Search

Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover and characterize cell types; however, the experiment-specific technical biases and analytic variability inherent to current pipelines may undermine its replicability. Meta-analysis is further hampered by the use of ad hoc naming conventions. Here we demonstrate our replication framework, MetaNeighbor, that quantifies the degree to which cell types replicate across datasets, and enables rapid identification of clusters with high similarity. We first measure the replicability of neuronal identity, comparing results across eight technically and biologically diverse datasets to define best practices for more complex assessments. We then apply this to novel interneuron subtypes, finding that 24/45 subtypes have evidence of replication, which enables the identification of robust candidate marker genes. Across tasks we find that large sets of variably expressed genes can identify replicable cell types with high accuracy, suggesting a general route forward for large-scale evaluation of scRNA-seq data.

BACKGROUND: Co-expression networks have been a useful tool for functional genomics, providing important clues about the cellular and biochemical mechanisms that are active in normal and disease processes. However, co-expression analysis is often treated as a black box with results being hard to trace to their basis in the data. Here, we use both published and novel single-cell RNA sequencing (RNA-seq) data to understand fundamental drivers of gene-gene connectivity and replicability in co-expression networks.

The number of individual cases of psychiatric disorders that can be ascribed to identified, rare, single mutations is increasing with great rapidity. Such mutations can be recapitulated in mice to generate animal models with direct etiological validity. Defining the underlying pathogenic mechanisms will require an experimental and theoretical framework to make the links from mutation to altered behavior in an animal or psychopathology in a human. Here, we discuss key elements of such a framework, including cell type-based phenotyping, developmental trajectories, linking circuit properties at micro and macro scales and definition of neurobiological phenotypes that are directly translatable to humans. © 2011 Mitchell et al; licensee BioMed Central Ltd.

The number of individual cases of psychiatric disorders that can be ascribed to identified, rare, single mutations is increasing with great rapidity. Such mutations can be recapitulated in mice to generate animal models with direct etiological validity. Defining the underlying pathogenic mechanisms will require an experimental and theoretical framework to make the links from mutation to altered behavior in an animal or psychopathology in a human. Here, we discuss key elements of such a framework, including cell type-based phenotyping, developmental trajectories, linking circuit properties at micro and macro scales and definition of neurobiological phenotypes that are directly translatable to humans. © 2011 Mitchell et al; licensee BioMed Central Ltd.

This study aims to describe and compare the gender-specific prevalence of chlamydia and gonorrhoea, sexual behaviours and experiences, and risk factors associated with sexually transmitted infections (STIs) among migrants versus rural and urban non-migrants in China. Data were abstracted from the Chinese Health and Family Life Survey conducted from 1999 to 2000, which provided a nationally representative adult (ages 20-64 years) sample. STI results were determined using a urine-based nucleic acid amplification assay. The prevalence of chlamydia for migrant women was triple that of rural non-migrant women. Migrants were more likely to engage in STI-associated risk behaviours than non-migrants (e.g. receiving money for sex). Among migrants, women were more likely than men to have STIs. The high STI prevalence among migrants highlights an urgent need to implement comprehensive prevention and intervention programmes targeting the cultural, social and structural needs of migrants in the city, especially migrant women.

This study aims to describe and compare the gender-specific prevalence of chlamydia and gonorrhoea, sexual behaviours and experiences, and risk factors associated with sexually transmitted infections (STIs) among migrants versus rural and urban non-migrants in China. Data were abstracted from the Chinese Health and Family Life Survey conducted from 1999 to 2000, which provided a nationally representative adult (ages 20-64 years) sample. STI results were determined using a urine-based nucleic acid amplification assay. The prevalence of chlamydia for migrant women was triple that of rural non-migrant women. Migrants were more likely to engage in STI-associated risk behaviours than non-migrants (e.g. receiving money for sex). Among migrants, women were more likely than men to have STIs. The high STI prevalence among migrants highlights an urgent need to implement comprehensive prevention and intervention programmes targeting the cultural, social and structural needs of migrants in the city, especially migrant women.

In this letter, we introduce a combined polarization and fluorescence imaging technique for the measurement of fluorescence yield on the surface of turbid media. We use the cross-polarization method to reject the specular reflection and enhance the diffusive backscattering from the turbid media. It has been found that the ratio image of fluorescence versus cross-polarized reflection is not sensitive to the geometry of fluorescence excitation and illumination, and provides a map of fluorescence yield on the surface of imaged subject. The technique reported in this letter may potentially solve the problem for imaging of early cancers which usually start from the superficial layer of tissue and have the fluorescence yield lower than surrounding normal tissue. (C) 2000 American Institute of Physics. [S0003-6951(00)00808-1].

Background and Objective: In nasopharyngeal cancer, conventional white light endoscopy does not provide adequate information to detect the flat/small lesion and identify the margin of observable tumor. In the present study, we evaluate the potential of light-induced fluorescence spectroscopic imaging for the localization of cancerous nasopharyngeal tissue. Study Design/Materials and Methods: We built a multiple channel spectrometer specifically for the investigation of fluorescence collected by a conventional endoscopic system. Nasopharyngeal fluorescence were measured in vivo from 27 subjects during the routine endoscopy. The biopsy specimens for histologic analysis were taken from the tissue sites where the fluorescence were measured. Results: Two algorithms to discriminate the nasopharyngeal carcinoma from normal tissue were created based on the good correlation between the tissue autofluorescence and histologic diagnosis. For the two-wavelength algorithm, carcinoma can be differentiated from normal tissue with a sensitivity and specificity of 93\% and 92\%, respectively. For the three-wavelength algorithm with compensation of variation of blood content in tissue, a sensitivity of 98\% and specificity of 95\% were achieved. Conclusion: Fluorescence endoscopic imaging used with the algorithms developed in this report is an efficient method for detecting the nasopharyngeal carcinoma. (C) 2000 Wiley-Liss, Inc.

We present an imaging technique for the correction of geometrical effects in fluorescence measurement of optically thick, turbid media such as human tissue. Specifically, we use the cross-polarization method to reject specular reflection and enhance the diffusive backscattering of polarized fluorescence excitation light from the turbid media. We correct the nonuniformity of the image field caused by the excitation- and-collection geometry of a fluorescence imaging system by normalizing the fluorescence image to the cross-polarized reflection image. The ratio image provides a map of relative fluorescence yield, defined as the ratio of emerging fluorescence power to incident excitation, over the surface of an imaged homogeneous turbid medium when fluorescence excitation-and-collection geometries vary in a wide range. We investigate the mechanism of ratio imaging by using Monte Carlo modeling. Our findings show that this technique could have a potential use in the detection of early cancer, which usually starts from a superficial layer of tissue, based on the contrast in the tissue fluorescence of an early lesion and of the surrounding normal tissue. (C) 2000 Optical Society of America OCIS codes: 170.0170, 110.7050, 170.3880, 170.4580, 170.6510.

A cross-polarization method has been used to eliminate the specular reflection and enhance the diffusive backscattering of fluorescence excitation light from tissue-like phantoms and skin tissue. We have demonstrated that the non-uniformity of excitation and collection of a fluorescence imaging system can be corrected by normalizing fluorescence signal to the cross-polarized reflection signal recorded from the same site. The ratio image of fluorescence vs, cross-polarized reflection provides a map of relative fluorescence yield over the tissue surface. This ratio imaging technique may hold the potential to detect early cancer, which usually starts from the superficial layer of tissue, based on the contrast in the fluorescence yield between early lesion and surrounding normal tissue. (C) 2000 Elsevier Science B.V. All rights reserved.

We present an imaging technique for the correction of geometrical effects in fluorescence measurement of optically thick, turbid media such as human tissue. Specifically, we use the cross-polarization method to reject specular reflection and enhance the diffusive backscattering of polarized fluorescence excitation light from the turbid media. We correct the nonuniformity of the image field caused by the excitation- and-collection geometry of a fluorescence imaging system by normalizing the fluorescence image to the cross-polarized reflection image. The ratio image provides a map of relative fluorescence yield, defined as the ratio of emerging fluorescence power to incident excitation, over the surface of an imaged homogeneous turbid medium when fluorescence excitation-and-collection geometries vary in a wide range. We investigate the mechanism of ratio imaging by using Monte Carlo modeling. Our findings show that this technique could have a potential use in the detection of early cancer, which usually starts from a superficial layer of tissue, based on the contrast in the tissue fluorescence of an early lesion and of the surrounding normal tissue. (C) 2000 Optical Society of America OCIS codes: 170.0170, 110.7050, 170.3880, 170.4580, 170.6510.

A cross-polarization method has been used to eliminate the specular reflection and enhance the diffusive backscattering of fluorescence excitation light from tissue-like phantoms and skin tissue. We have demonstrated that the non-uniformity of excitation and collection of a fluorescence imaging system can be corrected by normalizing fluorescence signal to the cross-polarized reflection signal recorded from the same site. The ratio image of fluorescence vs, cross-polarized reflection provides a map of relative fluorescence yield over the tissue surface. This ratio imaging technique may hold the potential to detect early cancer, which usually starts from the superficial layer of tissue, based on the contrast in the fluorescence yield between early lesion and surrounding normal tissue. (C) 2000 Elsevier Science B.V. All rights reserved.

In this letter, we introduce a combined polarization and fluorescence imaging technique for the measurement of fluorescence yield on the surface of turbid media. We use the cross-polarization method to reject the specular reflection and enhance the diffusive backscattering from the turbid media. It has been found that the ratio image of fluorescence versus cross-polarized reflection is not sensitive to the geometry of fluorescence excitation and illumination, and provides a map of fluorescence yield on the surface of imaged subject. The technique reported in this letter may potentially solve the problem for imaging of early cancers which usually start from the superficial layer of tissue and have the fluorescence yield lower than surrounding normal tissue. (C) 2000 American Institute of Physics. [S0003-6951(00)00808-1].

Background and Objective: In nasopharyngeal cancer, conventional white light endoscopy does not provide adequate information to detect the flat/small lesion and identify the margin of observable tumor. In the present study, we evaluate the potential of light-induced fluorescence spectroscopic imaging for the localization of cancerous nasopharyngeal tissue. Study Design/Materials and Methods: We built a multiple channel spectrometer specifically for the investigation of fluorescence collected by a conventional endoscopic system. Nasopharyngeal fluorescence were measured in vivo from 27 subjects during the routine endoscopy. The biopsy specimens for histologic analysis were taken from the tissue sites where the fluorescence were measured. Results: Two algorithms to discriminate the nasopharyngeal carcinoma from normal tissue were created based on the good correlation between the tissue autofluorescence and histologic diagnosis. For the two-wavelength algorithm, carcinoma can be differentiated from normal tissue with a sensitivity and specificity of 93\% and 92\%, respectively. For the three-wavelength algorithm with compensation of variation of blood content in tissue, a sensitivity of 98\% and specificity of 95\% were achieved. Conclusion: Fluorescence endoscopic imaging used with the algorithms developed in this report is an efficient method for detecting the nasopharyngeal carcinoma. (C) 2000 Wiley-Liss, Inc.

A cross-polarization method has been used to eliminate the specular reflection and enhance the diffusive backscattering of fluorescence excitation light from tissue-like phantoms and skin tissue. We have demonstrated that the non-uniformity of excitation and collection of a fluorescence imaging system can be corrected by normalizing fluorescence signal to the cross-polarized reflection signal recorded from the same site. The ratio image of fluorescence vs, cross-polarized reflection provides a map of relative fluorescence yield over the tissue surface. This ratio imaging technique may hold the potential to detect early cancer, which usually starts from the superficial layer of tissue, based on the contrast in the fluorescence yield between early lesion and surrounding normal tissue. (C) 2000 Elsevier Science B.V. All rights reserved.

We present an imaging technique for the correction of geometrical effects in fluorescence measurement of optically thick, turbid media such as human tissue. Specifically, we use the cross-polarization method to reject specular reflection and enhance the diffusive backscattering of polarized fluorescence excitation light from the turbid media. We correct the nonuniformity of the image field caused by the excitation- and-collection geometry of a fluorescence imaging system by normalizing the fluorescence image to the cross-polarized reflection image. The ratio image provides a map of relative fluorescence yield, defined as the ratio of emerging fluorescence power to incident excitation, over the surface of an imaged homogeneous turbid medium when fluorescence excitation-and-collection geometries vary in a wide range. We investigate the mechanism of ratio imaging by using Monte Carlo modeling. Our findings show that this technique could have a potential use in the detection of early cancer, which usually starts from a superficial layer of tissue, based on the contrast in the tissue fluorescence of an early lesion and of the surrounding normal tissue. (C) 2000 Optical Society of America OCIS codes: 170.0170, 110.7050, 170.3880, 170.4580, 170.6510.

Background and Objective: In nasopharyngeal cancer, conventional white light endoscopy does not provide adequate information to detect the flat/small lesion and identify the margin of observable tumor. In the present study, we evaluate the potential of light-induced fluorescence spectroscopic imaging for the localization of cancerous nasopharyngeal tissue. Study Design/Materials and Methods: We built a multiple channel spectrometer specifically for the investigation of fluorescence collected by a conventional endoscopic system. Nasopharyngeal fluorescence were measured in vivo from 27 subjects during the routine endoscopy. The biopsy specimens for histologic analysis were taken from the tissue sites where the fluorescence were measured. Results: Two algorithms to discriminate the nasopharyngeal carcinoma from normal tissue were created based on the good correlation between the tissue autofluorescence and histologic diagnosis. For the two-wavelength algorithm, carcinoma can be differentiated from normal tissue with a sensitivity and specificity of 93\% and 92\%, respectively. For the three-wavelength algorithm with compensation of variation of blood content in tissue, a sensitivity of 98\% and specificity of 95\% were achieved. Conclusion: Fluorescence endoscopic imaging used with the algorithms developed in this report is an efficient method for detecting the nasopharyngeal carcinoma. (C) 2000 Wiley-Liss, Inc.

In this letter, we introduce a combined polarization and fluorescence imaging technique for the measurement of fluorescence yield on the surface of turbid media. We use the cross-polarization method to reject the specular reflection and enhance the diffusive backscattering from the turbid media. It has been found that the ratio image of fluorescence versus cross-polarized reflection is not sensitive to the geometry of fluorescence excitation and illumination, and provides a map of fluorescence yield on the surface of imaged subject. The technique reported in this letter may potentially solve the problem for imaging of early cancers which usually start from the superficial layer of tissue and have the fluorescence yield lower than surrounding normal tissue. (C) 2000 American Institute of Physics. [S0003-6951(00)00808-1].