bluuebunny/crossref_metadata_2025 huggingface dataset:
Historical Film
Authors: Trafton John
Published: April 2016

From the advent of cinema to the present day, history has been brought to life on screen in many striking ways that have advanced motion picture technology and forged new relationships between viewers and the historical past. Historical films offer a privileged site for scholars of cinema, media, history, and many other disciplines to interrogate a nation’s relationship with the past. How cinema engages with the past, whether recent or distant, provides interesting case studies for how successive generations renegotiate cultural memory and understandings of how the past shapes the present. Historical films can bring into relief hidden or competing histories that either challenge or compliment prevailing narratives and authoritative accounts of the past, asking the viewer to consider the present as being shaped by multiple histories, rather than by one history. Historical films also suggest new ways of understanding the past, and, as a consequence, they also present new ways of understanding the present. Lastly, historical films can perform thought experiments about the past, deliberately departing from the historical print record in order to pose a different set of questions about a nation’s relationship with history. As such, historical films have garnered a tremendous level of scholarly interest, covering a broad range of research foci and subjects that are very useful in expanding discourses on national identity and historical memory. This article seeks to provide academics with ample resources and theoretical frameworks for conducting research on historical films or incorporating aspects of historical film studies into other disciplines. Starting with a general overview and scholarly approaches to historical films, the seminal works of Hayden White, Robert Rosenstone, and Vivian Sobchack are considered alongside newer approaches and scholarly journals, offering the scholar with an array of methodologies for bridging film studies to other fields. The article then examines in greater detail texts and studies concerned with a variety of questions and subissues pertaining to historical film studies—first with how film engages with memory (historical, cultural, personal, and national), then how historical films either interrogate or compound notions of national identity, and then how these ideas are explored in a variety of national and regional contexts. Next, the article turns toward the issues that stem from the scholarly approaches: how historical films can be used as a teaching tool, issues of genre and subgenre taxonomy, and how films themselves act as moments in history. Lastly, the article considers notions of authorship in historical cinema. Since many historical films are helmed by world-renowned filmmakers, the article ends with a section that explores repeated directorial engagements with history as a strong component of auteur cinema.
Roscoe Arbuckle
Authors: King Rob
Published: April 2016

Roscoe “Fatty” Arbuckle (b. 1887–d. 1933) was a comedian and filmmaker whose critical acclaim and popularity in the 1910s were entirely overshadowed by a career-destroying scandal in 1921. Following an early career as an illustrated song performer and several brief stints as a performer in Selig and Nestor film comedies, Arbuckle eventually found fame as “Fatty” after joining Mack Sennett’s legendary Keystone Film Company in 1913. Distinguished not only as an agile performer but also by his creative directing, Arbuckle achieved a level of autonomy unparalleled at Sennett’s studio, establishing his own East Coast unit of the company in Fort Lee, New Jersey, at the end of 1915. By this point, Arbuckle approached the critical stature of his former Keystone confrère Charles Chaplin as one of the few film comedians to be discussed seriously as a filmmaker, his work celebrated by commentators for its visual pictorialism. Arbuckle would go on to head his own studio, the Comique Film Corporation, in late 1916, where he wrote, directed, and starred in twenty two-reel comedies (which also mark the screen debuts of Buster Keaton). Four years later he graduated to features at Paramount, making him the first major male clown to star regularly in feature-length comedies. Yet these achievements would be swiftly annulled by the events of 5 September 1921, when the actress Virginia Rappe was discovered critically ill at a party at Arbuckle’s San Francisco hotel room, dying four days later. Allegations of violent rape saw Arbuckle tried three times for manslaughter, the first two trials ending in hung juries, the third in his acquittal; his career, however, could not be recuperated. In the wake of the Rappe scandal, Hollywood’s leaders moved quickly to form a new regulatory agency, the Motion Picture Producers and Distributors Association (MPPDA), whose first major decision was to ban Arbuckle from the screen. Nonetheless, with the support of his friends, Arbuckle was able to find consistent directorial work through the 1920s, initially uncredited but subsequently under the pseudonym William Goodrich (his father’s name). It was also under this pseudonym that Arbuckle directed two feature films, The Red Mill (1927, starring Marion Davies) and Special Delivery (1927, starring Eddie Cantor). He eventually returned to the screen in six Vitaphone two-reel talking comedies produced in 1932–1933, dying of a heart attack hours after he completed the last of these.
Douglas Sirk
Authors: Scheibel Will
Published: April 2016

The reputation of German director Douglas Sirk (b. 1897–d. 1987) rests on Hollywood films he made in the mid- to late 1950s that have since been canonized among the quintessential examples of film melodrama, both domestic (All That Heaven Allows, Written on the Wind, Imitation of Life) and romantic (Magnificent Obsession, The Tarnished Angels). While his most famous films were box-office hits at the time of their release, reviewers dismissed them for their sentimentality and heightened emotionalism, appeals to popular tastes, and implausible plots and emphasis on glossy spectacle that defied the privileged standards of social realism. Critics rediscovered Sirk’s films in the 1970s following the influence of Cahiers du Cinéma and the journal’s director-based approach to film appreciation during the postwar years, la politique des auteurs, and an academic interest in melodrama as a “progressive” genre that could expose and critique the ideology of the culture that produced it. As a result of this shift in taste politics and reading strategies, aided by the publication of Jon Halliday’s interview Sirk on Sirk in 1971, Sirk gained prominence as the auteur of melodrama par excellence, credited with subversively manipulating studio-assigned material through irony and parody, Brechtian distanciation, and modernist aesthetics of excess and self-reflexivity that could be found in the stylized artifice of his mise en scène. A legion of filmmakers, including Rainer Werner Fassbinder, Martin Scorsese, Pedro Almodóvar, and Todd Haynes, have cited Sirk’s films as a source of inspiration for their own screen practices of melodrama. Other films Sirk directed such as Summer Storm, A Scandal in Paris, All I Desire, There’s Always Tomorrow, and A Time to Love and a Time to Die have contributed to his association with Hollywood’s mid-century melodramas about doomed but passionate lovers and the ennui of bourgeois families, yet he also worked in action/adventures, suspense thrillers, musicals, and comedies. Further, he had a successful career in Germany under the name Detlef Sierck, first directing for the stage during the Weimar period and later for the film production company UFA (formerly Universum Film AG, now UFA GmbH), where he was responsible for turning Swedish singer Zarah Leander into a movie star. Sirk is best remembered for his collaborations with star Rock Hudson and producer Ross Hunter at Universal-International, which tend to dominate critical attention in the bibliographic entries that follow, practically dotting the routes of the historical developments in cinema studies as a contemporary discipline.
Reasonableness in International Law
Authors: Sartor Giovanni , Bongiovanni Giorgio , Valentini Chiara
Published: April 2016

The idea of reasonableness is pervasive in law. At the domestic, international, and transnational levels, this idea assists the law in responding to the many different aspects relevant to its operation in contemporary legal systems, which are characterized by a plurality of legal sources and claims of legal protection. The legal discourse resorts to reasonableness to characterize the expectations of the parties in a contractual relationship; the patterns of conduct to be assessed in order to ascribe criminal or civil liability; the exercise of institutional power; or the use of public resources by institutions. Moreover, reasonableness provides a legal standard for balancing different normative possibilities, measures, and arguments in relation to different circumstances. The law evaluates according to determinations of reasonableness beliefs and actions (i.e., epistemic and practical choices). When reasonableness is used as a legal standard, thoughts and actions violating it, namely, “unreasonable” thoughts and actions, are viewed as legally faulty. Unreasonable choices may be subject to annulment or revision, or they may be subject to requests for compensation by the parties negatively affected by them, or lead to further sanctions. On the contrary, reasonable private and public choices may successfully withstand legal challenges, and reasonable actions may be exempted from sanction even when they cause harm to others. We may say, in a first approximation, that a reasonable decision is a decision that meets to a sufficient extent the relevant standards, which may concern both the substance of the decision or the process through which it was achieved, and may concern both means-end efficiency and moral impartiality. Chiara Valentini gratefully acknowledges support by the “Ramón y Cajal” fellowship (RYC-2012-12175) and the Research Project “Global Constitutionalism and Global Justice: Philosophical Foundations” (DER2013- 48066-C2-1-R) both funded by the Spanish Ministerio de Economía y Competitividad.
Emancipation
Authors: Sorkin David
Published: April 2016

Since the early nineteenth century, “emancipation” has been the catch phrase used to designate the release of Jews from an inferior political status through the acquisition of equal rights. The term is inherently ambiguous: “Emancipation” conflates the status and its attainment, and it assumes a single goal and process of achievement. Many historians identify “equal rights” narrowly with national citizenship in the modern state, failing to account for the diversity of Jewish experiences across Europe. Jews gained equality through myriad processes, in such polities as the city-state, nation-state, or nationalities-state; they attained citizenship by residence (jus soli) or by descent (jus sanguinis). Equality included such statuses as corporate parity, juridical equality, recognition as the “subject” of a ruler or state, and local or municipal citizenship. Moreover, equality came in various forms and was often partial and nowhere irrevocable: it could be and was lost and regained. Emancipation involved virtually every aspect of Jewish life: occupations, education, religion, and communal solidarity. It had its enthusiastic proponents, who saw it as the messianic end of diasporic Jewish inferiority, and antagonists, who saw it as a threat to the existence of Judaism or Jews. While emancipation has been studied as a local, municipal, regional, national, and continent-wide development, there is no established consensus about so basic an issue as chronology. Some scholars who employ a narrow definition of equality date the process from the creation of modern citizenship during the French Revolution (1790–1791) (Dubnow) or write of a “long century” of emancipation extending from the American and French Revolutions to the Russian Revolution (Birnbaum and Katznelson 1995, cited under Anthologies). Others see an earlier inception with the Enlightenment debates about the Jews’ political status (circa 1770) (Katz 1973, cited under General Overviews), or the Peace of Westphalia’s promulgation of a toleration (1648) that eventually spilled over to the Jews (Baron 1960, cited under General Overviews). Some see the conclusion of the process around 1870 with the unifications of Germany and Italy and the restructuring of the Austro-Hungarian Empire (Katz 1973, cited under General Overviews); others date the end to the equality of Jews in Russia (April 1917), the minority rights treaties in the East Central European successor states, such as Poland and Czechoslovakia (1921–1925), and autonomy in Birobizhan (1934) and the new Soviet Constitution (1936) (Mahler 1941, cited under Document Collections). This entry surveys four centuries of emancipation (1550 to 1950). While many historians have equated emancipation with the modern Jewish experience itself, this article treats emancipation exclusively as a legal and political process.
Functional partitioning of local and distal gene expression regulation in multiple human tissues
Authors: Liu Xuanyao , Finucane Hilary K. , Gusev Alexander , Bhatia Gaurav , Gazal Steven , O’Connor Luke , Bulik-Sullivan Brendan , Wright Fred A. , Sullivan Patrick F. , Neale Benjamin M. , Price Alkes L.
Published: April 2016

Studies of the genetics of gene expression have served as a key tool for linking genetic variants to phenotypes. Large-scale eQTL mapping studies have identified a large number of local eQTLs, but the molecular mechanism of how genetic variants regulate expression is still unclear, particularly for distal eQTLs, which these studies are not well-powered to detect. In this study, we use a heritability partitioning approach to dissect the functional components of gene regulation. We make use of an existing method, stratified LD score regression, that leverages all variants (not just those that pass stringent significance thresholds) to partition heritability across functional categories, and we extend this method to partition local and distal gene expression heritability in 15 human tissues. The top enriched functional categories in local regulation of peripheral blood gene expression included super enhancers (5.18x), coding regions (3.73x), conserved regions (2.33x) and four histone marks (p<3x10-7for all enrichments); local enrichments were similar across the 15 tissues. We also observed substantial enrichments for distal regulation of peripheral blood gene expression: super enhancers (1.91x), coding regions (4.47x), conserved regions (4.51x) and two histone marks (p<3x10-7for all enrichments). Analyses of the genetic correlation of gene expression across tissues showed that local gene expression regulation is largely shared across tissues, but distal gene expression regulation is highly tissue-specific. Our results elucidate the functional components of the genetic architecture of local and distal gene expression regulation.
Evolutionary determinants of morphological polymorphism in colonial animals
Authors: Simpson Carl , Jackson Jeremy B.C. , Herrera-Cubilla Amalia
Published: April 2016

Colonial animals commonly exhibit morphologically polymorphic modular units that are phenotypically distinct and specialize in specific functional tasks. But how and why these polymorphic modules have evolved is poorly understood. Across colonial invertebrates there is wide variation in the degree of polymorphism from none in colonial ascidians, to extreme polymorphism in siphonophores such as the Portuguese Man of War. Bryozoa are a phylum of exclusively colonial invertebrates that uniquely exhibit almost the entire range of polymorphism from monomorphic species to others that rival siphonophores in their polymorphic complexity. Previous approaches to understanding the evolution of polymorphism have been based upon analyses of (1) the functional role of polymorphs or (2) presumed evolutionary costs and benefits based upon evolutionary theory that postulates polymorphism should only be evolutionarily sustainable in more “stable” environments because polymorphism commonly leads to the loss of feeding and sexual competence. Here we use bryozoans from opposite shores of the Isthmus of Panama to revisit the environmental hypothesis by comparison of faunas from distinct oceanographic provinces that differ greatly in environmental variability and we then examine the correlations between the extent of polymorphism in relation to patterns of ecological succession and variation in life histories. We find no support for the environmental hypothesis. Distributions of the incidence of polymorphism in the oceanographically unstable Eastern Pacific are indistinguishable from those in the more stable Caribbean. In contrast, the temporal position of species in a successional sequence is collinear with the degree of polymorphism because species with fewer types of polymorphs are competitively replaced by species with higher numbers of polymorphs on the same substrata. Competitively dominant species also exhibit patterns of growth that increase their competitive ability. The association between degrees of polymorphism and variations in life histories is fundamental to understanding of the macroevolution of polymorphism.
Expansion of the CRISPR toolbox in an animal with tRNA-flanked Cas9 and Cpf1 gRNAs
Authors: Port Fillip , Bullock Simon L
Published: April 2016

We present vectors for producing multiple CRISPR gRNAs from a single RNA polymerase II or III transcript inDrosophila. The system, which is based on liberation of gRNAs by processing of flanking t †RNAs, permits highly efficient multiplexing of Cas9-based mutagenesis. We also demonstrate that the †RNA-gRNA system markedly increases the efficacy of conditional gene disruption by Cas9 and can promote editing by the recently discovered RNA-guided endonuclease Cpf1.
Sensitive detection of rare disease-associated cell subsets via representation learning
Authors: Arvaniti Eirini , Claassen Manfred
Published: April 2016

Rare cell populations play a pivotal role in the initiation and progression of diseases like cancer. However, the identification of such subpopulations remains a difficult task. This work describes CellCnn, a representation learning approach to detect rare cell subsets associated with disease using high dimensional single cell measurements. Using CellCnn, we identify paracrine signaling and AIDS onset associated cell subsets in peripheral blood, and minimal residual disease associated populations in leukemia with frequencies as low as 0.005%.
Evaluating performance of metagenomic characterization algorithms usingin silicodatasets generated with FASTQSim
Authors: Shcherbina Anna , Ricke Darrell O. , Chiu Nelson
Published: April 2016

Background

In silicobacterial, viral, and human truth datasets were generated to evaluate available metagenomics algorithms. Sequenced datasets include background organisms, creating ambiguity in the true source organism for each read. Bacterial and viral datasets were created with even and staggered coverage to evaluate organism identification, read mapping, and gene identification capabilities of available algorithms. These truth datasets are provided as a resource for the development and refinement of metagenomic algorithms. Algorithm performance on these truth datasets can inform decision makers on strengths and weaknesses of available algorithms and how the results may be best leveraged for bacterial and viral organism identification and characterization.

Source organisms were selected to mirror communities described in the Human Microbiome Project as well as the emerging pathogens listed by the National Institute of Allergy and Infectious Diseases. The sixin silicodatasets were used to evaluate the performance of six leading metagenomics algorithms: MetaScope, Kraken, LMAT, MetaPhlAn, MetaCV, and MetaPhyler.

Results

Algorithms were evaluated on runtime, true positive organisms identified to the genus and species levels, false positive organisms identified to genus and species level, read mapping, relative abundance estimation, and gene calling. No algorithm out performed the others in all categories, and the algorithm or algorithms of choice strongly depends on analysis goals. MetaPhlAn excels for bacteria and LMAT for viruses. The algorithms were ranked by overall performance using a normalized weighted sum of the above metrics, and MetaScope emerged as the overall winner, followed by Kraken and LMAT.

Conclusions

Simulated FASTQ datasets with well-characterized truth data about microbial community composition reveal numerous insights about the relative strengths and weaknesses of the metagenomics algorithms evaluated. The simulated datasets are available to download from the Sequence Read Archive (SRP062063).
Looking for Energy in Population Data: How to Detect Self-Organization in Human Community Distribution
Authors: Casas-Busquet Josep M , Poch-Parés Agustí
Published: April 2016

In the present work we study the relationship between population allocation and the combined effects of urban size and energy consumption, for two given areas and through a major part of the twentieth century. Along these lines a general application model is laid down which relates city-growth rates to initial inhabitants and to exosomatic energy increment, the deviations from it showing order in space and time, as shown in a series of maps which hint at unaccounted socioeconomic factors. The study of the maps by means of spectral analysis allows finding patterns which reinforce over time, in such a manner that spatial frequencies can be determined whose weight increases up so granting surface evolution estimation.

Highlights

The regressions can be considered as a way to quantifying the population’s distribution

Slopes correlate well with commercial primary energy increments to a 0.9 coefficient

This result couples demography to energy and posits the emergence of self-order

Our model’s unexplained deviations show continuity in space

The topography of the maps has been typified through the methodology exposed herein
OncoPhase: Quantification of somatic mutation cellular prevalence using phase information
Authors: Chedom-Fotso Donatien , Ahmed Ahmed Ashour , Yau Christopher
Published: April 2016

The impact of evolutionary processes in cancer and its implications for drug response, biomarker validation and clinical outcome requires careful consideration of the evolving mutational landscape of the cancer. Genome sequencing allows us to identify mutations but the prevalence of those mutations in heterogeneous tumours must be inferred. We describe a method that we call OncoPhase to compute the prevalence of somatic point mutations from genome sequencing analysis of heterogeneous tumours that combines information from nearby phased germline variants. We show using simulations that the use of phased germline information can give improved prevalence estimates over the use of somatic variants only.
Control of Transposon-mediated Activation of theglpFKOperon ofEscherichia coliby two DNA binding Proteins
Authors: Zhang Zhongge , Saier Milton H.
Published: April 2016

Escherichia colicells deleted for the cyclic AMP (cAMP) receptor protein (Crp) gene (Δcrp) cannot utilize glycerol because cAMP-Crp is a required positive activator of glycerol utilization operonglpFK. We have previously shown that a transposon, Insertion Sequence 5 (IS5), can reversibly insert into the upstream regulatory region of the operon so as to activateglpFKand enable glycerol utilization. GlpR, which repressesglpFKtranscription, binds to theglpFKupstream region near the site of IS5insertion, and prevents insertion. We here show that the cAMP-Crp complex, which also binds to theglpFKupstream regulatory region, also inhibits IS5hopping into the activating site. This finding allowed us to identify conditions under which wild type cells can acquireglpFK-activating IS5insertions. Maximal rates of IS5insertion into the activating site require the presence of glycerol as well as a non-metabolizable sugar analogue that lowers cytoplasmic cAMP concentrations. Under these conditions, IS5insertional mutants accumulate and outcompete the wild type cells. Because of the widespread distribution of glucose analogues in nature, this mechanism of gene activation could have evolved by natural selection.
Automated population identification and sorting algorithms for high-dimensional single-cell data
Authors: Anchang Benedict , Plevritis Sylvia K.
Published: April 2016

Cell sorting or gating homogenous subpopulations from single-cell data enables cell-type specific characterization, such as cell-type genomic profiling as well as the study of tumor progression. This highlight summarizes recently developed automated gating algorithms that are optimized for both population identification and sorting homogeneous single cells in heterogeneous single-cell data. Data-driven gating strategies identify and/or sort homogeneous subpopulations from a heterogeneous population without relying on expert knowledge thereby removing human bias and variability. We further describe an optimized cell sorting strategy called CCAST based on Clustering, Classification and Sorting Trees which identifies the relevant gating markers, gating hierarchy and partitions that define underlying cell subpopulations. CCAST identifies more homogeneous subpopulations in several applications compared to prior sorting strategies and reveals simultaneous intracellular signaling across different lineage subtypes under different experimental conditions.
Analysis of Apoptosis and Necroptosis by Fluorescence-Activated Cell Sorting
Authors: Wallberg Fredrik , Tenev Tencho , Meier Pascal
Published: April 2016

Fluorescence-activated cell sorting (FACS) is a laser-based, biophysical technology that allows simultaneous multiparametric analysis. For the analysis of dying cells, fluorescently labeled Annexin V (Annexin VFITC) and propidium iodide (PI) are the most commonly used reagents. Instead of PI, 4′,6-diamidino-2-phenylindole (DAPI) can also be used. DAPI is a fluorescent stain that binds strongly to A-T-rich regions in DNA. DAPI and PI only inefficiently pass through an intact cell membrane and, therefore, preferentially stain dead cells. DAPI can be combined with Annexin VFITC and the potentiometric fluorescent dye, tetramethylrhodamine methyl ester (TMRM), which measures mitochondrial permeability transition and mitochondrial membrane depolarization. TMRM is a cell-permeable fluorescent dye that is sequestered to active mitochondria, and hence labels live cells. On apoptosis or necroptosis the TMRM signal is lost. The advantage of using Annexin VFITC/DAPI/TMRM is that the entire cell population is labeled, and it is easy to distinguish living (TMRM + /Annexin VFITC-/DAPI-) from dying or dead cells (apoptosis: TMRM-/Annexin VFITC + /DAPI-; necrosis: TMRM-/Annexin VFITC + /DAPI+). This is important because cell debris (fluorescent negative particles) must be avoided to establish the correct parameters for the FACS analysis, otherwise incorrect statistical values will be obtained. To obtain information on the cell concentration or absolute cell counts in a sample, it is recommended to add an internal microsphere counting standard to the flow cytrometric sample. This protocol describes the FACS analysis of cell death in HT1080 and L929 cells, but it can be readily adapted to other cell types of interest.
Synthetic Genetic Array Analysis
Authors: Kuzmin Elena , Costanzo Michael , Andrews Brenda , Boone Charles
Published: April 2016

Genetic interaction studies have been used to characterize unknown genes, assign membership in pathway and complex, and build a comprehensive functional map of a eukaryotic cell. Synthetic genetic array (SGA) methodology automates yeast genetic analysis and enables systematic mapping of genetic interactions. In its simplest form, SGA consists of a series of replica pinning steps that enable construction of haploid double mutants through automated mating and meiotic recombination. Using this method, a strain carrying a query mutation, such as a deletion allele of a nonessential gene or a conditional temperature-sensitive allele of an essential gene, can be crossed to an input array of yeast mutants, such as the complete set of approximately 5000 viable deletion mutants. The resulting output array of double mutants can be scored for genetic interactions based on estimates of cellular fitness derived from colony-size measurements. The SGA score method can be used to analyze large-scale data sets, whereas small-scale data sets can be analyzed using SGAtools, a simple web-based interface that includes all the necessary analysis steps for quantifying genetic interactions.
A Method for Genome Editing in Human Pluripotent Stem Cells
Authors: Smith Cory , Ye Zhaohui , Cheng Linzhao
Published: April 2016

Human pluripotent stem cells (PSCs) hold great potential for regenerative medicine and currently are being used as a research tool for basic discovery and disease modeling. To evaluate the role of a single genetic variant, a system of genome editing is needed to precisely mutate any desired DNA sequence in isolation and measure its effect on phenotype when compared to the isogenic parental PSC from which it was derived. This protocol describes the general targeting schemes used by researchers to edit PSCs to knock out, knock-in, or precisely alter a single nucleotide, covering conditions for electroporation, clonal isolation, and screening of edited PSCs for the targeted mutation. These recent advances simplify the procedure for genome editing, allowing individual researchers to induce nearly any desired mutation to further study its function or to reverse a disease-causing variant for future applications in regenerative medicine.
Transformation of Schizosaccharomyces pombe: Electroporation Procedure
Authors: Murray Johanne M. , Watson Adam T. , Carr Antony M.
Published: April 2016

Transformation of Schizosaccharomyces pombe with DNA requires the conditioning of cells to promote DNA uptake followed by cell growth under conditions that select and maintain the plasmid or integration event. The three main methodologies are electroporation, treatment with lithium cations, and transformation of protoplasts. This protocol describes transformation by electroporation. It involves pretreating S. pombe cells with dithiothreitol (DTT), which increases the transformation efficiency once the electric pulse is applied.
Transformation of Schizosaccharomyces pombe: Protoplast Procedure
Authors: Murray Johanne M. , Watson Adam T. , Carr Antony M.
Published: April 2016

Transformation of Schizosaccharomyces pombe with DNA requires the conditioning of cells to promote DNA uptake followed by cell growth under conditions that select and maintain the plasmid or integration event. The three main methodologies are electroporation, treatment with lithium cations, and transformation of protoplasts. The protocol for protoplast transformation, which is described here, is more complicated than those for electroporation or lithium acetate and thus less often used. However, for some strains, it remains the only reliable protocol.
Techniques to Distinguish Apoptosis from Necroptosis
Authors: Feoktistova Maria , Wallberg Fredrik , Tenev Tencho , Geserick Peter , Leverkus Martin , Meier Pascal
Published: April 2016

The processes by which cells die are as tightly regulated as those that govern cell growth and proliferation. Recent studies of the molecular pathways that regulate and execute cell death have uncovered a plethora of signaling cascades that lead to distinct modes of cell death, including “apoptosis,” “necrosis,” “autophagic cell death,” and “mitotic catastrophe.” Cells can readily switch from one form of death to another; therefore, it is vital to have the ability to monitor the form of death that cells are undergoing. A number of techniques are available that allow the detection of cell death and when combined with either knockdown approaches or inhibitors of specific signaling pathways, such as caspase or RIP kinase pathways, they allow the rapid dissection of divergent cell death pathways. However, techniques that reveal the end point of cell death cannot reconstruct the sequence of events that have led to death; therefore, they need to be complemented with methods that can distinguish all forms of cell death. Apoptotic cells frequently undergo secondary necrosis under in vitro culture conditions; therefore, novel methods relying on high-throughput time-lapse fluorescence video microscopy are necessary to provide temporal resolution to cell death events. Further, visualizing the assembly of multiprotein signaling hubs that can execute apoptosis or necroptosis helps to explore the underlying processes. Here we introduce a suite of techniques that reliably distinguish necrosis from apoptosis and secondary necrosis, and that enable investigation of signaling platforms capable of instructing apoptosis or necroptosis.
Genome Editing in Human Pluripotent Stem Cells
Authors: Smith Cory , Ye Zhaohui , Cheng Linzhao
Published: April 2016

Pluripotent stem cells (PSCs), defined by their capacity for self-renewal and differentiation into all cell types, are an integral tool for basic biological research and disease modeling. However, full use of PSCs for research and regenerative medicine requires the ability to precisely edit their DNA to correct disease-causing mutations and for functional analysis of genetic variations. Recent advances in DNA editing of human stem cells (including PSCs) have benefited from the use of designer nucleases capable of making double-strand breaks (DSBs) at specific sequences that stimulate endogenous DNA repair. The clustered, regularly interspaced short palindromic repeats (CRISPR)–Cas9 system has become the preferred designer nuclease for genome editing in human PSCs and other cell types. Here we describe the principles for designing a single guide RNA to uniquely target a gene of interest and describe strategies for disrupting, inserting, or replacing a specific DNA sequence in human PSCs. The improvements in efficiency and ease provided by these techniques allow individuals to precisely engineer PSCs in a way previously limited to large institutes and core facilities.
An exceptional 5:4 enantiomeric structure
Authors: Wachter Erin , Glazer Edith C. , Parkin Sean , Brock Carolyn Pratt
Published: April 2016

The only crystals that could be grown from racemic solutions of the PF6−salt of the resolvable cation [Ru(2,9-dimethyl-1,10-phenanthroline)2(dipyrido[3,2-d:2′,3′-f]quinoxaline)]2+have translational symmetry only (space groupP1), contain nine independent sets of ions, and include numerous independent solvent molecules (11 acetone, one diethyl ether and possibly several water molecules). Layers of hydrophobic cations alternate with layers containing most of the anions and solvent molecules. All nine cations have the same basic conformation, which is distorted by the presence of the methyl substituents on the two 1,10-phenanthroline ligands. Four pairs of enantiomeric cations within a layer are related by approximate inversion centers; the ninth cation, which shows no sign of disorder, makes the layer chiral. Within the cation layers stripes parallel to [110] of six cations alternate with stripes of three; the local symmetry and the cation orientations are different in the two stripes. These stripes are reflected in the organization of the anion/solvent layer. Theca80:20 inversion twinning found indicates that enantiomeric preference is transmitted less perfectly across the anion/solvent layer than within the cation layer. The structure is exceptional in having nine independent formula units and an unbalanced set (ratio 4:5) of resolvable enantiomers. The difficulty in growing crystals of this material is consistent with its structural complexity.
Geometry of trigonal boron coordination sphere in boronic acids derivatives – a bond-valence vector model approach
Authors: Czerwińska Karolina , Madura Izabela D. , Zachara Janusz
Published: April 2016

The systematic analysis of the geometry of three-coordinate boron in boronic acid derivatives with a common [CBO2] skeleton is presented. The study is based on the bond-valence vector (BVV) model [Zachara (2007).Inorg. Chem.46, 9760–9767], a simple tool for the identification and quantitative estimation of both steric and electronic factors causing deformations of the coordination sphere. The empirical bond-valence (BV) parameters in the exponential equation [Brown & Altermatt (1985).Acta Cryst.B41, 244–247]rijandb, for B—O and B—C bonds were determined using data deposited in the Cambridge Structural Database. The values obtained amount torBO= 1.364 Å,bBO= 0.37 Å,rBC= 1.569 Å,bBC= 0.28 Å, and they were further used in the calculation of BVV lengths. The values of the resultant BVV were less than 0.10 v.u. for 95% of the set comprising 897 [CBO2] fragments. Analysis of the distribution of BVV components allowed for the description of subtle in- and out-of plane deviations from the `ideal' (sp2) geometry of boron coordination sphere. The distortions specific for distinct groups of compounds such as boronic acids, cyclic and acyclic esters, benzoxaboroles and hemiesters were revealed. In cyclic esters the direction of strains was found to be controlled by the ring size effect. It was shown that thesynorantilocation of substituents on O atoms is decisive for the deformations direction for both acids and acyclic esters. The greatest strains were observed in the case of benzoxaboroles which showed the highest deviation from the zero value of the resultant BVV. The out-of-plane distortions, described by thevzcomponent of the resultant BVV, were ascertained to be useful in the identification of weak secondary interactions on the fourth coordination site of the boron centre.
Delivering a water treatment plant project using a collaborative project procurement approach
Authors: Walker Derek H.T. , Rahmani Farshid
Published: April 2016

Purpose

The purpose of this paper is to explore an interesting complex infrastructure construction case study project in which the initiation/design and delivery phases were managed differently, with diverse assumptions and workplace culture. It uses a recently developed collaboration and relationship-based procurement taxonomy to analyse the decision to commence a project and to deliver the project. The taxonomy tool reveals underlying assumptions and helps explain actions taken. The paper provides a window into the decision-making process. It also illustrates levels of innovation applied at the design and delivery phases.

Design/methodology/approach

A case study was undertaken, primarily using recorded and transcribed interviews, with five key senior participants in the project. This gathered a client, designer and contractor perspective that was subsequently analysed using a sense-making approach.

Findings

It is possible to start a project adopting a highly collaborative approach that maximises innovation, understanding complexity and developing a design that can then be delivered using a more traditional approach. The taxonomy used demonstrates that it is a useful visualisation tool for this purpose.

Research limitations/implications

The research was limited to the perspectives of only five individuals even though they were key decision-makers and had a robust overview of the project as a whole. The delivery phase was chosen as a matter of policy without the ability to break loose from that policy. The implications for beginning the initiation and design process in a highly collaborative hands-on mode influenced the understanding of all parties involved in the project in a positive direction. The case study was based in Australia, which has extensive experience of collaborative project delivery approaches.

Practical implications

The taxonomy and its ability to provide visualisation of the experienced collaboration presents a powerful tool in helping us understand how it may be useful and what limitations to collaboration exists.

Social implications

The paper illustrates the value of social interactions as alliance forms tend to consider triple bottom line issues and stakeholder engagement more highly than traditional, transnational approaches to project design and delivery.

Originality/value

The case study was unusual in its technical complexity; however, the main value of the paper is the application of the taxonomy and visualisation tool as a way to better understand how a project is being managed from a collaboration perspective.
Hybrid project delivery processes observed in constructor BIM innovation adoption
Authors: Gledson Barry J.
Published: April 2016

Purpose

Exploratory research was undertaken focusing upon an innovation adoption decision taken by a regional UK division of a large international contracting organisation implementing building information modelling (BIM) into their project delivery processes. The purpose of this paper was to gain new insights through observations of the process and analysis of the views of employees about organisational BIM adoption during the implementation stage of the innovation-decision process.

Design/methodology/approach

Case study research was performed focussing on initial BIM projects delivered by an early adopter organisation. Observations and semi-structured interviews were used as part of a data collection strategy, and an iterative research approach was adopted.

Findings

During implementation stages of BIM innovation adoption, organisations may have to make use of hybrid project delivery methods on initial adopter projects while also working concomitantly with existing systems, processes and personnel not yet ready to adapt to BIM methodology.

Originality/value

The work captures previously unseen phenomena of how such an organisation and its staff have adapted to BIM innovation adoption during a programme of organisational change. The identification of hybrid project delivery processes has generated further implications for practice and research into the effectiveness of construction production information management.
“Chasing a passion”: first-generation college graduates at work
Authors: Olson Joann S.
Published: April 2016

Purpose

– The purpose of this paper is to describe the college-to-work transition as experienced by first-generation college (FGC) graduates. First-generation graduates are often adjusting to workplaces that are significantly different from parents’ work environments.

Design/methodology/approach

– This phenomenological study explored the early-career learning experiences of six FGC graduates from the USA. All participants were working full-time and had graduated two to six years earlier.

Findings

– Three themes were identified: starting the job, being in the job, and releasing the past. Participants highlighted unanticipated aspects of their college-to-work transition, including dealing with workplace politics and family dynamics. They also described ambivalence between their current work and the desire to pursue a more compelling career or vocational passion.

Research limitations/implications

– All participants were white and from similar (rural) settings in one region of the USA. The qualitative nature of the study restricts generalization.

Practical implications

– This study suggests, given the distinction between first-generation students’ post-college work environments and that of their parents, that educators’ efforts to assist FGC students might appropriately extend to topics beyond graduation. FGC graduates should be alerted to the impact of shifts in social and cultural norms, and informed about changing family dynamics that may continue after leaving school.

Originality/value

– Previous research has highlighted the challenges facing FGC students. This is one of few studies that explores the experiences of FGC graduates in the workplace following graduation.
The rise and fall of the Australian DBA
Authors: Kortt Michael A. , Pervan Simon J , Hogan Owen
Published: April 2016

Purpose

– The purpose of this paper is to identify and discuss the drivers behind the rise and fall of the Australian Doctor of Business Administration (DBA) and to assess its future.

Design/methodology/approach

– Data covering the period 1993-2013 was sourced from the Commonwealth Department of Education and Training to provide a comprehensive analysis of the rise and fall of the Australian DBA.

Findings

– In Australia, the DBA was introduced in 1993. In the first 11 years of the programme, enrolments increased from only nine candidates in 1993 to 1,505 candidates in 2004. However, by 2013, the number of candidates had fallen to 869 candidates. The authors argue that the principal rationale for the dramatic fall in enrolments points to the challenges and issues of managing overseas candidates by second tier and regional universities rather than a decline in the market per se.

Practical implications

– The challenge for universities is to determine whether they can or are able to offer the DBA under a quality framework that requires academic rigour equal to the PhD.

Originality/value

– This paper presents – for the first time – the most comprehensive description of trends in the Australian DBA programme from its inception to the present day. It also offers valuable insights and cautionary lessons for other countries thinking of introducing or expanding their current DBA programmes.
IFRS and value relevance: evidence based on Canadian adoption
Authors: Okafor Oliver N. , Anderson Mark , Warsame Hussein
Published: April 2016

Purpose

– The purpose of this paper is to investigate whether financial information prepared and disclosed under International Financial Reporting Standards (IFRS) has incremental value relevance vs information prepared under generally accepted accounting principles (GAAP) in Canada.

Design/methodology/approach

– The authors employ a difference in differences methodology and estimate value relevance using: first, the adjusted R2 of regressions of stock price on book value and earnings; second, the adjusted R2 of regressions of stock returns on earnings and changes in earnings; and third, a time series incremental association return estimation. The authors use multiple models including a model similar to the Ohlson (1995) model and a modified Balachandran and Mohanram (2011) model to investigate value relevance in the period 2008-2013.

Findings

– The authors provide empirical evidence, based on unique Canadian environment, that accounting information prepared and disclosed under IFRS exhibits higher price and returns value relevance than accounting information prepared previously under local GAAP. Sensitivity analyses and yearly trends regressions produce collaborating evidence.

Originality/value

– The study provides early empirical evidence that value relevance increases in mandatory IFRS adoption, based on unique Canadian adoption. The Canadian adoption is unique because Canada: first, is the first G7 non-European country to adopt IFRS; second, had pursued a dual strategy of harmonizing with the US GAAP while supporting IFRS convergence; third, provided information environment that mitigates the problems associated with measuring the effects of IFRS adoption in the European countries where IFRS or its predecessor – international accounting standards – had permeated the reporting environment prior to the mandatory adoption in 2005; and fourth, allowed firms listed on the US exchanges to continue to use or adopt the US GAAP for financial reporting and thus, provided a group of benchmark firms drawn from the same social-political and economic environment as the treatment firms. The study clarifies prior inconsistent results from European samples.