A method for utilizing automated machine learning for histopathological classification of testis based on Johnsen scores.

We examined whether a tool for determining Johnsen scores automatically using artificial intelligence (AI) could be used in place of traditional Johnsen scoring to support pathologists' evaluations. Average precision, precision, and recall were assessed by the Google Cloud AutoML Vision platform. We obtained testicular tissues for 275 patients and were able to use haematoxylin and eosin (H&E)-stained glass microscope slides from 264 patients. In addition, we cut out of parts of the histopathology images (5.0 × 5.0 cm) for expansion of Johnsen's characteristic areas with seminiferous tubules. We defined four labels: Johnsen score 1-3, 4-5, 6-7, and 8-10 to distinguish Johnsen scores in clinical practice. All images were uploaded to the Google Cloud AutoML Vision platform. We obtained a dataset of 7155 images at magnification 400× and a dataset of 9822 expansion images for the 5.0 × 5.0 cm cutouts. For the 400× magnification image dataset, the average precision (positive predictive value) of the algorithm was 82.6%, precision was 80.31%, and recall was 60.96%. For the expansion image dataset (5.0 × 5.0 cm), the average precision was 99.5%, precision was 96.29%, and recall was 96.23%. This is the first report of an AI-based algorithm for predicting Johnsen scores.

Artificial intelligence for cellular phenotyping diagnosis of nasal polyps by whole-slide imaging.

BACKGROUND: artificial intelligence (AI) for cellular phenotyping diagnosis of nasal polyps by whole-slide imaging (WSI) is lacking. We aim to establish an AI chronic rhinosinusitis evaluation platform 2.0 (AICEP 2.0) to obtain the proportion of inflammatory cells for cellular phenotyping diagnosis of nasal polyps and to explore the clinical significance of different phenotypes of nasal polyps on the WSI. METHODS: a total of 453 patients were enrolled in our study. For the development of AICEP 2.0, 179 patients (WSIs) were obtained from the Third Affiliated Hospital of Sun Yat-Sen University (3HSYSU) from January 2008 to December 2018. A total of 24,625 patches were automatically extracted from the regions of interest under a 400× HPF by Openslide and the number of inflammatory cells in these patches was counted by two pathologists. For the application of AICEP 2.0 in a prospective cohort, 158 patients aged 14-70 years old with chronic rhinosinusitis with nasal polyps (CRSwNP) who had undergone endoscopic sinus surgery at 3HSYSU from June 2020 to December 2020 were included for preoperative demographic characteristics. For the application of AICEP 2.0 in a retrospective cohort, 116 patients with CRSwNP who had undergone endoscopic sinus surgery from May 2016 to June 2017 were enrolled for the recurrence rate. The proportion of inflammatory cells of these patients on WSI was calculated by our AICEP 2.0. FINDINGS: for AICEP 2.0, the mean absolute errors of the ratios of eosinophils, lymphocytes, neutrophils, and plasma cells were 1.64%, 2.13%, 1.06%, and 1.22%, respectively. The four phenotypes of nasal polyps were significantly different in clinical characteristics (including asthma, itching, sneezing, total IgE, peripheral eosinophils%, tissue eosinophils%, tissue neutrophils%, tissue lymphocytes%, tissue plasma cells%, and recurrence rate; P <0.05), but there were no significant differences in age distribution, onset time, total VAS score, Lund-Kennedy score, or Lund-Mackay score. The percentage of peripheral eosinophils was positively correlated with the percentage of tissue eosinophils (r = 0.560, P <0.001) and negatively correlated with tissue lymphocytes% (r = -0.489, P <0.001), tissue neutrophils% (r = -0.225, P = 0.005), and tissue plasma cells% (r = -0.266, P = 0.001) in WSIs.

[Values of cerebrospinal fluid cytochemistry in pediatric patients with ventriculoperitoneal shunt]. / Valores del análisis citoquímico de líquido cefalorraquídeo en pacientes con derivación ventrículo-peritoneal.

BACKGROUND: The ventriculo-peritoneal shunt (VPS) is the treatment for hydrocephalus, the cerebrospinal fluid (CSF) is evaluated for the management of its complications; however, information on the values of the cytochemistry in this population is insufficient. AIM: To describe the characteristics of the CSF cytochemistry of children in VPS management. METHODS: Descriptive observational study, developed in Bogotá (Colombia), from 2008 to 2016. VPS and related procedures records were reviewed. Patients between 6 months and 18 years were included. RESULTS: A total of 285 records were reviewed, 31 samples were entered. The CSF values were, respectively, for the median and 90% percentile: total leukocytes: 0 and 7 cells/mm3, neutrophils: 0 and 6.8 cells/mm3, lymphocytes: 0 and 2 cells/mm3, proteins: 13.4 and 67.2 mg/dL, glucose: 59 and 27.4 mg/dL. DISCUSSION: Glucose values evinced a normal rank towards the widest inferior limit with protein values exceeding the values expected. Cellularity is the variable with the lowest variation. CONCLUSIONS: The values of the CSF cytochemistry in patients with VPS are not comparable to those of the healthy population and should be interpreted according to the characteristics of this population.

Valores del análisis citoquímico de líquido cefalorraquídeo en pacientes con derivación ventrículo-peritoneal / Values of cerebrospinal fluid cytochemistry in pediatric patients with ventriculoperitoneal shunt

Resumen Introducción: La derivación ventrículo-peritoneal (DVP) es el tratamiento para la hidrocefalia. El líquido cefalorraquídeo (LCR) se evalúa para el manejo de sus complicaciones; sin embargo, la información de los valores del citoquímico en esta población es insuficiente. Objetivo: Describir las características del citoquímico del LCR de niños en manejo con DVP. Materiales y Métodos: Estudio de tipo observacional descriptivo, desarrollado en Bogotá (Colombia), entre el año 2008 y 2016. Se revisaron los registros de procedimientos de DVP y relacionados. Se incluyeron pacientes entre 6 meses y 18 años de edad. Resultados: Se revisaron 285 registros e ingresaron 31 muestras. Los valores de LCR fueron, respectivamente, para la mediana y al percentil 90%: leucocitos totales: 0 y 7 céls/mm3, neutrófilos: 0 y 6,8 céls/mm3, linfocitos: 0 y 2 céls/mm3, proteínas: 13,4 y 67,2 mg/dL, glucosa: 59 y 27,4 mg/dL. Discusión: Los valores de glucosa presentan un rango normal hacia el extremo inferior más amplio, con valores de proteínas mayores a los valores esperados. El rango de celularidad es la variable que presenta menor variación. Conclusiones: Los valores del citoquímico de LCR en paciente con DVP no son equiparables a los de la población sana y deben interpretarse según las características propias de esta población.

Background: The ventriculo-peritoneal shunt (VPS) is the treatment for hydrocephalus, the cerebrospinal fluid (CSF) is evaluated for the management of its complications; however, information on the values of the cytochemistry in this population is insufficient. Aim: To describe the characteristics of the CSF cytochemistry of children in VPS management. Methods: Descriptive observational study, developed in Bogotá (Colombia), from 2008 to 2016. VPS and related procedures records were reviewed. Patients between 6 months and 18 years were included. Results: A total of 285 records were reviewed, 31 samples were entered. The CSF values were, respectively, for the median and 90% percentile: total leukocytes: 0 and 7 cells/mm3, neutrophils: 0 and 6.8 cells/mm3, lymphocytes: 0 and 2 cells/mm3, proteins: 13.4 and 67.2 mg/dL, glucose: 59 and 27.4 mg/dL. Discussion: Glucose values evinced a normal rank towards the widest inferior limit with protein values exceeding the values expected. Cellularity is the variable with the lowest variation. Conclusions: The values of the CSF cytochemistry in patients with VPS are not comparable to those of the healthy population and should be interpreted according to the characteristics of this population.

Do pathologists agree with each other on the histological assessment of pT1b oesophageal adenocarcinoma?

Background: In early (T1) oesophageal adenocarcinoma (OAC), the histological profile of an endoscopic resection specimen plays a pivotal role in the prediction of lymph node metastasis and the potential need for oesophagectomy with lymphadenectomy. Objective: To evaluate the inter-observer agreement of the histological assessment of submucosal (pT1b) OAC. Methods: Surgical and endoscopic resection specimens with pT1b OAC were independently reviewed by three gastrointestinal pathologists. Agreement was determined by intraclass correlation coefficient for continuous variables, and Fleiss' kappa (κ) for categorical variables. Bland-Altman plots of the submucosal invasion depth were made. Results: Eighty-five resection specimens with pT1b OAC were evaluated. The agreement was good for differentiation grade (κ=0.77, 95% confidence interval (CI) 0.68-0.87), excellent for lymphovascular invasion (κ=0.88, 95% CI 0.76-1.00) and moderate for submucosal invasion depth using the Paris and Pragmatic classifications (κ=0.60, 95% CI 0.49-0.72 and κ=0.42, 95% CI 0.33-0.51, respectively). Systematic mean differences between pathologists were detected for the measurement of submucosal invasion depth, ranging from 297 µm to 602 µm. Conclusions: A substantial discordance was found between pathologists for the measurement of submucosal invasion depth in pT1b OAC. Differences may lead to an over- or underestimation of the lymph node metastasis risk, with grave implications for the treatment strategy. Review by a second gastrointestinal pathologist is recommended to improve differentiating between a favourable and an unfavourable histological profile.

Factors Affecting Ultrastructural Quality in the Prefrontal Cortex of the Postmortem Human Brain.

Electron microscopy (EM) studies of the postmortem human brain provide a level of resolution essential for understanding brain function in both normal and disease states. However, processes associated with death can impair the cellular and organelle ultrastructural preservation required for quantitative EM studies. Although postmortem interval (PMI), the time between death and preservation of tissue, is thought to be the most influential factor of ultrastructural quality, numerous other factors may also influence tissue preservation. The goal of the present study was to assess the effects of pre- and postmortem factors on multiple components of ultrastructure in the postmortem human prefrontal cortex. Tissue samples from 30 subjects were processed using standard EM histochemistry. The primary dependent measure was number of identifiable neuronal profiles, and secondary measures included presence and/or integrity of synapses, mitochondria, and myelinated axonal fibers. Number of identifiable neuronal profiles was most strongly affected by the interaction of PMI and pH, such that short PMIs and neutral pH values predicted the best preservation. Secondary measures were largely unaffected by pre- and postmortem factors. Together, these data indicate that distinct components of the neuropil are differentially affected by PMI and pH in postmortem human brain.

Control de calidad de la citología ginecológica: programa de calidad de la Sociedad Española de Citología. Resultados de la segunda ronda / The Spanish Society of Cytology: quality control program of gynecological cytology

Introducción. Las recomendaciones del cribado de cáncer de cérvix en España incluyen la participación en programas de control de calidad externos a los laboratorios de citología. La Sociedad Española de Citología (SEC) ha iniciado un programa de control de calidad de la citología ginecológica (CG). Objetivo. Presentar y analizar los resultados de la segunda ronda del control de calidad de la SEC. Material y métodos. Se incluyeron casos procesados mediante citología en medio líquido. Se escanearon las laminillas mediante la plataforma Aperio. Se seleccionaron 23 muestras procedentes de un banco de casos con al menos un 75% de acuerdo entre 4 expertos citopatólogos. Los diagnósticos de los casos para estudio incluyeron: uno negativo, 15 lesiones de bajo grado (4 ASCUS y 11 LSIL) y 7 lesiones de alto grado (uno ASCH y 6 HSIL). La CML correspondía a ThinPrep® en 16 casos y a SurePath® en 7. Se realizó el estudio de la correlación diagnóstica interobservador. Resultados. Participaron 16 hospitales. Las concordancias medias fueron: global 70,6% y por tipo de lesión 63,1%. En negativo 71,9%, en ASCUS 56,2%, en LSIL 69,5% y en HSIL 82,8%. Los casos discordantes correspondían con mayor frecuencia a negativos y a ASCUS. Se observó discordancia severa (HSIL/ASCH frente a negativo) en un 4,4% de los casos. Conclusiones. Nuestros resultados son similares a los descritos en la literatura, encontrando muy escasas discordancias severas (AU)

Introduction. In Spain, the guidelines for cervical cancer screening include a recommendation to enroll in external quality control programs. The Spanish Society of Cytology (SEC) has initiated its own quality control program of gynecological cytology (QCPGC). Aim. To describe and discuss the results of the second round of SEC¿s QCPGC. Material and method. The cases are selected by a group of expert cytologists. The cases with an agreement of 75% of four cytopathologists were used. The cases were scanned with Aperio. The scanned cases not available were excluded. We included a total of 23 cases, 1 negative, 15 low grade lesions (4 ASCUS and 11 LSIL) and 7 high grade lesions (1 ASCH and 6 HSIL). Sixteen cases were studied with ThinPrep™ platform and in 7 cases the SurePath™ platform was used. Results. Sixteen hospitals participated. The global mean concordance was 70.6%. The mean concordance in the type of lesion was 63.1%. The concordance was 71.9% in negative diagnoses, 56.2% in ASCUS, 69.5% in LSIL and 82.8% in HSIL The discordant cases were diagnosed more frequently as negative and ASCUS. 4.4% of cases had major discordances (HSIL or ASCH versus negatives). Conclusions: Our results are similar to those reported in the literature, with very little severe discordance. The method of exchanging slides does not allows continuous training, since the review of discordant cases can not be made. Therefore, methodological corrections are contemplated for future rounds (AU)

Differential diagnosis of well-differentiated squamous cell carcinoma from non-neoplastic oral mucosal lesions: New cytopathologic evaluation method dependent on keratinization-related parameters but not nuclear atypism.

BACKGROUND: The cytology of oral squamous cell carcinoma (SCC) is challenging because oral SCC cells tend to be well differentiated and lack nuclear atypia, often resulting in a false negative diagnosis. The purpose of this study was to establish practical cytological parameters specific to oral SCCs. METHODS: We reviewed 123 cases of malignancy and 53 of non-neoplastic lesions of the oral mucosa, which had been diagnosed using both cytology and histopathology specimens. From those, we selected 12 SCC and 4 CIS cases that had initially been categorized as NILM to ASC-H with the Bethesda system, as well as 4 non-neoplastic samples categorized as LSIL or ASC-H as controls, and compared their characteristic findings. After careful examinations, we highlighted five cytological parameters, as described in Results. Those 20 cytology samples were then reevaluated by 4 independent examiners using the Bethesda system as well as the 5 parameters. RESULTS: Five cytological features, (i) concentric arrangement of orangeophilic cells (indicating keratin pearls), (ii) large number of orangeophilic cells, (iii) bizarre-shaped orangeophilic cells without nuclear atypia, (iv) keratoglobules, and (v) uneven filamentous cytoplasm, were found to be significant parameters. All malignant cases contained at least one of those parameters, while none were observed in the four non-neoplastic cases with nuclear atypia. In reevaluations, the Bethesda system did not help the screeners distinguish oral SCCs from non-neoplastic lesions, while use of the five parameters enabled them to make a diagnosis of SCC. CONCLUSION: Recognition of the present five parameters is useful for oral SCC cytology. Diagn. Cytopathol. 2017;45:406-417. © 2017 Wiley Periodicals, Inc.

Biologically Relevant Heterogeneity: Metrics and Practical Insights.

Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.

The relevance of tissue thiol histochemistry to diagnostic hematopathology.

Expression analyses suggest that alterations of the antioxidant state of some diffuse large B-cell lymphomas can assist prognosis; reversibly oxidized thiols may serve as a surrogate marker for identifying such cases. Little is known about the distribution of free thiols and reversibly oxidized thiols in human tissues. We developed a staining technique that enables visualization of tissue thiols in situ using bright field microscopy and validated it using gastrointestinal tissue specimens. We used our thiol staining technique to assess benign tonsillectomy and diffuse large B-cell lymphoma specimens. The gastrointestinal series revealed the presence of free thiols within epithelial cells and cells of the lamina propria. Staining for reversibly oxidized thiols was robust in gastric foveolar cells, intestinal goblet cells and the mucus they produce. Tonsillectomy specimens exhibited diffuse presence of free thiols. Staining for reversibly oxidized thiols was confined to germinal center macrophages and sinus histiocytes. Among the diffuse large B-cell lymphoma specimens, we observed strong staining for free thiols within malignant cells. By contrast to benign B-cells, the malignant cells demonstrated pronounced and diffuse staining for reversibly oxidized thiols. We demonstrated intrinsic differences between benign and malignant cells.

External quality assessment for acid fast bacilli smear microscopy in eastern part of Ethiopia.

BACKGROUND: External quality assessment (EQA) of sputum smear microscopy is essential and indispensable component of any tuberculosis program. This study assessed the EQA of acid fast bacilli (AFB) smear microscopy through onsite evaluation, blinded rechecking and panel test. A one year study was conducted on eight health institution laboratories from December 2011 to December 2012. Onsite evaluation, blinded rechecking and panel tests were used to collect data. Data were analyzed using SPSS version 16. Sensitivity, specificity, predictive values, and proportions of false readings were calculated. The level of agreement was measured using Kappa (κ) value. RESULTS: Problems observed during onsite evaluation include shortages of materials, disinfectant, and poor storage and working condition. A total of 578 slides were collected for blinded rechecking, of which 102 (17.6%) were reported as positive by peripheral laboratories. The panel test revealed an overall error of 17 (25.25%) of which 14 (17.5%) were minor errors [low false negative 6 (7.5%) and low false positive 8 (10%)], and 3 (3.75%) were major errors (high false positive). The sensitivity, specificity, positive predictive values (PPV) and negative predictive values (NPV) of the peripheral laboratories were 83.5, 97.8, 91.7, and 95.7, respectively. The false readings at the peripheral laboratories were 32 (5.5%). Agreement on reading the slides was observed on 546 (94.5%) slides (K = 0.84, SE = 0.054). CONCLUSIONS: Lack of reagents, supplies, favorable working environment and AFB related technical problems were identified in the peripheral laboratories. High false negative error was found to be the predominant major error. A continuous and strong EQA scheme should be implemented to avoid reporting errors and produce quality sputum results.

Guidelines for the cytopathologic diagnosis of epithelioid and mixed-type malignant mesothelioma: Complementary Statement from the International Mesothelioma Interest Group, Also Endorsed by the International Academy of Cytology and the Papanicolaou Society of Cytopathology.

OBJECTIVE: To provide practical guidelines for the cytopathologic diagnosis of malignant mesothelioma. DATA SOURCES: Cytopathologists with an interest in the field involved in the International Mesothelioma Interest Group (IMIG) and the International Academy of Cytology (IAC) contributed to this update. Reference material includes peer-reviewed publications and textbooks. RATIONALE: This article is the result of discussions during and after the IMIG 2012 conference in Boston, followed by thorough discussions during the 2013 IAC meeting in Paris. Additional contributions have been obtained from cytopathologists and scientists who could not attend these meetings, with final discussions and input during the IMIG 2014 conference in Cape Town.

News from the Biological Stain Commission, no. 16.

In the 16(th) issue of News from the Biological Stain Commission (BSC) under the heading of Regulatory affairs, the Biological Stain Commission's International Affairs Committee presents information from the 28(th) meeting of CEN/TC 140 In vitro diagnostic medical devices held on October 23, 2013 in Berlin, Germany. Information is also presented from the 19(th) meeting of ISO/TC 212 Clinical laboratory testing and in vitro diagnostic test systems held on October 19 - 21, 2013 in Singapore.

Validation of a method to directly and specifically measure nitrite in biological matrices.

The bioactivity of nitric oxide (NO) is influenced by chemical species generated through reactions with proteins, lipids, metals, and its conversion to nitrite and nitrate. A better understanding of the functions played by each of these species could be achieved by developing selective assays able of distinguishing nitrite from other NO species. Nagababu and Rifkind developed a method using acetic and ascorbic acids to measure nitrite-derived NO in plasma. Here, we adapted, optimized, and validated this method to assay nitrite in tissues. The method yielded linear measurements over 1-300 pmol of nitrite and was validated for tissue preserved in a nitrite stabilization solution composed of potassium ferricyanide, N-ethylmaleimide and NP-40. When samples were processed with chloroform, but not with methanol, ethanol, acetic acid or acetonitrile, reliable and reproducible nitrite measurements in up to 20 sample replicates were obtained. The method's accuracy in tissue was ≈ 90% and in plasma 99.9%. In mice, during basal conditions, brain, heart, lung, liver, spleen and kidney cortex had similar nitrite levels. In addition, nitrite tissue levels were similar regardless of when organs were processed: immediately upon collection, kept in stabilization solution for later analysis or frozen and later processed. After ip nitrite injections, rapidly changing nitrite concentrations in tissue and plasma could be measured and were shown to change in significantly distinct patterns. This validated method could be valuable for investigations of nitrite biology in conditions such as sickle cell disease, cardiovascular disease, and diabetes, where nitrite is thought to play a role.

Cervical cancer biopsy reporting: a review.

The terminology for reporting human papillomavirus-associated squamous lesions in the cervix, both in tissue samples and cytology specimens, has suffered from many changes throughout the last years creating confusion in interpreting cervical biopsy and cytology reports by clinicians. This review presents a summary and discussion of the current terminology for reporting results of cervical biopsies and cytology with emphasis in the lower anogenital squamous terminology consensus recommendations for tissue specimens and the 2001 Bethesda Workshop for reporting cytology results. Microscopic features of cervical lesions in tissue samples and cytology specimens are presented. Biomarkers, including p16 and Ki-67, are discussed and how they can help the pathologist when dealing with difficult cases.

Accomplishments of the Trustees and laboratory staff of the Biological Stain Commission, 2002-2013.

During the 12 years from 2002 to 2013, the Trustees and laboratory personnel of the Biological Stain Commission (BSC) can claim many accomplishments. These accomplishments are itemized under 11 categories: continuous publication of the official journal, Biotechnic & Histochemistry; production of four special issues of Biotechnic & Histochemistry devoted to specific dyes or stains; standardization of staining and dye purity; mechanisms of staining and prediction of dye behavior; publication of books or book chapters; effects of fixation and processing on staining; cancer research; immunohistochemistry; BSC Laboratory activities; miscellaneous publications; and administrative accomplishments.

Subsite awareness in neuropathology evaluation of National Toxicology Program (NTP) studies: a review of select neuroanatomical structures with their functional significance in rodents.

This review article is designed to serve as an introductory guide in neuroanatomy for toxicologic pathologists evaluating general toxicity studies. The article provides an overview of approximately 50 neuroanatomical subsites and their functional significance across 7 transverse sections of the brain. Also reviewed are 3 sections of the spinal cord, cranial and peripheral nerves (trigeminal and sciatic, respectively), and intestinal autonomic ganglia. The review is limited to the evaluation of hematoxylin and eosin-stained tissue sections, as light microscopic evaluation of these sections is an integral part of the first-tier toxicity screening of environmental chemicals, drugs, and other agents. Prominent neuroanatomical sites associated with major neurological disorders are noted. This guide, when used in conjunction with detailed neuroanatomic atlases, may aid in an understanding of the significance of functional neuroanatomy, thereby improving the characterization of neurotoxicity in general toxicity and safety evaluation studies.

Validation of morphometric analyses of small-intestinal biopsy readouts in celiac disease.

BACKGROUND: Assessment of the gluten-induced small-intestinal mucosal injury remains the cornerstone of celiac disease diagnosis. Usually the injury is evaluated using grouped classifications (e.g. Marsh groups), but this is often too imprecise and ignores minor but significant changes in the mucosa. Consequently, there is a need for validated continuous variables in everyday practice and in academic and pharmacological research. METHODS: We studied the performance of our standard operating procedure (SOP) on 93 selected biopsy specimens from adult celiac disease patients and non-celiac disease controls. The specimens, which comprised different grades of gluten-induced mucosal injury, were evaluated by morphometric measurements. Specimens with tangential cutting resulting from poorly oriented biopsies were included. Two accredited evaluators performed the measurements in blinded fashion. The intraobserver and interobserver variations for villus height and crypt depth ratio (VH:CrD) and densities of intraepithelial lymphocytes (IELs) were analyzed by the Bland-Altman method and intraclass correlation. RESULTS: Unevaluable biopsies according to our SOP were correctly identified. The intraobserver analysis of VH:CrD showed a mean difference of 0.087 with limits of agreement from -0.398 to 0.224; the standard deviation (SD) was 0.159. The mean difference in interobserver analysis was 0.070, limits of agreement -0.516 to 0.375, and SD 0.227. The intraclass correlation coefficient in intraobserver variation was 0.983 and that in interobserver variation 0.978. CD3(+) IEL density countings in the paraffin-embedded and frozen biopsies showed SDs of 17.1% and 16.5%; the intraclass correlation coefficients were 0.961 and 0.956, respectively. CONCLUSIONS: Using our SOP, quantitative, reliable and reproducible morphometric results can be obtained on duodenal biopsy specimens with different grades of gluten-induced injury. Clinically significant changes were defined according to the error margins (2SD) of the analyses in VH:CrD as 0.4 and in CD3(+)-stained IELs as 30%.

Effects of pathology dyes on Raman bone spectra.

We report an overlooked source of artifacts for clinical specimens, where unexpected and normally negligible contaminants can skew the interpretation of results. During an ongoing study of bone fragments from diabetic osteomyelitis, strong Raman signatures were found, which did not correspond with normal bone mineral or matrix. In a bone biopsy from the calcaneus of a patient affected by diabetic osteomyelitis, Raman microspectroscopic analysis revealed regions with both abnormal mineral and degraded collagen in addition to normal bone. Additional bands indicated a pathological material. Stenotrophomonas maltophilia was identified in the wound culture by independent microbiologic examination. We initially assigned the unusual bands to xanthomonadin, a bacterial pigment from S. maltophilia. However, the same bands were also found more than a year later on a second specimen that had been noticeably contaminated with pathology marking dye. Drop deposition/Raman spectroscopy of commonly used pathology dyes revealed that a blue tissue-marking dye was responsible for the unusual bands in both specimens, even in the first specimen where there was no visible evidence of contamination.