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Papers by Dennis Wylie

Experiments designed to assess differential gene expression represent a rich resource for discove... more Experiments designed to assess differential gene expression represent a rich resource for discovering how DNA regulatory sequences influence transcription. Results derived from such experiments are usually quantified as continuous scores, such as fold changes, test statistics and p-values. We present a de novo motif discovery algorithm, SArKS, which uses a nonparametric kernel smoothing approach to identify promoter motifs correlated with elevated differential expression scores. SArKS has the capability to smooth over both motif sequence similarity and, in a second pass, over spatial proximity of multiple motifs to identify longer regions enriched in correlative motifs. We applied SArKS to simulated data, illustrating how SArKS can be used to find motifs embedded in random background sequences, and to two published RNA-seq expression data sets, one probing S. cerevisiae transcriptional response to anti-fungal agents and the other comparing gene expression profiles among cortical neu...

BMC Proc, 2011

Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pa... more Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pathway responses to B.melitensis, S.enterica Typhimurium and M.avium paratuberculosis Abstract Background: To decipher the complexity and improve the understanding of host-pathogen interactions, biologists must adopt new system level approaches in which the hierarchy of biological interactions and dynamics can be studied. This paper presents the application of systems biology for the cross-comparative analysis and interactome modeling of three different infectious agents, leading to the identification of novel, unique and common molecular host responses (biosignatures).

Vaccine, 2011

The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis... more The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis as such are classic examples of worldwide zoonoses for application of a systems biology approach for enhanced rational vaccine development. When used optimally, vaccines prevent disease manifestations, reduce transmission of disease, decrease the need for pharmaceutical intervention, and improve the health and welfare of animals, as well as indirectly protecting against zoonotic diseases of people. Advances in the last decade or so using comprehensive systems biology approaches linking genomics, proteomics, bioinformatics, and biotechnology with immunology, pathogenesis and vaccine formulation and delivery are expected to enable enhanced approaches to vaccine development. The goal of this paper is to evaluate the role of computational systems biology analysis of host:pathogen interactions (the interactome) as a tool for enhanced rational design of vaccines. Systems biology is bringing a new, more robust approach to veterinary vaccine

The Journal of Physical Chemistry B, 2006

Cell signaling dynamics mediate myriad processes in biology. It has become increasingly clear tha... more Cell signaling dynamics mediate myriad processes in biology. It has become increasingly clear that interand intracellular signaling reactions often occur in a spatially inhomogeneous environment and that it is important to account for stochastic fluctuations of certain species involved in signaling reactions. The importance of these effects enhances the difficulty of gleaning mechanistic information from observations of a few experimental reporters and highlights the significance of synergistic experimental and computational studies. When both stochastic fluctuations and spatial inhomogeneity must be included in a model simultaneously, however, the resulting computational demands quickly become overwhelming. In many situations the failure of standard coarse-graining methods (i.e., ignoring spatial variation or stochastic fluctuations) when applied to all components of a complex system does not exclude the possibility of successfully applying such coarsegraining to some components of the system. Following this approach alleviates computational cost but requires "hybrid" algorithms where some variables are treated at a coarse-grained level while others are not. We present an efficient algorithm for simulation of stochastic, spatially inhomogeneous reaction-diffusion kinetics coupled to coarse-grained fields described by (stochastic or deterministic) partial differential equations (PDEs). The PDEs could represent mean-field descriptions of reactive species present in large copy numbers or evolution of hydrodynamic variables that influence signaling (e.g., membrane shape or cytoskeletal motion). We discuss the approximations made to derive our algorithm and test its efficacy by applying it to problems that include many features typical of realistic cell signaling processes.

Proceedings of the National Academy of Sciences, 2007

Activation of T helper cells is necessary for the adaptive immune response to pathogens, and spur... more Activation of T helper cells is necessary for the adaptive immune response to pathogens, and spurious activation can result in organspecific autoimmunity (e.g., multiple sclerosis). T cell activation is initiated by membrane-proximal signaling that is predicated on the binding of the T cell receptor expressed on the T cell surface to peptide major histocompatibility complex (pMHC) molecules presented on the surface of antigen-presenting cells. These signaling processes regulate diverse outcomes, such as the ability of T cells to discriminate sensitively between stimulatory pMHC molecules and those that are characteristic of ''self,'' and the phenomenon of antagonism (wherein the presence of certain pMHC molecules impairs T cell receptor signaling). We describe a molecular model for membrane-proximal signaling in T cells from which these disparate observations emerge as two sides of the same coin. This development of a unified mechanism that is consistent with diverse data would not have been possible without explicit consideration of the stochastic nature of the pertinent biochemical events. Our studies also reveal that certain previously proposed concepts are not dueling ideas but rather are different stimuli-dependent manifestations of a unified molecular model for membrane-proximal signaling. This model may provide a conceptual framework for further investigations of early events that regulate T cell activation in response to self and foreign antigens and for the development of intervention protocols to inhibit aberrant signaling.

Epidemics, 2009

Background: Hepatitis C virus (HCV) causes significant morbidity and mortality in injecting drug ... more Background: Hepatitis C virus (HCV) causes significant morbidity and mortality in injecting drug users (IDU) worldwide. HCV vaccine candidates have shown promise for reducing the infectivity of acute infection and averting chronic infection, yet the impact of varying levels of vaccine efficacy and vaccine delivery strategies on the HCV epidemic in IDU has not been explored.

The Journal of Pathology: Clinical Research, 2016

The Journal of Clinical Endocrinology & Metabolism, 2015

Molecular testing for oncogenic mutations or gene expression in fine-needle aspirations (FNAs) fr... more Molecular testing for oncogenic mutations or gene expression in fine-needle aspirations (FNAs) from thyroid nodules with indeterminate cytology identifies a subset of benign or malignant lesions with high predictive value. This study aimed to evaluate a novel diagnostic algorithm combining mutation detection and miRNA expression to improve the diagnostic yield of molecular cytology. Surgical specimens and preoperative FNAs (n = 638) were tested for 17 validated gene alterations using the miRInform Thyroid test and with a 10-miRNA gene expression classifier generating positive (malignant) or negative (benign) results. Cross-sectional sampling of thyroid nodules with atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) or follicular neoplasm/suspicious for a follicular neoplasm (FN/SFN) cytology (n = 109) was conducted at 12 endocrinology centers across the United States. Qualitative molecular results were compared with surgical histopathology to determine diagnostic performance and model clinical effect. Mutations were detected in 69% of nodules with malignant outcome. Among mutation-negative specimens, miRNA testing correctly identified 64% of malignant cases and 98% of benign cases. The diagnostic sensitivity and specificity of the combined algorithm was 89% (95% confidence interval [CI], 73-97%) and 85% (95% CI, 75-92%), respectively. At 32% cancer prevalence, 61% of the molecular results were benign with a negative predictive value of 94% (95% CI, 85-98%). Independently of variations in cancer prevalence, the test increased the yield of true benign results by 65% relative to mRNA-based gene expression classification and decreased the rate of avoidable diagnostic surgeries by 69%. Multiplatform testing for DNA, mRNA, and miRNA can accurately classify benign and malignant thyroid nodules, increase the diagnostic yield of molecular cytology, and further improve the preoperative risk-based management of benign nodules with AUS/FLUS or FN/SFN cytology.

Clinical and translational gastroenterology, 2014

Current diagnostic tools for pancreatic cysts fail to reliably differentiate mucinous from nonmuc... more Current diagnostic tools for pancreatic cysts fail to reliably differentiate mucinous from nonmucinous cysts. Reliable biomarkers are needed. MicroRNAs (miRNA) may offer insights into pancreatic cysts. Our aims were to (1) identify miRNAs that distinguish benign from both premalignant cysts and malignant pancreatic lesions using formalin-fixed, paraffin-embedded (FFPE) pathology specimens; (2) identify miRNAs that distinguish mucinous cystic neoplasm (MCN) from branch duct-intraductal papillary mucinous neoplasm (BD-IPMN). A total of 69 FFPE pancreatic specimens were identified: (1) benign (20 serous cystadenoma (SCA)), (2) premalignant (10 MCN, 10 BD-IPMN, 10 main duct IPMN (MD-IPMN)), and (3) malignant (19 pancreatic ductal adenocarcinoma (PDAC)). Total nucleic acid extraction was performed followed by miRNA expression profiling of 378 miRNAs interrogated using TaqMan MicroRNA Arrays Pool A and verification of candidate miRNAs. Bioinformatics was used to generate classifiers. MiRN...

The Journal of molecular diagnostics : JMD, 2013

Implementation of highly sophisticated technologies, such as next-generation sequencing (NGS), in... more Implementation of highly sophisticated technologies, such as next-generation sequencing (NGS), into routine clinical practice requires compatibility with common tumor biopsy types, such as formalin-fixed, paraffin-embedded (FFPE) and fine-needle aspiration specimens, and validation metrics for platforms, controls, and data analysis pipelines. In this study, a two-step PCR enrichment workflow was used to assess 540 known cancer-relevant variants in 16 oncogenes for high-depth sequencing in tumor samples on either mature (Illumina GAIIx) or emerging (Ion Torrent PGM) NGS platforms. The results revealed that the background noise of variant detection was elevated approximately twofold in FFPE compared with cell line DNA. Bioinformatic algorithms were optimized to accommodate this background. Variant calls from 38 residual clinical colorectal cancer FFPE specimens and 10 thyroid fine-needle aspiration specimens were compared across multiple cancer genes, resulting in an accuracy of 96.1%...

Clinical Gastroenterology and Hepatology, 2014

Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) in combination with cytopathology i... more Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) in combination with cytopathology is the optimal method for diagnosis and staging of pancreatic ductal adenocarcinoma (PDAC) and other pancreatic lesions. Its clinical utility, however, can be limited by high rates of indeterminate or false-negative results. We aimed to develop and validate a microRNA (miRNA)-based test to improve preoperative detection of PDAC. Levels of miRNAs were analyzed in a centralized clinical laboratory by relative quantitative polymerase chain reaction in 95 formalin-fixed paraffin-embedded specimens and 228 samples collected by EUS-FNA during routine evaluations of patients with solid pancreatic masses at 4 institutions in the United States, 1 in Canada, and 1 in Poland. We developed a 5-miRNA expression classifier, consisting of MIR24, MIR130B, MIR135B, MIR148A, and MIR196, that could identify PDAC in well-characterized, formalin-fixed, paraffin-embedded specimens. Detection of PDAC in EUS-FNA samples increased from 78.8% by cytology analysis alone (95% confidence interval, 72.2%-84.5%) to 90.8% when combined with miRNA analysis (95% confidence interval, 85.6%-94.5%). The miRNA classifier correctly identified 22 additional true PDAC cases among 39 samples initially classified as benign, indeterminate, or nondiagnostic by cytology. Cytology and miRNA test results each were associated significantly with PDAC (P < .001), with positive predictive values greater than 99% (95% confidence interval, 96%-100%). We developed and validated a 5-miRNA classifier that can accurately predict which preoperative pancreatic EUS-FNA specimens contain PDAC. This test might aid in the diagnosis of pancreatic cancer by reducing the number of FNAs without a definitive adenocarcinoma diagnosis, thereby reducing the number of repeat EUS-FNA procedures.

Clinical Cancer Research, 2012

The diagnosis of pancreatic cystic lesions has increased dramatically. Most are benign, whereas s... more The diagnosis of pancreatic cystic lesions has increased dramatically. Most are benign, whereas some, such as intraductal papillary mucinous neoplasms (IPMN), represent precursors of pancreatic adenocarcinoma. Therapeutic stratification of IPMNs is challenging without precise information on dysplasia grade and presence of invasion. We assessed the diagnostic benefit of using miRNAs as biomarkers in pancreatic cyst fluid, focusing on IPMNs because of their frequency and malignant potential. RNA was extracted from 55 microdissected formalin-fixed, paraffin-embedded (FFPE) IPMN specimens, and 65 cyst fluid specimens aspirated following surgical resection. Expression of 750 miRNAs was evaluated with TaqMan miRNA Arrays using 22 FFPE and 15 cyst fluid specimens. Differential expression of selected miRNA candidates was validated in 33 FFPE and 50 cyst fluid specimens using TaqMan miRNA Assays. We identified 26 and 37 candidate miRNAs that distinguish low-grade from high-grade IPMNs using FFPE and cyst fluid specimens, respectively. A subset of 18 miRNAs, selected from FFPE and cyst fluid data, separated high-grade IPMNs from low-grade IPMNs, serous cystadenomas (SCA) and uncommon cysts, such as solid pseudopapillary neoplasms (SPN) and cystic pancreatic neuroendocrine tumors (PanNET). A logistic regression model using nine miRNAs allowed prediction of cyst pathology implying resection (high-grade IPMNs, PanNETs, and SPNs) versus conservative management (low-grade IPMNs, SCAs), with a sensitivity of 89%, a specificity of 100%, and area under the curve of 1. We found candidate miRNAs that helped identify patients with high-grade IPMN and exclude nonmucinous cysts. These classifiers will require validation in a prospective setting to ultimately confirm their clinical usefulness.

BMC Research Notes, 2011

Normalization is critical for accurate gene expression analysis. A significant challenge in the q... more Normalization is critical for accurate gene expression analysis. A significant challenge in the quantitation of gene expression from biofluids samples is the inability to quantify RNA concentration prior to analysis, underscoring the need for robust normalization tools for this sample type. In this investigation, we evaluated various methods of normalization to determine the optimal approach for quantifying microRNA (miRNA) expression from biofluids and tissue samples when using the TaqMan® Megaplex™ high-throughput RT-qPCR platform with low RNA inputs. We compared seven normalization methods in the analysis of variation of miRNA expression from biofluid and tissue samples. We developed a novel variant of the common mean-centering normalization strategy, herein referred to as mean-centering restricted (MCR) normalization, which is adapted to the TaqMan Megaplex RT-qPCR platform, but is likely applicable to other high-throughput RT-qPCR-based platforms. Our results indicate that MCR normalization performs comparable to or better than both standard mean-centering and other normalization methods. We also propose an extension of this method to be used when migrating biomarker signatures from Megaplex to singleplex RT-qPCR platforms, based on the identification of a small number of normalizer miRNAs that closely track the mean of expressed miRNAs. We developed the MCR method for normalizing miRNA expression from biofluids samples when using the TaqMan Megaplex RT-qPCR platform. Our results suggest that normalization based on the mean of all fully observed (fully detected) miRNAs minimizes technical variance in normalized expression values, and that a small number of normalizer miRNAs can be selected when migrating from Megaplex to singleplex assays. In our study, we find that normalization methods that focus on a restricted set of miRNAs tend to perform better than methods that focus on all miRNAs, including those with non-determined (missing) values. This methodology will likely be most relevant for studies in which a significant number of miRNAs are not detected.

Journal of the American Society of Cytopathology, 2015

ABSTRACT This study was to investigate the application of molecular testing to residual thyroid F... more ABSTRACT This study was to investigate the application of molecular testing to residual thyroid FNA material from needle rinses collected in Cytolyt.

Handouts and Slides by Dennis Wylie

Atelier morphosyntaxe, Laboratoire Dynamique du Langage, 2019

Adam J.R. Tallman (DDL) with Dennis Wylie, Anthony C. Woodbury, Gladys Camacho Rios, Hiroto Uc... more Adam J.R. Tallman (DDL)

with Dennis Wylie, Anthony C. Woodbury, Gladys Camacho Rios, Hiroto Uchihara, Kelsey Neely, Natalia Bermudez, Ambrocio Gutierrez, Cristian Juarez, Willem de Reuse, Patience Epps, Andrés Salanova, Eric Adell, Michael Everdell, Eric Campbell, Javier Carol

In this talk we discuss some foundational problems in the cross-linguistic comparison of wordhood and constituency. We present a solution to these problems and apply them to the study of 14 languages of the America (Chácobo (Pano), Yaminawa (Pano), Hup (Naduhup), Mebengokre (Ge), Chatino (Oto-Manguean), Quechua (Quechua), Mocoví (Guaicuruan), Zapotec (Oto-Manguean), Central Alaskan Yupik (Yupik-Inuit-Unangan), Apache (Na-Dene Athabaskan), Cherokee (Iroquioan), Naso (Chibchan), Chajul Ixil (Mayan), Southeastern Tepehuan (Uto-Aztecan), Chorote (Matacoan)). We argue for a new methodology that rests on rejection of a number of assumptions (often implicit) in descriptive and typological work: (i) the distinction between morphological and syntactic positions (ii) the distinction between morphosyntactic and phonological words; (iii) the distinction between wordhood and phrasehood diagnostics. Instead, we propose that an approach to cross-linguistic comparison of constituency that involves the systematic application of constituency diagnostics coded in a typological database that does not presuppose these distinctions. Languages are compared in terms of how many levels emerge out of the application of the diagnostics, the convergences between diagnostics, and the robustness of these convergences given the parameters of their application. We present a new set of terminology for describing sentence structure and comparing the results of constituency tests that we refer to as "flat structures" (based on a critical engagement and synthesis of the morphological and syntactic representations found in and Bickel and Zúñiga (2017) and Culicover and Jackendoff (2005)).

One of the most serious critiques of the investigation of constituency is methodological opportunism (e.g. Croft 2001; Croft 2010; Haspelmath 2011). Rather than lapsing into one of the two extremes of categorial universalism or categorial particularism (e.g. Haspelmath 2010), we deal with this problem by positing a novel concept referred to as the probability of chance convergence. This refers to the likelihood that two or more constituency diagnostics could have converged around the same result by chance given the number of tests applied and the morphosyntactic positions in the language. We also show how a metric of the probability of chance convergence can be computed. We argue that this methodology takes important steps towards overcoming language-internal and cross-linguistic methodological opportunism.

Our study has the following results:

. Languages vary in terms of whether and the extent to which a word constituent is motivated. This finding calls into question the whole framing of the debate on lexicalism (Marantz 1997; Wechsler 2005; Bruening 2018; Müller 2018) and wordhood generally (Blevins 2016; Geertzen et al. 2016).

. The distinction between grammatical and phonological word is not motivated in any language. This finding undermines some basic premises of certain formulations of Basic Linguistic Theory (e.g. Dixon 2010 and generative theories of phonological constituency such as prosodic phonology (Nespor & Vogel 1986).

We discuss other findings from this study and the future research that they could inspire. We also discuss the relevance of these findings for linguistic description.
References
Bickel, Balthasar, and Fernando Zuñiga. 2017. "The 'word' in polysynthetic languages: phonological and syntactic challenges." In The Oxford Handbook of Polysynthesis, edited by Michael Fortascue, Marianne Mithun and Nichols Evans, 158-186. Oxford: Oxford University Press.
Bickel, Balthasar, Kristine A. Hildebrandt, and René Schiering. 2009. "The distribution of phonological word domains: A probabilistic typology." In Phonological Domains: Universals and Deviations, edited by Janet Grijzenhout and Kabak Baris, 47-75. De Gruyter Mouton.
Blevins, James P. 2006. "Word-based morphology." Journal of Linguistics 42 (3): 531-573.
Blevins, James P. 2016. Word and Paradigm Morphology. Oxford: Oxford University Press.
Bresnan, Joan, and Sam A. McHombo. 1995. "The Lexical Integrity Principle: Evidence from Bantu." Natural Language & Linguistic Theory 13 (2): 181-254.
Bruening, Benjamin. 2018. "The lexicalist hypothesis: Both wrong and superfluous." Language 94 (1): 1-42.
Croft, William. 2010. "Radical Construction Grammar." In The Oxford Handbook of Construction Grammar, edited by Thomas Hoffman and Graeme Trousdale, 211-232. Oxford: Oxford University Press.
-. 2001. Radical Construction Grammar: Syntactic Theory in Typological Perspective. Oxford: Oxford University Press.
Croft, William. 2010. "Ten unwarranted assumptions in syntactic argumentation." In Language Usage and Language Structure, edited by Kasper Boye and Elisabeth Engberg-Pedersen, 313-350. Mouton de Gruyter.
Culicover, Peter W., and Ray Jackendoff. 2005. Simpler Syntax. Oxford: Oxford University Press.
Dixon, R.M.W, and Alexandra Y Aikhenvald. 2002. "Word: a typological framework." In Word: A cross-linguistic typology, edited by R.M.W. Dixon and Alexandra Y. Aikhenvald, 1-34. Cambridge: Cambridge University Press.
Dixon, R.M.W. 2010. Basic Linguistic Theory, Vol.2: Grammatical Topics. Oxford: Oxford University Press.
Dryer, Matthew. 2017. The myth of grammatical (morphosyntactic) words. ms.
Geertzen, Jeroen, James P Blevins, and Petar Milin. 2016. "The informativeness of linguistic unit bondaries." Italian Journal of Linguistics 28 (2): 1-24.
Halle, Morris, and Alec Marantz. 1993. "Distributed Morphology and the Pieces of Inflection." In The view from building 20, edited by Ken Halle and S.J. Keyser, 111-176. MIT Press.
Haspelmath, Martin. 2010. "Comparative concepts and descriptive categories in crosslinguistic studies." Language 86 (3): 663-687.
Haspelmath, Martin. 2011. "The indeterminacy of word segmentation and the nature of morphology and syntax." Folia Linguistica (Mouton de Gruyter - Societas Linguistica Europaea) 45 (1): 31-80.
Marantz, Alec. 1997. "No Escape from Syntax: Don't Try Morphological Analysis in the Pricavy of Your Own Lexicon." U Penn Working Papers in Linguistics 4 (2): 201-225.
Müller, Stefan. 2018. "The end of Lexicalism as we know it?" Language 94 (1): e54-e66.
Nespor, Marina, and Irene Vogel. 1986. Prosodic Phonology. Dordrecht: Foris Publications.
Schiering, René, Balthsar Bickel, and Kristine A. Hildebrandt. 2010. "The prosodic word is not unviersal, but emergent." Journal of Linguistics 46 (03): 657-709.
Wechsler, Stephen. 2008. "Dualist Syntax." Edited by Stefan Müller. Proceedings of the HPSG08 Conference. NICT, Keihanna, Japan: CSLI Publications. http://csli-publications.stanford.edu/.

Teaching materials by Dennis Wylie

Experiments designed to assess differential gene expression represent a rich resource for discove... more Experiments designed to assess differential gene expression represent a rich resource for discovering how DNA regulatory sequences influence transcription. Results derived from such experiments are usually quantified as continuous scores, such as fold changes, test statistics and p-values. We present a de novo motif discovery algorithm, SArKS, which uses a nonparametric kernel smoothing approach to identify promoter motifs correlated with elevated differential expression scores. SArKS has the capability to smooth over both motif sequence similarity and, in a second pass, over spatial proximity of multiple motifs to identify longer regions enriched in correlative motifs. We applied SArKS to simulated data, illustrating how SArKS can be used to find motifs embedded in random background sequences, and to two published RNA-seq expression data sets, one probing S. cerevisiae transcriptional response to anti-fungal agents and the other comparing gene expression profiles among cortical neu...

BMC Proc, 2011

Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pa... more Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pathway responses to B.melitensis, S.enterica Typhimurium and M.avium paratuberculosis Abstract Background: To decipher the complexity and improve the understanding of host-pathogen interactions, biologists must adopt new system level approaches in which the hierarchy of biological interactions and dynamics can be studied. This paper presents the application of systems biology for the cross-comparative analysis and interactome modeling of three different infectious agents, leading to the identification of novel, unique and common molecular host responses (biosignatures).

Vaccine, 2011

The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis... more The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis as such are classic examples of worldwide zoonoses for application of a systems biology approach for enhanced rational vaccine development. When used optimally, vaccines prevent disease manifestations, reduce transmission of disease, decrease the need for pharmaceutical intervention, and improve the health and welfare of animals, as well as indirectly protecting against zoonotic diseases of people. Advances in the last decade or so using comprehensive systems biology approaches linking genomics, proteomics, bioinformatics, and biotechnology with immunology, pathogenesis and vaccine formulation and delivery are expected to enable enhanced approaches to vaccine development. The goal of this paper is to evaluate the role of computational systems biology analysis of host:pathogen interactions (the interactome) as a tool for enhanced rational design of vaccines. Systems biology is bringing a new, more robust approach to veterinary vaccine

The Journal of Physical Chemistry B, 2006

Cell signaling dynamics mediate myriad processes in biology. It has become increasingly clear tha... more Cell signaling dynamics mediate myriad processes in biology. It has become increasingly clear that interand intracellular signaling reactions often occur in a spatially inhomogeneous environment and that it is important to account for stochastic fluctuations of certain species involved in signaling reactions. The importance of these effects enhances the difficulty of gleaning mechanistic information from observations of a few experimental reporters and highlights the significance of synergistic experimental and computational studies. When both stochastic fluctuations and spatial inhomogeneity must be included in a model simultaneously, however, the resulting computational demands quickly become overwhelming. In many situations the failure of standard coarse-graining methods (i.e., ignoring spatial variation or stochastic fluctuations) when applied to all components of a complex system does not exclude the possibility of successfully applying such coarsegraining to some components of the system. Following this approach alleviates computational cost but requires "hybrid" algorithms where some variables are treated at a coarse-grained level while others are not. We present an efficient algorithm for simulation of stochastic, spatially inhomogeneous reaction-diffusion kinetics coupled to coarse-grained fields described by (stochastic or deterministic) partial differential equations (PDEs). The PDEs could represent mean-field descriptions of reactive species present in large copy numbers or evolution of hydrodynamic variables that influence signaling (e.g., membrane shape or cytoskeletal motion). We discuss the approximations made to derive our algorithm and test its efficacy by applying it to problems that include many features typical of realistic cell signaling processes.

Proceedings of the National Academy of Sciences, 2007

Activation of T helper cells is necessary for the adaptive immune response to pathogens, and spur... more Activation of T helper cells is necessary for the adaptive immune response to pathogens, and spurious activation can result in organspecific autoimmunity (e.g., multiple sclerosis). T cell activation is initiated by membrane-proximal signaling that is predicated on the binding of the T cell receptor expressed on the T cell surface to peptide major histocompatibility complex (pMHC) molecules presented on the surface of antigen-presenting cells. These signaling processes regulate diverse outcomes, such as the ability of T cells to discriminate sensitively between stimulatory pMHC molecules and those that are characteristic of ''self,'' and the phenomenon of antagonism (wherein the presence of certain pMHC molecules impairs T cell receptor signaling). We describe a molecular model for membrane-proximal signaling in T cells from which these disparate observations emerge as two sides of the same coin. This development of a unified mechanism that is consistent with diverse data would not have been possible without explicit consideration of the stochastic nature of the pertinent biochemical events. Our studies also reveal that certain previously proposed concepts are not dueling ideas but rather are different stimuli-dependent manifestations of a unified molecular model for membrane-proximal signaling. This model may provide a conceptual framework for further investigations of early events that regulate T cell activation in response to self and foreign antigens and for the development of intervention protocols to inhibit aberrant signaling.

Epidemics, 2009

Background: Hepatitis C virus (HCV) causes significant morbidity and mortality in injecting drug ... more Background: Hepatitis C virus (HCV) causes significant morbidity and mortality in injecting drug users (IDU) worldwide. HCV vaccine candidates have shown promise for reducing the infectivity of acute infection and averting chronic infection, yet the impact of varying levels of vaccine efficacy and vaccine delivery strategies on the HCV epidemic in IDU has not been explored.

The Journal of Pathology: Clinical Research, 2016

The Journal of Clinical Endocrinology & Metabolism, 2015

Molecular testing for oncogenic mutations or gene expression in fine-needle aspirations (FNAs) fr... more Molecular testing for oncogenic mutations or gene expression in fine-needle aspirations (FNAs) from thyroid nodules with indeterminate cytology identifies a subset of benign or malignant lesions with high predictive value. This study aimed to evaluate a novel diagnostic algorithm combining mutation detection and miRNA expression to improve the diagnostic yield of molecular cytology. Surgical specimens and preoperative FNAs (n = 638) were tested for 17 validated gene alterations using the miRInform Thyroid test and with a 10-miRNA gene expression classifier generating positive (malignant) or negative (benign) results. Cross-sectional sampling of thyroid nodules with atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) or follicular neoplasm/suspicious for a follicular neoplasm (FN/SFN) cytology (n = 109) was conducted at 12 endocrinology centers across the United States. Qualitative molecular results were compared with surgical histopathology to determine diagnostic performance and model clinical effect. Mutations were detected in 69% of nodules with malignant outcome. Among mutation-negative specimens, miRNA testing correctly identified 64% of malignant cases and 98% of benign cases. The diagnostic sensitivity and specificity of the combined algorithm was 89% (95% confidence interval [CI], 73-97%) and 85% (95% CI, 75-92%), respectively. At 32% cancer prevalence, 61% of the molecular results were benign with a negative predictive value of 94% (95% CI, 85-98%). Independently of variations in cancer prevalence, the test increased the yield of true benign results by 65% relative to mRNA-based gene expression classification and decreased the rate of avoidable diagnostic surgeries by 69%. Multiplatform testing for DNA, mRNA, and miRNA can accurately classify benign and malignant thyroid nodules, increase the diagnostic yield of molecular cytology, and further improve the preoperative risk-based management of benign nodules with AUS/FLUS or FN/SFN cytology.

Clinical and translational gastroenterology, 2014

Current diagnostic tools for pancreatic cysts fail to reliably differentiate mucinous from nonmuc... more Current diagnostic tools for pancreatic cysts fail to reliably differentiate mucinous from nonmucinous cysts. Reliable biomarkers are needed. MicroRNAs (miRNA) may offer insights into pancreatic cysts. Our aims were to (1) identify miRNAs that distinguish benign from both premalignant cysts and malignant pancreatic lesions using formalin-fixed, paraffin-embedded (FFPE) pathology specimens; (2) identify miRNAs that distinguish mucinous cystic neoplasm (MCN) from branch duct-intraductal papillary mucinous neoplasm (BD-IPMN). A total of 69 FFPE pancreatic specimens were identified: (1) benign (20 serous cystadenoma (SCA)), (2) premalignant (10 MCN, 10 BD-IPMN, 10 main duct IPMN (MD-IPMN)), and (3) malignant (19 pancreatic ductal adenocarcinoma (PDAC)). Total nucleic acid extraction was performed followed by miRNA expression profiling of 378 miRNAs interrogated using TaqMan MicroRNA Arrays Pool A and verification of candidate miRNAs. Bioinformatics was used to generate classifiers. MiRN...

The Journal of molecular diagnostics : JMD, 2013

Implementation of highly sophisticated technologies, such as next-generation sequencing (NGS), in... more Implementation of highly sophisticated technologies, such as next-generation sequencing (NGS), into routine clinical practice requires compatibility with common tumor biopsy types, such as formalin-fixed, paraffin-embedded (FFPE) and fine-needle aspiration specimens, and validation metrics for platforms, controls, and data analysis pipelines. In this study, a two-step PCR enrichment workflow was used to assess 540 known cancer-relevant variants in 16 oncogenes for high-depth sequencing in tumor samples on either mature (Illumina GAIIx) or emerging (Ion Torrent PGM) NGS platforms. The results revealed that the background noise of variant detection was elevated approximately twofold in FFPE compared with cell line DNA. Bioinformatic algorithms were optimized to accommodate this background. Variant calls from 38 residual clinical colorectal cancer FFPE specimens and 10 thyroid fine-needle aspiration specimens were compared across multiple cancer genes, resulting in an accuracy of 96.1%...

Clinical Gastroenterology and Hepatology, 2014

Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) in combination with cytopathology i... more Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) in combination with cytopathology is the optimal method for diagnosis and staging of pancreatic ductal adenocarcinoma (PDAC) and other pancreatic lesions. Its clinical utility, however, can be limited by high rates of indeterminate or false-negative results. We aimed to develop and validate a microRNA (miRNA)-based test to improve preoperative detection of PDAC. Levels of miRNAs were analyzed in a centralized clinical laboratory by relative quantitative polymerase chain reaction in 95 formalin-fixed paraffin-embedded specimens and 228 samples collected by EUS-FNA during routine evaluations of patients with solid pancreatic masses at 4 institutions in the United States, 1 in Canada, and 1 in Poland. We developed a 5-miRNA expression classifier, consisting of MIR24, MIR130B, MIR135B, MIR148A, and MIR196, that could identify PDAC in well-characterized, formalin-fixed, paraffin-embedded specimens. Detection of PDAC in EUS-FNA samples increased from 78.8% by cytology analysis alone (95% confidence interval, 72.2%-84.5%) to 90.8% when combined with miRNA analysis (95% confidence interval, 85.6%-94.5%). The miRNA classifier correctly identified 22 additional true PDAC cases among 39 samples initially classified as benign, indeterminate, or nondiagnostic by cytology. Cytology and miRNA test results each were associated significantly with PDAC (P < .001), with positive predictive values greater than 99% (95% confidence interval, 96%-100%). We developed and validated a 5-miRNA classifier that can accurately predict which preoperative pancreatic EUS-FNA specimens contain PDAC. This test might aid in the diagnosis of pancreatic cancer by reducing the number of FNAs without a definitive adenocarcinoma diagnosis, thereby reducing the number of repeat EUS-FNA procedures.

Clinical Cancer Research, 2012

The diagnosis of pancreatic cystic lesions has increased dramatically. Most are benign, whereas s... more The diagnosis of pancreatic cystic lesions has increased dramatically. Most are benign, whereas some, such as intraductal papillary mucinous neoplasms (IPMN), represent precursors of pancreatic adenocarcinoma. Therapeutic stratification of IPMNs is challenging without precise information on dysplasia grade and presence of invasion. We assessed the diagnostic benefit of using miRNAs as biomarkers in pancreatic cyst fluid, focusing on IPMNs because of their frequency and malignant potential. RNA was extracted from 55 microdissected formalin-fixed, paraffin-embedded (FFPE) IPMN specimens, and 65 cyst fluid specimens aspirated following surgical resection. Expression of 750 miRNAs was evaluated with TaqMan miRNA Arrays using 22 FFPE and 15 cyst fluid specimens. Differential expression of selected miRNA candidates was validated in 33 FFPE and 50 cyst fluid specimens using TaqMan miRNA Assays. We identified 26 and 37 candidate miRNAs that distinguish low-grade from high-grade IPMNs using FFPE and cyst fluid specimens, respectively. A subset of 18 miRNAs, selected from FFPE and cyst fluid data, separated high-grade IPMNs from low-grade IPMNs, serous cystadenomas (SCA) and uncommon cysts, such as solid pseudopapillary neoplasms (SPN) and cystic pancreatic neuroendocrine tumors (PanNET). A logistic regression model using nine miRNAs allowed prediction of cyst pathology implying resection (high-grade IPMNs, PanNETs, and SPNs) versus conservative management (low-grade IPMNs, SCAs), with a sensitivity of 89%, a specificity of 100%, and area under the curve of 1. We found candidate miRNAs that helped identify patients with high-grade IPMN and exclude nonmucinous cysts. These classifiers will require validation in a prospective setting to ultimately confirm their clinical usefulness.

BMC Research Notes, 2011

Normalization is critical for accurate gene expression analysis. A significant challenge in the q... more Normalization is critical for accurate gene expression analysis. A significant challenge in the quantitation of gene expression from biofluids samples is the inability to quantify RNA concentration prior to analysis, underscoring the need for robust normalization tools for this sample type. In this investigation, we evaluated various methods of normalization to determine the optimal approach for quantifying microRNA (miRNA) expression from biofluids and tissue samples when using the TaqMan® Megaplex™ high-throughput RT-qPCR platform with low RNA inputs. We compared seven normalization methods in the analysis of variation of miRNA expression from biofluid and tissue samples. We developed a novel variant of the common mean-centering normalization strategy, herein referred to as mean-centering restricted (MCR) normalization, which is adapted to the TaqMan Megaplex RT-qPCR platform, but is likely applicable to other high-throughput RT-qPCR-based platforms. Our results indicate that MCR normalization performs comparable to or better than both standard mean-centering and other normalization methods. We also propose an extension of this method to be used when migrating biomarker signatures from Megaplex to singleplex RT-qPCR platforms, based on the identification of a small number of normalizer miRNAs that closely track the mean of expressed miRNAs. We developed the MCR method for normalizing miRNA expression from biofluids samples when using the TaqMan Megaplex RT-qPCR platform. Our results suggest that normalization based on the mean of all fully observed (fully detected) miRNAs minimizes technical variance in normalized expression values, and that a small number of normalizer miRNAs can be selected when migrating from Megaplex to singleplex assays. In our study, we find that normalization methods that focus on a restricted set of miRNAs tend to perform better than methods that focus on all miRNAs, including those with non-determined (missing) values. This methodology will likely be most relevant for studies in which a significant number of miRNAs are not detected.

Journal of the American Society of Cytopathology, 2015

ABSTRACT This study was to investigate the application of molecular testing to residual thyroid F... more ABSTRACT This study was to investigate the application of molecular testing to residual thyroid FNA material from needle rinses collected in Cytolyt.

Atelier morphosyntaxe, Laboratoire Dynamique du Langage, 2019

Adam J.R. Tallman (DDL) with Dennis Wylie, Anthony C. Woodbury, Gladys Camacho Rios, Hiroto Uc... more Adam J.R. Tallman (DDL)

with Dennis Wylie, Anthony C. Woodbury, Gladys Camacho Rios, Hiroto Uchihara, Kelsey Neely, Natalia Bermudez, Ambrocio Gutierrez, Cristian Juarez, Willem de Reuse, Patience Epps, Andrés Salanova, Eric Adell, Michael Everdell, Eric Campbell, Javier Carol

In this talk we discuss some foundational problems in the cross-linguistic comparison of wordhood and constituency. We present a solution to these problems and apply them to the study of 14 languages of the America (Chácobo (Pano), Yaminawa (Pano), Hup (Naduhup), Mebengokre (Ge), Chatino (Oto-Manguean), Quechua (Quechua), Mocoví (Guaicuruan), Zapotec (Oto-Manguean), Central Alaskan Yupik (Yupik-Inuit-Unangan), Apache (Na-Dene Athabaskan), Cherokee (Iroquioan), Naso (Chibchan), Chajul Ixil (Mayan), Southeastern Tepehuan (Uto-Aztecan), Chorote (Matacoan)). We argue for a new methodology that rests on rejection of a number of assumptions (often implicit) in descriptive and typological work: (i) the distinction between morphological and syntactic positions (ii) the distinction between morphosyntactic and phonological words; (iii) the distinction between wordhood and phrasehood diagnostics. Instead, we propose that an approach to cross-linguistic comparison of constituency that involves the systematic application of constituency diagnostics coded in a typological database that does not presuppose these distinctions. Languages are compared in terms of how many levels emerge out of the application of the diagnostics, the convergences between diagnostics, and the robustness of these convergences given the parameters of their application. We present a new set of terminology for describing sentence structure and comparing the results of constituency tests that we refer to as "flat structures" (based on a critical engagement and synthesis of the morphological and syntactic representations found in and Bickel and Zúñiga (2017) and Culicover and Jackendoff (2005)).

One of the most serious critiques of the investigation of constituency is methodological opportunism (e.g. Croft 2001; Croft 2010; Haspelmath 2011). Rather than lapsing into one of the two extremes of categorial universalism or categorial particularism (e.g. Haspelmath 2010), we deal with this problem by positing a novel concept referred to as the probability of chance convergence. This refers to the likelihood that two or more constituency diagnostics could have converged around the same result by chance given the number of tests applied and the morphosyntactic positions in the language. We also show how a metric of the probability of chance convergence can be computed. We argue that this methodology takes important steps towards overcoming language-internal and cross-linguistic methodological opportunism.

Our study has the following results:

. Languages vary in terms of whether and the extent to which a word constituent is motivated. This finding calls into question the whole framing of the debate on lexicalism (Marantz 1997; Wechsler 2005; Bruening 2018; Müller 2018) and wordhood generally (Blevins 2016; Geertzen et al. 2016).

. The distinction between grammatical and phonological word is not motivated in any language. This finding undermines some basic premises of certain formulations of Basic Linguistic Theory (e.g. Dixon 2010 and generative theories of phonological constituency such as prosodic phonology (Nespor & Vogel 1986).

We discuss other findings from this study and the future research that they could inspire. We also discuss the relevance of these findings for linguistic description.
References
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Bickel, Balthasar, Kristine A. Hildebrandt, and René Schiering. 2009. "The distribution of phonological word domains: A probabilistic typology." In Phonological Domains: Universals and Deviations, edited by Janet Grijzenhout and Kabak Baris, 47-75. De Gruyter Mouton.
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