bluuebunny/crossref_metadata_2025 huggingface dataset:
Vengeance in Popular Culture
Authors: Robson Peter
Published: December 2016

Vengeance or revenge has been characterized in popular culture in a range of different ways. Within theories of criminology and social psychology, its relationship to retribution has been examined along with notions of deterrence and rehabilitation. Vengeance has been prevalent within a range of various belief systems as well as in myths, legends, and sacred texts. While vengeance seems to be a feature in all cultures, its acceptance as an appropriate response has been less than clear. It has been weighed alongside a preference for forgiveness, and tensions between these two options against harm have come to the fore in more recent times.

A distinction can usefully be made between vengeance undertaken by the state and the community on the one hand, which might be termed the revenge of the legal process and that exacted by the individual or family. The vengeance theme has been a major feature of Western culture in its expression in Greek literature and theater, through classical authors like Shakespeare and Racine to the present day. There is a link to popular literature as well as the more elusive world of popular theater and its occasional forays into the revenge theme.

The major expression of revenge within mass cultural forms, however, has been in film. Initially production codes prevented revenge being shown as having a successful outcome. Since the 1970s, however, a major modern version of portraying revenge that recurs within modern cinema throughout the world has been the vigilante film. This model of vengeance operates on the notion of an individual responding to the failings of the official system of securing proportionate or effective retribution. There are particular recurring features in these films including a disruptive random unlawful event, the law taking its course, a system malfunction, a trigger to revenge, and a coda stressing the efficacy of vengeance. Along with this is a significant subgroup within the cinema of personal revenge, the rape-revenge film. There has been extensive scholarship on this type of film and its rather different elements. A distinction can be made on the basis of the nature and perceived audience between this trope and the wider world of vengeance movies.

There has been relatively limited coverage of the revenge theme in television. The changes in the forms of media provide fresh opportunities for coverage of the vengeance theme in the 21st century. The contrast between the community approach of law and that of the individual seeker after revenge are formally different, but in the end they both involve elements of vengeance.
Indonesia’s Colonial Sugar Industry
Authors: Knight Roger
Published: December 2016

Colonial Indonesia’s sugar industry, developed under Dutch and Sino-Indonesian auspices over a period of almost three centuries, beginning c. 1650, evolved into one which exhibited a unique configuration in which an industrialized sugar complex became embedded within much larger “peasant” economy of the farming of rice and “second” crops. It was on this agrarian and largely self-financed basis that Indonesia’s colonial sugar industry, located exclusively in the island of Java, became one of the leading sectors of the international sugar economy of the late colonial era, eventually even rivaling Cuba—the nonpareil of such producers—as an exporter to world markets. During the interwar Depression of the 1930s and subsequent decade of war and revolution, it lost much (and eventually all) of its international standing—yet managed to survive into Indonesia’s postcolonial era, albeit in an attenuated form. There were four main phases to the industry’s colonial-era history. The first, foundational phase, which saw the establishment of modern industrialized manufacture extended from the 1830s through to the 1880s. The second phase, from the 1880s to 1930, was the period of sugar’s peak expansion. The third phase, beginning in 1931 and ending in 1942, was one of retrenchment and (partial) recovery prior to the spread of the Second World War into Southeast Asia. The fourth phase, 1945–1958, was one of postwar reconstruction.
Decolonization in French West Africa
Authors: Chafer Tony
Published: December 2016

Studies of French decolonization in West Africa have traditionally treated it as a planned and reasonably smooth process. It has therefore been portrayed as a successful decolonization that stands in stark contrast to the much more conflictual decolonization processes in Indochina (1947–1954) and Algeria (1954–1962), which were marked by prolonged wars. This approach has tended to give pride of place to the role of individuals—members of France’s governing elites and African political leaders—who are portrayed as having successfully managed the transition to independence. While the importance of such individuals cannot be denied, it is important to recognize that French decolonization in West Africa was a contingent process. Shaped by the particular nature of French colonial rule in the region, the new international context after 1945, events on the ground, and—on the French side—the perceived need to maintain empire at all costs in order to restore French grandeur after the humiliation of defeat and occupation in the Second World War, it was a process that involved a multiplicity of French and African actors who were not in control of the policy agenda but who were, on the contrary, operating in a highly constrained context and constantly being forced to react to rapidly unfolding events. De Gaulle finally decided to grant independence in 1959, and within a year all the territories of former French West Africa had gained their political independence. However, political independence did not mean French withdrawal and the end of French dominance. There were many continuities between the colonial and postcolonial periods, which have been analyzed in a burgeoning literature on French neocolonialism in sub-Saharan Africa. Decolonization should therefore be seen as a process that started well before French rule formally ended in 1960 and that is—arguably—still ongoing.
Tropical Africa in the Global Economy
Authors: Austen Ralph A.
Published: December 2016

Tropical Africa has been in communication with the global economy since at least the last centuries bce through either land travel across the Sahara to the Mediterranean or navigation along the Indian Ocean coast. Despite recent archaeological research, not too much is known about this earliest trade. Only after Islam was firmly established in North Africa and the Indian Ocean do we have evidence of significant trade (slaves, gold, and ivory) and cultural exchange across these frontiers. Entrepôt cities now flourished in both the West and Central Sudan and the Swahili coast, where either camel caravans or large dhow vessels received export goods from indigenous Muslim merchants. During the 15th century European navigators opened up the Atlantic coast of Africa as well as a direct water route to the Indian Ocean. For the next 500 years Europeans dominated Africa’s global connections, initially seeking gold, then slaves for New World plantations, and later large quantities of less costly commodities such as vegetable oils, cocoa, coffee, and cotton. Initially Africa’s trans-Saharan and Indian Ocean commerce continued to operate under the control of Muslim rulers and merchants and even grew in volume, although declining in global significance. By the early 20th century European powers had established colonial regimes in almost all of tropical Africa, providing new infrastructures of political administration and mechanized transport (mainly railroads) that overcame the geographical barriers impeding commerce between the coasts and the continent’s interiors. However, limited capital and the spatial orientation of colonial transport undermined the dynamism of such advances. In the last stages of colonialism (c. 1945–1960) and the first decades of political independence, greater investments were made in both infrastructure and industrialization but with poor results leading, from the 1980s, to the global imposition of “structural adjustment” policies upon African states. During the early 21st century African economies experienced “miraculous” growth linked to a major new relationship with China.
Slavery in the South African Interior During the 19th Century
Authors: Morton Fred
Published: December 2016

The South African interior, roughly equivalent to the Highveld on the southern continental plateau, was in the 19th century a stage of numerous players and groups, acting in concert and in conflict with one another, as often dissolving as taking on board new members. The fortunes of Highveld inhabitants, occupiers, and passers-by fluctuated without periods of calm, and turned advantages to few. It was therefore not uncommon for the human flotsam and jetsam created by raiding, battles, and migrations, aggravated by drought and famine, to be subordinated by the survivors and forced to serve those with whom they had no prior allegiance or knowledge. Slavery in the interior was largely a by-product of staking out territory. Rather than generate slaves for sale in an external market, slavery on the Highveld was fed by the political impulse to aggregate followers and servants. An internal exchange emerged in some areas, and traders made a few transactions with coastal exporters, but the general pattern of enslavement was acquisition by raiding and distribution among raiders. The majority taken were youngsters and, to a lesser degree, women. As a rule, the menfolk were killed.
The Land Question in South Africa: 1913 and Beyond
Authors: Walker Cherryl
Published: December 2016

Since 1913, the “land question” in South Africa has revolved around the major inequalities in access to and rights over land between the black majority and the white minority of the population, and how these disparities should best be understood and overcome. The roots of this inequality are commonly traced back to the promulgation of the Natives Land Act in June 1913, which provided the legal framework for the subsequent division of the country into a relatively prosperous white heartland and a cluster of increasingly impoverished black reserves on the periphery. Historians have cautioned against according this legislation undue weight within the much longer history of colonization, capitalist penetration, and agrarian change that has shaped modern South Africa. The spatial divide of white core and black periphery has, however, been central to the political economy of 20th-century South Africa. Beginning in the 1950s, the apartheid government attempted to maintain white hegemony, drive an urban–industrial economy, and deflect political resistance by turning these reserves into the ethnic “homelands” of African people. This involved increasingly repressive policies of urban influx control, population relocation, and the tribalization of local administration in the reserves.

Since the transition to democracy in 1994, the post-apartheid state has struggled to develop an effective land reform program that can address the crosscutting demands for land redistribution, local development, and representative government that this history has bequeathed. For many analysts, these ongoing challenges mean that “the land question” remains unresolved; for others it means that the question is itself in need of reformulation. In order to review these developments, a three-part periodization is used to organize the discussion: (1) the segregation era (1910–1948), (2) the apartheid era (1948–1990), and (3) the transition to democracy and the post-apartheid era that began in 1990.
The New Deal
Authors: Wall Wendy L.
Published: December 2016

The New Deal generally refers to a set of domestic policies implemented by the administration of Franklin Delano Roosevelt in response to the crisis of the Great Depression. Propelled by that economic cataclysm, Roosevelt and his New Dealers pushed through legislation that regulated the banking and securities industries, provided relief for the unemployed, aided farmers, electrified rural areas, promoted conservation, built national infrastructure, regulated wages and hours, and bolstered the power of unions. The Tennessee Valley Authority prevented floods and brought electricity and economic progress to seven states in one of the most impoverished parts of the nation. The Works Progress Administration offered jobs to millions of unemployed Americans and launched an unprecedented federal venture into the arena of culture. By providing social insurance to the elderly and unemployed, the Social Security Act laid the foundation for the U.S. welfare state.

The benefits of the New Deal were not equitably distributed. Many New Deal programs—farm subsidies, work relief projects, social insurance, and labor protection programs—discriminated against racial minorities and women, while profiting white men disproportionately. Nevertheless, women achieved symbolic breakthroughs, and African Americans benefited more from Roosevelt’s policies than they had from any past administration since Abraham Lincoln’s. The New Deal did not end the Depression—only World War II did that—but it did spur economic recovery. It also helped to make American capitalism less volatile by extending federal regulation into new areas of the economy.

Although the New Deal most often refers to policies and programs put in place between 1933 and 1938, some scholars have used the term more expansively to encompass later domestic legislation or U.S. actions abroad that seemed animated by the same values and impulses—above all, a desire to make individuals more secure and a belief in institutional solutions to long-standing problems. In order to pass his legislative agenda, Roosevelt drew many Catholic and Jewish immigrants, industrial workers, and African Americans into the Democratic Party. Together with white Southerners, these groups formed what became known as the “New Deal coalition.” This unlikely political alliance endured long after Roosevelt’s death, supporting the Democratic Party and a “liberal” agenda for nearly half a century. When the coalition finally cracked in 1980, historians looked back on this extended epoch as reflecting a “New Deal order.”
Erotic Representations of the Divine
Authors: Greenberg Yudit Kornberg
Published: December 2016

Erotic representations of the divine occupy a pivotal place in religious myths, poetry, liturgy, and theology. Reading eros as a category of religious love highlights its ubiquitous presence in sacred literary sources; moreover, it renders the nexus of erotic love and the divine critical to comprehending religiosity as an immanent and embodied phenomenon, rather than as an abstract idea. As an embodied phenomenon, religious love is subject to an investigation of topics such as gender and sexuality, and its multiple cultural meanings and contexts. Western philosophers such as Plato, Aristotle, (Pseudo-)Dionysius, and the Neoplatonist renaissance thinker Leone Ebreo, delineate a hierarchy or a “ladder of love” differentiating lesser and higher subjects and objects of love from love of the particular, to the universal, cosmic, and divine. An interrelated distinction is ascertained between “desire” as a state of lack often seen as a lower state, and “love” as the higher state, in which fulfillment and joy of the union with the object of one’s love is achieved. Love and desire as marked yet interrelated emotions are contextualized in religious phenomena cross-culturally, most obviously in theistic frameworks in which a personal and intimate relationship with the divine is an ideal. Poetry and autobiography are the most common genre of depicting the intimate and passionate encounter of human and divine. Despite the prominence of male voices in the sources, the contributions of medieval Christian and Muslim women mystics to this literature are significant. Key base-texts from which mystics and philosophers are inspired and draw upon to elucidate their own personal experience of yearning for the divine, include the biblical Song of Songs, Bhagavata Purana (Book 10), and the Gitagovinda. Although the yearning for the divine, associated with an emotional, embodied state and therefore seen as problematic from a rational perspective, this yearning is also a cherished state, even for rationalists such as the medieval Jewish thinker Moses Maimonides. The significance of erotic love for the divine is confirmed, not only by Sufi and Hindu bhakti poets such as Rumi and Jayadeva, but also by philosophers such as Ibn Arabi and Rupa-Goswami. The idiom of erotic desire and love for God is particularly poignant and integral not only in poetry but also in theology, as exemplified in Hindu bhakti and Christian theology. Exploring the meanings of erotic love in religious poetry, theology, liturgy, and the history of religion more broadly offers a rich scholarly and personal medium for contemplating the reality of human and divine nature.
Martin Luther’s Sacramental Theology
Authors: Jensen Gordon A.
Published: December 2016

Martin Luther’s emphasis on the sacraments as a visible, tactile means by which the justifying action of God is conveyed to the believer brings the pastoral heart of the Reformation into clear focus. As Luther continued to explore how justification, the “first and chief article” (Smalcald Articles 2 in BC 301), was the measuring stick by which all theology is evaluated, he was forced to define and clarify his understanding of the sacraments as a “more than verbal” (Robert W. Jenson, Visible Words: The Interpretation and Practice of Christian Sacraments [Philadelphia: Fortress, 1978], 5) word that proclaims the promises of God and makes those promises a reality. Using this and other, correlated criteria, Luther justifies the reduction in the number of sacraments found in the Roman Catholic Church of his time. The sacramental controversies that arose in the 1520s also force him to shape and clarify the interconnected nature of the sacramental elements, the word, and faith. By 1530, Luther’s sacramental theology had matured and could be defined by the “sacramental unity” between the word, faith, and earthly elements. This sacramental union also provided the foundational basis for his insistence on the efficacy of the sacraments, since this union was intimately connected to God’s promise of the gospel, proclaimed and enacted.
Multilingualism in Rural Africa
Authors: Di Carlo Pierpaolo , Good Jeff , Ojong Diba Rachel
Published: December 2016

The pervasiveness of multilingualism throughout the African continent has led it to be viewed as Africa’s “lingua franca.” Nevertheless, sociolinguistic research on this topic has concentrated mostly on urbanized areas, even though the majority of Africans still live in rural regions, and rural multilingualism is clearly of much older provenance than its urban counterpart. In urban domains, individual language repertoires are dominated by the interplay between European ex-colonial languages, African lingua francas, and local languages, and language ideologies emphasize the ordering of languages in a hierarchy that is tied to social status. The situation in rural areas is clearly distinct, though it has yet to be thoroughly investigated.

Early work on language use in rural Africa tended to background the presence of multilingualism and was dominated by an approach that viewed each community (or “tribe”) as having its own language. Thanks to the progressive adoption of ethnographic methods of inquiry, facilitated by language documentation research especially since the beginning of the 21st century, it has been possible to more effectively study areas of high linguistic diversity in West and Central Africa which demonstrate that multilingualism plays an integral role in structuring social relations. Available case studies document the presence of individuals with linguistic repertoires that are primarily oriented around local languages, ideologies, and practices and that do not clearly fit with what is known from urban environments. The most important theme that emerges from this work is the extent to which rural multilingualism is linked to the specific dynamics holding among communities that are near to each other rather than being a reflection of a more general, externally imposed value system.

While this result makes it difficult to characterize rural multilingualism as a single, coherent phenomenon, it does point to the utility of a shared toolkit of research strategies for exploring it in more detail. In particular, ethnographic methods are required in order to ascertain the major local social divisions which language choice both reflects and constructs in these areas, and it is additionally important to focus on how individual repertoires are tied to specific life histories rather than to assume that groupings that are salient to the outside researcher (e.g., “villages” or “compounds”) are the relevant units of analysis.

Finally, investigation of multilingualism in rural Africa is not only valuable for what it reveals about social dynamics on the continent, but it also seems likely to yield important insights for the study of sociolinguistics more broadly.
Number in Language
Authors: Acquaviva Paolo
Published: December 2016

Number is the category through which languages express information about the individuality, numerosity, and part structure of what we speak about. As a linguistic category it has a morphological, a morphosyntactic, and a semantic dimension, which are variously interrelated across language systems. Number marking can apply to a more or less restricted part of the lexicon of a language, being most likely on personal pronouns and human/animate nouns, and least on inanimate nouns. In the core contrast, number allows languages to refer to ‘many’ through the description of ‘one’; the sets referred to consist of tokens of the same type, but also of similar types, or of elements pragmatically associated with one named individual. In other cases, number opposes a reading of ‘one’ to a reading as ‘not one,’ which includes masses; when the ‘one’ reading is morphologically derived from the ‘not one,’ it is called a singulative. It is rare for a language to have no linguistic number at all, since a ‘one–many’ opposition is typically implied at least in pronouns, where the category of person discriminates the speaker as ‘one.’ Beyond pronouns, number is typically a property of nouns and/or determiners, although it can appear on other word classes by agreement. Verbs can also express part-structural properties of events, but this ‘verbal number’ is not isomorphic to nominal number marking. Many languages allow a variable proportion of their nominals to appear in a ‘general’ form, which expresses no number information. The main values of number-marked elements are singular and plural; dual and a much rarer trial also exist. Many languages also distinguish forms interpreted as paucals or as greater plurals, respectively, for small and usually cohesive groups and for generically large ones. A broad range of exponence patterns can express these contrasts, depending on the morphological profile of a language, from word inflections to freestanding or clitic forms; certain choices of classifiers also express readings that can be described as ‘plural,’ at least in certain interpretations. Classifiers can co-occur with other plurality markers, but not when these are obligatory as expressions of an inflectional paradigm, although this is debated, partly because the notion of classifier itself subsumes distinct phenomena. Many languages, especially those with classifiers, encode number not as an inflectional category, but through word-formation operations that express readings associated with plurality, including large size. Current research on number concerns all its morphological, morphosyntactic, and semantic dimensions, in particular the interrelations of them as part of the study of natural language typology and of the formal analysis of nominal phrases. The grammatical and semantic function of number and plurality are particularly prominent in formal semantics and in syntactic theory.
Extreme Natural Hazards, Disaster Epidemiology, and Public Health Implications
Authors: Noji Eric K. , Khan Anas A. , Al-Aseri Zohair
Published: December 2016

The fields of disaster medicine and public health preparedness have developed considerably with the natural hazards and humanitarian disasters over the past half-century. Developing countries, particularly Small Island Developing States and Least Developed Countries, are disproportionately affected. In April and May 2015, two massive earthquakes in Nepal killed more than 8,400 people, injured 20,000, and reduced 300,000 houses to rubble. In March 2016, Cyclone Pam destroyed homes, schools, infrastructure, and livelihoods on the Pacific island of Vanuatu, affecting half the population, including 82,000 children. Most recently, Hurricane Matthew, a Category 4 tropical storm struck parts of Haiti violently on 4 October 2016 causing the largest humanitarian emergency since the 2010 earthquake. The Directorate of Civil Protection of Haiti has so far confirmed over 500 deaths, 339 injuries, and 75 people missing. The number of evacuees is 175,509 people scattered in 224 temporary shelters. Among the approximate 2.1 million people affected, UNICEF estimates that 894,057 are children. Nearly 1,410,774 people need humanitarian assistance, including 592,581 children. All three nations will take years to recover. However, the catastrophic Great East Japan earthquake and tsunami on March 11, 2011, and Hurricane Sandy, whose storm surge hit New York City on October 29, 2012, flooding streets, tunnels, and subway lines, and cutting power in every borough of the city sent clear messages that developed countries are also vulnerable to such severe disasters. To cite “Superstorm Sandy” again, the New York Stock Exchange was closed on October 29 and 30, 2012 as a result of power outages and flooding in the Wall Street area. Such a closure for weather-related reasons had not happened since 1888!

Unsustainable development practices, ecosystem degradation, and poverty, as well as climate variability and extremes have led to an increase in both natural and man-made disaster risk at a rate that poses a threat to lives and development efforts. Fortunately, over the past decade, the public health approach to disasters has changed significantly. Terms such as prevention, mitigation, preparedness, recovery, and resilience are now part of the vocabulary of public health officials in national and international organizations, and more importantly, they are used to advance the cause of reducing mortality and morbidity from disasters. We now know much about the cause and nature of disasters and about populations at risk, and that knowledge allows us to anticipate some of the effects a disaster may have on the health of an affected community. This expanding body of epidemiological research has provided a basis for increasingly effective prevention and intervention strategies.
SED-ML web tools: generate, modify and export standard-compliant simulation studies
Authors: Bergmann Frank T , Nickerson David , Waltemath Dagmar , Scharm Martin
Published: December 2016

The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions.

Availability and Implementation

http://sysbioapps.dyndns.org/SED-ML_Web_Tools/.
Primerize-2D: automated primer design for RNA multidimensional chemical mapping
Authors: Tian Siqi , Das Rhiju
Published: December 2016

Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications.

Availability and Implementation

http://primerize2d.stanford.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array
Authors: Gross Jeffrey A. , Lefebvre François , Lutz Pierre-Eric , Bacot François , Vincent Daniel , Bourque Guillaume , Turecki Gustavo
Published: December 2016

Investigating 5-methylcytosine (5mC) has led to many hypotheses regarding molecular mechanism underlying human diseases and disorders. Many of these studies, however, utilize bisulfite conversion alone, which cannot distinguish 5mC from its recently discovered oxidative product, 5-hydroxymethylcytosine (5hmC). Furthermore, previous array-based technologies do not have the necessary probes to adequately investigate both modifications simultaneously. In this manuscript, we used technical replicates of DNA from human brain, human blood, and human saliva, in combination with oxidative bisulfite conversion and Illumina’s Infinium MethylationEPIC array, to analyze 5mC and 5hmC at more than 650 000 and 450 000 relevant loci, respectively, in the human genome. We show the presence of loci with detectable 5mC and 5hmC to be equally distributed across chromosomes and genomic features, while also being present in genomic regions with transcriptional regulatory properties. We also describe 2528 5hmC sites common across tissue types that show a strong association with immune-related functions. Lastly, in human brain, we show that 5hmC accounts for one-third of the total signal from bisulfite-converted data. As such, not only do our results confirm the efficacy and sensitivity of pairing oxidative bisulfite conversion and the EPIC array to detect 5mC and 5hmC in all three tissue types, but they also highlight the importance of dissociating 5hmC from 5mC in future studies related to cytosine modifications.
Going Off Road
Authors: Anciano Carlos , Brown Craig , Bowling Mark
Published: December 2016

The ability to reach the peripheral pulmonary nodule/mass with bronchoscopy has improved greatly over the past several years with the use of Electromagnetic navigational bronchoscopy; however, many of these lesions are unable to be adequately sampled due to their location outside the bronchial airways. We report the first use of the transbronchial access tool that creates a pathway from the bronchial airway through the lung parenchyma into the targeted lung abnormality.
Our Experience on Silicone Y-Stent for Severe COPD Complicated With Expiratory Central Airway Collapse
Authors: Ozgul Mehmet A. , Cetinkaya Erdogan , Cortuk Mustafa , Iliaz Sinem , Tanriverdi Elif , Gul Sule , Ozgul Guler , Onaran Hilal , Abbasli Kenan , Dincer Huseyin E.
Published: December 2016

Background:

Expiratory central airway collapse (ECAC) is abnormal central airway narrowing during expiration. ECAC involves 2 different pathophysiological entities as tracheobronchomalacia and excessive dynamic airway collapse (EDAC). Although the exact cause is unknown, chronic obstructive pulmonary disease (COPD) is frequently accompanied by ECAC. Although there are various publications on the relationship between COPD and ECAC, there are very few data for stent placement in patients with tracheobronchomalacia accompanied severe COPD. We share our results for stenting in ECAC among patients with severe COPD.

Methods:

The data in this case series were collected retrospectively. The ECAC diagnosis was made during flexible bronchoscopy with severe COPD. Silicone Y-stents were placed via rigid bronchoscopy under general anesthesia.

Results:

A total of 9 patients’ (7 men) data were evaluated with an average age of 67±10.73 years. One patient experienced stent migration on the second day of stenting prompting stent removal. Another patient died 1 month after stenting. Consequently, we evaluated the follow-up data of remaining 7 patients. The changes in forced expiratory volume 1 was not significant for these 7 cases (P=0.51). The modified Medical Research Council (mMRC) score improvement was statistically significant (P=0.03). Functional status improvement was observed in 4 of 7 patients. Of the 7 patients, mean additional follow-up bronchoscopic interventions requirement was 2.2 times.

Conclusions:

Our study showed significant decrease in mMRC score with stenting for ECAC in severe COPD. For 2 patients, we experienced severe complications during short-term follow-up period after stenting. Additional follow-up bronchoscopic interventions were required.
Pulmonologist-Performed Per-Esophageal Needle Aspiration of Parenchymal Lung Lesions Using an EBUS Bronchoscope
Authors: Steinfort Daniel P. , Farmer Michael W. , Irving Louis B. , Jennings Barton R.
Published: December 2016

Background:

Transesophageal introduction of the endobronchial ultrasound (EBUS) videobronchoscope allows pulmonologists to perform endoscopic ultrasound fine-needle aspiration (EUS-B-FNA) of mediastinal lesions. Safety, diagnostic accuracy, and feasibility of EUS-B-FNA in evaluation of pulmonary parenchymal lesions are not established.

Methods:

All patients undergoing pulmonologist-performed EUS-B-FNA of parenchymal lung lesions at 2 tertiary centers were included in this prospective observational cohort study.

Results:

EUS-B-FNA sampling of parenchymal lesions was performed in 27 patients. Mean (±SD) lesion size was 36±16 mm. Seven lesions were ≤18 mm. Pneumothorax occurred in 1 patient (3.7%, 95% confidence interval, 0.001%-19%). Ten target lesions (36%) were in locations inaccessible to bronchoscopic sampling via the airways, and 9 lesions were inaccessible to EBUS-guided transbronchial needle aspiration and in locations associated with low diagnostic yield from radial EBUS. EUS-B-FNA was diagnostic in 26 patients (96%), and sensitivity of EUS-B-FNA was 100% (95% confidence interval, 87%-100%) for both lung cancer (n=21) and for pulmonary metastatic lesions (n=5).

Conclusions:

Pulmonologist-performed EUS-B-FNA is safe and accurate in the evaluation parenchymal lung lesions. Diagnostic accuracy is high. EUS-B-FNA may achieve access to sites not amenable to other forms of bronchoscopic sampling, or increase diagnostic accuracy in patients where anatomic position predicts a low diagnostic yield.
Genotypic complexity of Fisher’s geometric model
Authors: Hwang Sungmin , Park Su-Chan , Krug Joachim
Published: December 2016

Fisher’s geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from the nonlinear mapping of phenotypes to fitness. Of particular interest is the occurrence of reciprocal sign epistasis, which is a necessary condition for multipeaked genotypic fitness landscapes. Here we compute the probability that a pair of randomly chosen mutations interacts sign-epistatically, which is found to decrease with increasing phenotypic dimensionn, and varies non-monotonically with the distance from the phenotypic optimum. We then derive expressions for the mean number of fitness maxima in genotypic landscapes composed of all combinations ofLrandom mutations. This number increases exponentially withL, and the corresponding growth rate is used as a measure of the complexity of the landscape. The dependence of the complexity on the model parameters is found to be surprisingly rich, and three distinct phases characterized by different landscape structures are identified. Our analysis shows that the phenotypic dimension, which is often referred to as phenotypic complexity, does not generally correlate with the complexity of fitness landscapes and that even organisms with a single phenotypic trait can have complex landscapes. Our results further inform the interpretation of experiments where the parameters of Fisher's model have been inferred from data, and help to elucidate which features of empirical fitness landscapes can be described by this model.
Histone H3K4 and H3K36 methylation promotes recruitment, but not activity, of the NuA3 histone acetyltransferase complex inS. cerevisiae
Authors: Martin Benjamin J.E. , McBurney Kristina L. , Maltby Vicki E. , Jensen Kristoffer N. , Brind’Amour Julie , Howe LeAnn J.
Published: December 2016

Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. InS. cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14, whichin vitrobind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9 respectively. However the relativein vivocontributions of these histone PTMs in targeting NuA3 is unknown. Here we show thatin vivoH4K4 and H3K36 methylation, but not acetylated or crotonylated H3K9, recruit NuA3 to transcribed genes. Through genome-wide colocalization and by mutational interrogation, we demonstrate that the PHD finger of Yng1, and the PWWP domain of Pdp3 independently target NuA3 to H3K4 and H3K36 methylated chromatin respectively. In contrast, we find no evidence to support the YEATS domain of Taf14 functioning in NuA3 recruitment. Collectively our results suggest that the presence of multiple histone-PTM binding domains within NuA3, rather than restricting it to nucleosomes containing distinct combinations of histone PTMs, can serve to increase the range of nucleosomes bound by the complex. Interestingly however, the simple presence of NuA3 is insufficient to ensure acetylation of the associated nucleosomes, suggesting a secondary level of acetylation regulation that does not involve control of HAT-nucleosome interactions
Inference of Multiple-wave Admixtures by Length Distribution of Ancestral Tracks
Authors: Ni Xumin , Yang Xiong , Yuan Kai , Feng Qidi , Guo Wei , Ma Zhiming , Xu Shuhua
Published: December 2016

The ancestral tracks in admixed genomes are of valuable information for population history inference. A few methods have been developed to infer admixture history based on ancestral tracks. Nonetheless, these methods suffered the same flaw that only population admixture history under some specific models can be inferred. In addition, the inference of history might be biased or even unreliable if the specific model is deviated from the real situation. To address this problem, we firstly proposed a general discrete admixture model to describe the admixture history with multiple ancestral populations and multiple-wave admixtures. We next deduced the length distribution of ancestral tracks under the general discrete admixture model. We further developed a new method,MultiWaver, to explore the multiple-wave admixture histories. Our method could automatically determine an optimal admixture model based on the length distribution of ancestral tracks, and estimate the corresponding parameters under this optimal model. Specifically, we used a likelihood ratio test (LRT) to determine the number of admixture waves, and implemented an expectation??maximization (EM) algorithm to estimate parameters. We used simulation studies to validate the reliability and effectiveness of our method. Finally, good performance was observed when our method was applied to real datasets of African Americans, Mexicans, Uyghurs, and Hazaras.
Cell reprogramming modelled as transitions in a hierarchy of cell cycles
Authors: Hannam R. , Annibale A. , Kühn R.
Published: December 2016

We construct a model of cell reprogramming (the conversion of fully differentiated cells to a state of pluripotency, known as induced pluripotent stem cells, or iPSCs) which builds on key elements of cell biology viz. cell cycles and cell lineages. Although reprogramming has been demonstrated experimentally, much of the underlying processes governing cell fate decisions remain unknown. This work aims to bridge this gap by modelling cell types as a set of hierarchically related dynamical attractors representing cell cycles. Stages of the cell cycle are characterised by the configuration of gene expression levels, and reprogramming corresponds to triggering transitions between such configurations. Two mechanisms were found for reprogramming in a two level hierarchy: cycle specific perturbations and a noise induced switching. The former corresponds to adirectedperturbation that induces a transition into a cycle-state of a different cell type in the potency hierarchy (mainly a stem cell) whilst the latter is a priori undirected and could be induced, e.g., by a (stochastic) change in the cellular environment. These reprogramming protocols were found to be effective in large regimes of the parameter space and make specific predictions concerning reprogramming dynamics which are broadly in line with experimental findings.
Effects of miRNAs on myocardial apoptosis by modulating mitochondria related proteins
Authors: Zhao Yanfang , Ponnusamy Murugavel , Dong Yanhan , Zhang Lei , Wang Kun , Li Peifeng
Published: December 2016

Myocardial apoptosis play a vital role in pathogenesis of cardiovascular diseases. The intrinsic pathway of apoptosis (mitochondrial apoptosis pathway) and abnormal mitochondrial fission and fusion have a detrimental effect on cells under a variety of intracellular stresses including hypoxia, oxidative stress, drug toxicity or DNA damage and contributes to the development of heart failure (HF), myocardial infarction (MI), diabetic cardiomyopathy and ischaemia/reperfusion injury (I/R). MicroRNAs (miRNAs) are endogenous short non‐coding RNAs, which target 3′‐untranslated region of mRNA to switch off gene expression. They play crucial roles in regulating complicated cardiac signalling and transcriptional events during cardiac development as well as in diseased condition. In this review, we summarize the molecular mechanism of mitochondrial apoptosis in cardiac cells and influence of miRNAs on them. MiRNAs regulate cardiac mitochondrial apoptosis by exert their effects on mitochondrial fission and fusion, reactive oxygen species (ROS) generation and Ca2+ homeostasis, Bcl‐2 family members, and other mitochondrial function proteins. This advancement in understanding mechanism of cardiac cells death provides us new therapy targets for cardiovascular diseases associated with mitochondrial dysfunctions.
The second earthquake: how the Italian state generated hope and uncertainty in post‐disaster L'Aquila
Authors: Bock Jan‐Jonathan
Published: December 2016

Recent analyses of the state have emphasized its inability to generate hope among citizens, suggesting that neoliberalism and globalization erode its protective power. However, this article suggests that the state still features as a coveted agent of support, in particular during unstable times. After the 2009 L'Aquila earthquake, the Italian state became the key actor responsible for emergency aid, restoration, and urban redevelopment. Dedication and the performance of compassion produced expectations of swift improvement. Hope became dependent on state authority. A few years later, uncertainty replaced hope, as promises for recovery remained unrealized. The state morphed from an agent of hope into the source of hopelessness, generating uncertainty and a sense of crisis. Since the state is revealed through its effects, this article highlights the need to trace state power in intimate human emotional experience, such as hope or despair. The production of a specific condition of uncertainty reveals the significance of state power in human life, particularly during times of personal or collective crisis.
The Ecology Of Neighborhood Participation and The Reproduction Of Political Conflict
Authors: Deener Andrew
Published: December 2016

Building on three years of participant observation and 30 life‐history interviews with activists in the Los Angeles community of Venice, this article introduces an ecological perspective to examine neighborhood participation and the reproduction of political conflict. As the official local space of community politics, the city‐funded Venice Neighborhood Council has experienced dramatic conflict. Observers have framed the conflict as occurring between liberal and conservative groups. Despite the history of conflict between so‐called ‘groups', the individuals involved are in flux. Venice is a complex arrangement of different neighborhoods and multiple interests. Tensions between long‐term neighborhood affiliations, formal bureaucracy and grassroots organizations affect how activists weigh competing associations embedded in the spatial landscape. The ecology of neighborhood participation underscores that conflict is not an outcome of stable substantive positions, but rather it occurs as the reassembling of overlapping and competing interests over time.
A Large‐Sample Test of a Semi‐Automated Clavicle Search Engine to Assist Skeletal Identification by Radiograph Comparison
Authors: D'Alonzo Susan S. , Guyomarc'h Pierre , Byrd John E. , Stephan Carl N.
Published: December 2016

In 2014, a morphometric capability to search chest radiograph databases by quantified clavicle shape was published to assist skeletal identification. Here, we extend the validation tests conducted by increasing the search universe 18‐fold, from 409 to 7361 individuals to determine whether there is any associated decrease in performance under these more challenging circumstances. The number of trials and analysts were also increased, respectively, from 17 to 30 skeletons, and two to four examiners. Elliptical Fourier analysis was conducted on clavicles from each skeleton by each analyst (shadowgrams trimmed from scratch in every instance) and compared to the search universe. Correctly matching individuals were found in shortlists of 10% of the sample 70% of the time. This rate is similar to, although slightly lower than, rates previously found for much smaller samples (80%). Accuracy and reliability are thereby maintained, even when the comparison system is challenged by much larger search universes.