New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

Cattle with Hair Whorl Patterns above the Eyes are More Behaviorally Agitated During Restraint

The article focuses on the temperament of cattle depending on the position of hair whorl. The article was published in the journal Applied Animal Behaviour Science.

Serpentine Cattle Chute Gives Handling Advantages

The article discusses the efficiency of a curved chute as opposed to a straight chute when leading cattle into a conveyor restrainer. The article was published in The National Provisioner in 1984.

Bos Indicus-Cross Feedlot Cattle with Excitable Temperaments have Tougher Meat and a Higher Incidence of Borderline Dark Cutters

The article was published in the journal Meat Science, Vol. 46, No.4. The focus is data collected for cattle temperament and the quality of meat produced.

Selected Articles from Beef Cattle Science Handbook Volume 19

The articles within the handbook are: "Livestock Psychology and Handling-Facility Design", "Design of Corrals, Squeeze Chutes, and Dip Vats", "Handling Feedlot Cattle", and "Reducing Transportation Stresses".

The Feasibility of Using Vocalization Scoring as an Indicator of Poor Welfare During Cattle Slaughter

The article discusses the vocalization of cattle in six slaughter plants and the results indicate that "vocalization scoring could be used as a simple method for detecting welfare problems that need to be corrected".

Welfare of Cattle during Slaughter and the Prevention of Nonambulatory (downer) cattle

The article focuses on keeping cattle calm and removing distractions that would scare cattle back from the chute.

Designing Meat Packing Plant Handling Facilities for Cattle and Hogs

The focus is on design, more specifically, "animal handling facilities which are labor saving and reduce bruise losses". The article studies: Unloading Chutes, Stockyard Design, Hog Plant Stockyard, General Purpose Small Stockyard, Beef Stockyard, Cattle Crowding Pens, Hog Crowding Pens, Slopes in Chutes and Crowding Pens, Single File Chutes General Recommendations, Single File Chutes for Cattle, Slaughter Restrainers,

Double Rail Restrainer for Handling Beef Cattle

The summary of the article reads "A new double rail conveyor restrainer for handling cattle at the slaughter plant is described. It has improved safety and ergonomics compared to the V restrainer conveyor it replaces. Cattle ride astride a moving conveyor. This design could also be adapted for veterinary work."

Pointers on Design and Operation of Cattle Restrainer Systems

The article discusses the importance of design and the people who run handling systems.

The Reluctance of Cattle to Change a Learned Choice May Confound Preference Tests

The conclusion of the article states "it appears that previously learned choices may affect future choices in Y-mazes for cattle. Another area that needs to be researched is the effects of a mildly aversive treatment versus a severely aversive treatment on the tendency of a bovine to resist changing a learned choice".

The Design and Construction of Facilities for Handling Cattle

The article focuses on the following: Cattle Perception, How to prevent Balking, Solid Fences, Flight Zone, Curved Race more Efficient, Curved Race and Crowd Pen Dimensions, Loading Ramps, Working Corral for a Large Ranch, Squeeze Chutes and Headgates, Calf Tables, Artificial Insemination Chute, New Restraint Ideas, Dipping Vats, Bruise and Injury Prevention, Washable Facilities.

Chart of bill of timber in bridges, culverts, cattle-guard and roadways, signed by S.D. Woodruff

Chart of bill of timber in bridges, culverts, cattle-guard and roadways, signed by S.D. Woodruff, Oct. 18, 1855.

Pay roll voucher from the Engineer Department of Port Dalhousie and Thorold Railway Extension for repairs to fences and cattle guards etc. in the months of April and May. This document is attached to a time sheet, May 11, 1857

Pay roll voucher from the Engineer Department of Port Dalhousie and Thorold Railway Extension for repairs to fences and cattle guards etc. in the months of April and May. This document is attached to a time sheet, May 11, 1857.

Universal history, from the creation of the world to the begining of the eighteenth century

UANL