Disease-Gene Association Using a Genetic Algorithm

Understanding the relationship between genetic diseases and the genes associated with them is an important problem regarding human health. The vast amount of data created from a large number of high-throughput experiments performed in the last few years has resulted in an unprecedented growth in computational methods to tackle the disease gene association problem. Nowadays, it is clear that a genetic disease is not a consequence of a defect in a single gene. Instead, the disease phenotype is a reflection of various genetic components interacting in a complex network. In fact, genetic diseases, like any other phenotype, occur as a result of various genes working in sync with each other in a single or several biological module(s). Using a genetic algorithm, our method tries to evolve communities containing the set of potential disease genes likely to be involved in a given genetic disease. Having a set of known disease genes, we first obtain a protein-protein interaction (PPI) network containing all the known disease genes. All the other genes inside the procured PPI network are then considered as candidate disease genes as they lie in the vicinity of the known disease genes in the network. Our method attempts to find communities of potential disease genes strongly working with one another and with the set of known disease genes. As a proof of concept, we tested our approach on 16 breast cancer genes and 15 Parkinson's Disease genes. We obtained comparable or better results than CIPHER, ENDEAVOUR and GPEC, three of the most reliable and frequently used disease-gene ranking frameworks.

A sequential analysis of therapist scaffolding and child concept formation in narrative therapy

Narrative therapy is a postmodern therapy that takes the position that people create self-narratives to make sense of their experiences. To date, narrative therapy has compiled virtually no quantitative and very little qualitative research, leaving gaps in almost all areas of process and outcome. White (2006a), one of the therapy's founders, has recently utilized Vygotsky's (1934/1987) theories of the zone of proximal development (ZPD) and concept formation to describe the process of change in narrative therapy with children. In collaboration with the child client, the narrative therapist formalizes therapeutic concepts and submits them to increasing levels of generalization to create a ZPD. This study sought to determine whether the child's development proceeds through the stages of concept formation over the course of a session, and whether therapists' utterances scaffold this movement. A sequential analysis was used due to its unique ability to measure dynamic processes in social interactions. Stages of concept formation and scaffolding were coded over time. A hierarchical log-linear analysis was performed on the sequential data to develop a model of therapist scaffolding and child concept development. This was intended to determine what patterns occur and whether the stated intent of narrative therapy matches its actual process. In accordance with narrative therapy theory, the log-linear analysis produced a final model with interactions between therapist and child utterances, and between both therapist and child utterances and time. Specifically, the child and youth participants in therapy tended to respond to therapist scaffolding at the corresponding level of concept formation. Both children and youth and therapists also tended to move away from earlier and toward later stages of White's scaffolding conversations map as the therapy session advanced. These findings provide support for White's contention that narrative therapists promote child development by scaffolding child concept formation in therapy.

Manuscript of James Cummings- August 28, 1860

Transcript (spelling and grammar retained): Chippawa [Chippewa] 28th August 1860 My Dear Sir I duly received your very kind letter of the 24th [June] asking me to communicate such facts of general interest connected with my career during the War with the United States. I have no objection to afford you such information as came under my own observation; nevertheless I do so, with the understanding, I have no desire to be my own trumpeter. With respect to your circular wherein you state you have been for several years collecting materials for a History of the late War between the United States & Great Britain, for which you are now gathering further materials to add to your collection, concerning the Second War for Independence. I am rather at a loss to know, what is meant by the second war; If you allude to the petty Rebellion, it could not be called a War, Those that caused the outbreak were very soon put down, by the Loyal people of the Province without the aid of Regular Troops being satisfied with the Independence they enjoyed. With respect to the several questions names in your circular: To the 1st I would say, this locality is made memorable by the battle of Chippawa [Chippewa] which took place about a mile above the village on the ground I pointed out to you, when I had the pleasure of seeing you a few days ago, with Mr Porter of the Niagara Falls, of which I believe you took sketches at the time. 2nd I have no historical documents of any value; so many years having gone past, the most of my old papers have either been lost or destroyed, I however came across two letters, one dated Queenston 9th July 1812 from Lt. Col. Nicholl Quarter Master General of Militia, the other from Lt. Col Myers Deputy Quarter Master General of the Regular Army date Fort George 23rd same month, directed to me in the hand writing of each of those officers as Deputy Quarter Master General of Militia, which letters I shall be obliged you would return at as early a day possible, as I wish to place them with tome others in the case, I have had made to hold the cocked hat & feather I wore during that eventful period, which I am sorry I did not exhibit when you was at my house; with reference to it I now enclose a letter from Lt. Col. Clark, residing at Port Dalhousie he was Captain & Adjutant of Militia in the War of 1812__ I send the letter in proof of the cock’d hat it is a lengthy one, but you may find time to turn over it, as I shall also place it in the hat case__ 3rd Where are [but] [for] traditionary [sic] witnesses residing in this vicinity – Col Clark above named Mr Merritt of St. Catharines, & Mr Kerby of Brantford are the only ones I now recollect, who could offord [sic] you any statistical information. 4th I have no pictorial sketches of any Military Movements or fortifications. As regards my own career, which you appear [ ? ] of knowing__ I was first a Lieutenant in a volunteer flank company stationed on the river side opposite [Navy] Island not far from the battle ground of Chippawa [Chippewa], I got promotion as Lieutenant of Cavalry before I got my Cavalry dress completed in three days more, I was called by General Brock to Fort George, was appointed Deputy Quarter Master General of Militia with the rank of Captain s the accompanying letters will show. I was at the battle of Stony Creek, several skirmishes at the Cross Roads, when the American army [ ? ] Fort George, at the taking of Col. Boerstler at the Beaver Dam, & had the honor of receiving Colonel Chapens sword at the surrender, who commanded a company of volunteer Horse Men was at the taking of 15 regulars & two officers at Fort Schlosser—was with Col. Bishop at the taking of Black Rock, near him when he fell, three men of the 8th Reg. more killed in the Boat I was in – I was at Chippawa battle, and the last, not the least in Lundy’s lane battle, which the Americans call the battle of Bridge [Waters]. I had forgot; there was another small affair at Corks Mill where I was. I could write a little history of events, but have not the time to do so. If what I have stated will be of any service for the purpose you require I shall feel happy. The history of the late War was published at Toronto in the Anglo American Magazine. Did you ever see it, I have the Books, there were however several errors which came under my notice, which I could have corrected. If my time would permit I could give you a more detailed statement of events. I trust however you may succeed with your publication , and I shall be most happy to hear from you at all times—I related many little occurances verbally to you when here, which I thought not necessary to repeat again as you would have a perfect recollection of them. Be pleased to return the letters for the purpose I require them. I am My Dear Sir Your respectful friend James Cummings

John Adams Smith letter, Jan. 14, 1813

Transcript: New York Jan. 14. 1813. My dear uncle, I had nearly concluded to have made my [jaunt?] earlier than I had mentioned in my last letter to you, for Swartout had intended to have written by me to Father & yourself; having [Louisa?] concluded not so soon to depart he sends me his letters which I forward in mail, I shall hope to have letters from home soon, it is a great pleasure to hear from any of you. I said last week in Hollands letter mentioning [bladeworth?] account, I have explained to him. It is a mistake about me agreeing to pay Mr. [Dening?] [their?] account. Caroline mentions to me your jaunt to [Sophia?], but I regret our friend there should be unpleasantly situated. I have not yet seen Col. Willett but will see him as mentioned. I have neglected to go there for some time which has been remiss in me. We have nothing new I believe unless it be that Armstrong & Jones of Philadelphia have been nominated as Secretarys of War & the Navy & [cer?] this in all probability may be appointed. There may be room for speculation, but perhaps it is not probable that Canada will be ceded to American Valor in the year 1813. There is a Bill before congress by which it may be made penal to enter on board American vessels, either British subjects or naturalized Americans, which it is presoomed by many will [spon?] the accommodation of Peace – may be yes may be no – the proof of the pudding is in the eating of it. I imagine pacification is not so near at hand although it is much to be desired. Whatever might be for the honor & prosperity of the Country I would strenuously advocate, aloof from partial & party considerations. We have not a word as yet what the Council at Albany may be thinking of as yet. I suppose these things will come in time, perhaps untimely to many. I desire for the present not to be found among the untimely. I am your sincerely, with love to all. John Adams Smith