboptimal antimicrobial exposure, defined as an AUC[0-24]MIC ratio of less than 100.

Acute Disease↗
PubMed2000

Induction of differentiation and apoptosis- a possible strategy in the treatment of adult acute myelogenous leukemia.

A differentiation block with accumulation of immature myeloid cells characterizes acute myelogenous leukemia (AML). However, native AML cells often show some morphological signs of differentiation that allow a classification into different subsets, and further differentiation may be induced by exposure to various soluble mediators, e.g., all trans-retinoic acid (ATRA) and several cytokines. Combination therapy with ATRA and chemotherapy should now be regarded as the standard treatment for the acute promyelocytic leukemia variant of AML. Several agents can induce leukemic cell differentiation for other AML subtypes, although these effects differ between patients. Differentiation may then be associated with induction of apoptosis, and differentiation-inducing therapy may therefore become useful in combination with intensive chemotherapy to increase the susceptibility of AML blasts to drug-induced apoptosis. However, it should be emphasized that differentiation and apoptosis can occur as separate events with different regulation in AML cells, and future studies in AML should therefore focus on: A) the identification of new agents with more predictable effects on differentiation and apoptosis; B) the use of clinical and laboratory parameters to define new subsets of AML patients in which differentiation/apoptosis induction has a predictable and beneficial effect, and C) further characterization of how AML blast sensitivity to drug-induced apoptosis is modulated by differentiation induction.

Adult↗
PubMed1991

[Polydactyly of the hands. Recommendation for expanded classification].

The few anatomical findings summarized in the literature have now been expanded by our own anatomical dissections on four hands of still-born infants with postaxial polydactyly, and by intra-operative microsurgical investigations of 25 polydactylous hands. New experimentally-based knowledge of embryology helps interpret the morphogenesis and specific anatomy of polydactyly. It can be postulated that both the location and definite form of polydactyly are a function of the location and extent of initial excessive cell proliferation and disturbance of cell necrosis in the hand blastema. The conclusive discussion of special findings regarding anatomical structures shows regular pattern formations which lend themselves to a broader classification. The classification of malformations of the hand by Temtamy and McKusick was used as a framework for the classification of polydactyly, whether it was existing as an isolated form or as part of a syndrome. The osteological types I to VI found by Wassel in thumb duplication are confirmed by our anatomical findings. Special coding of anatomical findings enabled us to identify four variants and three forms, depending on the development of the digital palmar arteries and nerves. For the triphalangeal pre-axial fingers and the post-axial fifth finger, the five osteological types described by Müller and those described by Duhamel are increased to ten. Comparison with our anatomical findings shows four variants of these osteological types. For post-axial polydactyly, types XI through XIV, existing in three variants, have been defined.

Fingers↗
PubMed1984

Brucella classification and regional distribution.

The most significant advances in the field of Brucella classification since the last meeting have been in the field of Brucella phages reviewed by Corbel & Morgan (1980) Handbuch der Bakteriellen Infektionen bei Tieren, 4, Ed Blobel & Schliesser) and Corbel & Morgan (Bergey's Manual of Determinative Bacteriology. In press). The Berkeley phages, especially the BK2 variant has been found to be able to lyse smooth B. melitensis, as well as smooth strains of the other species. A further advance has been the isolation of phages which lyse rough strains of B. abortus as well as B. canis and B. ovis. The most recent comprehensive account of the world-wide distribution of brucellosis has been given by Hansen and Müller (1982. Tierarztl Umschau 37, 564-570), supplemented by recent reviews by Morgan, Hellman, Weber, Meyer, and Wundt (1980) in Handbuch der Bakteriellen Infektionen bei Tieren 4). Except in those countries where B. abortus infection has been eradicated in cattle, the disease still remains a world-wide problem in cattle, sheep, goats and pigs as well as in wild animal reservoirs in certain parts of the world.

Bacteriophage Typing↗
PubMed2005

Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral.

BACKGROUND: Genetic testing for hereditary cancer syndromes contributes to the medical management of patients who may be at increased risk of one or more cancers. BRCA1 and BRCA2 testing for hereditary breast and ovarian cancer is one such widely used test. However, clinical testing methods with high sensitivity for deleterious mutations in these genes also detect many unclassified variants, primarily missense substitutions. METHODS: We developed an extension of the Grantham difference, called A-GVGD, to score missense substitutions against the range of variation present at their position in a multiple sequence alignment. Combining two methods, co-occurrence of unclassified variants with clearly deleterious mutations and A-GVGD, we analysed most of the missense substitutions observed in BRCA1. RESULTS: A-GVGD was able to resolve known neutral and deleterious missense substitutions into distinct sets. Additionally, eight previously unclassified BRCA1 missense substitutions observed in trans with one or more deleterious mutations, and within the cross-species range of variation observed at their position in the protein, are now classified as neutral. DISCUSSION: The methods combined here can classify as neutral about 50% of missense substitutions that have been observed with two or more clearly deleterious mutations. Furthermore, odds ratios estimated for sets of substitutions grouped by A-GVGD scores are consistent with the hypothesis that most unclassified substitutions that are within the cross-species range of variation at their position in BRCA1 are also neutral. For most of these, clinical reclassification will require integrated application of other methods such as pooled family histories, segregation analysis, or validated functional assay.

Amino Acid Sequence↗
PubMed2024

Obesity: exploring its connection to brain function through genetic and genomic perspectives.

Obesity represents an escalating global health burden with profound medical and economic impacts. The conventional perspective on obesity revolves around its classification as a "pure" metabolic disorder, marked by an imbalance between calorie consumption and energy expenditure. Present knowledge, however, recognizes the intricate interaction of rare or frequent genetic factors that favor the development of obesity, together with the emergence of neurodevelopmental and mental abnormalities, phenotypes that are modulated by environmental factors such as lifestyle. Thirty years of human genetic research has unveiled >20 genes, causing severe early-onset monogenic obesity and ~1000 loci associated with common polygenic obesity, most of those expressed in the brain, depicting obesity as a neurological and mental condition. Therefore, obesity's association with brain function should be better recognized. In this context, this review seeks to broaden the current perspective by elucidating the genetic determinants that contribute to both obesity and neurodevelopmental and mental dysfunctions. We conduct a detailed examination of recent genetic findings, correlating them with clinical and behavioral phenotypes associated with obesity. This includes how polygenic obesity, influenced by a myriad of genetic variants, impacts brain regions associated with addiction and reward, differentiating it from monogenic forms. The continuum between non-syndromic and syndromic monogenic obesity, with evidence from neurodevelopmental and cognitive assessments, is also addressed. Current therapeutic approaches that target these genetic mechanisms, yielding improved clinical outcomes and cognitive advantages, are discussed. To sum up, this review corroborates the genetic underpinnings of obesity, affirming its classification as a neurological disorder that may have broader implications for neurodevelopmental and mental conditions. It highlights the promising intersection of genetics, genomics, and neurobiology as a foundation for developing tailored medical approaches to treat obesity and its related neurological aspects.

Humans↗
PubMed2005

Phylogenetic analysis of the main neutralization and hemagglutination determinants of all human adenovirus prototypes as a basis for molecular classification and taxonomy.

Human adenoviruses (HAdV) are responsible for a wide spectrum of diseases. The neutralization epsilon determinant (loops 1 and 2) and the hemagglutination gamma determinant are relevant for the taxonomy of HAdV. Precise type identification of HAdV prototypes is crucial for detection of infection chains and epidemiology. epsilon and gamma determinant sequences of all 51 HAdV were generated to propose molecular classification criteria. Phylogenetic analysis of epsilon determinant sequences demonstrated sufficient genetic divergence for molecular classification, with the exception of HAdV-15 and HAdV-29, which also cannot be differentiated by classical cross-neutralization. Precise sequence divergence criteria for typing (<2.5% from loop 2 prototype sequence and <2.4% from loop 1 sequence) were deduced from phylogenetic analysis. These criteria may also facilitate identification of new HAdV prototypes. Fiber knob (gamma determinant) phylogeny indicated a two-step model of species evolution and multiple intraspecies recombination events in the origin of HAdV prototypes. HAdV-29 was identified as a recombination variant of HAdV-15 (epsilon determinant) and a speculative, not-yet-isolated HAdV prototype (gamma determinant). Subanalysis of molecular evolution in hypervariable regions 1 to 6 of the epsilon determinant indicated different selective pressures in subclusters of species HAdV-D. Additionally, gamma determinant phylogenetic analysis demonstrated that HAdV-8 did not cluster with -19 and -37 in spite of their having the same tissue tropism. The phylogeny of HAdV-E4 suggested origination by interspecies recombination between HAdV-B (hexon) and HAdV-C (fiber), as in simian adenovirus 25, indicating additional zoonotic transfer. In conclusion, molecular classification by systematic sequence analysis of immunogenic determinants yields new insights into HAdV phylogeny and evolution.

Adenovirus Infections, Human↗
PubMed1977

Primary clear cell carcinoma of the ovary. An analysis of 15 cases with review of the literature.

The clinical and pathological findings in 15 primary "pure" clear cell carcinoma of the ovary included in the Magee-Womens Hospital Tumor Registry from 1947 through 1974 are discussed. The ages of the patients ranged from 35 to 75 years (mean 53). The most common clinical finding was an abdominal mass in 14 cases. At surgery, five patients had extraovarian spread, one accompanied by ascitis. The tumors varied in diameter from 4 cm to 17 cm (mean 10.5 cm); grossly, about one-third were cystic, one-third solid and one-third had combined cystic and solid areas. Microscopically, four basic patterns were seen: papillary, tubular, solid, and cystic, and in several an admixture of the above. Clear cells predominated in 48% of the cases and 23% displayed hobnail cells. Most patients were treated by TAH & BSO or variants thereof, some followed by radiation or chemotherapy. Four patients died with cancer within 35 months after diagnosis; two others died of unrelated causes three and 12 years later. The actuarial survival was computed as 55% at five years. Five patients were stages as IIb (FIGO classification); four died with tumor and the remaining patient is alive with recurrent tumor in the pelvis 18 months after the original diagnosis. Three patients with tumors displaying the cystic pattern are still alive; two with a predominantly papillary pattern and vascular permeation are dead. It is suggested that survival rates in these 15 cases may be related more to the extent of the lesion at the initial presentation than to the gross or microscopic pattern.

Adenocarcinoma↗
PubMed2005

Classification of types of intraductal papillary-mucinous neoplasm of the pancreas: a consensus study.

Now that more than two decades have passed since the first reports of intraductal papillary-mucinous neoplasms (IPMNs), it has become clear that IPMN consists of a spectrum of neoplasms with both morphological and immunohistochemical variations. At a meeting of international experts on pancreatic precursor lesions held in 2003, it was agreed that a consensus classification of IPMN subtypes should be established to enable a more detailed analysis of the clinicopathological significance of the variations. Based on our experience and on information from the literature, we selected representative histological examples of IPMNs and defined a consensus nomenclature and criteria for classifying variants as distinctive IPMN subtypes including gastric type, intestinal type, pancreatobiliary type, and oncocytic type. These definitions can be used for further analyses of the clinicopathological significance of the variations of IPMN.

Biomarkers, Tumor↗
PubMedDate not supplied

[Differential diagnostic considerations in microcephalic dwarfism].

PURPOSE: While the rare Seckel-Syndrome is defined by clear criteria, clinical and radiologic findings for microcephalic osteodysplastic primordial dwarfism (MOPD) make an exact diagnosis and classification difficult. By comparing our patients to previously described cases of MOPD we evaluate the hypothesis that this disorder has a greater heterogeneity than has been believed up until now. Furthermore the differential diagnosis of the MOPD-complex is discussed. RESULTS: Two cases that show typical growth retardation, microcephalus and facial anomalies as well as osteodysplastic deformities including hip dysplasia are presented. The parents of both children are consanguineous and of Arabic race. In one of the children growth hormone levels were noticeably decreased. In discrepancy to the Seckel-syndrome both children showed no signs of mental retardation, therefore the classification into the heterogeneous group of microcephalic osteodysplastic primordial dwarfism (MOPD) is the most likely diagnosis. CONCLUSION: It is suggested that microcephalic osteodysplastic primordial dwarfism (MOPD) has a greater clinical and radiological expression than has been assumed up until now. Whether our results are merely a variant or suggest a new subtype of the MOPD can only be resolved by further cases. The exact pathogenesis of the disease currently remains unknown but the most probable cause is an autosomal recessive inheritance.

Abnormalities, Multiple↗
PubMedDate not supplied

Acute leukemias in children from the city of Kiev and Kiev region after the Chernobyl NPP catastrophe.

During 1993-1997, 247 cases of childhood acute leukemia (AL) were analyzed among inhabitants of the city of Kiev and Kiev region, excluding the most contaminated areas belonging to the strict control zone. The criteria of an FAB classification supplemented by immunophenotyping data were applied. The AL pattern was shown to be quite typical except for several peculiar features characteristic of this regional group of patients, especially the absence of age peaks in children with acute myelogenous leukemias (AML), increased frequency of the T1 variant in T-cell acute lymphoblastic leukemia (ALL), and higher levels of M4 and M5 variants in AML. A typical variant of M5a-AML with minimal signs of differentiation was found.

Child↗
PubMed1993

Raynaud's phenomenon.

The classification of Raynaud's phenomenon has been complicated by various confusing labels, including Raynaud's disease and Raynaud's syndrome. To improve clarity and to allow for uniformity in reporting, most investigators agree that only the terms primary and secondary Raynaud's phenomenon should be used for patient classification. The prevalence of Raynaud's phenomenon seems to vary among different populations and different climates, suggesting genetic and environmental influences on its expression. The concept that Raynaud's phenomenon is the manifestation of a generalized vasospastic disorder has been addressed by studies of migraine headaches, variant angina, and the pulmonary vascular circulation. Current data suggest that the pathophysiology of Raynaud's phenomenon is complex and multifactorial, involving the endothelium, neuroreceptor expression, and locally produced mediators that affect vascular responses. New and old diagnostic tools used to measure digital circulation continue to be tested in an effort to define a better method of evaluating patients. Occupational causes of Raynaud's phenomenon continue to be an important health problem despite efforts to control vibratory tool usage. The role of beta-blockers in the induction of Raynaud's phenomenon has been questioned, but the use of chemotherapeutic agents is a definite risk factor. A new radical surgical approach for severe refractory Raynaud's phenomenon was described. Intravenous prostaglandins continue to appear helpful in the treatment of severe Raynaud's phenomenon, and oral prostaglandins are beginning to be studied.

Humans↗
PubMed2000

Structural similarities and differences in Staphylococcus aureus exfoliative toxins A and B as revealed by their crystal structures.

Staphylococcal aureus epidermolytic toxins (ETs) A and B are responsible for the induction of staphylococcal scalded skin syndrome, a disease of neonates and young children. The clinical features of this syndrome vary from localized blisters to severe exfoliation affecting most of the body surface. Comparison of the crystal structures of two subtypes of ETs-rETA (at 2.0 A resolution), rETB (at 2.8 A resolution), and an active site variant of rETA, Ser195Ala at 2.0 A resolution has demonstrated that their overall topology resembles that of a "trypsin-like" serine protease, but with significant differences at the N- and C-termini and loop regions. The details of the catalytic site in both ET structures are very similar to those in glutamate-specific serine proteases, suggesting a common catalytic mechanism. However, the "oxyanion hole," which is part of the catalytic sites of glutamate specific serine proteases, is in the closed or inactive conformation for rETA, yet in the open or active conformation for rETB. The ETs contain a unique amphipathic helix at the N-terminus, and it appears to be involved in optimizing the conformation of the catalytic site residues. Determination of the structure of the rETA catalytic site variant, Ser195Ala, showed no significant perturbation at the active site, establishing that the loss of biological and esterolytic activity can be attributed solely to disruption of the catalytic serine residue. Finally, the crystal structure of ETs, together with biochemical data and mutagenesis studies, strongly confirms the classification of these molecules as "serine proteases" rather than "superantigens."

Amino Acid Sequence↗
PubMed1989

The neuronal ceroid lipofuscinoses.

The neuronal ceroid lipofuscinoses are clinical disorders associated with the accumulation of autofluorescent waxy pigments within cells of several different tissues. Such syndromes always have neurological manifestations. Variations in clinical course, genetics, pathogenesis, and possibly treatment occur in each of the several forms listed under this category. Ten subtypes have now been recognized: (1) chronic, juvenile (Batten type); (2) acute, late infantile (Bielschowsky type); (3) subacute-chronic, adult (Kufs type); (4) acute, infantile (Santavuori-Haltia type); (5) congenital (Norman-Wood type); (6) acute, adult (Zeman-Dyken type); (7) acute-subacute childhood (Bielschowsky variant); (8) chronic, childhood with pervasiveness (Edathodu-Dyken type); (9) chronic, infantile with autism (Dyken type); and (10) chronic, juvenile with ataxia and spasticity (Dyken type). By far the most common of these are the first four disorders listed. It is proposed that this present classification of neuronal ceroid lipofuscinosis is more comprehensive than previous ones and fails to support the hypothesis that this disorder represents a unitary disease process, rather than different diseases with similar characteristics. At present, each of the neuronal ceroid lipofuscinosis types are of unknown etiology.

Humans↗
PubMed1998

Anaplastic large cell lymphoma: a concept reviewed.

The development of the concept of anaplastic large cell lymphoma is reviewed. The subtypes of the tumor proposed in the literature, including the so-called Hodgkin's-like variant, are discussed both on morphological and clinical grounds. The more recent information on the genetic and molecular characteristics of the tumor (i.e. 2;5 translocation, formation of the NPM/ALK hybrid gene, and production of a specific protein) are presented: their possible implications in the future classification and clinical management of the neoplasm are discussed.

Journal Article↗