Bio-inspired optimization & sampling technique for side-chain packing in MCCE

The prediction of proteins' conformation helps to understand their exhibited functions, allows for modeling and allows for the possible synthesis of the studied protein. Our research is focused on a sub-problem of protein folding known as side-chain packing. Its computational complexity has been proven to be NP-Hard. The motivation behind our study is to offer the scientific community a means to obtain faster conformation approximations for small to large proteins over currently available methods. As the size of proteins increases, current techniques become unusable due to the exponential nature of the problem. We investigated the capabilities of a hybrid genetic algorithm / simulated annealing technique to predict the low-energy conformational states of various sized proteins and to generate statistical distributions of the studied proteins' molecular ensemble for pKa predictions. Our algorithm produced errors to experimental results within .acceptable margins and offered considerable speed up depending on the protein and on the rotameric states' resolution used.

A Multi-Objective Genetic Algorithm with Side Effect Machines for Motif Discovery

Understanding the machinery of gene regulation to control gene expression has been one of the main focuses of bioinformaticians for years. We use a multi-objective genetic algorithm to evolve a specialized version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find, test different multi-objective scoring schemes and probabilistic models for the background sequence models and report our results on a synthetic dataset and some biological benchmarking suites. We conclude with a comparison of our algorithm with some widely used motif discovery algorithms in the literature and suggest future directions for research in this area.

SYNTHESIS OF CYCLIC AZOBENZENE ANALOGUES FOR INCORPORATION INTO OLIGONUCLEOTIDES, PEPTIDES AND POLYMERS

(A) In recent years, considerable amount of effort has contributed towards enhancing our understanding of the new photoswitch, cyclic azobenzene, particularly from the theoretical point of view. However, the challenging part with this system was poor efficiency of its synthesis from 2,2’- dinitrodibenzyl and lack of effective methods for further modification which would be useful to incorporate this system into biomolecules as a photoswitch. We report the synthesis of cyclic azobenzene and analogues from 2,2’-dinitrodibenzyl, which would allow for further incorporation of this cyclic azobenzene into biomolecules. Reaction of 2,2’-dinitrodibenzyl with zinc metal powder in the presence of triethylammonium formate buffer (pH-9.5) gave a cyclic azoxybenzene, 11,12-dihydrodibenzo[c,g][1,2]diazocine-5-oxide. The latter compound was converted into cyclic azobenzene analogues (bromo-, chloro-, cyano-, and carboxyl) through subsequent transformations. The carboxylic acid analogue was reacted with D-threoninol to give the corresponding amide, which readily undergoes photo-isomerization upon illumination with light. Upon illumination with light at 400 nm, approximately 70% of cis- isomer of amide was isomerized to trans- isomer. It was observed that cis- to trans- isomerization reached the maximum steady state of light transmission after approximately 40 min, whereas the trans- to cis- isomerization approximately acquired in 2 h to regain full recovery of light transmission. Cyclic azobenzene phosphoramidite was synthesized from DMT-protected D-threoninol linked cyclic azobenzene. (B) In recent years, there has been considerable interest invested towards the synthesis of azobenzene analogues for incorporation into proteins. Among the many azobenzene analogues, the synthesis of bi-functional cyclic azobenzene analogues for the incorporation into proteins is relatively new. In this thesis, we report the synthesis of a cyclic azobenzene biscarboxylic acid from 4-(bromomethyl)benzonitrile. (C) Azobenzene has been widely used in the field of polymer science to study the surface morphology and surface properties of polymers. In this thesis, we report the incorporation of cyclic azobenzene into a commercial polymer 2- (hydroxyethyl)methacrylate. Samples collected after 24 h from the reaction solution showed approximately 9% of incorporation of cyclic azobenzene into polymer compared to samples collected after 10 h, which showed approximately 6% incorporation.

Niagara River (Ontario) Remedial Action Plan fonds, 1984-1997, n.d.

The Niagara River Remedial Action Plan was part of an initiative to restore the integrity of the Great Lakes Basin ecosystem. In 1972, the Great Lakes Water Quality Agreement was signed by both Canada and the United States to demonstrate their commitment to protecting this valuable resource. An amendment in 1987 stipulated that Remedial Action Plans (RAPs) be implemented in 43 ecologically compromised areas known as Areas of Concern. The Niagara River was designated as one of these areas by federal and provincial governments and the International Joint Commission, an independent and binational organization that deals with issues concerning the use and quality of boundary waters between Canada and the United States. Although the affected area included parts of both the Canadian and American side of the river, Remedial Action Plans were developed separately in both Canada and the United States. The Niagara River (Ontario) RAP is a three-stage process requiring collaboration between numerous government agencies and the public. Environment Canada, the Ontario Ministry of the Environment, and the Niagara Peninsula Conservation Authority are the agencies guiding the development and implementation of the Niagara River (Ontario) RAP. The first stage is to determine the severity and causes of the environmental degradation that resulted in the location being designated an Area of Concern; the second stage is to identify and implement actions that will restore and protect the health of the ecosystem; and the third stage is to monitor the area to ensure that the ecosystem’s health has been restored. Stage one of the RAP commenced in January 1989 when a Public Advisory Committee (PAC) was established. This committee was comprised of concerned citizens and representatives from various community groups, associations, industries and municipalities. After several years of consultation, the Niagara River (Ontario) Remedial Action Plan Stage 2 Report was released in 1995. It contained 16 goals and 37 recommendations. Among them was the need for Canadians and Americans to work more collaboratively in order to successfully restore the water quality in the Niagara River. Stage three of the Niagara River (Ontario) RAP is currently ongoing, but it is estimated that it will be completed by 2015. At that point, the Niagara River Area of Concern will be delisted, although monitoring of the area will continue to ensure it remains healthy.

Draft News Release - Great Lakes Water Quality Agreement

A News Release draft to be sent to "100 newspapers, radio and television stations (virtually all those with offices within 20 miles of the Lakes), make them available to the Press Gallery, special interest groups, trade publication and Mayors etc. of Great Lake-side communities". The release discusses the need for an upgrade to "the 1972 Canada-U.S. Great Lakes Water Quality agreement". Within the document, O'Sullivan is quoted that the agreement "should be upgraded to become a treaty with the United States, so that after all the effort which has already been put into tyring to clean up the Great Lakes we the provision which provides for cancellation by either party giving twelve months (notice) to do so". The total report is 61 pages in length.

Photograph - Julia Cleveland Woodruff, Side angle Pose

Black and white photograph, mounted on board, 7 cm x 4 cm, of Julia in a side angle face pose. This photo was taken by Fred Pfaff of Peach Street, Erie, Pennsylvania.

Photograph - Margaret Julia Woodruff Band, Side Angle Lace Dress

Black and white photograph, 23 cm x 17 cm, of Margaret Julia Woodruff Band in a seated position, taken from a side angle. She is wearing a lace dress. The photo was taken by Dudley Hoyt of New York.

The Influence of the Media on Shaping Perceptions of Leadership in Sport: A Within and Between Groups Design

An experimental design that included both between-group and within-group designs was used to assess media influence on perceptions of sport leadership. Participants were recruited and randomly assigned to three groups, where each group completed two separate survey sessions regarding leader personality traits and behaviours. During the second survey session, experimental Groups 1 and 2 watched a video on a separate, respective sport leader prior to filling out the survey. There were a total of 104 participants (N = 104) for the first session, and 99 (N = 99) participants completed the second session. One-way ANOVA, factorial repeated measures ANOVA, and ANCOVA were used for data analysis. Results indicate a significant change in Group 2’s results after watching the video clip, thus rejecting the null hypotheses. Results and implications are discussed, highlighting their relationships to sport and media related theories and sport management practice.

American Falls from Canadian side, Niagara, U.S.A.

The description reads "(12) American Falls from the Canadian side, Niagara, U.S.A."

Whirlpool and River View from Canadian side, Niagara

The description of the image reads "(18) Looking over the 'Whirlpool' and down the River - from Canadian side - Niagara, U.S.A."

Horseshoe Falls, Canada Side

The description of the image reads "29 Horseshoe Fall - Canada Side".

(A) Photoregulation of DNA Functions by Cyclic Azobenzene-tethered Oligonucleotides (B) Site-specific Fluorescent Labeling of DNA using Inverse Electron Demand Diels-Alder Reaction between trans-Cyclooctene Derivatives and BODIPY-Tetrazine Adducts

(A) Most azobenzene-based photoswitches require UV light for photoisomerization, which limit their applications in biological systems due to possible photodamage. Cyclic azobenzene derivatives, on the other hand, can undergo cis-trans isomerization when exposed to visible light. A shortened synthetic scheme was developed for the preparation of a building block containing cyclic azobenzene and D-threoninol (cAB-Thr). trans-Cyclic azobenzene was found to thermally isomerize back to the cis-form in a temperature-dependent manner. cAB-Thr was transformed into the corresponding phosphoramidite and subsequently incorporated into oligonucleotides by solid phase synthesis. Melting temperature measurement suggested that incorporation of cis-cAB into oligonucleotides destabilizes DNA duplexes, these findings corroborate with circular dichroism measurement. Finally, Fluorescent Energy Resonance Transfer experiments indicated that trans-cAB can be accommodated in DNA duplexes. (B) Inverse Electron Demand Diels-Alder reactions (IEDDA) between trans-olefins and tetrazines provide a powerful alternative to existing ligation chemistries due to its fast reaction rate, bioorthogonality and mutual orthogonality with other click reactions. In this project, an attempt was pursued to synthesize trans-cyclooctene building blocks for oligonucleotide labeling by reacting with BODIPY-tetrazine. Rel-(1R-4E-pR)-cyclooct-4-enol and rel-(1R,8S,9S,4E)-Bicyclo[6.1.0]non-4-ene-9-ylmethanol were synthesized and then transformed into the corresponding propargyl ether. Subsequent Sonogashira reactions between these propargylated compounds with DMT-protected 5-iododeoxyuridine failed to give the desired products. Finally a methodology was pursued for the synthesis of BODIPY-tetrazine conjugates that will be used in future IEDDA reactions with trans-cyclooctene modified oligonucleotides.

Cross sections of excavation required to make a ditch on the earth side of the railroad near Port Dalhousie

Cross sections of excavation required to make a ditch on the earth side of the railroad near Port Dalhousie. This is a 12 page booklet of hand- drawn charts and diagrams which is slightly stained. Text is not affected, Mar. 1860.

Envelope with a laurel wreath containing the initials W.N. on the back side

Envelope with a laurel wreath containing the initials W.N. on the back side. The envelope has a 2 cent stamp on it, but it is not addressed, n.d.

Chart of station 2, crop sections of the old back ditch on the south side of the feeder, station 45, station 118 and the total length from the culvert to lot no. 5

Chart of station 2, crop sections of the old back ditch on the south side of the feeder, station 45, station 118 and the total length from the culvert to lot no. 5. This is signed by Fred Holmes, April 13, 1857.