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Zhao B.,University of Illinois at Chicago | Duan V.,Illinois Mathematics and Science Academy | Yau S.S.-T.,Tsinghua University
Journal of Theoretical Biology | Year: 2011

A novel clustering method is proposed to classify genes or genomes. This method uses a natural representation of genomic data by binary indicator sequences of each nucleotide (adenine (A), cytosine (C), guanine (G), and thymine (T)). Afterwards, the discrete Fourier transform is applied to these indicator sequences to calculate spectra of the nucleotides. Mathematical moments are calculated for each of these spectra to create a multidimensional vector in a Euclidean space for each gene or genome sequence. Thus, each gene or genome sequence is realized as a geometric point in the Euclidean space. Finally, pairwise Euclidean distances between these points (i.e. genome sequences) are calculated to cluster the gene or genome sequences. This method is applied to three sets of data. The first is 34 strains of coronavirus genomic data, the second is 118 of the known strains of Human rhinovirus (HRV), and the third is 30 bacteria genomes. The distance matrices are computed based on the three sets, showing the distances from each point to the others. We used the complete linkage clustering algorithm to build phylogenetic trees to indicate how the distances among these sequence correspond to the evolutionary relationship among these sequences. This genome representation provides a powerful and efficient method to classify genomes and is much faster than the widely acknowledged multiple sequence alignment method. © 2011 Elsevier Ltd.


Mundle S.D.,Janssen Services LLC. | Mundle S.D.,Illinois Mathematics and Science Academy | Marathe A.S.,Rush University Medical Center | Chelladurai M.,Janssen Services LLC.
Critical Reviews in Oncology/Hematology | Year: 2013

A phenomenon of serum tumor biomarker surge or flare that ensues shortly after initiating cancer therapy and that may precede the actual therapeutic response-related decline is poorly understood and remains under-appreciated. However, it may have a significant clinical implication as it could be misinterpreted in clinical practice as therapeutic failure and lead to a premature discontinuation of potentially effective therapy. Therefore, in the present study, attempts have been made to understand the behavior of this phenomenon with respect to a reported median incidence, duration, and its relationship to clinical response. The results of these analyses suggest a significantly lower incidence of this phenomenon with carcinoembryonic antigen (CEA) as determined in colorectal cancer and prostate specific antigen (PSA) in prostate cancer as compared to the other biomarkers studied (p=0.006). Furthermore, regardless of the type of biomarker or the extent of its incidence, a therapy-related initial surge appears to correlate with eventual response to therapy. Although, the biologic significance of this phenomenon is currently elusive, two distinct hypothesis-generating cases with CEA and alpha-fetoprotein (AFP) are presented that, if supported by further research, would provide insights into the role of a biomarker surge in overall tumor growth control by cancer therapy. © 2012 Elsevier Ireland Ltd.


Wu J.,Fermi National Accelerator Laboratory | Shi Y.,Illinois Mathematics and Science Academy | Zhu D.,Illinois Mathematics and Science Academy
Journal of Instrumentation | Year: 2012

A low-power time-to-digital convertor (TDC) for an application inside a vacuum has been implemented based on the Wave Union TDC scheme in a low-cost field-programmable gate array (FPGA) device. Bench top tests have shown that a time measurement resolution better than 30 ps (standard deviation of time differences between two channels) is achieved. Special firmware design practices are taken to reduce power consumption. The measurements indicate that with 32 channels fitting in the FPGA device, the power consumption on the FPGA core voltage is approximately 9.3 mW/channel and the total power consumption including both core and I/O banks is less than 27 mW/channel. © 2012 IOP Publishing Ltd and SISSA.


Ramanathan M.,Argonne National Laboratory | Skudlarek G.,Argonne National Laboratory | Wang H.H.,Illinois Mathematics and Science Academy | Darling S.B.,Argonne National Laboratory
Nanotechnology | Year: 2010

Palladium has been extensively studied as a material for hydrogen sensors because of the simplicity of its reversible resistance change when exposed to hydrogen gas. Various palladium films and nanostructures have been used, and different responses have been observed with these diverse morphologies. In some cases, such as with nanowires, the resistance will decrease, whereas in others, such as with thick films, the resistance will increase. Each of these mechanisms has been explored for several palladium structures, but the crossover between them has not been systematically investigated. Here we report on a study aimed at deciphering the nanostructure-property relationships of ultrathin palladium films used as hydrogen gas sensors. The crossover in these films is observed at a thickness of ∼ 5nm. Ramifications for future sensor developments are discussed. © 2010 IOP Publishing Ltd.


Kalinich A.O.,Illinois Mathematics and Science Academy
Information Processing Letters | Year: 2012

Partially-ordered set games, also called poset games, are a class of two-player combinatorial games. The playing field consists of a set of elements, some of which are greater than other elements. Two players take turns removing an element and all elements greater than it, and whoever takes the last element wins. Examples of poset games include Nim and Chomp. We investigate the complexity of computing which player of a poset game has a winning strategy. We give an inductive procedure that modifies poset games to change the nim-value which informally captures the winning strategies in the game. For a generic poset game G, we describe an efficient method for constructing a game ¬G such that the first player has a winning strategy if and only if the second player has a winning strategy on G. This solves the long-standing problem of whether this construction can be done efficiently. This construction also allows us to reduce the class of Boolean formulas to poset games, establishing a lower bound on the complexity of poset games. © 2011 Elsevier B.V. All rights reserved.


Lee J.,Illinois Mathematics and Science Academy | Jayathilaka L.P.,University of Illinois at Chicago | Gupta S.,University of Illinois at Chicago | Huang J.-S.,University of Illinois at Chicago | Lee B.-S.,University of Illinois at Chicago
Journal of the American Society for Mass Spectrometry | Year: 2012

Stimulated by the interest in developing gold compounds for treating cancer, gold ion- angiotensin peptide interactions are investigated by mass spectrometry. Under the experimental conditions used, the majority of gold ion-angiotensin peptide complexes contain gold in the oxidation states I and III. Both ESI-MS and MALDI-TOF MS detect singly/multiply charged ions for mononuclear/multinuclear gold-attached peptides, which are represented as [peptide+a Au (I)+b Au(III)+(e - a -3b) H]e+, where a,b≤0 and e is charge. ESI-MS data shows singly/multiply charged ions of Au(I)-peptide and Au(III)-peptide complexes. This study reveals that MALDITOF MS mainly detects singly charged Au(I)-peptide complexes, presumably due to the ionization process. The electrons in the MALDI plume seem to efficiently reduce Au(III) to Au(I). MALDI also tends to enhance the higher polymeric forms of gold-peptide complexes regardless of the laser power used. Collision-induced dissociation experiments of the mononuclear and dinuclear gold-attached peptide ions for angiotensin peptides show that the gold ion (a soft acid) binding sites are in the vicinity of Cys (a soft ligand), His (a major anchor of peptide for metal ion chelation), and the basic residue Arg. Data also suggests that the abundance of gold-attached peptides increases with higher gold concentration until saturation, after which an increase in gold ion concentration leads to the aggregation and/or precipitation of gold-bound peptides. © American Society for Mass Spectrometry, 2012.


Getman R.B.,Northwestern University | Miller J.H.,Illinois Mathematics and Science Academy | Wang K.,Illinois Mathematics and Science Academy | Snurr R.Q.,Northwestern University
Journal of Physical Chemistry C | Year: 2011

Metal-organic frameworks (MOFs) are permanently porous solids, which are promising hydrogen storage materials. However, the maximum H2 adsorption energies in MOFs are only around 10 Kj·mol-1, leading to small adsorption capacities at ambient temperature. In this work we use ab initio calculations and grand canonical Monte Carlo (GCMC) simulations to explore metal alkoxide functionalization for improving H2 storage in IRMOF-1, IRMOF-10, IRMOF-16, UiO-68, and UMCM-150. We examine functionalization with lithium, magnesium, manganese, nickel, and copper alkoxides. We show that lithium and magnesium alkoxides physically bind H2 and manganese, nickel, and copper alkoxides chemically bind H2. H2 binding energies calculated with quantum mechanics are -10, -22, -20, -78, and -84 Kj·mol-1, respectively, for the first hydrogen molecule. Of these, lithium and manganese alkoxides bind H2 too weakly to enhance adsorption at ambient temperature, even at 100 bar. Owing to the strong binding energies, Ni and Cu exhibit high uptake at low pressure, but metal alkoxide sites saturate at pressures as low as 1 bar. They thus exhibit poor deliverable capacities [wt % (100 bar) - wt % (2 bar)]. Magnesium alkoxide exhibits low uptake at low pressure and high uptake at high pressure and is a promising functional group for enhanced ambient-temperature hydrogen storage in all MOFs studied. © 2010 American Chemical Society.


Acosta A.M.,Northwestern University | Dewald H.A.,Illinois Mathematics and Science Academy | Dewald J.P.A.,Northwestern University
Journal of Rehabilitation Research and Development | Year: 2011

Robotic systems currently used in upper-limb rehabilitation following stroke rely on some form of visual feedback as part of the intervention program. We evaluated the effect of a video game environment (air hockey) on reaching in stroke with various levels of arm support. We used the Arm Coordination Training 3D system to provide variable arm support and to control the hockey stick. We instructed seven subjects to reach to one of three targets covering the workspace of the impaired arm during the reaching task and to reach as far as possible while playing the video game. The results from this study showed that across subjects, support levels, and targets, the reaching distances achieved with the reaching task were greater than those covered with the video game. This held even after further restricting the mapped workspace of the arm to the area most affected by the flexion synergy (effectively forcing subjects to fight the synergy to reach the hockey puck). The results from this study highlight the importance of designing video games that include specific reaching targets in the workspace compromised by the expression of the flexion synergy. Such video games would also adapt the target location online as a subject's success rate increases.


Anjur S.S.,Illinois Mathematics and Science Academy
American Journal of Physiology - Advances in Physiology Education | Year: 2011

Student test score percentages in the Physiology and Disease (PAD) course at the Illinois Mathematics and Science Academy, a high school for students of the state of Illinois gifted in math and science, were studied over a period of 5 yr. Inquiry-based laboratory experiences in the course were slowly converted during this time from partly student centered and mostly teacher led to completely student centered beginning in fall 2008. Quarterly analysis of the effect of increased inquiry upon average weekly report submissions of 400 students over 4 yr showed a significant improvement in submission (P > 0.0002) between quarters 1 and 2 and also improvement from year to year between the academic years of 2006/2007 and 2009/2010 (P > 0.0001). A comparison of student test score percentages from 346 students in 4 major tests showed a significant increase (P > 0.0125) beginning in the academic year of 2008/2009, when the conversion of all laboratories in the course from partly student centered to completely student centered was concluded compared with scores over the 2 yr from 2006/2007 up to this point. There was also a significant difference (P > 00001) in test score percentages between the individual tests themselves over the 4 yr studied. Taking the study a step further, the 35 students registered in the two PAD classes offered in the fall 2010 semester were divided in each of their classes into student-centered and teacher-centered groups, with the former designing all their experiments and the latter following instructions from the teacher. Student score percentages on specific test questions from the four major tests that focused on transfer of student understanding were compared between these two groups. There was a significant improvement (P > 0.012) when students designed their own laboratories (student-centered group) compared with doing what the teacher asked (teacher-centered group). There was also a significant difference between these student score percentages among the individual tests (P > 0.0001). These data suggest that an increase in student-centered experiments may lead to a corresponding increase in test performance on questions involving student transfer. © 2011 The American Physiological Society.


Lee J.,Illinois Mathematics and Science Academy | Gupta S.,University of Illinois at Chicago | Huang J.-S.,University of Illinois at Chicago | Jayathilaka L.P.,University of Illinois at Chicago | Lee B.-S.,University of Illinois at Chicago
Analytical Biochemistry | Year: 2013

A strategy using reversed-phase high-performance liquid chromatography (HPLC), thin layer chromatography (TLC), mass spectrometry (MS), nuclear magnetic resonance (NMR), chemical synthesis, and MTT (3-(4,5-dimethylthiazol-2- yl)-2,5-diphenyltetrazolium bromide) cell viability assay to identify allicin as the active anticancer compound in aqueous garlic extract (AGE) is described. Changing the pH of AGE from 7.0 to 5.0 eliminated interfering molecules and enabled a clean HPLC separation of the constituents in AGE. MTT assay of the HPLC fractions identified an active fraction. Further analysis by TLC, MS, and NMR verified the active HPLC fraction as allicin. Chemically synthesized allicin was used to provide further confirmation. The results clearly identify the active compound in AGE as allicin. © 2013 Elsevier Inc. All rights reserved.

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