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PubMed2025

Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS).

Probabilistic spatial modelling techniques developed on large-scale tumor-immune Atlases (~35M individually mapped cells; 50,000 high power fields) were used to characterize predictive features of treatment-responsive lung cancer. We identified CD8+FoxP3+ cell density as a robust pre-treatment biomarker for outcomes across disease stages and therapy types. In parallel, single-cell RNAseq studies of CD8+FoxP3+ T-cells revealed an activated, early effector phenotype, substantiating an anti-tumor role, and contrasting with CD4+FoxP3+ T-regulatory cells. A spatial biomarker was developed using an empirical probabilistic model to define the immediate cell neighbors or niche surrounding CD8+FoxP3+ cells and proximity to the tumor-stromal boundary. The resultant 'Diversity of Niches Unlocking Treatment Sensitivity (DONUTS)' are more prevalent than the CD8+FoxP3+ cells themselves, mitigating sampling error in small biopsies. Further, the DONUTS only require four markers, are additive to PD-L1, and associate with tertiary lymphoid structure counts. Taken together, the DONUTS represent a next-generation predictive biomarker poised for clinical implementation.

AstroPath↗
PubMed2000

A quantitative evaluation of SAGE.

Serial Analysis of Gene Expression (SAGE) is an innovative technique that offers the potential of cataloging both the identity and relative frequencies of mRNA transcripts in a given poly(A(+)) RNA preparation. Although it is a very effective approach for determining the expression of mRNA populations, there are significant biases in the observed results that are inherent in the experimental process. These are caused by sampling error, sequencing error, nonuniqueness, and nonrandomness of tag sequences. The quantitative information desired from SAGE experiments consists of estimates of the number of genes and the frequency distribution of transcript copy numbers. Of additional concern is the extent to which a given tag sequence can be assumed to be unique to its gene. The present study takes these mathematical biases into account and presents a basis for maximum likelihood estimation of gene number and transcript copy frequencies given a set of experimental results. These estimates of the true state of genomic expression are markedly different from those based directly on the observations from the underlying experiments. It also is shown that while in many cases it is probable that a given tag sequence is unique within the genome, in larger genomes this cannot be safely assumed.

Computer Simulation↗
PubMed2003

Characterization of the probabilistic traveling salesman problem.

We show that stochastic annealing can be successfully applied to gain new results on the probabilistic traveling salesman problem. The probabilistic "traveling salesman" must decide on an a priori order in which to visit n cities (randomly distributed over a unit square) before learning that some cities can be omitted. We find the optimized average length of the pruned tour follows E(L(pruned))=sqrt[np](0.872-0.105p)f(np), where p is the probability of a city needing to be visited, and f(np)-->1 as np--> infinity. The average length of the a priori tour (before omitting any cities) is found to follow E(L(a priori))=sqrt[n/p]beta(p), where beta(p)=1/[1.25-0.82 ln(p)] is measured for 0.05< or =p< or =0.6. Scaling arguments and indirect measurements suggest that beta(p) tends towards a constant for p<0.03. Our stochastic annealing algorithm is based on limited sampling of the pruned tour lengths, exploiting the sampling error to provide the analog of thermal fluctuations in simulated (thermal) annealing. The method has general application to the optimization of functions whose cost to evaluate rises with the precision required.

Journal Article↗
PubMed2004

Treatment of EXAFS data taken in the fluorescence mode in non-linear conditions.

The aim of this work is to investigate the possibility of extracting correct structural parameters from fluorescence EXAFS data taken at high count rates with an energy-resolving detector. This situation is often encountered on third-generation synchrotron radiation sources which provide a high flux on the sample. Errors caused by pulse pile-up in the extraction of structural information have been quantified in a real experiment, and different approaches to the problem of data correction have been elaborated. The different approaches are discussed in a comparison of the ability of each kind of correction to recover the correct structural parameters. The result of our analysis is that it is possible to work in non-linear conditions and correct the data, if the response of the acquisition system is known. Reliable structural information can be obtained with data acquired up to a count rate equal to approximately 60% of the inverse of the dead time.

Journal Article↗
PubMed1983

The hamster ear sebaceous glands. I. Examination of the regional variation by stripped skin planimetry.

A stripped skin planimetric method was developed to measure the ear sebaceous gland areas using a Numonics Graphics Calculator. The ear skin was manually separated from the cartilage and the area of the sebaceous gland units observed from the underside was determined. This procedure is less time-consuming than standard histologic techniques. Using stripped skin planimetry, it was demonstrated that the sebaceous gland size was greatest at the basal region of the ear and decreased toward the periphery. Regional variations in the density of the sebaceous gland units were also observed. In using the ear sebaceous model system it is important to standardize the site of biopsy in order to avoid sampling errors. The increase in ear sebaceous gland area from weaning to sexual maturity in the male hamster parallels the increase in flank organ area. This observation suggests that the ear and the flank organ sebaceous glands are comparable sebaceous models since they show a similarity in their response to the changing hormone levels during sexual maturation.

Animals↗
PubMed2001

A comparison of phenotypic variation and covariation patterns and the role of phylogeny, ecology, and ontogeny during cranial evolution of new world monkeys.

Similarity of genetic and phenotypic variation patterns among populations is important for making quantitative inferences about past evolutionary forces acting to differentiate populations and for evaluating the evolution of relationships among traits in response to new functional and developmental relationships. Here, phenotypic co variance and correlation structure is compared among Platyrrhine Neotropical primates. Comparisons range from among species within a genus to the superfamily level. Matrix correlation followed by Mantel's test and vector correlation among responses to random natural selection vectors (random skewers) were used to compare correlation and variance/covariance matrices of 39 skull traits. Sampling errors involved in matrix estimates were taken into account in comparisons using matrix repeatability to set upper limits for each pairwise comparison. Results indicate that covariance structure is not strictly constant but that the amount of variance pattern divergence observed among taxa is generally low and not associated with taxonomic distance. Specific instances of divergence are identified. There is no correlation between the amount of divergence in covariance patterns among the 16 genera and their phylogenetic distance derived from a conjoint analysis of four already published nuclear gene datasets. In contrast, there is a significant correlation between phylogenetic distance and morphological distance (Mahalanobis distance among genus centroids). This result indicates that while the phenotypic means were evolving during the last 30 millions years of New World monkey evolution, phenotypic covariance structures of Neotropical primate skulls have remained relatively consistent. Neotropical primates can be divided into four major groups based on their feeding habits (fruit-leaves, seed-fruits, insect-fruits, and gum-insect-fruits). Differences in phenotypic covariance structure are correlated with differences in feeding habits, indicating that to some extent changes in interrelationships among skull traits are associated with changes in feeding habits. Finally, common patterns and levels of morphological integration are found among Platyrrhine primates, suggesting that functional/developmental integration could be one major factor keeping covariance structure relatively stable during evolutionary diversification of South American monkeys.

Animals↗
PubMed1996

Image quantitation of intestinal metaplasia in entire gastrectomy specimens from Swedish and Japanese patients.

The aim of this work was to investigate the extension of intestinal metaplasia (IM), as well as to quantitate various components of IM (namely sialomucins, sulfomucins and Paneth cells), in entire gastrectomy specimens from Swedish and Japanese patients. The length of the gastric mucosa was assessed by morphometry. The percent of sections with IM was regarded as the extension of IM in the specimens. Histochemically labeled sialomucins, sulfomucins and Paneth cells (the 3 main findings in gastric IM) were quantified in separate sections with the aid of an image analyzer. In total, 1,321 sections corresponding to 6 gastrectomy specimens were quantified. Sialomucins and sulfomucins were more extensively distributed in the 4 specimens with carcinoma than in the 2 without carcinoma (one having a peptic ulcer and the other, hereditary gastric cancer syndrome (HGCS) without carcinoma). On the other hand, quantitative analysis in Swedish specimens indicated that the highest values for sialomucins, sulfomucins and Paneth cells were present in HGCS. When Swedish and Japanese specimens with adenocarcinoma were compared, only sulfomucins (denoting Types II and III IM) were significantly higher in those carrying an intestinal-type carcinoma (ITC) than in those with diffuse-type carcinoma (DTC). The results substantiate those obtained with gastric biopsies by other authors. On the other hand, the mucosal extension and the amount of sulfomucins are not comparable parameters (since that mucin was not equally distributed, but "concentrated" in certain areas in the mucosa). One possible conclusion is that the focal distribution of acidic mucins and of Paneth cells in the gastric mucosa may strongly influence their detection rate in gastric biopsies. Thus, haphazard biopsy of the gastric mucosa may fail to sample areas with sulfomucins in population studies aiming to detect individuals at risk. Such sampling errors in gastric biopsies may explain the conflicting results on this subject appearing in the literature.

Gastrectomy↗
PubMed2004

Clinical strategies -- interactive case discussions.

Interactive case discussions held during the symposium illustrate the practical challenges and dilemmas faced in the management of Barrett's oesophagus. Opinions of the faculty and audience varied widely on how proton pump inhibitor therapy should be used, especially in patients with short-segment Barrett's oesophagus. The therapeutic goal that received most support was to achieve sufficient acid control to keep the patient symptom free and heal any oesophagitis. At the same time, the patient should be reassured of the low risk associated with the endoscopic findings. When long-segment Barrett's oesophagus is detected, it should be assessed in detail, with targeted biopsy of any irregular-surfaced metaplastic mucosa and four quadrant biopsies every 2 cm, to diagnose intestinal metaplasia and to screen for dysplasia or cancer. Repeat endoscopy and biopsy may be appropriate to achieve a sensitive initial assessment because of potential sampling error. Proton pump inhibitor therapy, often twice daily, was considered a requirement for most cases of long-segment Barrett's oesophagus. There was disagreement over the role of surveillance, although proponents viewed it as worthwhile even in patients at low risk for the development of adenocarcinoma, mainly for medico-legal reasons. Endoscopic mucosal resection was seen to be appropriate in carefully selected patients with high-grade dysplasia, depending on factors such as age and comorbidity, the extent of high-grade dysplasia, findings on endoscopic ultrasound and the length of Barrett's oesophagus.

Anti-Ulcer Agents↗
PubMed2006

Acetic acid-enhanced magnification endoscopy in the diagnosis of specialized intestinal metaplasia, dysplasia and early cancer in Barrett's oesophagus.

BACKGROUND: Barrett's surveillance is prone to sampling error. Aim To determine whether enhanced magnification endoscopy using acetic acid instillation improves diagnostic accuracy of specialized intestinal metaplasia/dysplasia in Barrett's oesophagus. METHODS: We examined the detection rate of the specialized intestinal metaplasia/dysplasia in 64 consecutive patients with Barrett's oesophagus using acetic acid to enhance mucosal pit patterns. Histology was compared with the previous findings at recent conventional surveillance in 62 patients. We also examined the inter-/intra-observer agreement in the assessment of the enhanced magnification endoscopy pit pattern findings. RESULTS: Histology revealed columnar-lined oesophagus in six (9%) patients, specialized intestinal metaplasia in 49 (77%), low-grade dysplasia in five (8%), high-grade dysplasia in one (2%), and adenocarcinoma in three (5%). There was discordance between the histologic findings from conventional surveillance with random biopsy. Fifteen patients (24%) had a histological upgrade with enhanced magnification endoscopy. There was a high detection rate of specialized intestinal metaplasia even in short segment Barrett's oesophagus (74%), and additionally, there were two cancers, one with 2-cm Barrett's oesophagus and one ultra-short (1 cm). The mean kappa values for inter- and intra-observer agreement in assessing the pit patterns were 0.571 (0.041) and 0.709 (0.038), respectively. CONCLUSIONS: Enhanced magnification endoscopy allows clear visualization of the epithelial pit patterns within Barrett's oesophagus, and targeted biopsy results in a high yield of specialized intestinal metaplasia and dysplasia.

Acetic Acid↗
PubMed1991

DNA ploidy studies of benign and malignant tumours: comparison of flow cytometry and image analysis techniques using two types of cytological specimen.

DNA ploidy studies were carried out on Feulgen stained smears and cytocentrifuge preparations from 35 malignant tumours and four benign neoplasms using the CAS image analyser. The smears were prepared from scrapings from fresh tumour tissue whereas the cytocentrifuge preparations were prepared from single nuclear suspensions from paraffin-embedded cell blocks from the same tumour. Histograms obtained by image analysis of the tumour scrapes were compared with those obtained on the cytocentrifuge preparations. Concordant results were obtained in four benign tumours (100%) and 32 malignant tumours (91%). The results obtained by image analysis were also compared with results obtained by flow cytometry of the tumour tissue. Discordant results were obtained for three malignant tumours. Possible reasons for the discrepancy include sampling error, tumour heterogeneity and selective loss of cell populations during processing.

Base Sequence↗
PubMed1997

Cytohistological correlation as a measure of quality assurance of a cytology laboratory.

In a hospital-based cytology screening programme for the early detection of preinvasive lesions of the uterine cervix, 166 women with abnormal smears (human papillomavirus (HPV) changes, cervical intraepithelial neoplasia (CIN) and invasive carcinoma) were referred to the central colposcopy clinic between January 1989 and December 1991. The colposcopist (V.S.) was able to take a direct biopsy in 156 cases. In the remaining 10-cases, biopsy could not be taken because of unsatisfactory colposcopy. A cytohistological correlation was obtained in 121/156 (77.5%) cases, and the remaining 35 cases showed a disparity in diagnosis. These were reviewed by one of us (P.S.) and the reasons for underdiagnosis/false negatives and overdiagnosis/false-positive results were analysed. It was found that sampling error was the cause of false negativity and underdiagnosis in most cases while interpretative errors resulted in the overdiagnosis and false-positive smears. The reasons for interpretative errors were studied in detail.

Cytodiagnosis↗
PubMed2006

Endoscopic ultrasound-guided FNA biopsy of bile duct and gallbladder: analysis of 53 cases.

OBJECTIVE: Endoscopic retrograde cholangiopancreaticography (ERCP)-guided brushing has been the standard of practice for surveillance and detection of carcinoma in the biliary tree. Few studies have evaluated the role of endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) in diagnosing clinically suspected cholangiocarcinoma. The role of this method in diagnosing clinically suspected gallbladder malignancies has not been extensively evaluated in the USA. This study investigates the role of EUS-FNA in the diagnosis of clinically suspected biliary tree and gallbladder malignancies in a large patient series. METHODS: EUS-FNAs were obtained from 46 bile duct and seven gallbladder lesions. On-site rapid interpretation was provided using air-dried Diff Quik stained smears. In addition, alcohol fixed Papanicoloau stained smears and Thin Prep preparations (Cytye Corp., Marlborough, MA, USA) were evaluated before providing a final cytological diagnosis. Tissue biopsies and/or clinical follow-up were used as the standards to determine operating characteristics for EUS-FNA. RESULTS: The mean ages for bile duct and gallbladder lesions were 66 years (range: 37-84 years), and 69 years (range 49-86 years), respectively. All cases diagnosed as suspicious/malignant on preliminary evaluation were confirmed on final cytological interpretation (27/27). The operating characteristics show that EUS-FNA is highly specific (100%) with sensitivity rates of 87% and 80% from clinically suspected malignancies of biliary tract and gallbladder, respectively. Sampling error in three cases and associated acute inflammation in two cases resulted in false-negative diagnoses. CONCLUSIONS: EUS-FNA of biliary tree and gallbladder carcinoma is highly specific and should be considered for evaluation of clinically suspicious lesions. Marked inflammation may result in false-negative diagnoses.

Bile Duct Neoplasms↗
PubMed1976

Bone mass in maintenance haemodialysis. Prospective study with sequential biopsies.

The change of bone mass during maintenance haemodialysis was studied in 20 patients. Iliac crest biopsies were obtained at a 9 - 16 months interval. Two biopsies were taken in order to give an independent estimate of the sampling error. 22 individuals in the same age group without skeletal disease who died from traffic accidents or from violent deaths were used as controls. Undecalcified sections of bone (Masson-Goldner-stain) were evaluated by micromorphometry. At the beginning of the study osteosclerosis (i.e. volumetric density of bone above x +/- 2 SD in control patients) was found in 14 out of 20 patients. Volumetric density of bone only increased in one of the patients during the observation period. A significant decrease of volumetric density of bone was found in 5 out of 20 patients. This could be attributed to prolonged immobilisation in two cases and to inadequate protein- and calorie-intake in two cases. No predisposing factor could be found in the fifth case. It is concluded that loss of spongy bone mass (osteopenia) is not an invariable result of haemodialysis.

Adult↗
PubMed1988

Incomplete septal cirrhosis: histopathological aspects.

We have reviewed 60 liver specimens from 47 patients with the diagnosis of incomplete septal cirrhosis observed between 1968 and 1987. In reaching this diagnosis evaluation of the following histological features appeared to be helpful: parenchymal nodularity, thin incomplete septa, hypoplastic portal tracts, increased number of venous channels, abnormal spacing between portal tracts and veins, crowding of reticulin fibres between adjacent zones of hyperplastic parenchyma, hyperplasia of hepatocytes and dilated sinusoids. These histological features were not specific for incomplete septal cirrhosis as they were also present--although less evident and less frequent--in a series of 87 non-cirrhotic liver specimens. Reticulin stains were an essential adjunct to assess the architectural disturbance, which was often inconspicuous in needle biopsies. Histological features indicating a specific aetiology were lacking in the great majority of cases. On histological and clinical grounds, incomplete septal cirrhosis resembles idiopathic portal hypertension, nodular regenerative hyperplasia and partial nodular transformation; in these entities an obliterative portal venopathy with non-uniformity of portal blood supply to the parenchyma has been suggested as a pathogenic mechanism. In the present study phlebosclerotic lesions of the portal vein were found in only two cases. This might be explained by sampling error or, alternatively, the hypoplastic portal tracts observed might be a functional equivalent of obliterative portal venopathy resulting in a deficient portal blood supply. Non-uniformity of blood supply to the parenchyma may explain the similarities between incomplete septal cirrhosis and the diseases mentioned.

Humans↗
PubMed1989

Diagnostic reliability of histological and cytological fine needle biopsies from focal liver lesions.

In 175 consecutive cases of ultrasonically detected focal liver lesions both cytological and histological fine needle biopsies were performed using two different 0.6 mm needles. The cytological and histological material was evaluated blindly and separately by two examiners, who had no access to clinical data. In 65 cases a reliable final diagnosis as defined by autopsy or surgical biopsy within 6 months could be reached. Eleven cases of benign liver lesions were correctly classified by the two examiners by both cytological and histological fine needle biopsies, resulting in a predictive value of 100% for a malignant diagnosis. The predictive value for a benign diagnosis was 85% for both examiners' evaluation of cytological fine needle biopsies, while it was 73% and 85%, respectively, for histological fine needle biopsies. At reevaluation both sampling error and difficulties in interpretation of biopsies of poor quality were responsible for the false benign diagnosis. The origin of the primary tumour was correctly diagnosed in about 50% of the cases by both techniques. Correct tumour typing could most often be made by both methods in cases of hepatocellular carcinoma, breast carcinoma, colonic carcinoma and small cell carcinoma of the lung.

Adult↗
PubMed1993

The histological diagnosis of clinically documented cases of cryptogenic organizing pneumonia: diagnostic features in transbronchial biopsies.

Eleven cases of clinically diagnosed cryptogenic organizing pneumonia were examined in order to establish the histological features found at transbronchial biopsy and to correlate this with open lung biopsy which followed in six cases. The essential pathological feature was the presence of buds of granulation tissue (Masson bodies) indicating organization of a persistent exudate by fibroblasts and capillaries within alveoli, with preservation of the alveolar architecture. In addition, both acute and chronic inflammatory cells were present in the interstitium. These features, combined with the clinical history, were sufficient for a diagnosis in seven of the 11 cases on transbronchial biopsies. Four biopsies lacked these features. Patients proceeded to open lung biopsy in addition to the two with histological features of cryptogenic organizing pneumonia on transbronchial biopsy, but where the clinician wanted to eliminate other pathology because of rapid clinical deterioration. Five of the six cases coming to open lung biopsy confirmed cryptogenic organizing pneumonia with Masson bodies within alveoli, but changes were focal in three with very few Masson bodies in one. One case which had the features on transbronchial biopsy lacked them in the open lung biopsy. Transbronchial biopsy, therefore, can yield diagnostic material in the majority of patients with cryptogenic organizing pneumonia while open lung biopsy, which is considered the gold standard for interstitial lung disease, may yield negative results because of sampling error and the rapid evolution and changing pattern of the disease.

Adult↗
PubMed2006

Variations on a theme: sources of heterogeneity in the form of the interspecific relationship between abundance and distribution.

1. A positive interspecific relationship between abundance and distribution is widely considered to be one of the most general patterns in ecology. However, the relationship appears to vary considerably across assemblages, from significant positive to significant negative correlations and all shades in between. 2. This variation has led to the suggestion that the abundance-distribution relationship has multiple forms, with the corollary that different patterns may inform about, or have different, causes. However, this variation has never been formally quantified, nor has it been determined whether the observed variation is indicative of sampling error in estimating a single effect or of real heterogeneity in such relationships. Here, we use the meta-analytical approach to assess variation in abundance-distribution relationships, and to test different hypotheses for it. 3. Analysis of 279 relationships found a mean effect size of 0.655, which was both highly significantly different from zero and indicative of a strong positive association between abundance and distribution. However, effect sizes were highly heterogeneous, supporting the contention that this relationship does indeed have multiple forms. 4. Most notably, relationships vary significantly in strength across realms, with the strongest in the marine and intertidal, intermediate relationships for terrestrial and parasitic assemblages, and the weakest relationships in freshwater systems. Effect sizes in all of the aquatic realms are homogeneous, suggesting that realm is an important source of the heterogeneity observed across all studies. We posit that this may be because the different spatial structure of the environment in each realm affects the opportunity for the dispersal of individuals between sites. 5. Some of the remaining heterogeneity in effect sizes for terrestrial assemblages could be explained by partitioning assemblages by habitat, scale, biogeographical region and taxon, but considerable heterogeneity in effect sizes for terrestrial and parasitic assemblages remained unexplained.

Amphibians↗
PubMed1984

Specificity of plasma cells in the rheumatoid synovium. I. Immunoglobulin class of antiglobulin-producing cells.

Plasma cells synthesizing rheumatoid factors (RF) were identified by fluorescent staining of sections of synovium and macrophage-depleted cells from dispersed synovial tissue. The latter avoided problems related to sampling errors in studying tissue sections and in the uncertainty raised by the staining of macrophages with intracellular complexes. Plasma cells producing IgG predominated, and seropositive patients had a higher proportion of IgM producers than seronegative subjects. None the less, in both groups of patients more than 90% of the IgM plasma cells were synthesizing RF, whereas the corresponding figure for IgG was between 50% and 60%. Only around 10% of IgA plasma cells were positive for RF. The high percentage of IgM plasma cells making RF would tend to argue for an IgG-specific response and against direct polyclonal activation as the stimulus. The percentage of IgG-producing cells positive for RF is also consistent with a dominant response to IgG. Accepting the difference in the relative proportion of total IgM- to IgG-producing plasma cells in seropositive as against seronegative patients, the close similarity between the two groups in the fraction of cells making RF favours the view that the two groups have a comparable underlying immunopathology dependent on IgG autosensitization. From the technical standpoint, the dispersed cell method gives results in line with those obtained with sections but which are easier to read, whereas the fluorescent techniques described give clear and reproducible results for the detection of RF of different heavy-chain isotype.

Adult↗