The University of Kansas: Journals@KU
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Appropriate normalization is critical to improve reproducibility of tissue ChIP-seq
Full text linkChromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technology for studying genetic and epigenetic regulation. However, ChIP-seq data can be heavily affected by variations in chromatin amount and composition, ChIP enrichment, library preparation, and sequencing depth, affecting its overall reproducibility across biological replicates. Here, we evaluated four ChIP-seq normalization methods utilizing triplicate Foxa1 ChIP-seq data performed in prostate cancer tissues from three mice. We found that count-per-million (CPM) normalization, although not affecting peak calling in individual samples, is very useful for visualization and comparison of peak distribution and intensity across samples. By contrast, equal-read normalization improves both peak identification and intensity comparison. Moreover, spike-in normalization took advantage of spike-in chromatin ChIP to correct technical variations in ChIP-seq, including ChIP enrichment, sample preparation, and sequencing. Lastly, input-adjusted spike-in normalization further accounts for differences in input chromatin amount across samples, which is especially crucial for tissue ChIP-seq that often starts with different amounts of input chromatin. Overall, our study demonstrated that appropriate normalization is essential to improve the reproducibility and comparability of ChIP-seq experiments and highlighted the importance of input-adjusted spike-in normalization for tissue ChIP-seq.
Deconstructing the “Special Relationship”:: The Cultural Erosion of American Popular Support for Israel
No full textThis article attempts to explain the growing criticism of Israel among young Americans, most recently on display in the widespread demonstrations across American university campuses in response to the Israel-Hamas war, through the unlikely engagement with American studies. Employing scholarship from multiple fields, it sheds light on the eroding cultural foundations of the so-called “special relationship” between the U.S. and Israel by highlighting the evolving ways through which the once celebrated image of Israel has been deconstructed in American eyes and transformed into something far less sympathetic and more controversial. Rather than approach any specific facet or field the article casts a wider interdisciplinary net that connects the broad and diverse body of existing scholarship surveying the cultural representations of Israel across American film, television, literature, and popular culture in recent decades. By integrating various academic discourses, usually detached from one another, into a single cohesive narrative, the article reconceptualizes them as part of an overarching cultural process of deconstructing Israel’s romanticized image in the American public eye that has unfolded since the 1980s. In doing so, the article explains, at least to some extent, why many young Americans, especially those who came of age in recent decades, have become much more critical of Israel, at times hostile to it, than previous generations. The conclusion evaluates the potential impact the cultural deconstruction could have on the future of U.S.-Israel relations and considers ways in which it might inform foreign policymaking and possibly diminish American popular support for Israel
Educational Copying – the “Very Antithesis of Fair Dealing” or Within Copyright’s “Breathing Space”? Part 1: Statutory Provisions
Full text linkThis article is part of a three-part series that seeks an understanding of circumstances in which educational institutions may engage in educational copying (making unauthorized multiple copies of course readings for student use) in five common law countries: Australia, Canada, New Zealand, the United Kingdom, and the United States. Part 1 considers copyright’s purpose and justifications and then surveys the parameters of copyright law—including users’ rights (copyright exceptions or limitations)—and licensing arrangements as presented in the copyright statutes of the five countries
На пользу Советского Союза: собственные корреспонденты New York Times в Москве в годы Второй мировой войны
Full text linkThe New York Times was one of the first American newspapers to have its own foreign correspondent in Soviet Russia in the 1920s. From August 1921 to the mid-1930s, its first reporter in Moscow was Walter Duranty, who had a favorable view of the Soviet experiment and praised the development of the Soviet Union under Stalin. This admiration granted him exclusive access to high-ranking Soviet officials. After Duranty, two other reporters covered prewar Moscow for The New York Times: Harold Denny (1934-1939) and G.E.R. Gedye (1939-July 18, 1940).
This article explores previously unresearched aspects of the complex and often opaque interactions between American journalists and Soviet diplomats during World War II. A month after the start of the Winter War, Soviet authorities reintroduced strict press censorship, rendering the presence of American newspaper correspondents in Moscow largely ineffective. Foreign correspondents wererestricted to sending home English-translated prefabricated news authorized by Soviet censors. Consequently, by the fall of 1940, leading American newspapers had closed their Moscow bureaus. The remaining correspondents operated under heavy censorship, preventing them from fully reporting what they learned in the Soviet Union. This censorship coincided with the deterioration of Soviet-American relations in 1940 and the first half of 1941.The situation changed swiftly after Germany invaded the Soviet Union on June 22, 1941. As this article demonstrates, American diplomats and reporters were aware of the possibility of a German attack on the USSR in advance, though they could not confirm when or if it would occur. Alongside diplomatic and military support from the United States and Great Britain, the Anglo-American pressadopted a more favorable stance toward the Soviet Union. Leading newspapers covering international affairs returned, and The New York Times re-established its Moscow bureau in July 1941. In the private talks with the Soviet officials the represenatives of The New York Times sought to position itself as closely aligned with President Roosevelt. This status allowed it to maintain correspondents in the Soviet Union throughout the war. However, The New York Times failed to regain its prewar status as the premier source of exclusive news and semi-official rumors.In this regard, its correspondents in Turkey and Europe had significantly greater access to diplomatic and military sources than those in Moscow.The New York Times was one of the first American newspapers to have itsown foreign correspondent in Soviet Russia in the 1920s. From August 1921 to themid-1930s, its first reporter in Moscow was Walter Duranty, who had a favorableview of the Soviet experiment and praised the development of the Soviet Unionunder Stalin. This admiration granted him exclusive access to high-ranking Sovietofficials. After Duranty, two other reporters covered prewar Moscow for The NewYork Times: Harold Denny (1934-1939) and G.E.R. Gedye (1939-July 18, 1940).This article explores previously unresearched aspects of the complex andoften opaque interactions between American journalists and Soviet diplomatsduring World War II. A month after the start of the Winter War, Soviet authoritiesreintroduced strict press censorship, rendering the presence of American newspapercorrespondents in Moscow largely ineffective. Foreign correspondents wererestricted to sending home English-translated prefabricated news authorized bySoviet censors. Consequently, by the fall of 1940, leading American newspapershad closed their Moscow bureaus. The remaining correspondents operated underheavy censorship, preventing them from fully reporting what they learned inthe Soviet Union. This censorship coincided with the deterioration of Soviet-American relations in 1940 and the first half of 1941.The situation changed swiftly after Germany invaded the Soviet Union onJune 22, 1941. As this article demonstrates, American diplomats and reporterswere aware of the possibility of a German attack on the USSR in advance, thoughthey could not confirm when or if it would occur. Alongside diplomatic and militarysupport from the United States and Great Britain, the Anglo-American pressadopted a more favorable stance toward the Soviet Union. Leading newspaperscovering international affairs returned, and The New York Times re-establishedits Moscow bureau in July 1941. In the private talks with the Soviet officials therepresenatives of The New York Times sought to position itself as closely alignedwith President Roosevelt. This status allowed it to maintain correspondents in theSoviet Union throughout the war. However, The New York Times failed to regainits prewar status as the premier source of exclusive news and semi-official rumors.In this regard, its correspondents in Turkey and Europe had significantly greateraccess to diplomatic and military sources than those in Moscow
Cellular and Structural Analyses of Intervertebral Disc Degeneration in NFAT1 Deficient Mice
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