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PubMed2006

Lemur responses to edge effects in the Vohibola III classified forest, Madagascar.

Forest edges are dynamic zones characterized by the penetration (to varying depths and intensities) of conditions from the surrounding environment (matrix) into the forest interior. Although edge effects influence many tropical organisms, they have not been studied directly in primates. Edge effects are particularly relevant to lemurs because of the highly fragmented forest landscapes found in Madagascar. In this study, data are presented regarding how the densities of six lemur species (Avahi laniger, Cheirogaleus major, Eulemur rubriventer, Hapalemur griseus griseus, Microcebus rufus, and Propithecus diadema edwardsi) varied between six 500-m interior transects and six 500-m edge transects in the Vohibola III Classified Forest in SE Madagascar. Diurnal (n = 433) and nocturnal (n = 128) lemur surveys were conducted during June-October 2003 and May-November 2004. A. laniger, E. rubriventer, and H. g. griseus exhibited a neutral edge response (no differences in densities between habitats). M. rufus and P. d. edwardsi had a positive edge response (higher densities in edge habitats), which may be related to edge-related variations in food abundance and quality. Positive edge responses by M. rufus and P. d. edwardsi may ultimately be detrimental due to edge-related anthropogenic factors (e.g., hunting by local people). The negative edge response exhibited by C. major (lower densities in edge habitats) may result from heightened ambient temperatures that inhibit torpor in edge habitats.

Animals↗

PubMed2004

Classifying structural joint damage in rheumatoid arthritis as progressive or nonprogressive using a composite definition of joint radiographic change: a preliminary proposal.

OBJECTIVE: To categorize radiographic joint damage as progressive or nonprogressive in individuals with rheumatoid arthritis (RA) participating in clinical studies. METHODS: Using the total Sharp radiographic damage score, erosion score, and joint space narrowing (JSN) score for 751 serial films of the hand/wrist and forefoot obtained from 190 patients with early RA during 6-60 months of followup (mean 31 months), various threshold values for progression of joint damage were evaluated singly and in various combinations. For each patient, the progression rate was estimated from the linear regression line for all available radiographic time points. After preliminary screening, 23 candidate definitions were tested to select a definition that discriminated well between radiographic progression and radiographic nonprogression. RESULTS: The definition selected describes radiographic nonprogression in individual patients as an increase of < or =0.1 in the standardized response mean of the trimmed population (the central 95% of patients) for > or =5 of 6 change measures (erosion scores and JSN scores for the fingers, wrists, and feet). Using this definition, 59% of the 190 patients with early RA were defined as having nonprogressive radiographic damage. Moreover, 95% of 95 patients with progression of the total Sharp score at or below the median and 24% of 95 patients with progression of the total Sharp score above the median were defined as having nonprogressive joint damage (chi(2) = 98, P < 0.0001), as were 97% of patients in the lowest quintile of total Sharp score progression rates and none of the patients in the highest progression quintile. Patients defined as nonprogressors had significantly lower baseline levels of C-reactive protein and lower erythrocyte sedimentation rates compared with patients defined as progressors, and those patients in the nonprogressive joint damage group more frequently had American College of Rheumatology 20% and 50% improvement criteria responses, "good" improvements (decrease of > or =1.2) in the Disease Activity Score, and > or =50% decreases in the swollen joint counts during the first 2 years of followup. CONCLUSION: RA joint damage in an observational cohort can be classified as progressive or nonprogressive with the use of a composite definition. Validation and/or refinement of this definition is needed by utilizing the data from controlled clinical trials that compare placebo with active treatment.

Antirheumatic Agents↗

PubMed2005

Classifying antibodies using flow cytometry data: class prediction and class discovery.

Classifying monoclonal antibodies, based on the similarity of their binding to the proteins (antigens) on the surface of blood cells, is essential for progress in immunology, hematology and clinical medicine. The collaborative efforts of researchers from many countries have led to the classification of thousands of antibodies into 247 clusters of differentiation (CD). Classification is based on flow cytometry and biochemical data. In preliminary classifications of antibodies based on flow cytometry data, the object requiring classification (an antibody) is described by a set of random samples from unknown densities of fluorescence intensity. An individual sample is collected in the experiment, where a population of cells of a certain type is stained by the identical fluorescently marked replicates of the antibody of interest. Samples are collected for multiple cell types. The classification problems of interest include identifying new CDs (class discovery or unsupervised learning) and assigning new antibodies to the known CD clusters (class prediction or supervised learning). These problems have attracted limited attention from statisticians. We recommend a novel approach to the classification process in which a computer algorithm suggests to the analyst the subset of the "most appropriate" classifications of an antibody in class prediction problems or the "most similar" pairs/ groups of antibodies in class discovery problems. The suggested algorithm speeds up the analysis of a flow cytometry data by a factor 10-20. This allows the analyst to focus on the interpretation of the automatically suggested preliminary classification solutions and on planning the subsequent biochemical experiments.

Antibodies, Monoclonal↗

PubMed2007

Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells.

Viruses can reproduce their progenies only within a host cell, and their actions depend both on its destructive tendencies toward a specific host cell and on environmental conditions. Therefore, knowledge of the subcellular localization of viral proteins in a host cell or virus-infected cell is very useful for in-depth studying of their functions and mechanisms as well as designing antiviral drugs. An analysis on the Swiss-Prot database (version 50.0, released on May 30, 2006) indicates that only 23.5% of viral protein entries are annotated for their subcellular locations in this regard. As for the gene ontology database, the corresponding percentage is 23.8%. Such a gap calls for the development of high throughput tools for timely annotating the localization of viral proteins within host and virus-infected cells. In this article, a predictor called "Virus-PLoc" has been developed that is featured by fusing many basic classifiers with each engineered according to the K-nearest neighbor rule. The overall jackknife success rate obtained by Virus-PLoc in identifying the subcellular compartments of viral proteins was 80% for a benchmark dataset in which none of proteins has more than 25% sequence identity to any other in a same location site. Virus-PLoc will be freely available as a web-server at http://202.120.37.186/bioinf/virus for the public usage. Furthermore, Virus-PLoc has been used to provide large-scale predictions of all viral protein entries in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The results thus obtained have been deposited in a downloadable file prepared with Microsoft Excel and named "Tab_Virus-PLoc.xls." This file is available at the same website and will be updated twice a year to include the new entries of viral proteins and reflect the continuous development of Virus-PLoc.

Cells↗

PubMed2004

Classifying enzymes from selectivity fingerprints.

Fingerprints of lipases and esterases have been recorded by using an array of chiral fluorogenic aliphatic esters of increasing chain length (C(4)-C(16)). Classification of the enzyme series was carried out with selectivity data by clustering and principal component analysis (PCA). Enzymes were classified on the basis of selectivity for chain length (C(4)-C(6) vs. C(10)-C(16)) and of middle-chain-length (C(8)-C(10)) reactivity. A minimum set of nine substrates was defined by cluster analysis of relative reactivities of each substrate for the different enzymes. This selectivity-based analysis is general. It does not require a common reference substrate to react with all enzymes or vice versa, and is independent of knowing the exact concentration of active protein in the enzyme samples.

Cluster Analysis↗

PubMed2002

Can true papillary neoplasms of breast and their mimickers be accurately classified by cytology?

BACKGROUND: The cytologic accuracy in assessing malignancy in papillary breast neoplasms (PBNs) is controversial. This is further complicated by overlapping features observed in other breast lesions that produce papillary-like tissue fragments. METHODS: The authors reviewed 22 fine-needle aspirates (FNAs) from histologically proven papillary neoplasms: papillary carcinoma (PCA; 10 aspirates) and intraductal papilloma (IDP; 12 aspirates). They also reviewed 8 FNAs in which a papillary neoplasm was suggested by cytology but not confirmed by follow-up biopsy: fibroadenoma (6), mucinous carcinoma (1), and cribriform ductal carcinoma in situ (1). RESULTS: Papillary carcinoma can be distinguished from IDP by the higher cellularity, more complex papillae with thin disorganized fronds, mild to moderate nuclear atypia, and prominent dissociation with many single papillae. Fibrovascular cores (FVCs) were more common in PCA than IDP in which detached fibrous tissue fragments were frequently seen. Atypical IDP exhibited features intermediate between PCA and IDP. Apocrine metaplasia was variably present in IDP, atypical IDP, and fibroadenoma but absent in all carcinomas. Intraductal papilloma can be distinguished from fibroadenoma by their broad ruffled branches, scalloped borders, and tiny tongue-like projections. True papillae were commonly covered by tall columnar cells. Myoepithelial cells were few in IDP but were numerous in fibroadenoma. The epithelial fragments in nonpapillary lesions presented as cellular spheres and/or complex sheets with finger-like projections but lacked FVCs and columnar cells. CONCLUSIONS: Papillary breast neoplasms can be accurately classified by cytology. Closer evaluation of the tissue fragments architecture and the background can help in separating PBN from their mimics.

Adenocarcinoma, Mucinous↗

PubMed2026

Awake Craniotomy for Eloquent Region Glioblastoma Classified by Tumor Location-A Retrospective and Prospective Cohort Study.

INTRODUCTION: The efficacy of awake craniotomy (AC) with intraoperative mapping for glioblastoma (GBM) in eloquent regions remains debated. This study aims to evaluate functional and survival outcomes of GBM patients undergoing AC stratified by tumor locations. METHODS: A combined retrospective (2015-2023, n = 114: 43 AC vs. 71 standard craniotomy) and prospective cohort (2023-2025, n = 28: 13 AC vs. 15 standard craniotomy) of GBM patients with motor/language-eloquent tumors was analyzed. Tumors were classified into motor subtypes (I: precentral gyrus; II: premotor/supplementary motor; III: internal capsule posterior limb; IV: other) and language subtypes (I: Broca's/precentral; II: postcentral/supramarginal gyrus; III: Wernicke's; IV: insular; V: other). Outcomes included extent of resection (EOR), postoperative motor/language recovery, overall survival (OS), and progression-free survival (PFS). RESULTS: The retrospective cohort demonstrated that AC has advantages in functional preservation across various motor/language subtypes. However, AC was associated with significantly deteriorated survival outcomes specifically in precentral gyrus GBMs. A prospective cohort study, enrolling only precentral gyrus GBMs for validation, yielded results consistent with the retrospective findings: worsened OS and PFS (OS: HR = 3.223, p = 0.0450; PFS: HR = 2.374, p = 0.0476); reduced EOR (AC: 74.3% ± 5.3%; standard craniotomy: 86.9% ± 12.3%, p = 0.0470); and better motor recovery. CONCLUSIONS: Functional preservation and survival outcomes of AC in GBM exhibited subtype-specific correlations with tumor locations. AC with intraoperative mapping effectively preserves neurological function in GBM patients. However, for tumors involving the precentral gyrus, the AC approach carries greater risks than benefits and should be considered with caution. TRIAL REGISTRATION: Strategic Intervention on Preserving Motor Function During Awake Craniotomy: NCT05143788. Strategic Intervention on Preserving Language Function During Awake Craniotomy: NCT05143775.

Adult↗

PubMedDate not supplied

A systematic procedure for identifying and classifying children with dyscalculia among primary school children in India.

This paper describes the procedures adopted by two independent studies in India for identifying and classifying children with dyscalculia in primary schools. For determining the presence of dyscalculia both inclusionary and exclusionary criteria were used. When other possible causes of arithmetic failure had been excluded, figures for dyscalculia came out as 5.98% (15 cases out of 251) in one study and 5.54% (78 out of 1408) in the second. It was found in the latter study that 40 out of the 78 (51.27%) also had reading and writing problems. The findings are discussed in the light of previous studies.

Child↗

PubMed2004

Changes of chemical composition and dough rheology in two fractions of sieve-classified Polish spring wheat flour.

The study of chemical composition and dough rheology changes in sieve-classified two fractions (up to 60 and 60-240 microm particles) of wheat flour was the subject of this study. The straight grade flours were obtained by the milling of three Polish varieties of spring wheat, differing in particle size index (PSI) values. The flours were separated with the use of an SZ-1 laboratory sifter. The yield of fine fraction was in the range 50.0-55.7%. The obtained fractions were assayed for the content and composition of free lipids, gluten proteins, damaged starch, ash, water absorption and amylograph viscosity. Dough rheology (extrusion in OTMS cell, alveograph and farinograph tests) and baking trials were also performed. The content of free lipids, including the non-polar and phospholipids was lower and the content of glycolipids was higher in fine flours. Those fractions were more rich in linoleic acid but the lower content of oleic and linolenic acids resulted in a higher oxidizability index of free lipids. Fine flours contained less ash and significantly more damaged starch. At the same time, they were characterized by a higher content of wet gluten, water absorption, amylograph viscosity and better dough parameters. This was reflected in the bread volume, which was higher by 6.3-10.7%. The influence of the changes in composition and the content of free lipids upon the rheology of the dough after the 90 days flour storage has not been defined unambiguously and requires further research.

Absorption↗

PubMed1992

Chromosomal in situ suppression hybridization of immunologically classified mitotic cells in hematologic malignancies.

Chromosomal in situ suppression (CISS) hybridization was performed with library DNA from sorted human chromosomes 8, 9, 15, 17, 21, and 22 on immunologically stained bone marrow cells of four patients with a hematologic neoplasm, including two patients with myelodysplastic syndrome and trisomy 8, one patient with promyelocytic leukemia bearing the translocation t(15;17)(q22;q11-12), and one patient with chronic myeloid leukemia and the translocation t(9;22)(q34;q11). In all patients, the results of conventional karyotype analysis could be confirmed by one- or two-color CISS hybridization using the appropriate chromosome-specific libraries. Our results show that CISS hybridization can detect both numerical and structural chromosome changes in immunologically classified cells with high specificity and reliability. The fact that chromosome spreads of very poor quality can now be included in such analyses is a decisive advantage of this approach. In addition, the suitability of this approach for interphase cytogenetics is discussed.

Chromosome Aberrations↗

PubMed2004

Development of a statistical approach to classifying treatment response in individual children with ADHD.

The use of cognitive tests as measures of treatment response in individual children with ADHD has not been adequately evaluated or commonly applied by clinicians. This is most likely due to a lack of suitable assessment tasks as well as clinicians' limited awareness of the appropriate statistical techniques for analysing cognitive change in individuals. This study investigated the application of statistical decision rules to the cognitive and behavioural measures of individual children with ADHD in order to classify a significant, positive response to medication. The previously reported data of 14 children with ADHD (combined type; ADHD-CT) were re-analysed to investigate changes in function following a low- and high-dose of stimulant medication (2.5 mg and 7.5 mg dexamphetamine, respectively). The performances of 14 age-, gender- and IQ-matched controls was also analysed to provide an estimate of the false-positive classification rate. Overall, the decision rule yielded a high sensitivity and high specificity to treatment response. In the high-dose condition, 71% of children with ADHD demonstrated improvements in both cognitive and behavioural function. This study demonstrates an evidence-based approach to evaluating concurrent cognitive and behavioural improvement in individual children with ADHD following treatment with stimulant medication.

Attention Deficit Disorder with Hyperactivity↗

PubMed1994

Difference in sero-diagnostic values among KL-6-associated mucins classified as cluster 9.

KL-6 classified as Cluster 9 (MUC-I) is a circulating high-molecular-weight mucin-like molecule. Serum level of KL-6 was measured by a sandwich assay using KL-6 antibody as not only a catcher but also as a tracer. We established 2 additional monoclonal antibodies (MAbs), LISA 101 and EH-123, reacting with KL-6 epitopes different from the epitope recognized by KL-6 antibody. The KL-6-associated mucins detected by the sandwich assay using LISA 101 or EH-123 antibody as a catcher and KL-6 antibody as a tracer were designated as LISA 1-6 and CAM 123-6 respectively. The diagnostic values as the serum markers of KL-6, LISA 1-6 and CAM 123-6 were evaluated measuring their levels in the same serum from healthy individuals and from patients with pulmonary, pancreatic and breast adenocarcinomas. KL-6 was increased abnormally at high rates of more than 50% in pancreatic cancer and in benign lung diseases, LISA 1-6 only in pancreatic cancer, and CAM 123-6 only in pulmonary adenocarcinoma. In benign lung diseases, however, LISA 1-6 and CAM 123-6 were increased abnormally at the rates of only 5.3% and 0% respectively. These observations clearly indicate that LISA 1-6 and CAM 123-6 constitute a part of KL-6, but that they are superior to KL-6 as tumor markers for pancreatic cancer and for pulmonary adenocarcinoma respectively, because of their much lower false-positive rates.

Adenocarcinoma↗

PubMed1991

Significance of classifying antiarrhythmic actions since the cardiac arrhythmia suppression trial.

The Cardiac Antiarrhythmic Suppression Trial (CAST) showed flecainide and encainide induced excess mortality compared with placebo. Labeling drugs as Class 1C is based on clinical observations, comprising measurements of the electrocardiographic parameters QRS. H-V and J-T intervals and of effective refractory period (ERP) as follows: 1--(QRS) wide, 2--(HV) long, 3--(ERP) unchanged, 4--(JT) unchanged. In vitro electrophysiology helped to explain the clinical findings. Flecainide and encainide rendered Na channels as nonconducting, but F and E were only slowly released from the channels after repolarization. At any given drug concentration, a proportion of total channels were eliminated, and the steady-state proportion increased at rising heart rate. It is not proven that the properties that lead to classification of a drug as 1C were those that caused excess deaths in the CAST. The proarrhythmic tendency of 1C drugs can be reduced by beta-blockade, and the mechanisms of adrenergic arrhythmogenicity are discussed. Propafenone is both a 1C drug and a beta-blocker, and its pharmacologic profile is reviewed to illustrate how it resembles and differs from flecainide and encainide. Some features of the CAST are assessed with particular reference to the extent to which conclusions drawn from the results may be justifiably extrapolated to other drugs classified as 1C.

Anilides↗

PubMed1992

Classifying antiarrhythmic actions: by facts or speculation.

Classification of antiarrhythmic actions is reviewed in the context of the results of the Cardiac Arrhythmia Suppression Trials, CAST 1 and 2. Six criticisms of the classification recently published (The Sicilian Gambit) are discussed in detail. The alternative classification, when stripped of speculative elements, is shown to be similar to the original classification. Claims that the classification failed to predict the efficacy of antiarrhythmic drugs for the selection of appropriate therapy have been tested by an example. The antiarrhythmic actions of cibenzoline were classified in 1980. A detailed review of confirmatory experiments and clinical trials during the past decade shows that predictions made at the time agree with subsequent results. Classification of the effects drugs actually have on functioning cardiac tissues provides a rational basis for finding the preferred treatment for a particular arrhythmia in accordance with the diagnosis.

Animals↗

PubMedDate not supplied

Novel approach for classifying chemicals according to skin sensitizing potency by non-radioisotopic modification of the local lymph node assay.

The murine local lymph node assay (LLNA) is currently recognized as a stand-alone sensitization test for determining the sensitizing potential of chemicals, and it has the advantage of yielding a quantitative endpoint that can be used to predict the sensitization potency of chemicals. The EC3 has been proposed as a parameter for classifying chemicals according to the sensitization potency. We previously developed a non-radioisotopic endpoint for the LLNA based on 5-bromo-2'-deoxyuridine (BrdU) incorporation (non-RI LLNA), and we are proposing a new procedure to predict the sensitization potency of chemicals based on comparisons with known human contact allergens. Nine chemicals (i.e. diphencyclopropenone, p-phenylenediamine, glutaraldehyde, cinnamicaldehyde, citral, eugenol, isopropyl myristate, propyleneglycol and hexane) categorized as human contact allergen classes 1-5 were tested by the non-RI LLNA with the following reference allergens: 2,4-dinitrochlorobenzene (DNCB) as a class 1 human contact allergen, isoeugenol as a class 2 human contact allergen and alpha-hexylcinnamic aldehyde (HCA) as a class 3 human contact allergen. Consequently, nine test chemicals were almost assigned to their correct allergen class. The results suggested that the new procedure for non-RI LLNA can provide correct sensitization potency data. Sensitization potency data are useful for evaluating the sensitization risk to humans of exposure to new chemical products. Accordingly, this approach would be an effective modification of LLNA with regard to its experimental design. Moreover, this procedure can be applied also to the standard LLNA with radioisotopes and to other modifications of the LLNA.

Allergens↗

PubMed1986

Use of a monoclonal antibody to classify neurons isolated from the head region of Hydra.

A mouse monoclonal antibody (JD1) to Hydra attenuata using the peroxidase-antiperoxidase (PAP) method revealed unipolar, bipolar, and multipolar sensory and ganglion cells in the head region of H. littoralis. Neurons isolated from macerated hypostomes and tentacles were classified according to the number of their cytoplasmic processes and the position of the cilium, when present, relative to the perikaryon. PAP-stained sensory cells had an apical ciliary cone, whereas ganglion cells did not. Neurons with cytoplasmic processes longer than 50 microns stained faintly, whereas those with processes shorter than 50 microns in length stained mainly dense brown. Unipolar neurons had an oval, crescent, round, or elliptic perikaryon with a single short axon. The perikaryal shape of bipolar neurons varied from round to tall triangular, short triangular, crescent, oval, or elliptic with two oppositely directed symmetric or asymmetric processes. Asymmetric processes were present in a bipolar sensory cell with a long apical cilium typical of gastrodermal sensory cells. One type of bipolar ganglion cell had a short perikaryal cilium. Another type had neurites longer than 50 microns. We found seven morphological variations of multipolar neurons, including one with an apical knob, two with a short perikaryal cilium, two with cytoplasmic loops near the perikaryon, one with perpendicular processes projecting from the major neurites, and one with a branched process longer than 50 microns opposite a tangled mass of neurites.

Animals↗

PubMedDate not supplied

Quantification of white matter and gray matter volumes from three-dimensional magnetic resonance volume studies using fuzzy classifiers.

We accurately measured white matter (WM) and gray matter (GM) from three-dimensional (3D) volume studies, using a fuzzy classification technique. The new segmentation method is a modification of a recently published method developed for T1 parametric images. 3D MR images were transformed into pseudo forms of T1 parametric images and segmented into WM and GM voxel fraction images with a set of standardized fuzzy classifiers. This segmentation method was validated with synthesized 3D MR images as phantoms. These phantoms were developed from cryosectioned human brain images located in the superior, middle, and inferior regions of the cerebrum. Phantom volume measurements revealed that, generally, the difference between measured and actual volumes was less than 3% for 1.5-mm simulated brain slices. The average cerebral GM/WM ratio calculated from 3D MR studies in four subjects was 1.77, which compared favorably with the estimate of 1.67 derived from anatomical data. Results indicate that this is an accurate and rapid method for quantifying WM and GM from Tl-weighted 3D volume studies.

Brain↗

PubMed1995

Malignant histiocytosis: a reassessment of cases formerly classified as histiocytic neoplasms and review of the literature.

Malignant histiocytosis (MH) and true histiocytic lymphoma (THL) are hematopoietic malignancies of the mononuclear phagocytic system distinguished from each other by clinical presentation and presumed cell of origin. THL present as a localized mass derived from the fixed tissue histiocyte which may or may not disseminate. MH originates from the circulating monocyte or tissue macrophage and is characterized by a syndrome of systemic symptoms, pancytopenia, adenopathy, hepatosplenomegaly, and wasting. The distinction between MH and THL is at times arbitrary and overlap exists between these syndromes. The clinicopathologic studies that defined these entities were performed prior to the development of immunophenotyping and other molecular techniques currently used to ensure proper classification of hematopoietic malignancies. Nine patients from the University of Minnesota originally diagnosed with MH were retrospectively analyzed using a panel of antibodies reactive against T cell, B cell, and myelomonocytic antigens. Only one patient was reclassified as a possible histiocytic malignancy after reevaluation. Similar immunophenotyping studies have also shown cases previously diagnosed as MH or THL express lymphoid antigens, and would now be classified as Ki-1 positive anaplastic large cell lymphoma (ALCL) or some other hematopoietic neoplasm. These results indicate true histiocytic neoplasms are extremely rare, and previous concepts concerning clinical presentation and therapeutic outcome of the entities are inaccurate. In this paper we summarize the results of multiple retrospective analyses of cases previously diagnosed as MH or THL, including our experience at University of Minnesota, to illustrate the overall rarity of these entities. The current literature on malignant histiocytic disorders is reviewed, and the clinical presentation of patients determined to have histiocytic malignancies using contemporary analytical techniques is discussed.

Histiocytic Disorders, Malignant↗