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PubMed2003

Improving lopinavir genotype algorithm through phenotype correlations: novel mutation patterns and amprenavir cross-resistance.

BACKGROUND: Current genotypic algorithms suggest that the HIV-1 protease inhibitors (PI) lopinavir (LPV) and amprenavir (APV) have distinct resistance profiles. However, phenotypic data indicate that cross-resistance is more common than expected. METHODS: Protease genotype (GT) and phenotype (PT) from 1418 patient viruses with reduced PI susceptibility and/or resistance-associated mutations (training data) were analyzed. Samples were classified as LPV resistant by GT (GT-R) if six or more LPV mutations were present, and by PT (PT-R) if the 50% inhibitory concentration (IC(50)) fold-change (FC) was over 10. RESULTS: There were 182 samples (13%) that were GT-S but PT-R for LPV. A comparison of the mutation prevalence in PT-R/GT-S samples with that in PT-S/GT-S samples identified mutations associated with LPV PT-R. Several previously defined LPV mutations were found to have a stronger than average effect (e.g., M46I/L, I54V/T, V82A/F), and new variants at known positions (e.g., I54A/M/S, V82S) were identified. Other mutations, including known APV resistance mutations, were found to contribute to reduced LPV susceptibility. A new LPV genotypic interpretation algorithm was constructed that improved overall genotypic/phenotypic concordance from 80% to 91%. The algorithm demonstrated a concordance rate of 90% when tested on 523 new samples. Cross-resistance between APV and LPV was greater in samples with primary APV resistance mutations than in those lacking them. CONCLUSIONS: The current LPV mutation score does not fully account for many resistant viruses. Consequently, cross-resistance between LPV and APV is underappreciated. Phenotypic results from large and diverse patient virus populations should be used to guide the development of more accurate GT interpretation algorithms.

Algorithms↗

PubMed2002

Human migrations and population structure: what we know and why it matters.

The increasingly obvious medical relevance of human genetic variation is fueling the development of a rich interface between medical genetics and the study of human genetic history. A key feature of this interface is a step increase in the size and diversity of genetic data sets, permitting a range of new questions to be addressed concerning our evolutionary history. Similarly, methodologies first developed to study genetic history are being tailored to address medical challenges, including mapping genes that influence diseases and variable drug reactions. In this paper we do not attempt a comprehensive review of human genetic history. Rather we briefly outline some of the complications and challenges in the study of human genetic history, drawing particular attention to new opportunities created by the explosive growth in genetic information and technologies. First we discuss the complexity of human migration and demographic history, taking both a genetic and archaeological perspective. Then we show how these apparently academic issues are becoming increasingly important in medical genetics, focusing on association studies, the common disease/common variant hypothesis, the evaluation of variable drug response, and inferences about gene function from patterns of genetic variation. Finally we describe some of the inferential approaches available for interpreting human genetic variation, focusing both on current limitations and future developments.

Chromosome Mapping↗

PubMed1999

Profile validity standards for MMPI and MMPI-2 F scales.

Although numerous indices of validity have been developed for the MMPI and MMPI-2, interest in the F scale and its variants continues, especially among practicing clinicians. The use of the binomial for assessing standards for random answering and possibly for judgments of malingering offers another approach for the interpretation of F-scale scores. The theoretical binomial distribution and Monte Carlo data are in accord. Cut-off scores of 24 for the MMPI and 23 for the MMPI-2 suggest random responses, and scores of 40 and 37, respectively, suggest clinical interpretation rather than randomness of responding.

Humans↗

PubMed1978

3. The laboratory investigation of monoclonal gammopathies.

The monoclonal gammopathies are a group of disorders characterized by proliferation of a single clone of plasma cells that produce a homogeneous, monoclonal (M) protein. The structure of immunoglobulins, relationship of normal (polyclonal) immunoglobulins to myeloma and macroglobulin (monoclonal) immunoglobulins, pattern of monoclonal immunoglobulin overproduction, and laboratory methods for the recognition and study of monoclonal proteins in the serum and urine are reviewed. Interpretation of these laboratory tests is emphasized. The demonstration of a monoclonal protein in the serum or urine of a patient suggests multiple myeloma or one of its variants (solitary plasmacytoma of bone, extramedullary plasmacytoma, or plasma cell leukemia); Waldenström's macroglobulinemia or, occasionally, lymphoma; heavy-chain diseases (gamma, alpha, and mu); primary amyloidosis; and monoclonal gammopathies of undertermined significance. The electrophoretic and immunoelectrophoretic patterns found in the monoclonal gammopathies are discussed. Periodic electrophoresis of the serum and urine is essential in the follow-up and management of patients with a monoclonal gammopathy.

Amyloidosis↗

PubMed1999

[Results of routine intraoperative cholangiography].

Most bile duct injuries result from an incorrect interpretation of bile duct anatomy. In 500 laparoscopic cholecystectomies we used a modified technique of cholecystcholangiography. This method is very easy and needs only 5 minutes. We found variants of bile duct anatomy in 74 cases and occult bile duct stones in 20 patients. We recommend this method which decreases the risk of bile duct injuries and gives the opportunity to approximate the golden standard of conventional cholecystectomy.

Cholangiography↗

PubMed2002

Influence of functional MDR1 gene polymorphisms on P-glycoprotein activity in CD34+ hematopoietic stem cells.

BACKGROUND AND OBJECTIVES: Expression of the multidrug resistance P-glycoprotein, a transmembrane drug transporter, is influenced by recently described polymorphisms of the human MDR1 gene. Hematopoietic cells, such as lymphocytes, and hematopoietic stem cells, express P-glycoprotein, but the effect of MDR1 gene polymorphisms on P-glycoprotein activity in stem cells is unknown. We investigated whether T-129C, G26677T and C3435T polymorphisms influence P-glycoprotein function in stem cells. DESIGN AND METHODS: P-glycoprotein function was evaluated in immunomagnetically purified bone marrow CD34+ cells from 33 healthy bone marrow donors by the flow cytometric rhodamine 123-efflux assay. For T-129C and C3435T, bone marrow donors were genotyped by polymerase chain reaction amplification followed by MspA1I and DpnII digestion analyses, respectively. For the analysis of C2677T, exon 21 was sequenced. RESULTS: P-glycoprotein function was not different among the C3435T genotypes (CC, 38.2 +/- 3.5%; n=17; CT, 42.2 +/- 3.3%; n=11; and TT, 45.0 +/- 5.3%; n=5) nor was it among the C2677T genotypes (CC, 39.4 +/- 2.4%; n=27; CT, 43.7 +/- 6.4%; n=5; and TT, 54.3%; n=1). Among the 33 subjects, three were heterozygotes for the 129C allele (CT) and no mutant homozygote was identified. P-glycoprotein was similar in heterozygotes (TC, 50.6 +/- 2.9%) and wild-type subjects (TT, 39.5 +/- 2.4%). INTERPRETATION AND CONCLUSIONS: These findings suggest that the known functional MDR1 gene polymorphisms are not major determinants of P-glycoprotein function in hematopoietic stem cells. Other genetic variants might influence P-glycoprotein activity in this cell type.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1983

Thyroid papillary carcinoma. Pathological and philosophical controversies.

An encapsulated thyroid tumor with a papillary architecture is statistically much more likely to be a hyperplastic follicular adenoma than a papillary carcinoma, for the latter are uncommonly encapsulated. Hyperfunction of such a tumor is diagnostic of an adenoma. Various histopathologic features are useful in the differential diagnosis, but these are more accurately termed guidelines than criteria. The presence of psammoma bodies, fibrovascular stalks of papillae and pale nuclear changes are probably the most reliable histopathologic features of a carcinoma. The value of needle biopsy as a diagnostic tool for the screening of thyroid nodules is emphasized. Encapsulated variants of papillary carcinoma are discussed, including the rare pure follicular variant and those intermixed with adenomatous components, suggesting the possibility that some papillary carcinomas might arise in a preexisting adenoma. When the histopathologic diagnosis is equivocal, a benign interpretation is favored since encapsulated papillary carcinomas are very low grade, have an unusually favorable prognosis, and need no further resection. The polarization in past years of clinicians into radical and conservative operative fractions is reviewed. This stemmed from different interpretations of the presence of lymph node metastases in a majority of cases and the high frequency of intraglandular microscopic dissemination of neoplasm. It is clear that biological behavior of this unusual cancer is more important than a literal interpretation of the pathologic findings as a determinant for patient management. The surgical pathologist should be mindful that he plays an important role in patient management, not only by providing a diagnosis but also by serving as a consultant to the surgeon in pathologic correlation.

Adenocarcinoma↗

PubMed2005

Approximating filtered scale-variant signals.

We develop theorems that place limits on the point-wise approximation of the responses of filters, both linear shift invariant (LSI) and linear shift variant (LSV), to input signals and images that are LSV in the following sense: they can be expressed as the outputs of systems with LSV impulse responses, where the shift variance is with respect to the filter scale of a single-prototype fillter. The approximations take the form of LSI approximations to the responses. We develop tight bounds on the approximation errors expressed in terms of filter durations and derivative (Sobolev) norms. Finally, we find application of the developed theory to defoveation of images, deblurring of shift-variant blurs, and shift-variant edge detection.

Algorithms↗

PubMed1999

Interpretation of genetic test results for hereditary nonpolyposis colorectal cancer: implications for clinical predisposition testing.

CONTEXT: Genetic testing for cancer predisposition is evolving from purely research applications to affecting clinical management. OBJECTIVE: To determine how often genetic test results for hereditary nonpolyposis colorectal cancer (HNPCC) can be definitively interpreted and used to guide clinical management. DESIGN: Case-series study conducted in 1996 to 1998 in which a complete sequence analysis of hMSH2 and hMLH1 coding sequence and flanking intronic regions was performed. Mutations were categorized as protein truncating and missense. In the case of missense alterations, additional analyses were performed in an effort to assess pathogenicity. SETTING AND PARTICIPANTS: Families were identified by self-referral or health care provider referral to a cancer genetics program. Participants and kindreds were classified into 1 of 4 categories: (1) Amsterdam criteria for HNPCC, (2) modified Amsterdam criteria for HNPCC, (3) young age at onset, or (4) HNPCC-variant. In addition, each proband was classified according to the Bethesda guidelines for identification of individuals with HNPCC. MAIN OUTCOME MEASURE: Alterations of hMSH2 and hMLH1 genes. RESULTS: Twenty-seven alterations of hMSH2 and hMLH1 were found in 24 of 70 families (34.3%). Of these, deleterious mutations that could be used with confidence in clinical management were identified in 25.7% (18/70) of families. The rates of definitive results for families fulfilling Amsterdam criteria, modified Amsterdam criteria, young age at onset, HNPCC-variant, and Bethesda guidelines were 27 (39.3%), 13 (18.2%), 12 (16.7%), 11 (15.8%), and 21 (30.4%), respectively. The prevalence of missense mutations, genetic heterogeneity of the syndrome, and limited availability of validated functional assays present a challenge in the interpretation of genetic test results of HNPCC families. CONCLUSIONS: The identification of pathogenic mutations in a significant subset of families for whom the results may have marked clinical importance makes genetic testing an important option for HNPCC and HNPCC-like kindreds. However, for the majority of individuals in whom sequence analysis of hMSH2 and hMLH1 does not give a definitive result, intensive follow-up is still warranted.

Adaptor Proteins, Signal Transducing↗

PubMed1994

Primary intracranial pleomorphic angioleiomyoma--a new morphologic variant. An immunohistochemical and electron microscopic study.

BACKGROUND: Angioleiomyomas usually are benign subcutaneous neoplasms that occur most often in extremities of middle-aged individuals. Very few cases have been described in other locations; none along the neuroaxis. An intracranial example of angioleiomyoma displaying unusual morphologic features not seen in the typical peripheral variants of this tumor is described. METHODS: The tumor was studied with conventional histology, immunohistochemistry with morphometric calculation of proliferation index, immunoelectron microscopy, and DNA flow cytometry. RESULTS: The tumor was composed of large epithelioid and pleomorphic cells filled with intermediate filaments positive for desmin and vimentin. Scattered cells also expressed myosin and muscle-specific actin. Smooth muscle cell differentiation was confirmed by ultrastructural demonstration of subplasmalemmal dense bodies, attachment plaques, and discontinuous basal lamina. The proliferation index with proliferating cell nuclear antigen (PCNA) monoclonal antibody was 75.78%, whereas it was only 4.22% with Ki67 monoclonal antibodies adopted to paraffin material (MIB-1). CONCLUSION: The tumor represents a unique morphologic variant of a pleomorphic angioleiomyoma. Cellular pleomorphism and a strong reaction for PCNA in numerous cells suggested that the lesion was malignant. However, the absence of mitotic figures, a small number of Ki-67-positive cells, a diploic DNA pattern, and a low proliferation index in flow cytometry all supported the concept that this neoplasm represented an unusual histologic variant of benign angiogenic leiomyoma. Encapsulation and demarcation of the surgical specimen and the survival of the patient for more than 4 years without recurrence after resection support this interpretation.

Adult↗

PubMed1986

Dental metric assessment of the omo fossils: implications for the phylogenetic position of Australopithecus africanus.

The discovery of Australopithecus afarensis has led to new interpretations of hominid phylogeny, some of which reject A. africanus as an ancestor of Homo. Analysis of buccolingual tooth crown dimensions in australopithecines and Homo species by Johanson and White (Science 202:321-330, 1979) revealed that the South African gracile australopithecines are intermediate in size between Laetoli/hadar hominids and South African robust hominids. Homo, on the other hand, displays dimensions similar to those of A. afarensis and smaller than those of other australopithecines. These authors conclude, therefore, that A. africanus is derived in the direction of A. robustus and is not an ancestor of the Homo clade. However, there is a considerable time gap (ca. 800,000 years) between the Laetoli/Hadar specimens and the earliest Homo specimens; "gracile" hominids from Omo fit into this chronological gap and are from the same geographic area. Because the early specimens at Omo have been designated A. afarensis and the later specimens classified as Homo habilis, Omo offers a unique opportunity to test hypotheses concerning hominid evolution, especially regarding the phylogenetic status of A. africanus. Comparisons of mean cheek teeth breadths disclosed the significant (P less than or equal to 0.05) differences between the Omo sample and the Laetoli/Hadar fossils (P4, M2, and M3), the Homo fossils (P3, P4, M1, M2, and M1), and A. africanus (M3). Of the several possible interpretations of these data, it appears that the high degree of similarity between the Omo sample and the South African gracile australopithecine material warrants considering the two as geographical variants of A. africanus. The geographic, chronologic, and metric attributes of the Omo sample argue for its lineal affinity with A. afarensis and Homo. In conclusion, a consideration of hominid postcanine dental metrics provides no basis for removing A. africanus from the ancestry of the Homo lineage.

Animals↗

PubMedDate not supplied

Fetal heart rate monitoring: interpretation and collaborative management.

Effective intrapartum fetal heart rate (FHR) monitoring requires ongoing collaboration among health care providers. Nurses, midwives, and physicians must have a shared understanding of 1) how FHR tracings are interpreted, 2) which FHR patterns are associated with actual or impending fetal acidemia, 3) when and within what time frame the physician or the midwife should be notified of variant FHR patterns, 4) how quickly physicians and midwives should respond when notified of variant patterns, and 5) the indications for and optimal timing of interventions such as operative delivery. This article reviews the literature on FHR monitoring and includes a discussion of the advantages and limitations of different monitoring modalities. An overview of those FHR patterns are associated with presumed fetal acidemia is presented, as well as sample multidisciplinary FHR monitoring guidelines and an exercise in intrapartum FHR pattern evaluation that can be used to initiate development of local FHR monitoring patterns.

Acidosis↗

PubMed2005

Controlled reduction of the humidity induces a shortcut recovery reaction in the photocycle of photoactive yellow protein.

The photocycle of the blue-light photoreceptor protein Photoactive Yellow Protein (PYP) was studied at reduced relative humidity (RH). Photocycle kinetics and spectra were measured in thin films of PYP in which the relative humidity was set at values between 29 and 98% RH with saturated solutions of various salts. We show that in this range, approximately 200 water molecules per PYP molecule are released from the film. As humidity decreased, photocycle transition rates changed, until at low humidity (RH < 50%) an authentic photocycle was no longer observed and the absorption spectrum of the dark, equilibrium state of PYP started to shift to 355 nm, that is, to a form resembling that of pB(dark). At moderately reduced humidity (i.e., >50% RH), an authentic photocycle is still observed, although its characteristics differ from those in solution. As humidity decreases, the rate of ground state recovery increases, while the rate of depletion of the first red-shifted intermediate pR dramatically decreases. The latter observation contrasts all so-far known modulations of the rate of the transition of the red-shifted- to the blue-shifted intermediates of PYP, which is consistently accelerated by all other modulations of the mesoscopic context of the protein. Under these same conditions, the long-lived, blue-shifted intermediate was formed not only with slower kinetics than in solution but also to a smaller extent. Global analysis of these data indicates that in this low humidity environment the photocycle can take a different route than in solution, that is, part of pG recovers directly from pR. These experiments on wild-type PYP, in combination with observations on a variant of PYP obtained by site-directed mutagenesis (the E46Q mutant protein), further document the context dependence of the photocycle transitions of PYP and are relevant for the interpretation of results obtained in both spectroscopic and diffraction studies with crystalline PYP.

Bacterial Proteins↗

PubMed1993

A molecular variant of angiotensinogen associated with preeclampsia.

Pregnancy-induced hypertension (PIH) is a heterogeneous disorder which complicates 5-7% of all pregnancies and remains a leading cause of maternal, fetal and neonatal morbidity and mortality. Severe preeclampsia is the most distinctive and life-threatening form; a multi-system disorder more common in first pregnancies, it is characterized by high blood pressure and proteinuria. In a series of Caucasian women with pregnancy-induced hypertension, we have observed a significant association of preeclampsia with a molecular variant of angiotensinogen, T235, found previously to be associated with essential hypertension. This finding is corroborated in a sample ascertained in Japan. Together, these observations support a new pathophysiological interpretation of preeclampsia and of its relation to some forms of essential hypertension.

Angiotensinogen↗

PubMed1963

ADDITIONAL STUDIES ON THE TRANSFERRINS OF CORD SERUM AND CEREBROSPINAL FLUID; VARIATION IN CARBOHYDRATE PROSTHETIC GROUPS.

Serum transferrins have been examined in 392 samples from full-term infants and from premature infants at various stages of growth. The characteristic transferrin pattern of the infants by starch gel electrophoresis contained a single prominent iron-binding component accompanied by 4 faint, slower migrating components. An additional faint component was present in the sera of infants heterozygous for a transferrin variant. The faint components migrated slightly more rapidly than the corresponding components in the stepwise pattern produced by the action of neuraminidase in removing sialic acid from transferrin. The interpretation is presented that the faint components may represent the absence of multi-unit carbohydrate prosthetic groups on the transferrin molecule in the infant. A similar interpretation is possible for the slow migrating transferrins of cerebrospinal fluid.

Blood Protein Electrophoresis↗

PubMed1973

Cross-stimulation of monoclonal antibodies in anamnestic responses.

Immunization of BALB/c mice with Group A streptococcal vaccines leads to the induction of high levels of monoclonal antibody populations. Subsequent immunization of these mice with Group A-variant streptococcal vaccines induces a significant level of monoclonal antibody of A-variant antigen specificity revealed by labeled group A-variant polysaccharide. During these course Av and Av' immunizations, the monoclonal Group A-specific antibodies were also restimulated to levels usually higher than the variant-specific antibodies. With two exceptions, these homogeneous antibody populations were not cross-reactive in vitro with the related antigen. Such cross-stimulation of monoclonal antibodies was interpreted as a function of particular membrane properties of the Ig receptor-bearing memory cells which, for restimulation, would only require the structurally closely related antigen which serves as a backbone to the original antigen, and not necessarily the exact fit of the homologous immunodominant group.

Animals↗

PubMed2002

Primary brain CD30+ ALK1+ anaplastic large cell lymphoma ('ALKoma'): the first case with a combination of 'not common' variants.

BACKGROUND: Primary central nervous system lymphomas (PCNSLs) are rare tumors, mostly represented by diffuse large B cells. PCNSLs with a T phenotype are less frequently reported; even rarer are anaplastic large cell lymphomas (ALCLs). PCNSL ALCLs are commonly represented, like their systemic counterpart, by a variably prevalent amount of large pleomorphic tumor cells ('hallmark cells'), and this feature enhances their recognition. Patient and methods We report the first case of primary brain CD30+ ALK-1+ ALCL with a T-cell phenotype, showing the combination of both the 'lymphohistiocytic' and the 'small cell' variants of the disease. A few elements consistent with 'hallmark cells' were recognizable. However, these cells were never prominent, increasing diagnostic difficulties. Immunohistochemistry results were critical for the correct interpretation. Our findings also differ from the majority of PCNSL ALCLs for the absence of tumor necrosis and the lack of prominent mitotic activity. The neuroimaging picture was not specific. A comparison with literature data concerning the clinical/instrumental features shows a very frequent meningeal involvement in PCNSL ALCLs, in contrast to the majority of PCNSLs. CONCLUSION: The occurrence of such a rare form of ALCL may widen the spectrum of differential diagnoses in PCNSL and their recognition may allow a rapid diagnosis, thus encouraging adequate treatment, which should take into account the high rate of meningeal involvement observed in these cases.

Adult↗

PubMed2000

Mesotheliomas with deciduoid morphology: a morphologic spectrum and a variant not confined to young females.

Deciduoid mesotheliomas are rare with only four previously reported cases, all affecting the peritoneum of young females. We describe another six cases (three men and three women; age range 52-65 yrs, median 55 yrs; five peritoneal and one pleural). Three patients had an occupational history of asbestos exposure. The deciduoid appearance predominated in four cases, whereas in two it represented a minor component within conventional tubulopapillary epithelioid mesothelioma. All tumors were strongly cytokeratin-positive (including CK5/6) and all showed at least focal staining for thrombomodulin, HBME-1, and calretinin. All were negative for epithelial mucin (D/PAS), CEA, BerEP4, LeuM1 (CD15), CD21, CD35, and S100 protein. Five of six cases (83%) were vimentin-positive and two (33%) were focally positive for alpha-smooth muscle actin. A differential diagnosis of gastrointestinal autonomic nerve tumor (GANT) had been initially considered from the morphology of one case, and we found positivity for some of the "neuronal" markers described in GANTs. This prompted us to apply such a panel to the other five tumors, accepting that the cytokeratin positivity encountered in all of our cases would exclude GANT. All cases of deciduoid mesothelioma (100%) were positive for PGP 9.5 and NSE and four of six (66%) were positive for NKI/C3. Weak focal staining (<5% cells) for synaptophysin was seen in two of six tumors. All cases were chromogranin-negative. All cases examined by electron microscopy showed desmosomes and smooth microvilli without rootlets but no neuroendocrine granules. In conclusion, a deciduoid morphology appears to be part of the histopathologic spectrum encountered in epithelioid mesothelioma. This variant is not confined to female patients and occurs over a wider age range than previously recognized. The overlapping immunophenotype with GANTs illustrates that caution should be exercised when interpreting positivity for "neuronal" markers in this context. An immunohistochemical panel that includes cytokeratins should always be used.

Aged↗