@article{price_longtin_conley-payton_osborne_johanningsmeier_bitzer_breidt_2020, title={Modeling buffer capacity and pH in acid and acidified foods}, volume={85}, ISSN={["1750-3841"]}, DOI={10.1111/1750-3841.15091}, abstractNote={AbstractStandard ionic equilibria equations may be used for calculating pH of weak acid and base solutions. These calculations are difficult or impossible to solve analytically for foods that include many unknown buffering components, making pH prediction in these systems impractical. We combined buffer capacity (BC) models with a pH prediction algorithm to allow pH prediction in complex food matrices from BC data. Numerical models were developed using Matlab software to estimate the pH and buffering components for mixtures of weak acid and base solutions. The pH model was validated with laboratory solutions of acetic or citric acids with ammonia, in combinations with varying salts using Latin hypercube designs. Linear regressions of observed versus predicted pH values based on the concentration and pK values of the solution components resulted in estimated slopes between 0.96 and 1.01 with and without added salts. BC models were generated from titration curves for 0.6 M acetic acid or 12.4 mM citric acid resulting in acid concentration and pK estimates. Predicted pH values from these estimates were within 0.11 pH units of the measured pH. Acetic acid concentration measurements based on the model were within 6% accuracy compared to high‐performance liquid chromatography measurements for concentrations less than 400 mM, although they were underestimated above that. The models may have application for use in determining the BC of food ingredients with unknown buffering components. Predicting pH changes for food ingredients using these models may be useful for regulatory purposes with acid or acidified foods and for product development.}, number={4}, journal={JOURNAL OF FOOD SCIENCE}, author={Price, Robert E. and Longtin, Madyson and Conley-Payton, Summer and Osborne, Jason A. and Johanningsmeier, Suzanne D. and Bitzer, Donald and Breidt, Fred}, year={2020}, month={Apr}, pages={918–925} }
 @article{lobo_bitzer_vouk_2012, title={Locally Invertible Multidimensional Convolutional Encoders}, volume={58}, ISSN={["1557-9654"]}, DOI={10.1109/tit.2011.2178129}, abstractNote={A polynomial matrix is said to be locally invertible if it has an invertible subsequence map of equal size between its input and output sequence spaces. This paper examines the use of these matrices, which we call locally invertible encoders, for generating multidimensional convolutional codes. We discuss a novel method of encoding and inverting multidimensional sequences using the subsequence map. We also show that the overlapping symbols between consecutive input subsequences obtained during the sequence inversion can be used to determine if the received sequence is the same as the transmitted codeword.}, number={3}, journal={IEEE TRANSACTIONS ON INFORMATION THEORY}, author={Lobo, Ruben and Bitzer, Donald L. and Vouk, Mladen A.}, year={2012}, month={Mar}, pages={1774–1782} }
 @article{xing_bitzer_alexander_vouk_stomp_2009, title={Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation}, volume={37}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkn917}, abstractNote={We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3′-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3′-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3′-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences.}, number={2}, journal={NUCLEIC ACIDS RESEARCH}, author={Xing, Chuanhua and Bitzer, Donald L. and Alexander, Winser E. and Vouk, Mladen A. and Stomp, Anne-Marie}, year={2009}, month={Feb}, pages={591–601} }
 @article{may_vouk_bitzer_2006, title={Classification of Escherichia coli K-12 ribosome binding sites}, volume={25}, ISSN={["0739-5175"]}, DOI={10.1109/memb.2006.1578668}, abstractNote={Drawing on parallels between genetic information processing in living organisms and the processing of communications data, we develop an error-control coding-based translation initiation classification system that uses an eleven base classification window. An overview of channel codes and a summary of the translation initiation process are presented. Parallels between the two are drawn and a brief review of a channel code model for translation initiation is shown. A block-code Bayesian classifier is presented and the results of applying the system to the translation start site location problem for Escherichia coli K-12 is discussed.}, number={1}, journal={IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE}, author={May, EE and Vouk, MA and Bitzer, DL}, year={2006}, pages={90–97} }
 @inbook{lobo_bitzer_vouk_2006, title={Locally Invertible Multivariate Polynomial Matrices}, ISBN={9783540354819 9783540354826}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/11779360_33}, DOI={10.1007/11779360_33}, abstractNote={A new class of rectangular zero prime multivariate polynomial matrices are introduced and their inverses are computed. These matrices are ideal for use in multidimensional systems involving input-output transformations. We show that certain multivariate polynomial matrices, when transformed to the sequence space domain, have an invertible subsequence map between their input and output sequences. This invertible subsequence map can be used to derive the polynomial inverse matrix together with a set of pseudo-inverses. All computations are performed using elementary operations on the ground field without using any polynomial operations.}, booktitle={Coding and Cryptography}, publisher={Springer Berlin Heidelberg}, author={Lobo, Ruben G. and Bitzer, Donald L. and Vouk, Mladen A.}, year={2006}, pages={427–441} }
 @article{lobo_bitzer_vouk_2006, title={Locally invertible multivariate polynomial matrices}, number={3969}, journal={Lecture Notes in Computer Science}, author={Lobo, R. G. and Bitzer, D. L. and Vouk, M. A.}, year={2006}, pages={427–441} }
 @article{starmer_stomp_vouk_bitzer_2006, title={Predicting Shine-Dalgarno sequence locations exposes genome annotation errors}, volume={2}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.0020057}, abstractNote={In prokaryotes, Shine–Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of synthesis. Thus, accurate characterization of SD sequences enhances our understanding of how an organism's transcriptome relates to its cellular proteome. We implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo–oligo hybridization and created a new metric, relative spacing (RS), to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3′ tails. In 18 prokaryote genomes, we identified 2,420 genes out of 58,550 where the strongest binding in the translation initiation region included the start codon, deviating from the expected location for the SD sequence of five to ten bases upstream. We designated these as RS+1 genes. Additional analysis uncovered an unusual bias of the start codon in that the majority of the RS+1 genes used GUG, not AUG. Furthermore, of the 624 RS+1 genes whose SD sequence was associated with a free energy release of less than −8.4 kcal/mol (strong RS+1 genes), 384 were within 12 nucleotides upstream of in-frame initiation codons. The most likely explanation for the unexpected location of the SD sequence for these 384 genes is mis-annotation of the start codon. In this way, the new RS metric provides an improved method for gene sequence annotation. The remaining strong RS+1 genes appear to have their SD sequences in an unexpected location that includes the start codon. Thus, our RS metric provides a new way to explore the role of rRNA–mRNA nucleotide hybridization in translation initiation.}, number={5}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Starmer, J. and Stomp, A. and Vouk, M. and Bitzer, D.}, year={2006}, month={May}, pages={454–466} }
 @inbook{barnes_bitzer_vouk_2005, title={Experimental Analysis of the Q-Matrix Method in Knowledge Discovery}, volume={3488}, ISBN={9783540258780 9783540319498}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/11425274_62}, DOI={10.1007/11425274_62}, abstractNote={The q-matrix method, a new method for data mining and knowledge discovery, is compared with factor analysis and cluster analysis in analyzing fourteen experimental data sets. This method creates a matrix-based model that extracts latent relationships among observed binary variables. Results show that the q-matrix method offers several advantages over factor analysis and cluster analysis for knowledge discovery. The q-matrix method can perform fully unsupervised clustering, where the number of clusters is not known in advance. It also yields better error rates than factor analysis, and is comparable in error to cluster analysis. The q-matrix method also allows for automatic interpretation of the data sets. These results suggest that the q-matrix method can be an important tool in automated knowledge discovery.}, booktitle={Lecture Notes in Computer Science}, publisher={Springer Berlin Heidelberg}, author={Barnes, Tiffany and Bitzer, Donald and Vouk, Mladen}, year={2005}, pages={603–611} }
 @article{may_vouk_bitzer_rosnick_2004, title={An error-correcting code framework for genetic sequence analysis}, volume={341}, ISSN={["1879-2693"]}, DOI={10.1016/j.jfranklin.2003.12.009}, abstractNote={A fundamental challenge for engineering communication systems is the problem of transmitting information from the source to the receiver over a noisy channel. This same problem exists in a biological system. How can information required for the proper functioning of a cell, an organism, or a species be transmitted in an error introducing environment? Source codes (compression codes) and channel codes (error-correcting codes) address this problem in engineering communication systems. The ability to extend these information theory concepts to study information transmission in biological systems can contribute to the general understanding of biological communication mechanisms and extend the field of coding theory into the biological domain. In this work, we review and compare existing coding theoretic methods for modeling genetic systems. We introduce a new error-correcting code framework for understanding translation initiation, at the cellular level and present research results for Escherichia coli K-12. By studying translation initiation, we hope to gain insight into potential error-correcting aspects of genomic sequences and systems.}, number={1-2}, journal={JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS}, author={May, EE and Vouk, MA and Bitzer, DL and Rosnick, DI}, year={2004}, pages={89–109} }
 @article{may_vouk_bitzer_rosnick_2004, title={Coding theory based models for protein translation initiation in prokaryotic organisms}, volume={76}, ISSN={["0303-2647"]}, DOI={10.1016/j.biosystems.2004.05.017}, abstractNote={Our research explores the feasibility of using communication theory, error control (EC) coding theory specifically, for quantitatively modeling the protein translation initiation mechanism. The messenger RNA (mRNA) of Escherichia coli K-12 is modeled as a noisy (errored), encoded signal and the ribosome as a minimum Hamming distance decoder, where the 16S ribosomal RNA (rRNA) serves as a template for generating a set of valid codewords (the codebook). We tested the E. coli based coding models on 5′ untranslated leader sequences of prokaryotic organisms of varying taxonomical relation to E. coli including: Salmonella typhimurium LT2, Bacillus subtilis, and Staphylococcus aureus Mu50. The model identified regions on the 5′ untranslated leader where the minimum Hamming distance values of translated mRNA sub-sequences and non-translated genomic sequences differ the most. These regions correspond to the Shine–Dalgarno domain and the non-random domain. Applying the EC coding-based models to B. subtilis, and S. aureus Mu50 yielded results similar to those for E. coli K-12. Contrary to our expectations, the behavior of S. typhimurium LT2, the more taxonomically related to E. coli, resembled that of the non-translated sequence group.}, number={1-3}, journal={BIOSYSTEMS}, author={May, EE and Vouk, MA and Bitzer, DL and Rosnick, DI}, year={2004}, pages={249–260} }
 @article{rodman_mcallister_bitzer_cepeda_abbitt_2002, title={Forensic speaker identification based on spectral moments}, volume={9}, ISSN={["1350-1771"]}, DOI={10.1558/sll.2002.9.1.22}, abstractNote={A new method for doing text-independent speaker identification geared to forensic situations is presented. By analysing ‘isolexemic’ sequences, the method addresses the issues of very short criminal exemplars and the need for open-set identification. An algorithm is given that computes an average spectral shape of the speech to be analysed for each glottal pulse period. Each such spectrum is converted to a probability density function and the first moment (i.e. the mean) and the second moment about the mean (i.e. the variance) are computed. Sequences of moment values are used as the basis for extracting variables that discriminate among speakers. Ten variables are presented all of which have sufficiently high inter- to intraspeaker variation to be effective discriminators. A case study comprising a ten-speaker database, and ten unknown speakers, is presented. A discriminant analysis is performed and the statistical measurements that result suggest that the method is potentially effective. The report represents work in progress.}, number={1}, journal={FORENSIC LINGUISTICS-THE INTERNATIONAL JOURNAL OF SPEECH LANGUAGE AND THE LAW}, author={Rodman, R and McAllister, D and Bitzer, D and Cepeda, L and Abbitt, P}, year={2002}, pages={22–43} }
 @article{vouk_bitzer_klevans_1999, title={Workflow and end-user quality of service issues in Web-based education}, volume={11}, ISSN={["1558-2191"]}, DOI={10.1109/69.790839}, abstractNote={The option of obtaining education over networks is quickly becoming a reality for all those who have access to the Internet and the World Wide Web (WWW). However, at present, network-based education (NBE) over the WWW and the Internet in general faces a number of pitfalls. The problems range from inadequate end-user quality of service (QoS), to inadequate materials, to shortcomings in learning paradigms, and to missing or inappropriate student assessment and feedback mechanisms. In this paper, we discuss some major issues that, although mostly solved for NBE, still face Web-based education (WEE). These include the required workflow-oriented technological and quality of service support. In discussing the issues, we use examples from a wide-area NBE/WBE system called NovaNET and a WEE system called Web Lecture System (WLS). We recommend that WEE system developers construct operational user (workflow) profiles before building their content and interfaces. Our experience is that, especially for synchronous WEE systems, user-level round-trip keystroke delays should not exceed about 250 ms and the overall availability of the system (including network-related service failures) should be at least 0.95. We also suggest that a successful WEE system will have a sound auto-adaptive knowledge assessment component, a "virtual" laboratory capability, and a set of strong collaborative functions.}, number={4}, journal={IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING}, author={Vouk, MA and Bitzer, DL and Klevans, RL}, year={1999}, pages={673–687} }
 @inproceedings{rodman_mcallister_bitzer_freeman_1998, title={Automated lip-sync animation as a telecommunications aid for the hearing impaired}, booktitle={Proceedings, 1998 IEEE 4th Workshop Interactive Voice Technology for Telecommunications Applications: IVTTA '98, September 29th-30th, 1998, Turino, Italy}, publisher={New York: Institute of Electrical and Electronics Engineers, Inc.; Piscataway, NJ: IEEE Service Center}, author={Rodman, R. D. and McAllister, D. F. and Bitzer, D. L. and Freeman, A. S.}, year={1998}, pages={202–208} }
 @misc{bitzer_dholakia_koorapaty_vouk_1998, title={On locally invertible rate-1/n convolutional encoders}, volume={44}, ISSN={["1557-9654"]}, DOI={10.1109/18.651074}, abstractNote={A locally invertible convolutional encoder has a local inverse defined as a full rank w/spl times/w matrix that specifies a one-to-one mapping between equal-length blocks of information and encoded bits. In this correspondence, it is shown that a rate-1/n convolutional encoder is nondegenerate and noncatastrophic if and only if it is locally invertible. Local invertibility is used to obtain upper and lower bounds on the number of consecutive zero-weight branches in a convolutional codeword. Further, existence of a local inverse can be used as an alternate test for noncatastrophicity instead of the usual approach involving computation of the greatest common divisor of n polynomials.}, number={1}, journal={IEEE TRANSACTIONS ON INFORMATION THEORY}, author={Bitzer, DL and Dholakia, A and Koorapaty, H and Vouk, MA}, year={1998}, month={Jan}, pages={420–422} }
 @article{mcallister_rodman_bitzer_freeman_1998, title={Speaker independence in automated lip-sync for audio-video communication}, volume={30}, ISSN={["0169-7552"]}, DOI={10.1016/S0169-7552(98)00216-5}, abstractNote={By analyzing the absolute value of the Fourier transform of a speaker's voice signal we can predict the position of the mouth for English vowel sounds. This is without the use of text, speech recognition or mechanical or other sensing devices attached to the speaker's mouth. This capability can reduce the time required for mouth animation considerably. We expect it to be competitive eventually with the speech/text driven solutions which are becoming popular. Our technique would require much less interaction from the user and no knowledge of phonetic spelling. We discuss the problems of producing an algorithm that is speaker independent. The goal is to avoid having to measure mouth movements off video for each speaker's training sounds. We have discovered that eliminating variation due to pitch yields moments which are mouth shape dependent but not speaker dependent. This implies that careful construction of predictor surfaces can produce speaker independent prediction of mouth motion for English vowels.}, number={20-21}, journal={COMPUTER NETWORKS AND ISDN SYSTEMS}, author={McAllister, DF and Rodman, RD and Bitzer, DL and Freeman, AS}, year={1998}, month={Nov}, pages={1975–1980} }
 @inproceedings{rodman_bitzer_mcallister_1997, title={Lip synchronization as an aid to the hearing disabled}, number={1997}, booktitle={AVIOS 97: Proceedings of the American Voice Input/Output Society (AVIOS), September 1997}, publisher={San Jose, Calif.: American Voice Input/Output Society Society}, author={Rodman, R. D. and Bitzer, D. L. and McAllister, D. F.}, year={1997}, pages={233–248} }
 @inproceedings{rodman_mcallister_bitzer_1997, title={Lip synchronization for animation}, booktitle={Computer graphics: Proceedings, annual conference series, 1997: SIGGRAPH 97 Conference proceedings, August 3-8, 1997}, publisher={New York, N.Y.: Association for Computing Machinery}, author={Rodman, R. D. and McAllister, D. F. and Bitzer, D. L.}, year={1997}, pages={225–226} }
 @inproceedings{mcallister_bitzer_rodman_1997, title={Lip synchronization of speech}, booktitle={Proceedings of the Audio Visual Speech Processing Conference '97, October 1997}, author={McAllister, D. F. and Bitzer, D. L. and Rodman, R. D.}, year={1997}, pages={133–136} }
 @inproceedings{rodman_mcallister_bitzer_1997, title={Toward speaker independence in automated lip-sync}, number={1997}, booktitle={Compugraphics '97: Proceedings of the International Conference on Computational Graphics and Visualization Techniques, December 1997}, publisher={Portugal}, author={Rodman, R. D. and McAllister, D. F. and Bitzer, D. L.}, year={1997}, pages={1–5} }
 @misc{bitzer_vouk_srinivasan_lo_dholakia_gonzalez_lee_wang_koorapaty_1995, title={System for encoding and decoding of convolutionally encoded data}, volume={5381425}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Bitzer, D. L. and Vouk, M. A. and Srinivasan, V. and Lo, S. K. and Dholakia, A. and Gonzalez, E. M. and Lee, T. M. and Wang, L. and Koorapaty, H.}, year={1995} }