Faculty of Science

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Open Access
11B and 23 Na solid-state NMR and density functional theory studies of electric field gradients at boron sites in ulexite
(Royal Society of Chemistry, 2013-07-31) Zhou, Bing; Michaelis, Vladimir K.; Kroeker, Scott; Wren, John E. C.; Yao, Yefeng; Sherriff, Barbara L.; Pan, Yuanming
Nuclear magnetic resonance (NMR) parameters of 11B in borates and borosilicates, unlike those of many other nuclei such as 29Si and 27Al, vary only over limited ranges and have been thought to be insensitive to local structural environments. High-resolution NMR spectroscopy at high (14 T) and ultrahigh (21 T) fields yield precise 11B and 23Na NMR parameters for ulexite, which contains the pentaborate polyanion ([B5O6(OH)6]3−) as the fundamental building block (FBB). These NMR parameters are compared with ab initio theoretical calculations as implemented in WIEN2K, including optimization of the ulexite structure, determination of the electric field gradients (EFG) and consequently the nuclear quadrupole interaction (QI) parameters at the five distinct B sites, and calculations of the density of states (DOS). These calculations show that the magnitudes and signs of the EFG for [3]B and [4]B are determined by multiple factors, including the electron distributions in the B 2pz orbitals and their interactions with Ca-3p/O-2s orbitals. Most importantly, the calculated B 2pz orbitals at all B sites in ulexite are predominantly affected by the atoms within the fundamental building block, resulting in the insensitivity of the 11B QI parameters to the weak interunit interactions among FBB. Calculations with the water molecules removed from the ulexite structure provide further support for the strong intraunit interactions in FBB as a cause for the poor sensitivity of 11B NMR parameters to local structural environments, including hydrogen bonding, in borates.
Open Access
A Directional Antenna in a Matching Liquid for Microwave Radar Imaging
(2015-11-10) Latif, Saeed I.; Flores Tapia, Daniel; Rodriguez Herrera, Diego; Solis Nepote, Mario; Pistorius, Stephen; Shafai, Lotfollah
The detailed design equations and antenna parameters for a directional antenna for breast imaging are presented in this paper. The antenna was designed so that it could be immersed in canola oil to achieve efficient coupling of the electromagnetic energy to the breast tissue. Ridges were used in the horn antenna to increase the operating bandwidth. The antenna has an exponentially tapered section for impedance matching. The double-ridged horn antenna has a wideband performance from 1.5 GHz to 5 GHz (3.75 GHz or 110% of impedance bandwidth), which is suitable for breast microwave radar imaging. The fabricated antenna was tested and compared with simulated results, and similar bandwidths were obtained. Experiments were conducted on breast phantoms using these antennas, to detect a simulated breast lesion. The reconstructed image from the experiments shows distinguishable tumor responses indicating promising results for successful breast cancer detection.
Open Access
A method of spatial correction for acoustic positioning biotelemetry
(2016-02-03) Charles, C.; Gillis, D. M; Hrenchuk, L. E; Blanchfield, P. J
Abstract Background It has been stated that there is a certain amount of intrinsic error inherent in all remote sensing methods, including acoustic telemetry, which has gained popularity in both freshwater and marine environments to record fine-scale movements over small spatial scales. We performed stationary tag trials on three freshwater lakes where we placed transmitters at known locations around the lakes and used radio-acoustic positioning and telemetry (RAPT) system-derived location data to assess the measurement and systematic biases of the system. We used a geostatistical technique called ordinary kriging to deal with the systematic errors and a state-space model to represent the measurement error of the data. Furthermore, we applied the kriging correction and a continuous-time correlated random walk model in a state-space framework to predict locations of a lake trout. Results The stationary tagging trials produced a complex pattern of spatial error within each lake that could not properly be accounted for by a simple filtering process. Using fivefold cross-validation, positioning error was reduced from 93 to 99 % in three small lakes. We also identified tag depth as a potential source of measurement error. The application of a state-space model resulted in the contraction of home ranges of lake trout by 10–32 % and a 3–32 % reduction in total distance travelled. Conclusions Our results indicate that the systematic biases were a greater source of error than the measurement errors using a RAPT system. Consequently, the addition of a state-space model had relatively little effect on the quality of the spatial correction compared with the kriging method. The kriging method was able to compensate for the systematic biases produced by the RAPT systems and in turn increased the quality of data returned.
Open Access
A New Mathematical Model for Assessing Therapeutic Strategies for HIV Infection
(2002-1-1) Gumel, A. B.; Zhang, Xue-Wu; Shivakumar, P. N.; Garba, M. L.; Sahai, B. M.
The requirements for the eradication of HIV in infected individuals are unknown. Intermittent administration of the immune activator interleukin-2 (IL-2) in combination with highly-active antiretroviral therapy (HAART) has been suggested as an effective strategy to realize long-term control of HIV replication in vivo. However, potential latent virus reservoirs are considered to be a major impediment in achieving this goal. In this paper, a new mathematical model is designed and used to monitor the interactions between HIV, CD4+ T-cells, CD8+ T-cells, productively infected and latently infected CD4+ T-cells, and to evaluate therapeutic strategies during the first 3 years of HIV infection. The model shows that current anti-HIV therapies, including intermittent IL-2 and HAART, are insufficient in achieving eradication of HIV. However, it suggests that the HIV eradication may indeed be theoretically feasible if such therapy is administered continuously (without interruption) under some specified conditions. These conditions may realistically be achieved using an agent (such as a putative anti-HIV vaccine) that brings about a concomitant increase in the proliferation of HIVspecific CD4+ T- and CD8+ T-cells and the differentiation of CD8+ T-cells into anti-HIV cytotoxic T lymphocytes (CTLs).
Open Access
A privacy-preserving distributed filtering framework for NLP artifacts
(2019-09-07) Sadat, Md Nazmus; Aziz, Md Momin Al; Mohammed, Noman; Pakhomov, Serguei; Liu, Hongfang; Jiang, Xiaoqian
Abstract Background Medical data sharing is a big challenge in biomedicine, which often hinders collaborative research. Due to privacy concerns, clinical notes cannot be directly shared. A lot of efforts have been dedicated to de-identifying clinical notes but it is still very challenging to accurately locate and scrub all sensitive elements from notes in an automatic manner. An alternative approach is to remove sentences that might contain sensitive terms related to personal information. Methods A previous study introduced a frequency-based filtering approach that removes sentences containing low frequency bigrams to improve the privacy protection without significantly decreasing the utility. Our work extends this method to consider clinical notes from distributed sources with security and privacy considerations. We developed a novel secure protocol based on private set intersection and secure thresholding to identify uncommon and low-frequency terms, which can be used to guide sentence filtering. Results As the computational cost of our proposed framework mostly depends on the cardinality of the intersection of the sets and the number of data owners, we evaluated the framework in terms of these two factors. Experimental results demonstrate that our proposed method is scalable in various experimental settings. In addition, we evaluated our framework in terms of data utility. This evaluation shows that the proposed method is able to retain enough information for data analysis. Conclusion This work demonstrates the feasibility of using homomorphic encryption to develop a secure and efficient multi-party protocol.
Open Access
A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919
(2019-02-06) Nickol, Michaela E; Kindrachuk, Jason
Abstract Background In the spring of 1918, the “War to End All Wars”, which would ultimately claim more than 37 million lives, had entered into its final year and would change the global political and economic landscape forever. At the same time, a new global threat was emerging and would become one of the most devastating global health crises in recorded history. Main text The 1918 H1N1 pandemic virus spread across Europe, North America, and Asia over a 12-month period resulting in an estimated 500 million infections and 50–100 million deaths worldwide, of which ~ 50% of these occurred within the fall of 1918 (Emerg Infect Dis 12:15-22, 2006, Bull Hist Med 76:105-115, 2002). However, the molecular factors that contributed to the emergence of, and subsequent public health catastrophe associated with, the 1918 pandemic virus remained largely unknown until 2005, when the characterization of the reconstructed pandemic virus was announced heralding a new era of advanced molecular investigations (Science 310:77-80, 2005). In the century following the emergence of the 1918 pandemic virus we have landed on the Moon, developed the electronic computer (and a global internet), and have eradicated smallpox. In contrast, we have a largely remedial knowledge and understanding of one of the greatest scourges in recorded history. Conclusion Here, we reflect on the 1918 influenza pandemic, including its emergence and subsequent rapid global spread. In addition, we discuss the pathophysiology associated with the 1918 virus and its predilection for the young and healthy, the rise of influenza therapeutic research following the pandemic, and, finally, our level of preparedness for future pandemics.
Open Access
Acid-base regulation in the Dungeness crab (Metacarcinus magister): effects of predicted future changes in environmental pCO2
(Marine Biology, 2013) Hans, Stephanie; Fehsenfeld, Sandra; Weihrauch, Dirk
Rising seawater pCO2 (ocean acidification) presents a challenge for marine organisms. To counteract disturbances, many aquatic crustaceans excrete/accumulate acid-base equivalents through their gills; however, not much is known about the role of ammonia in this response. The present study investigated the effects of elevated pCO2 on acid-base and ammonia regulation in the Dungeness crab, Metacarcinus magister on the whole animal and the isolated gill level. Hemolymph pCO2 and [HCO3-] increased in M. magister acclimated to elevated pCO2 while pH remained stable. Additionally, hemolymph [Na+], [Ca2+], and [SO42-] were significantly increased. When challenged with varying pH during gill perfusion, the pH of the artificial hemolymph remained relatively unchanged. Overall, ammonia production and excretion were reduced in crabs acclimated to elevated pCO2, demonstrating that either amino acid metabolism is reduced in response to this particular stress, or nitrogenous wastes are excreted in an alternative form.
Open Access
Adaptive multiple imputations of missing values using the class center
(2022-04-28) Phiwhorm, Kritbodin; Saikaew, Charnnarong; Leung, Carson K.; Polpinit, Pattarawit; Saikaew, Kanda R.
Abstract Big data has become a core technology to provide innovative solutions in many fields. However, the collected dataset for data analysis in various domains will contain missing values. Missing value imputation is the primary method for resolving problems involving incomplete datasets. Missing attribute values are replaced with values from a selected set of observed data using statistical or machine learning methods. Although machine learning techniques can generate reasonably accurate imputation results, they typically require longer imputation durations than statistical techniques. This study proposes the adaptive multiple imputations of missing values using the class center (AMICC) approach to produce effective imputation results efficiently. AMICC is based on the class center and defines a threshold from the weighted distances between the center and other observed data for the imputation step. Additionally, the distance can be an adaptive nearest neighborhood or the center to estimate the missing values. The experimental results are based on numerical, categorical, and mixed datasets from the University of California Irvine (UCI) Machine Learning Repository with introduced missing values rate from 10 to 50% in 27 datasets. The proposed AMICC approach outperforms the other missing value imputation methods with higher average accuracy at 81.48% which is higher than those of other methods about 9 – 14%. Furthermore, execution time is different from the Mean/Mode method, about seven seconds; moreover, it requires significantly less time for imputation than some machine learning approaches about 10 – 14 s.
Open Access
Advances in Matrices, Finite and Infinite, with Applications
(2013-7-17) Shivakumar, P. N.; Psarrakos, Panayiotis; Sivakumar, K. C.; Zhang, Yang
Open Access
Advances in Matrices, Finite and Infinite, with Applications 2014
(2014-9-7) Shivakumar, P. N.; Psarrakos, Panayiotis J.; Sivakumar, K. C.; Zhang, Yang; da Fonseca, Carlos M.
Open Access
AI-based sensor information fusion for supporting deep supervised learning
(MDPI, 2019-03) Leung, Carson K.; Braun, Peter; Cuzzocrea, Alfredo
In recent years, artificial intelligence (AI) and its subarea of deep learning have drawn the attention of many researchers. At the same time, advances in technologies enable the generation or collection of large amounts of valuable data (e.g., sensor data) from various sources in different applications, such as those for the Internet of Things (IoT), which in turn aims towards the development of smart cities. With the availability of sensor data from various sources, sensor information fusion is in demand for effective integration of big data. In this article, we present an AI-based sensor-information fusion system for supporting deep supervised learning of transportation data generated and collected from various types of sensors, including remote sensed imagery for the geographic information system (GIS), accelerometers, as well as sensors for the global navigation satellite system (GNSS) and global positioning system (GPS). The discovered knowledge and information returned from our system provides analysts with a clearer understanding of trajectories or mobility of citizens, which in turn helps to develop better transportation models to achieve the ultimate goal of smarter cities. Evaluation results show the effectiveness and practicality of our AI-based sensor information fusion system for supporting deep supervised learning of big transportation data.
Open Access
Alternative BNIP3 splicing in alveolar rhabdomyosarcomal cells
(2023-04) Fernando, Amy; Whyard, Steve (Biological Sciences); Ghavami, Saeid (Human Anatomy and Cell Science); Gordon, Joseph; Wilkins, Olivia
Several cellular phenotypes drive tumorigenesis in alveolar rhabdomyosarcoma. These phenotypes may be attenuated via treatment with non-steroidal antiinflammatory drugs, like aspirin, tolfenamic acid, and indomethacin, which interfere with intracellular prostaglandin synthesis and induce cell death. Recent data suggest that this mechanism may be mediated by differential splicing of the cell death gene BNIP3, such that full-length BNIP3 could promote cell death, while short BNIP3 could inhibit it. Additional data indicate that oncogenic cytokines from the TGF-β family may also be involved in this mechanism. This honours thesis examines whether indomethacin alters cell death, BNIP3 splicing, and other alveolar rhabdomyosarcoma phenotypes. To assess this, RT-PCR and fluorescent imaging assays were performed on the RH30 cell line. Results of these experiments indicate that a 2.0 μM concentration of indomethacin alters the cell death phenotype. However, they also provide preliminary evidence that the expression levels of full-length and short BNIP3 are unchanged. Accordingly, drug treatments did not change calcium signalling pathways. Furthermore, this text examined the role of TGF-β cytokines in this molecular pathway. To help establish the role of TGF-β in alveolar rhabdomyosarcoma, a statistical analysis of a previously generated secretome dataset was performed. It determined that the three TGF-β isoforms are differentially secreted in alveolar and embryonal rhabdomyosarcoma. However, qRT-PCR results indicate that indomethacin exposure does not change TGF- β1 expression. Collectively, this thesis provides preliminary evidence that indomethacin exposure induces cell death in RH30s independently of alternative BNIP3 splicing.
Open Access
Ammonia excretion in Caenorhabditis elegans: Physiological and molecular characterization of the rhr-2 knock-out mutant
(Comp Biochem Physiol A, 2016) Adlimoghaddam, Aida; O'Donnell, Michael J.; Kormish, Jay; Banh, Sheena; Treberg, Jason R.; Merz, David; Weihrauch, Dirk
Previous studies have shown the free living soil nematode Caenorhabditis elegans (N2 strain) to be ammonotelic. Ammonia excretion was suggested to take place partially via the hypodermis, involving the Na+/K+-ATPase (NKA), V-ATPase (VAT), carbonic anhydrase, NHX-3 and a functional microtubule network and at least one Rh-like ammonia transporter RHR-1. In the current study we show that a second Rh-protein, RHR-2, is highly expressed in the hypodermis, here also in the apical membrane of that tissue. To further characterize the role of RHR-2 in ammonia excretion, a knock-out mutant rhr-2(ok403), further referred to as Δrhr-2, was employed. Compared to wild-type worms (N2), this mutant showed a lower rate of ammonia excretion and a lower hypodermal H+ excretion rate. At the same time rhr-1, nka, vat, and nhx-3 showed higher mRNA expression levels when compared to N2. Also, in contrast to N2 worms, Δrhr-2 did not show enhanced ammonia excretion rates when exposed to a low pH environment, suggesting that RHR-2 represents the apical NH3 pathway that allows ammonia trapping via the hypodermis in N2 worms. A hypothetical model for the mechanism of hypodermal ammonia excretion is proposed on the basis of data in this and previous investigations.
Open Access
An Investigation of Knowledge Retention Using Two-Stage Exams in Undergraduate Biology
(2024-07-04) Judge, Abby
Although active learning is typically thought of as an in-class experience, this concept can be further applied to assessments as well. Two-stage exams allow for the unique experience of students working collaboratively during examinations, following the completion of the individual stage. Although two-stage exams have been shown to improve student learning gains, the effects of two-stage exams on retention of course content remains variable. I examined the effects of two-stage exams on knowledge retention at various Bloom’s level (Remember, Understand, and Apply) to determine whether two-stage exams promote knowledge retention at various levels of cognitive thinking. A two-stage in-class test followed by the re-testing of questions answered individually or in groups at subsequent time points (5, 48, and 85 days) allowed testing for knowledge retention. Our results indicate that group questions improve knowledge retention at relatively long time periods across all Bloom’s levels while also promoting retention at more complex Bloom’s levels at intermediate and relatively long time periods. Additionally, our analysis reveals that an average of 40% of individual only questions are forgotten by the final exam, while only an average of 19.5% of group questions are forgotten by the final exam. These results indicate that two-stage exams promote the ability to retain complex information at relatively long time periods.
Open Access
An OpenMP-based tool for finding longest common subsequence in bioinformatics
(2019-04-11) Shikder, Rayhan; Thulasiraman, Parimala; Irani, Pourang; Hu, Pingzhao
Abstract Objective Finding the longest common subsequence (LCS) among sequences is NP-hard. This is an important problem in bioinformatics for DNA sequence alignment and pattern discovery. In this research, we propose new CPU-based parallel implementations that can provide significant advantages in terms of execution times, monetary cost, and pervasiveness in finding LCS of DNA sequences in an environment where Graphics Processing Units are not available. For general purpose use, we also make the OpenMP-based tool publicly available to end users. Result In this study, we develop three novel parallel versions of the LCS algorithm on: (i) distributed memory machine using message passing interface (MPI); (ii) shared memory machine using OpenMP, and (iii) hybrid platform that utilizes both distributed and shared memory using MPI-OpenMP. The experimental results with both simulated and real DNA sequence data show that the shared memory OpenMP implementation provides at least two-times absolute speedup than the best sequential version of the algorithm and a relative speedup of almost 7. We provide a detailed comparison of the execution times among the implementations on different platforms with different versions of the algorithm. We also show that removing branch conditions negatively affects the performance of the CPU-based parallel algorithm on OpenMP platform.
Open Access
Analyses of Physcomitrella patens Ankyrin Repeat Proteins by Computational Approach
(2016-6-27) Mahmood, Niaz; Tamanna, Nahid
Ankyrin (ANK) repeat containing proteins are evolutionary conserved and have functions in crucial cellular processes like cell cycle regulation and signal transduction. In this study, through an entirely in silico approach using the first release of the moss genome annotation, we found that at least 54 ANK proteins are present in P. patens. Based on their differential domain composition, the identified ANK proteins were classified into nine subfamilies. Comparative analysis of the different subfamilies of ANK proteins revealed that P. patens contains almost all the known subgroups of ANK proteins found in the other angiosperm species except for the ones having the TPR domain. Phylogenetic analysis using full length protein sequences supported the subfamily classification where the members of the same subfamily almost always clustered together. Synonymous divergence (dS) and nonsynonymous divergence (dN) ratios showed positive selection for the ANK genes of P. patens which probably helped them to attain significant functional diversity during the course of evolution. Taken together, the data provided here can provide useful insights for future functional studies of the proteins from this superfamily as well as comparative studies of ANK proteins.
Open Access
Analysis of Cluster Interconnection Schemes in 802.15.4 Beacon Enabled Networks
(2008-1-1) Mišić, Jelena; Udayshankar, Ranjith
In this paper, we consider the interconnection of IEEE 802.15.4 beacon enabled network clusters. We discuss two types of interconnections. One type can be achieved by using the PAN coordinator node as the bridging device and the other type is achieved by using ordinary network nodes as bridge nodes. We discuss design and performance issues of both kinds of interconnections.
Open Access
Analysis of high resolution FTIR spectra from synchrotron sources using evolutionary algorithms
(Journal of Molecular Spectroscopy, 2015-04-17) van Wijngaarden, Jennifer; Desmond, Durell; Leo Meerts, W.
Room temperature Fourier transform infrared spectra of the four-membered heterocycle trimethylene sulfide were collected with a resolution of 0.00096cm−1 using synchrotron radiation from the Canadian Light Source from 500 to 560cm−1. The in-plane ring deformation mode (ν13) at ∼529cm−1 exhibits dense rotational structure due to the presence of ring inversion tunneling and leads to a doubling of all transitions. Preliminary analysis of the experimental spectrum was pursued via traditional methods involving assignment of quantum numbers to individual transitions in order to conduct least squares fitting to determine the spectroscopic parameters. Following this approach, the assignment of 2358 transitions led to the experimental determination of an effective Hamiltonian. This model describes transitions in the P and R branches to J′=60 and Ka′=10 that connect the tunneling split ground and vibrationally excited states of the ν13 band although a small number of low intensity features remained unassigned. The use of evolutionary algorithms (EA) for automated assignment was explored in tandem and yielded a set of spectroscopic constants that re-create this complex experimental spectrum to a similar degree. The EA routine was also applied to the previously well-understood ring puckering vibration of another four-membered ring, azetidine (Zaporozan et al., 2010). This test provided further evidence of the robust nature of the EA method when applied to spectra for which the underlying physics is well understood.
Open Access
Analysis of the Complex Quadrupole Hyperfine Patterns for Two Chlorine Nuclei in the Rotational Spectrum of 2,5-Dichlorothiophene
(The Journal of Physical Chemistry A, 2021-07-13) Daudet, Gabrielle; van Wijngaarden, Jennifer
The rotational spectrum of 2,5-dichlorothiophene (DCT) was measured for the first time using Fourier transform microwave spectroscopy from 5.5-19 GHz. Dense hyperfine splitting patterns due to the two quadrupolar chlorine nuclei (I=3/2) were resolved and assigned for the 35Cl-35Cl, 37Cl-35Cl and 37Cl-37Cl isotopologues as well as for the two 13C and one 34S analogs with two 35Cl atoms allowing derivation of their respective nuclear quadrupole coupling tensors. The rotational constants obtained from fitting the spectra of the six isotopic species allowed derivation of the experimental geometry of DCT for comparison with the equilibrium structure computed at the MP2/aug-cc-pVTZ level. This revealed that the electron withdrawing effect of chlorine causes small distortions to the ring geometry relative to thiophene including a 1.1o increase in the two S-C-C angles and a 0.012 Å increase to the two S-C bonds.
Open Access
Analysis of the Coriolis perturbed rovibrational spectrum of the CO asymmetric stretch and CC symmetric stretch of trimethylene oxide
(Journal of Molecular Spectroscopy, 2020-06-12) Mahassneh, Omar; van Wijngaarden, Jennifer
Rotationally-resolved vibrational spectra of trimethylene oxide (c-C3H6O) were recorded using synchrotron radiation from the Canadian Light Source between 400 and 1200 cm−1 with a resolution of 0.000959 cm−1. The dense spectra are composed of transitions arising from excitation of several fundamental vibrations as well as hotbands and combination bands involving the very low frequency ring puckering (ν18) vibration at ~53 cm−1. To date, 3452 transitions have been assigned corresponding to the CO asymmetric stretch (ν23) at ~1008 cm−1 and the CC symmetric stretch (ν6) at ~1033 cm−1 which are coupled via second order c-type Coriolis interaction. An additional perturbation from a lower energy state was observed and attributed to a first order b-type interaction with a state that is likely the combination of the CC asymmetric stretching (ν24) at ~937 cm−1 and ring puckering motions. An additional 916 transitions involving the CO stretching mode were assigned to two hotbands that originate in the first and second excited ring puckering states of trimethylene oxide. Accurate band centers for the ν6, ν23, ν23 + ν18, ν23 + 2ν18 and ν24 + ν18 vibrational states were determined and are compared with harmonic and anharmonic frequency estimates at the MP2 and DFT B3LYP levels using the 6-311++G(d,p) basis set. The analysis of additional features at lower frequency is in progress and will be reported in a subsequent article.