In East Asia, the relationship between script and language is determined to a great extent by the... more In East Asia, the relationship between script and language is determined to a great extent by the typological character of the languages involved. This is particularly so because sinographic writing generally relies on the syllable as the smallest unit of sound expressible. However, many languages that have adapted Sinitic writing throughout history display complex syllable structure not easily expressible by the monosyllabically inclined sinograph. Moreover, some languages have even displayed changing syllable structure throughout documented history. This article examines the so-called “monosyllabicization” of the Vietnamese language, and its impact on the history of the sinographic vernacular script known as Chữ Nôm. I argue that by the 17th century, the emergent monosyllabic character of Vietnamese was remarked upon by elites as a new justification for embracing vernacular writing, previously considered uncouth.
Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a he... more Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a heterogeneous manner that makes diagnosis inconsistent and management challenging. Biomarkers offer the potential to objectively identify injury status, severity, and phenotype by measuring the relative concentrations of endogenous molecules in readily accessible biofluids. Through a data-driven, discovery approach, novel biomarker candidates for TBI were identified in the serum lipidome of adult male Sprague-Dawley rats in the first week following moderate controlled cortical impact (CCI). Serum samples were analyzed in positive and negative modes by ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). A predictive panel for the classification of injured and uninjured sera samples, consisting of 26 dysregulated species belonging to a variety of lipid classes, was developed with a cross-validated accuracy of 85.3% using omniClassifier software to optimize feature selection. ...
This article examines David Damrosch’s notion of “scriptworlds”—spheres of cultural and intellect... more This article examines David Damrosch’s notion of “scriptworlds”—spheres of cultural and intellectual transfusion, defined by a shared script—as it pertains to early modern Vietnam’s abandonment of sinographic writing in favor of a latinized alphabet. The Vietnamese case demonstrates a surprisingly rapid readjustment of deeply held attitudes concerning the nature of writing, in the wake of the alphabet’s meteoric successes. The fluidity of “language ethics” in early modern Vietnam (a society that had long since developed vernacular writing out of an earlier experience of diglossic literacy) suggests that the durability of a “scriptworld” depends on the nature and history of literacy in the societies under question.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2012
Histopathological images acquired from different experimental set-ups often suffer from batch-eff... more Histopathological images acquired from different experimental set-ups often suffer from batch-effects due to color variations and scale variations. In this paper, we develop a novel scale normalization model for histopathological images based on nuclear area distributions. Results indicate that the normalization model closely fits empirical values for two renal tumor datasets. We study the effect of scale normalization on classification of renal tumor images. Scale normalization improves classification performance in most cases. However, performance decreases in a few cases. In order to understand this, we propose two methods to filter extracted image features that are sensitive to image scaling and features that are uncorrelated with scaling factor. Feature filtering improves the classification performance of cases that were initially negatively affected by scale normalization.
Kidney neoplasms are classified by light microscopy using the World Health Organization (WHO) sys... more Kidney neoplasms are classified by light microscopy using the World Health Organization (WHO) system. The WHO system defines histopathologic tumor subtypes with distinct clinical behavior and underlying genetic mutations. In adults, the common malignant subtypes are variants of renal cell carcinoma (RCC). Histopathologic classification is critical for clinical management of RCC, but is becoming more complex with recognition of novel tumor subtypes, development of procedures yielding small diagnostic biopsies, and emergence of molecular therapies directed at tumor gene activity. Therefore, classification systems based on gene expression are likely to become essential for diagnosis, prognosis and treatment of kidney tumors. Recent DNA microarray studies have shown that clinically relevant renal tumor subtypes are characterized by distinct gene expression profiles, which are useful for discovery of novel diagnostic and prognostic biomarkers. In this review, we summarize the WHO classif...
The differential diagnosis of clear cell, papillary, and chromophobe renal cell carcinoma is clin... more The differential diagnosis of clear cell, papillary, and chromophobe renal cell carcinoma is clinically important, because these tumor subtypes are associated with different pathobiology and clinical behavior. For cases in which histopathology is equivocal, immunohistochemistry and quantitative reverse transcriptase-polymerase chain reaction can assist in the differential diagnosis by measuring expression of subtype-specific biomarkers. Several renal tumor biomarkers have been discovered in expression microarray studies. However, due to heterogeneity of gene and protein expression, additional biomarkers are needed for reliable diagnostic classification. We developed novel bioinformatics systems to identify candidate renal tumor biomarkers from the microarray profiles of 45 clear cell, 16 papillary, and 10 chromophobe renal cell carcinomas; the microarray data was derived from 2 independent published studies. The ArrayWiki biocomputing system merged the microarray data sets into a si...
Combining multiple microarray datasets increases sample size and leads to improved reproducibilit... more Combining multiple microarray datasets increases sample size and leads to improved reproducibility in identification of informative genes and subsequent clinical prediction. Although microarrays have increased the rate of genomic data collection, sample size is still a major issue when identifying informative genetic biomarkers. Because of this, feature selection methods often suffer from false discoveries, resulting in poorly performing predictive models. We develop a simple meta-analysis-based feature selection method that captures the knowledge in each individual dataset and combines the results using a simple rank average. In a comprehensive study that measures robustness in terms of clinical application (i.e., breast, renal, and pancreatic cancer), microarray platform heterogeneity, and classifier (i.e., logistic regression, diagonal LDA, and linear SVM), we compare the rank average meta-analysis method to five other meta-analysis methods. Results indicate that rank average met...
In East Asia, the relationship between script and language is determined to a great extent by the... more In East Asia, the relationship between script and language is determined to a great extent by the typological character of the languages involved. This is particularly so because sinographic writing generally relies on the syllable as the smallest unit of sound expressible. However, many languages that have adapted Sinitic writing throughout history display complex syllable structure not easily expressible by the monosyllabically inclined sinograph. Moreover, some languages have even displayed changing syllable structure throughout documented history. This article examines the so-called “monosyllabicization” of the Vietnamese language, and its impact on the history of the sinographic vernacular script known as Chữ Nôm. I argue that by the 17th century, the emergent monosyllabic character of Vietnamese was remarked upon by elites as a new justification for embracing vernacular writing, previously considered uncouth.
Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a he... more Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a heterogeneous manner that makes diagnosis inconsistent and management challenging. Biomarkers offer the potential to objectively identify injury status, severity, and phenotype by measuring the relative concentrations of endogenous molecules in readily accessible biofluids. Through a data-driven, discovery approach, novel biomarker candidates for TBI were identified in the serum lipidome of adult male Sprague-Dawley rats in the first week following moderate controlled cortical impact (CCI). Serum samples were analyzed in positive and negative modes by ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). A predictive panel for the classification of injured and uninjured sera samples, consisting of 26 dysregulated species belonging to a variety of lipid classes, was developed with a cross-validated accuracy of 85.3% using omniClassifier software to optimize feature selection. ...
This article examines David Damrosch’s notion of “scriptworlds”—spheres of cultural and intellect... more This article examines David Damrosch’s notion of “scriptworlds”—spheres of cultural and intellectual transfusion, defined by a shared script—as it pertains to early modern Vietnam’s abandonment of sinographic writing in favor of a latinized alphabet. The Vietnamese case demonstrates a surprisingly rapid readjustment of deeply held attitudes concerning the nature of writing, in the wake of the alphabet’s meteoric successes. The fluidity of “language ethics” in early modern Vietnam (a society that had long since developed vernacular writing out of an earlier experience of diglossic literacy) suggests that the durability of a “scriptworld” depends on the nature and history of literacy in the societies under question.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2012
Histopathological images acquired from different experimental set-ups often suffer from batch-eff... more Histopathological images acquired from different experimental set-ups often suffer from batch-effects due to color variations and scale variations. In this paper, we develop a novel scale normalization model for histopathological images based on nuclear area distributions. Results indicate that the normalization model closely fits empirical values for two renal tumor datasets. We study the effect of scale normalization on classification of renal tumor images. Scale normalization improves classification performance in most cases. However, performance decreases in a few cases. In order to understand this, we propose two methods to filter extracted image features that are sensitive to image scaling and features that are uncorrelated with scaling factor. Feature filtering improves the classification performance of cases that were initially negatively affected by scale normalization.
Kidney neoplasms are classified by light microscopy using the World Health Organization (WHO) sys... more Kidney neoplasms are classified by light microscopy using the World Health Organization (WHO) system. The WHO system defines histopathologic tumor subtypes with distinct clinical behavior and underlying genetic mutations. In adults, the common malignant subtypes are variants of renal cell carcinoma (RCC). Histopathologic classification is critical for clinical management of RCC, but is becoming more complex with recognition of novel tumor subtypes, development of procedures yielding small diagnostic biopsies, and emergence of molecular therapies directed at tumor gene activity. Therefore, classification systems based on gene expression are likely to become essential for diagnosis, prognosis and treatment of kidney tumors. Recent DNA microarray studies have shown that clinically relevant renal tumor subtypes are characterized by distinct gene expression profiles, which are useful for discovery of novel diagnostic and prognostic biomarkers. In this review, we summarize the WHO classif...
The differential diagnosis of clear cell, papillary, and chromophobe renal cell carcinoma is clin... more The differential diagnosis of clear cell, papillary, and chromophobe renal cell carcinoma is clinically important, because these tumor subtypes are associated with different pathobiology and clinical behavior. For cases in which histopathology is equivocal, immunohistochemistry and quantitative reverse transcriptase-polymerase chain reaction can assist in the differential diagnosis by measuring expression of subtype-specific biomarkers. Several renal tumor biomarkers have been discovered in expression microarray studies. However, due to heterogeneity of gene and protein expression, additional biomarkers are needed for reliable diagnostic classification. We developed novel bioinformatics systems to identify candidate renal tumor biomarkers from the microarray profiles of 45 clear cell, 16 papillary, and 10 chromophobe renal cell carcinomas; the microarray data was derived from 2 independent published studies. The ArrayWiki biocomputing system merged the microarray data sets into a si...
Combining multiple microarray datasets increases sample size and leads to improved reproducibilit... more Combining multiple microarray datasets increases sample size and leads to improved reproducibility in identification of informative genes and subsequent clinical prediction. Although microarrays have increased the rate of genomic data collection, sample size is still a major issue when identifying informative genetic biomarkers. Because of this, feature selection methods often suffer from false discoveries, resulting in poorly performing predictive models. We develop a simple meta-analysis-based feature selection method that captures the knowledge in each individual dataset and combines the results using a simple rank average. In a comprehensive study that measures robustness in terms of clinical application (i.e., breast, renal, and pancreatic cancer), microarray platform heterogeneity, and classifier (i.e., logistic regression, diagonal LDA, and linear SVM), we compare the rank average meta-analysis method to five other meta-analysis methods. Results indicate that rank average met...
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