Bioinformatics construction of the human cell surfaceome

Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane proteins located at the surface of human cells (human cell surfaceome). We explored the genetic diversity of the human cell surfaceome at different levels, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression. By integrating expression information from a variety of sources, we were able to identify surfaceome genes with a restricted expression in normal tissues and/or differential expression in tumors, important characteristics for putative tumor targets. A high-throughput and efficient quantitative real-time PCR approach was used to validate 593 surfaceome genes selected on the basis of their expression pattern in normal and tumor samples. A number of candidates were identified as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma. Several candidate genes were also identified as coding for cell surface cancer/testis antigens. The human cell surfaceome will serve as a reference for further studies aimed at characterizing tumor targets at the surface of human cells.

DNA polymorphisms as tools for spinal cord injury research

Study Design: Data mining of single nucleotide polymorphisms (SNPs) in gene pathways related to spinal cord injury (SCI). Objectives: To identify gene polymorphisms putatively implicated with neuronal damage evolution pathways, potentially useful to SCI study. Setting: Departments of Psychiatry and Orthopedics, Faculdade de Medicina, Universidade de Sao Paulo, Brazil. Methods: Genes involved with processes related to SCI, such as apoptosis, inflammatory response, axonogenesis, peripheral nervous system development and axon ensheathment, were determined by evaluating the `Biological Process` annotation of Gene Ontology (GO). Each gene of these pathways was mapped using MapViewer, and gene coordinates were used to identify their polymorphisms in the SNP database. As a proof of concept, the frequency of subset of SNPs, located in four genes (ALOX12, APOE, BDNF and NINJ1) was evaluated in the DNA of a group of 28 SCI patients and 38 individuals with no SC lesions. Results: We could identify a total of 95 276 SNPs in a set of 588 genes associated with the selected GO terms, including 3912 nucleotide alterations located in coding regions of genes. The five non-synonymous SNPs genotyped in our small group of patients, showed a significant frequency, reinforcing their potential use for the investigation of SCI evolution. Conclusion: Despite the importance of SNPs in many aspects of gene expression and protein activity, these gene alterations have not been explored in SCI research. Here we describe a set of potentially useful SNPs, some of which could underlie the genetic mechanisms involved in the post trauma spinal cord damage.

Early diagnostic and endoscopic dilatation for the treatment of acquired upper airway stenosis after intubation in children

Background: Upper airway stenosis (UAS) after endotracheal intubation is a common problem in children. Most literature refers to a surgical treatment for these lesions. Laryngotracheal reconstruction and cricotracheal resection are used for low- and high-grade stenosis, but decannulation is not always possible immediately after surgery. Purpose: The aim of this study was to verify the feasibility and results of endoscopic dilatations for treatment of subglottic stenosis. Method: The study encompassed a 12-year retrospective analysis of patients treated for UAS in a tertiary center. All children were symptomatic at the time of the endoscopic diagnosis. The stenosis was graded according to the Myer-Cotton criteria. Endoscopic dilatation was initiated immediately after the diagnosis. Children with grade IV stenosis underwent surgery. Results: Children with tracheal stenosis and no involvement of the subglottic area did not respond to endoscopic dilatations and underwent surgery. There were 45 children with grade I stenosis, 12 with grade II, 7 with grade III, and 4 with grade IV lesions. Patients with grade I, II, and III stenosis were a] I treated by endoscopic dilatations alone and were decannulated when asymptomatic. The average time for decannulation was 18.90 +/- 26.07 months for grade 1, 32.5 +/- 27.08 months for grade 11, and 27.57 +/- 20.60 months for grade III stenosis (P < .01, for grade II vs grade III). Conclusion: Grade I, II, and III subglottic stenoses can be safely managed by early endoscopic dilatations with a high rate of success and low rate of morbidity but require a significantly long period of treatment. (C) 2008 Elsevier Inc. All rights reserved.

Social anxiety disorder: what are we losing with the current diagnostic criteria?

Objective: To assess the rate of comorbidities and the functional impairment associated with the social anxiety disorder (SAD), with an emphasis on the so-called subthreshold clinical signs and symptoms. Method: Psychiatric comorbidities and psychosocial functioning were evaluated in 355 volunteers (college students) who had been diagnosed as SAD (n = 141), Subthreshold SAD (n = 92) or Controls (n = 122). Results: The rate of comorbidities was 71.6% in the SAD group and 50% in subjects with Subthreshold SAD, both significantly greater than Controls (28.7%). Concerning psychosocial functioning, the SAD group had higher impairment than the other two groups in all domains evaluated, and subjects with Subthreshold SAD presented intermediate values. Conclusion: The rates of psychiatric comorbidities and the impairment of psychosocial functioning increase progressively along the spectrum of social anxiety. The fact that Subthreshold SAD causes considerable disability and suffering in comparison with control subjects justifies a review of the validity of the diagnostic criteria.

Diagnostic model based on Raman spectra of normal, hyperplasia and prostate adenocarcinoma tissues in vitro

This study evaluated the use of Raman spectroscopy to identify the spectral differences between normal (N), benign hyperplasia (BPH) and adenocarcinoma (CaP) in fragments of prostate biopsies in vitro with the aim of developing a spectral diagnostic model for tissue classification. A dispersive Raman spectrometer was used with 830 nm wavelength and 80 mW excitation. Following Raman data collection and tissue histopathology (48 fragments diagnosed as N, 43 as BPH and 14 as CaP), two diagnostic models were developed in order to extract diagnostic information: the first using PCA and Mahalanobis analysis techniques and the second one a simplified biochemical model based on spectral features of cholesterol, collagen, smooth muscle cell and adipocyte. Spectral differences between N, BPH and CaP tissues, were observed mainly in the Raman bands associated with proteins, lipids, nucleic and amino acids. The PCA diagnostic model showed a sensitivity and specificity of 100%, which indicates the ability of PCA and Mahalanobis distance techniques to classify tissue changes in vitro. Also, it was found that the relative amount of collagen decreased while the amount of cholesterol and adipocyte increased with severity of the disease. Smooth muscle cell increased in BPH tissue. These characteristics were used for diagnostic purposes.

Further evidences on a new diagnostic approach for monitoring human Leishmania (L.) infantum chagasi infection in Amazonian Brazil

This was a prospective study carried out during a period over 2 years (May/2006-September/2008) with a cohort of 1,099 individuals of both genders, aged 1 year old and older, from an endemic area of American visceral leishmaniasis (AVL) in Para state, Brazil. The object was to analyze the prevalence and incidence of human Leishmania (L.) infantum chagasi infection as well as the dynamics evolution of its clinical-immunological profiles prior identified: (1) asymptomatic infection (AI); (2) symptomatic infection (SI = AVL); (3) sub-clinical oligosymptomatic infection (SOI); (4) sub-clinical resistant infection (SRI) and; (5) indeterminate initial infection (III). The infection diagnosis was performed by using both the indirect fluorescent antibody test and leishmanin skin test with amastigotes and promastigotes antigens of L. (L.) i. chagasi, respectively. A total of 187 cases of infection were recorded in the prevalence (17%), 117 in the final incidence (6.9%), and 304 in the accumulated prevalence (26.7%), which provided the following distribution into the clinical-immunological profiles: AI, 51.6%; III, 22.4%; SRI, 20.1%; SOI, 4.3%; and SI (=AVL), 1.6%. The major finding regarding the dynamics evolution of infection was concerned to III profile, from which the cases of infection evolved to either the resistant profiles, SRI (21 cases, 30.8%) and AI (30 cases, 44.1%), or the susceptible SI (=AVL; 1 case, 1.5%); the latter 16 cases remained as III till the end of the study. These results provided the conclusion that this diagnostic approach may be useful for monitoring human L. (L.) i. chagasi infection in endemic area and preventing the high morbidity of severe AVL cases.

Effect of Disease Severity and Optic Disc Size on Diagnostic Accuracy of RTVue Spectral Domain Optical Coherence Tomograph in Glaucoma

PURPOSE. To evaluate the effect of disease severity and optic disc size on the diagnostic accuracies of optic nerve head (ONH), retinal nerve fiber layer (RNFL), and macular parameters with RTVue (Optovue, Fremont, CA) spectral domain optical coherence tomography (SDOCT) in glaucoma. METHODS. 110 eyes of 62 normal subjects and 193 eyes of 136 glaucoma patients from the Diagnostic Innovations in Glaucoma Study underwent ONH, RNFL, and macular imaging with RTVue. Severity of glaucoma was based on visual field index (VFI) values from standard automated perimetry. Optic disc size was based on disc area measurement using the Heidelberg Retina Tomograph II (Heidelberg Engineering, Dossenheim, Germany). Influence of disease severity and disc size on the diagnostic accuracy of RTVue was evaluated by receiver operating characteristic (ROC) and logistic regression models. RESULTS. Areas under ROC curve (AUC) of all scanning areas increased (P < 0.05) as disease severity increased. For a VFI value of 99%, indicating early damage, AUCs for rim area, average RNLI thickness, and ganglion cell complex-root mean square were 0.693, 0.799, and 0.779, respectively. For a VFI of 70%, indicating severe damage, corresponding AUCs were 0.828, 0.985, and 0.992, respectively. Optic disc size did not influence the AUCs of any of the SDOCT scanning protocols of RTVue (P > 0.05). Sensitivity of the rim area increased and specificity decreased in large optic discs. CONCLUSIONS. Diagnostic accuracies of RTVue scanning protocols for glaucoma were significantly influenced by disease severity. Sensitivity of the rim area increased in large optic discs at the expense of specificity. (Invest Ophthalmol Vis Sci. 2011;92:1290-1296) DOI:10.1167/iovs.10-5516

Screening for Alzheimer`s Disease Among Illiterate Elderly: Accuracy Analysis for Multiple Instruments

One of the challenges in screening for dementia in developing countries is related to performance differences due to educational and cultural factors. This study evaluated the accuracy of single screening tests as well as combined protocols including the Mini-Mental State Examination (MMSE), Verbal Fluency animal category (VF), Clock Drawing test (CDT), and Pfeffer Functional Activities Questionnaire (PFAQ) to discriminate illiterate elderly with and without Alzheimer`s disease (AD) in a clinical sample. Cross-sectional study with 66 illiterate outpatients diagnosed with mild and moderate AD and 40 illiterate normal controls. Diagnosis of AD was based on NINCDS-ADRDA. All patients were submitted to a diagnostic protocol including a clinical interview based on the CAMDEX sections. ROC curves area analyses were carried out to compare sensitivity and specificity for the cognitive tests to differentiate the two groups (each test separately and in two by two combinations). Scores for all cognitive (MMSE, CDT, VF) and functional assessments (PFAQ) were significantly different between the two groups (p < 0.001). The best screening instruments for this sample of illiterate elderly were the MMSE and the PFAQ. The cut-off scores for the MMSE, VF, CDT, and PFAQ were 17.5, 7.5, 2.5, and 11.5, respectively. The most sensitive combination came from the MMSE and PFAQ (94.1%), and the best specificity was observed with the combination of the MMSE and CDT (89%). Illiterate patients can be successfully screened for AD using well-known screening instruments, especially in combined protocols.

Post-craniotomy headache: A proposed revision of IHS diagnostic criteria

Seventy-nine patients with intracranial aneurysms were evaluated in the presurgical period, and followed up to 6 months after surgery. We compare patients who fulfilled with those that did not post-craniotomy headache (PCH) diagnostic criteria, according to the International Classification of Headache Disorders. Semistructured interviews, headache diaries, Short Form-36 and McGill Pain Questionnaire were used. Seventy-two patients (91%) had headaches during the follow-up period. The incidence of PCH according to the International Headache Society diagnostic criteria was 40%. Age, sex, type of surgery, temporomandibular disorder, vasospasm, presence and type of previous headaches, and subarachnoid haemorrhage were not related to headache classification. There were no differences in the quality of life, headache frequency and characteristics or pain intensity between patients with headache that fulfilled or not PCH criteria. We proposed a revision of the diagnostic criteria for PCH, extending the headache outset after surgery from 7 to 30 days, and including the presence of headaches after surgery in patients with no past history of headaches, or an increase in headache frequency during the first 30 days of the postsurgical period followed by a decrease over time. Using these criteria we would classify 65% of our patients as having PCH.

Patient Characteristics as Predictors of Image Quality and Diagnostic Accuracy of MDCT Compared With Conventional Coronary Angiography for Detecting Coronary Artery Stenoses: CORE-64 Multicenter International Trial

OBJECTIVE. The purpose of the study was to investigate patient characteristics associated with image quality and their impact on the diagnostic accuracy of MDCT for the detection of coronary artery stenosis. MATERIALS AND METHODS. Two hundred ninety-one patients with a coronary artery calcification (CAC) score of <= 600 Agatston units (214 men and 77 women; mean age, 59.3 +/- 10.0 years [SD]) were analyzed. An overall image quality score was derived using an ordinal scale. The accuracy of quantitative MDCT to detect significant (>= 50%) stenoses was assessed using quantitative coronary angiography (QCA) per patient and per vessel using a modified 19-segment model. The effect of CAC, obesity, heart rate, and heart rate variability on image quality and accuracy were evaluated by multiple logistic regression. Image quality and accuracy were further analyzed in subgroups of significant predictor variables. Diagnostic analysis was determined for image quality strata using receiver operating characteristic (ROC) curves. RESULTS. Increasing body mass index (BMI) (odds ratio [OR] = 0.89, p < 0.001), increasing heart rate (OR = 0.90, p < 0.001), and the presence of breathing artifact (OR = 4.97, p = 0.001) were associated with poorer image quality whereas sex, CAC score, and heart rate variability were not. Compared with examinations of white patients, studies of black patients had significantly poorer image quality (OR = 0.58, p = 0.04). At a vessel level, CAC score (10 Agatston units) (OR = 1.03, p = 0.012) and patient age (OR = 1.02, p = 0.04) were significantly associated with the diagnostic accuracy of quantitative MDCT compared with QCA. A trend was observed in differences in the areas under the ROC curves across image quality strata at the vessel level (p = 0.08). CONCLUSION. Image quality is significantly associated with patient ethnicity, BMI, mean scan heart rate, and the presence of breathing artifact but not with CAC score at a patient level. At a vessel level, CAC score and age were associated with reduced diagnostic accuracy.

Diagnostic transitions in mild cognitive impairment subtypes

Background: At least for a subset of patients, the clinical diagnosis of mild cognitive impairment (MCI) may represent an intermediate stage between normal aging and dementia. Nevertheless, the patterns of transition of cognitive states between normal cognitive aging and MCI to dementia are not well established. In this study we address the pattern of transitions between cognitive states in patients with MCI and healthy controls, prior to the conversion to dementia. Methods: 139 subjects (78% women, mean age, 68.5 +/- 6.1 years; mean educational level, 11.7 +/- 5.4 years) were consecutively assessed in a memory clinic with a standardized clinical and neuropsychological protocol, and classified as cognitively healthy (normal controls) or with MCI (including subtypes) at baseline. These subjects underwent annual reassessments (mean duration of follow-up: 2.7 +/- 1.1 years), in which cognitive state was ascertained independently of prior diagnoses. The pattern of transitions of the cognitive state was determined by Markov chain analysis. Results: The transitions from one cognitive state to another varied substantially between MCI subtypes. Single-domain MCI (amnestic and non-amnestic) more frequently returned to normal cognitive state upon follow-up (22.5% and 21%, respectively). Among subjects who progressed to Alzheimer`s disease (AD), the most common diagnosis immediately prior conversion was multiple-domain MCI (85%). Conclusion: The clinical diagnosis of MCI and its subtypes yields groups of patients with heterogeneous patterns of transitions between one given cognitive state to another. The presence of more severe and widespread cognitive deficits, as indicated by the group of multiple-domain amnestic MCI may be a better predictor of AD than single-domain amnestic or non-amnestic deficits. These higher-risk individuals could probably be the best candidates for the development of preventive strategies and early treatment for the disease.