bluuebunny/crossref_metadata_2025 huggingface dataset:
Rural Industrialization and Migration in the People’s Republic of China
Authors: Goldstein Alice , Goldstein Sidney , Shengzu Gu
Published: February 2016

The modernization/development process, both historically in Europe and in developing nations of the twentieth century, has involved the transformation of the labor force from one primarily engaged in agricultural pursuits to one largely involved in secondary- and tertiary-sector activities. This change has often been brought about in stages, beginning with the introduction of nonagricultural work in rural areas—proto-industrialization—as a supplement to industrial development in urban locations, concomitant with or followed by massive migration of the rural population into cities. Proto-industrialization may have been a response to population pressure, serving as a means to provide work for the surplus rural labor force when cultivable land became overtaxed and as a way for households to gain much-needed additional income during periods of agricultural shortfall.
The Criminal Courts in “Young America”: Bucks County, Pennsylvania, 1820–1860, with Some Comparisons to Massachusetts and South Carolina
Authors: Little Craig B.
Published: February 2016

Historians generally agree that crime, especially serious violence and disorder in America’s urban areas, increased during the first half of the nineteenth century, then leveled off, and eventually declined to the end of the century (Ferdinand 1978, 1980; Lane 1968,1979; Warner 1968). The need to improve institutions of control seemed apparent to many city dwellers in the early part of the century. Their responses, which remain part of our criminal justice system, included urban policing, large-scale penitentiaries, and specialized facilities, such as houses of refuge and reform schools for juvenile offenders. While the story of these urban developments has been well told previously (for example, Barnes 1927; Lane 1967; Rothman 1971; Platt 1969; Johnson 1978; Schneider 1980; Monkkonen 1981; Harring 1983), comparatively little is known about crime and control in peripheral communities, even though less than one-tenth of the American population was urban in 1820 and only one-quarter in 1860.
Comments on the Underenumeration of the U.S. Census, 1850–1880
Authors: Parkerson Donald H.
Published: February 2016

As furstenberg et al. (1979: 497) suggested over a decade ago, “The enormous promise of quantitative history can only be fulfilled when we are intimately acquainted with the limitations of our sources of information.” This collection of articles follows that suggestion by assessing the limitations of perhaps the most important source of information for social science researchers: the U.S. census. Certainly the degree of underenumeration may seriously affect research in many disciplines. For example, our estimates of migration rates might be inflated. In the process of nominal record linkage, researchers typically assume that those who are not listed in the linked census document out-migrated, when in reality many may simply have been missed by the census taker. As a result, past populations (especially in cities) may appear to have been much more mobile than they actually were. Census underenumeration might also exaggerate voter turnout. If the census in a particular community listed 1,215 eligible voters and election returns showed that 1,150 voted in an election, the voter turnout would be estimated at 95%. However, if just 10% of the eligible voters were not counted by the census taker, the estimated level of voter participation would decline to 85%. Finally, our understanding of the rural economy in the past might be affected by underenumeration. Agricultural production might be overstated if the more successful landowning farmers were more often enumerated and less productive farm tenants were missed. In short, the accuracy of the U.S. census should be a central concern to social science historians.
The Flexible House: The Housing Backlog and the Persistence of Lodging, 1891–1951
Authors: Harris Richard
Published: February 2016

Lodging was once common. In 1900 about one-quarter of U.S. households contained a lodger or lodging family. Almost as many more took one in at some point in the life of the household. Since then, rising incomes have enabled more people to maintain their own household. Today, lodging is quite rare and is confined largely to the poor.

A good deal has been written about lodging, mostly by social historians concerned with its implications for daily life. We have been told that lodiging was part of the immigrant experience, that it helped even out household income over the life cycle, that it augmented the clout of women within the household, and that in larger cities it supported a subculture among single men and women (Modell and Hareven 1973).
On Class, the Logic of Solidarity, and the Civilizing Process: Workers, Priests, and Alcohol in Dutch Shoemaking Communities, 1900–1920
Authors: Kalb Don
Published: February 2016

There is an economic logic and a moral logic and it is futile to argue as to which we give priority since they are different expressions of the same “kernel” of human relationship.

—E. P. Thompson, 1961

Class is certainly a key concept of social history just as civilization is for the figurational sociology of Norbert Elias and his followers. Each of these traditions needs to come to terms with the other. Notwithstanding fundamentally divergent assumptions, interests, and styles, both traditions would gain from a closer examination of each other's concepts, subjects, and methods.
Wifely Duties
Authors: Zeigler Sara L.
Published: February 2016

Although many Americans casually refer to the “institution” of marriage, most rarely consider the implications of that terminology. One enters into marriage by participating in fairly well-defined rites, and couples are warned of the solemnity of the undertaking. But seldom do the parties enter into marriage with a thorough understanding of what it means to subject oneself to governance by thelawof marriage.

The law is widely recognized as an institution that may profoundly affect the choices and lives of individuals. It is designed to affect individual behavior, encouraging “appropriate” actions by penalizing those that are seen as problematic for society. Its rules allow for the balancing of competing rights, and the courts provide a remedy when the rules are broken. Marriage law provides ground rules to govern the specific relationship characterized by a lifetime sexual and economic partnership between a man and a woman and endorses that relationship by giving it legal force.
The Political Consequences of Suffrage Exclusion
Authors: Harvey Anna L.
Published: February 2016

By the close of the first decade following ratification of constitutional female suffrage in the United States, it had become commonplace to read of female political leaders bemoaning the inefficacy of women's lobbying organizations, which despite their lobbying efforts did not engage in any electoral activity such as the mobilization of female voters (see, for example,NYT10 March 1928: 3;NYT31 March 1931: 22). That this should have been the case raises an interesting question: Why not? That is, given the likelihood that women's votes would have increased the efficacy of these lobbying efforts, why weren't the leaders of women's lobbying organizations, in particular those of the former suffrage machine, the National League of Women Voters (NLWV), pursuing those votes?
Bringing Political Economy Back In
Authors: Frader Laura L.
Published: February 2016

As other contributors to this roundtable suggest, the practices of social and labor history as we have known them have been in methodological and epistemological turmoil for some time. The dominant paradigms that guided much of the work of social historians in the 1960s, 1970s, and 1980s have been thrown into question by poststructuralism and by the emergence of new analytical perspectives on gender, race, and ethnicities. Attention to culture and to the meanings that historical subjects imposed on the habits of everyday life, as well as to the constitutive power of language and cultural practices, have now become a central aspect of much historical work that has sought to analyze the operations of gender, race, and ethnicities as the subjects of social history and the history of working people in particular.
Resuscitating Class
Authors: O. Rose Sonya
Published: February 2016

A sense of crisis and uncertainty seems pervasive among many social historians and historical sociologists who have studied the relationship between economic disadvantage and protest politics. Within the last five or so years, edited volumes and special issues of journals have encouraged scholars to “bring class back in,” to explore what some worry is the “end of labor history,” or to “rethink working-class history” in the wake of postmodernism, the turn to discursive and cultural analysis, and the growing number of scholars whose substantive interests involve issues of race and gender.

Even those who celebrate the rich diversity of subject matters explored by contemporary labor and working-class historians are worried about scholars jumping ship because “engaged history, in possession at least of the conceit of making a difference, has moved elsewhere, to other subject areas,” to quote Ira Katznelson (1994: 7). I myself have chosen to take a “leave of absence” from studying the mutual constitution of gender and class.
Introduction
Authors: Naragon Michael D. , Brown Marguerite
Published: February 2016

This issue brings together economists, sociologists, and historians in the study of migration and labor markets. The editors of the journal have turned the authors into unwitting collaborators, and in that sense these articles stand on their own. But one of the pleasures of being involved in the editorial process of an interdisciplinary journal is the opportunity it provides for drawing meaningful connections in the scholarship of diverse fields. We linked these separate contributions because together they help reconstruct the social and economic systems that channeled human migration. Each author makes important contributions to his respective field. Combined, their efforts illustrate what can be gained through the interdisciplinary nature of social science methodology.
The Agenda for “Social Science History”
Authors: Kousser J. Morgan
Published: February 2016

I want to take as my texts today statements made to me in correspondence and conversation by two senior quantitative historians. Each statement illustrates what I believe to be misjudgments about the proper methodological priorities for quantitative historians in America today. To spare these historians from publicity which their casual statements were not intended to invite, but mostly to protect myself against reprisal, I shall not name them here.

The first statement arose because I assigned a particular book in my American Political History course. Some of my colleagues, students, and I were critical of the methodology employed in the book, and a student suggested we might reanalyze the data, employing different techniques. The data set, however, was rather obscure and was apparently not available at any major archive. When I wrote to the author, rather brashly asking for a copy of his computer tapes, I was informed that he had “lost interest” in the project after the first year or so and discarded most of the tapes and IBM cards.
The Relevance of Bellah’s “Civil Religion” Thesis to a Theory of Secularization
Authors: Fenn Richard K.
Published: February 2016

A nation is minimally constituted by a population which shares two experiences, that of occupation of the same territory and of exposure to the exercise of a central state authority. Some societies are more self-sufficient in their economies and cultures than others; some societies surrender more or less political autonomy to a larger body than the nation. Nations, however, are generally the whole of which other bodies are the parts; the nation, in turn, is not usually part of another, larger whole. Edward Shils argues that the state creates conditions which are conducive to a national culture. By giving a population a “common focus of attention,” a common experience of the state’s exercise of its authority among those who share the same territory, and a belief in the legitimacy of the state’s power, conditions are generated which lead, often if not always, to a central culture which defines and expresses the history of the nation, the meaning of membership in the nation, and its basic commitments. Such a national belief-system is the “civil” or “civic” religion which a variety of historians and sociologists have located in American schools, national ceremonies, the regalia of office, and in political rhetoric. It is this culture which provides a non-theoretical answer to the question of what makes a nation “more than” the interaction of organizations and groups coordinated and controlled by a central state. But it is also this culture which becomes the source of new ambiguities concerning the grounds and limits of political authority.
Exploratory Analysis of Aggregate Voting Behavior: Presidential Elections in New Hampshire, 1896–1972
Authors: McCarthy John L. , Tukey John W.
Published: February 2016

This paper presents a new statistical method that is well-suited to building and testing theories of change. An exploratory, robust two-way analysis of New Hampshire’s county-level presidential election returns for the past eighty years illustrates how this general technique can help to clarify theoretical concepts as well as to reveal systematic regularities in empirical data.

Because two-way analysis involves a number of novel techniques, this paper is primarily a methodological exposition. It devotes much more attention to step-by-step details of how the analysis was carried out, and the accompanying exhibits contain much more detailed information than normally would be the case for reporting results of such research.

In contrast to classical methods, the techniques presented in this paper are intended primarily for exploration of data rather than for statistical inference. They require very few assumptions about the data, and they are not unduly influenced by extreme or missing values. Graphic and semi-graphic devices keep the analyst close to the data and make it possible to display many numbers simultaneously in contrast to simple single-number summaries which can conceal information. Removing obvious regularities in the data facilitates discovery of other underlying patterns.
The Language of A Cold Warrior: A Content Analysis of Harry Truman’s Public Statements
Authors: Sorenson Dale
Published: February 2016

Americans struggled with paranoia in the early 1950s. Many believed the most extravagant charges about the presence of Communists in the United States. Others had no firm convictions about the threat of Communism but tolerated an unrestricted search for disloyal citizens. To a later generation, there seems to have been little connection between the degree of danger and the public’s alarm.

A recent attempt to explain this national paranoia holds the Truman administration responsible for creating an unreasoning anti-Communist mentality. According to Athan Theoharis and Richard Freeland, members of the Truman administration exaggerated the dangers of international and domestic Communism. The public heard that the United States was “imminently threatened by a massive ideologically based assault upon everything Americans valued.” The administration’s excessively moralistic rhetoric portrayed the Soviet Union as the “Anti-Christ.” This strident anti-Communism created a public mood that Joseph McCarthy and others exploited for their political advantage. Thus, one of McCarthy’s major victims—the Truman administration—created the preconditions for McCarthyism.
The Historian’s Role in the Making of Public Policy
Authors: McCurley James
Published: February 2016

Some eight or nine years ago, David Nixon—a political scientist from Penn State University—was struck by the open dumping of industrial wastes into Pittsburgh’s rivers. Research on the topic indicated that under terms of the River and Harbor Refuse Act of 1899, the U.S. Army Corps of Engineers maintained responsibility for issuing permits to private concerns for the discharge of wastes into the nation’s waterways. The Act had also been successfully employed by the Justice Department in prosecuting a handful of past offenders. When the Corps’ district office in Pittsburgh denied any knowledge about such permits, David and a biologist friend began taking water samples from the Monongahela River in Pittsburgh. Subsequent chemical analyses of more than 400 samples verified the polluted condition of the stream caused by certain industrial sources. Upon taking his evidence to the district U.S. Attorney’s office, David Nixon persuaded Richard Thornburgh to file charges which were upheld by the federal district court in 1971—although final resolution would not come until years later. The suit eventually involved the Pennsylvania Chemical Corporation, U.S. Steel, Wheeling-Pittsburgh Steel, and Jones & Laughlin Steel, but David Nixon’s goal was to induce the government to enforce clear violations of existing law. In that regard, President Richard Nixon revived enforcement of the 1899 Refuse Act by Executive Order in December, 1971, and the “permit program” became the basis of enforcement for compliance with the Water Pollution Control Act Amendments of 1972. For more than 20 years prior to 1971, federal efforts to abate water pollution struggled to find some means to enforce compliance and in the process expended well over a billion dollars, without any apparent knowledge of the 1899 law.
Herbert Gutman’s The Black Family in Slavery and Freedom, 1750-1925: Demographic Perspectives
Authors: Modell John
Published: February 2016

Throughout his distinguished career, Herbert Gutman has displayed a rare genius for dredging up the most gloriously obscure historical evidence and deriving from it new perspectives on the largest themes. The Black Family is another triumph of this kind: my awe of Professor Gutman’s energy and insight is enhanced by this volume. At the same time, Gutman makes clear that the volume is not demographic in its intent. Since my commentary is to be from a demographic perspective, I will take particular pains to direct this perspective to the purposes Gutman sets forth in The Black Family. These are identified by the author as discerning “what sustained common slave beliefs and behavior,” rather than merely documenting “regularities in behavior,” the latter being Gutman’s characterization of the results of the application of quantitative methods (1976). My task, then, is to examine the links that Gutman establishes between demographic argument and explanation, in his sense, and to assess their adequacy. No demographer, I suspect, would have undertaken the kind of investigation Gutman assays; but demographic skills would have served Gutman’s intentions. I will here try to be severe with this imposing volume, recognizing the importance and aptness of its central thesis, and the audacity of its author’s empirical reach, but questioning the adequacy of his demography to his own ends.
Slave Mortality: Analysis of Evidence from Plantation Records
Authors: Steckel Richard H.
Published: February 2016

Since the inception of slavery in North America the free population has been concerned with the mortality of the slave population. Slaveowners were concerned with mortality for purposes of estimating the profitability of slave investments. Opponents of slavery and the slave trade used actual and presumed slave mortality experience as arguments for abolishing the system. Death rates were viewed as a measure of demographic performance that reflected the quality of slave life. It was argued that death rates reflected, and were in part determined by, such factors as diet, physical treatment, and the quality of medical care and housing—all under the control of the slaveowners. Consequently, information on deaths was used as a standard for evaluating the severity of the slave system and for assessing regional and international differences in slavery. In the postbellum period, scholars researched and debated various issues in slave mortality. The modern discussion includes issues in the levels and determinants of slave mortality, but research has concentrated on levels, possibly due to inadequate data for extensive research on determinants of mortality.
Contexts and pragmatics learning: Problems and opportunities of the study abroad research
Authors: Taguchi Naoko
Published: February 2016

Despite different epistemologies and assumptions, all theories in second language (L2) acquisition emphasize the centrality of context in understanding L2 acquisition. Under the assumption that language emerges from use in context, the cognitivist approach focuses on distributions and properties of input to infer both learning objects and process of acquisition. The interactionist approach views context more narrowly by analyzing how a particular linguistic item is attended and processed during a task-based interaction, and how it becomes intake as learning outcomes. For socially-oriented theories such as the sociocultural theory and language socialization, learning is fundamentally situated in context. Through mediated participation in learning as social practice, learners come to appropriate linguistic knowledge. Context is also fundamental in the complex, dynamic systems theory, which views learning as a non-linear, adaptive process emerging through an interaction of resources and individuals within a given context. All of these theories give the central power to context to describe and explain L2 learning. Context serves as the site where acquisition is examined. Context also helps explain the process and outcomes of acquisition.
Challenging Official Propaganda? Public Opinion Leaders on Sina Weibo
Authors: Nip Joyce Y. M. , Fu King-wa
Published: February 2016

This article examines the prominence of various user categories as opinion leaders, defined as initiators, agenda setters or disseminators, in 29 corruption cases exposed on Sina Weibo. It finds that ordinary citizens made up the largest category of initiators but that their power of opinion leadership was limited as they had to rely on media organizations to spread news about the cases. News organizations and online media were the main opinion leaders. Government and Party bodies initiated a fair number of cases and, despite not being strong agenda setters or disseminators, were able to dominate public opinion owing to the fact that news organizations and online media mainly published official announcements about the cases. Media organizations also played a secondary role as the voice of the people. While individuals from some other user categories were able to become prominent opinion leaders, news workers are likely to be the most promising user category to challenge official propaganda.
Human Papillomavirus in the Aetiology and Prevention of Genital Cancers
Authors: Muñoz Nubia
Published: February 2016

In the first part of this paper the molecular epidemiological evidence linking HPV to cervical cancer and other genital cancers is reviewed based mainly on the research work of the author. In the second part, the implications of the epidemiological findings for the prevention of cervical cancer are discussed in two areas: in primary prevention by the use of prophylactic HPV vaccines and in secondary prevention by increasing the accuracy of cervical cancer screening.
A New Period in the Cyprus Conflict: Can Anastasiadis and Akıncı Change the Status Quo?
Authors: Direkli Mehmet
Published: February 2016

A new leading actor has been added to the Cyprus Conflict. The winner of the Presidential elections held on the morning of Sunday, 26 April 2015, in the Turkish Republic of Northern Cyprus (Kuzey Kıbrıs Türk Cumhuriyeti – TRNC) was the independent candidate Mustafa Akıncı. Both Nicos Anastasiades, who was elected President of the Republic of Cyprus in 2013, and Akıncı are rare leaders supporting the Fifth Annan Plan, which was rejected in a referendum by the Greek Cypriots in 2004. One of the most vital catalysts that could play a role in the resolution of the Cyprus Conflict is a charismatic leader who aims for the resolution of the conflict. Whether the current Presidents have this personality and can change the current balances that are monopolized by the conservatives-nationalists on the Island will be revealed as a result of the negotiations. This article briefly tackles the UN parameters relative to the Cyprus Conflict and addresses the problems awaiting Presidents Anastasiades and Akıncı during the peace negotiations that have started anew.
Gabriel and the Virgin: The Secret of the Annunciation
Authors: Altmann Simon
Published: February 2016

It has long been known that the vast majority of the Annunciation pictures show the Virgin on their right. All former studies, including one by the present author, treat this as a problem of left-right or mirror symmetry. This is not correct: this symmetry exchanges the right and left hands and such a transformation is not permitted: Gabriel, must always be represented as right-handed. That this is so emerged from the study of a database that we have created, which contains 1007 Annunciations from C3 to 1750. Details of this database, which the author intends to put in the public domain in due course, and of other results, will be left for a further paper. It is a sufficient example here that from C3 to 1400 Gabriel shows his right hand to the Virgin in 62 items out of 93, and the left hand in only two. Even from 1401 to 1750 the Angel shows his right hand to the Virgin 278 times and only 22 for the left. A brief pictorial study of the evolution of the Annunciation paintings from C3 onwards shows why the right-handedness of Gabriel made it easier for the painter to present him on the left. A summary table of the results obtained from the database is provided. This study offers some explanation of the fact pointed out in a former paper that sculptural representations of the Annunciation are often variant, with the Virgin on the left.
A novel dietary improvement strategy: examining the potential impact of community-supported agriculture membership
Authors: Vasquez Angie , Sherwood Nancy E , Larson Nicole , Story Mary
Published: February 2016

Objective

To investigate the use of community-supported agriculture (CSA) as an employer-based health promotion intervention.

Design

Quasi-experimental study using a convenience sample of employees at three employers.

Setting

Participants and controls from three Minnesota employers completed baseline and follow-up health assessments and surveys about their experiences with CSA.

Subjects

A total of 324 participants purchased a CSA share and were eligible for study inclusion. Study participants were matched by age, sex, employer and occupation to a non-randomized control group of individuals who did not purchase a CSA share but completed health assessments during the same time frame as the study participants.

Results

The majority of participants were female, white, middle-aged and highly educated. The most common reason for purchasing a CSA share was a desire for fresh food, and the majority of participants were satisfied with their experience. Participants reported a significant increase in the number of vegetables present in the household and the frequency of family meals. The frequency of eating out decreased significantly, especially at fast-food restaurants. Participants also reported an increase in the amount and variety of produce consumed. However, health assessment data did not show significant changes in dietary intake, health status or BMI.

Conclusions

CSA participation was associated with improvement in some aspects of the household environment and dietary behaviours. Further research is needed to determine whether employer-based CSA interventions may also lead to improvements in dietary intake and health.
Public health nutrition capacity: assuring the quality of workforce preparation for scaling up nutrition programmes
Authors: Shrimpton Roger , du Plessis Lisanne M , Delisle Hélène , Blaney Sonia , Atwood Stephen J , Sanders David , Margetts Barrie , Hughes Roger
Published: February 2016

Objective

To describe why and how capacity-building systems for scaling up nutrition programmes should be constructed in low- and middle-income countries (LMIC).

Design

Position paper with task force recommendations based on literature review and joint experience of global nutrition programmes, public health nutrition (PHN) workforce size, organization, and pre-service and in-service training.

Setting

The review is global but the recommendations are made for LMIC scaling up multisectoral nutrition programmes.

Subjects

The multitude of PHN workers, be they in the health, agriculture, education, social welfare, or water and sanitation sector, as well as the community workers who ensure outreach and coverage of nutrition-specific and -sensitive interventions.

Results

Overnutrition and undernutrition problems affect at least half of the global population, especially those in LMIC. Programme guidance exists for undernutrition and overnutrition, and priority for scaling up multisectoral programmes for tackling undernutrition in LMIC is growing. Guidance on how to organize and scale up such programmes is scarce however, and estimates of existing PHN workforce numbers – although poor – suggest they are also inadequate. Pre-service nutrition training for a PHN workforce is mostly clinical and/or food science oriented and in-service nutrition training is largely restricted to infant and young child nutrition.

Conclusions

Unless increased priority and funding is given to building capacity for scaling up nutrition programmes in LMIC, maternal and child undernutrition rates are likely to remain high and nutrition-related non-communicable diseases to escalate. A hybrid distance learning model for PHN workforce managers’ in-service training is urgently needed in LMIC.
Evaluation of molecular variability in germplasm of vanilla (Vanilla planifoliaG. Jackson in Andrews) in Southeast Mexico: implications for genetic improvement and conservation
Authors: Ramos-Castellá Alma Laura , Iglesias-Andreu Lourdes G. , Martínez-Castillo Jaime , Ortíz-García Matilde , Andueza-Noh Rubén Humberto , Octavio-Aguilar Pablo , Luna-Rodríguez Mauricio
Published: February 2016

Molecular variability of vanilla (Vanilla planifolia) and three wild species was assessed to explore the possible sources of variation that can be used for crop improvement. A total of 154 ISSR loci were analysed by the UPGMA, assignment tests of individuals (STRUCTURE) and indices of genetic diversity. The assignment tests were done at two levels: first considering the four species and then only the accessions ofV. planifolia. The molecular analysis indicated 99.3% polymorphism among all species and 70.45% withinV. planifolia. The UPGMA showed the separation of these four species into three groups and groupedV. planifoliaaccessions into three subgroups. The more genetically differentiated accessions were of the Rayada morphotype and a wild accession was from Oaxaca, followed by a wild accession from Quintana Roo; all the commercial accessions ofV. planifolia(Mansa morphotype) were grouped together. The STRUCTURE analysis differentiated betweenV. planifoliaand the three wild species, and among the accessions of the Mansa and Rayada morphotypes and the wild accessions. The STRUCTURE analysis also indicated the presence of mixed individuals. These results are of great importance since the accessions ofV. planifoliathat are genetically more differentiated are the most threatened due to the scarcity of these individuals, the destruction of habitat and replacement by the commercial morphotype. These individuals should be salvaged and used to expand the genetic background of vanilla.
Space Weather Gains National and International Attention
Authors: Kelleher Shannon
Published: February 2016

A heightened understanding of geomagnetic disturbances in a high-tech world encourages policy changes in the United States and abroad.
Mapping gene regulatory circuitry of Pax6 during neurogenesis
Authors: Thakurela Sudhir , Tiwari Neha , Schick Sandra , Garding Angela , Ivanek Robert , Berninger Benedikt , Tiwari Vijay K
Published: February 2016

Pax6 is a highly conserved transcription factor among vertebrates and is important in various aspects of the central nervous system development. However, the gene regulatory circuitry of Pax6 underlying these functions remains elusive. We find that Pax6 targets a large number of promoters in neural progenitors cells. Intriguingly, many of these sites are also bound by another progenitor factor, Sox2, which cooperates with Pax6 in gene regulation. A combinatorial analysis of Pax6-binding data set with transcriptome changes in Pax6-deficient neural progenitors reveals a dual role for Pax6, in which it activates the neuronal (ectodermal) genes while concurrently represses the mesodermal and endodermal genes, thereby ensuring the unidirectionality of lineage commitment towards neuronal differentiation. Furthermore, Pax6 is critical for inducing activity of transcription factors that elicit neurogenesis and repress others that promote non-neuronal lineages. In addition to many established downstream effectors, Pax6 directly binds and activates a number of genes that are specifically expressed in neural progenitors but have not been previously implicated in neurogenesis. The in utero knockdown of one such gene, Ift74, during brain development impairs polarity and migration of newborn neurons. These findings demonstrate new aspects of the gene regulatory circuitry of Pax6, revealing how it functions to control neuronal development at multiple levels to ensure unidirectionality and proper execution of the neurogenic program.
High-resolution phylogenetic microbial community profiling
Authors: Singer Esther , Bushnell Brian , Coleman-Derr Devin , Bowman Brett , Bowers Robert M , Levy Asaf , Gies Esther A , Cheng Jan-Fang , Copeland Alex , Klenk Hans-Peter , Hallam Steven J , Hugenholtz Philip , Tringe Susannah G , Woyke Tanja
Published: February 2016

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake’s water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.
Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria
Authors: Zhu Bo , Ibrahim Muhammad , Cui Zhouqi , Xie Guanlin , Jin Gulei , Kube Michael , Li Bin , Zhou Xueping
Published: February 2016

Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.
Self-renewal of CD133hi cells by IL6/Notch3 signalling regulates endocrine resistance in metastatic breast cancer
Authors: Sansone Pasquale , Ceccarelli Claudio , Berishaj Marjan , Chang Qing , Rajasekhar Vinagolu K. , Perna Fabiana , Bowman Robert L. , Vidone Michele , Daly Laura , Nnoli Jennifer , Santini Donatella , Taffurelli Mario , Shih Natalie N. C. , Feldman Michael , Mao Jun J. , Colameco Christopher , Chen Jinbo , DeMichele Angela , Fabbri Nicola , Healey John H. , Cricca Monica , Gasparre Giuseppe , Lyden David , Bonafé Massimiliano , Bromberg Jacqueline
Published: February 2016

The mechanisms of metastatic progression from hormonal therapy (HT) are largely unknown in luminal breast cancer. Here we demonstrate the enrichment of CD133hi/ERlo cancer cells in clinical specimens following neoadjuvant endocrine therapy and in HT refractory metastatic disease. We develop experimental models of metastatic luminal breast cancer and demonstrate that HT can promote the generation of HT-resistant, self-renewing CD133hi/ERlo/IL6hi cancer stem cells (CSCs). HT initially abrogates oxidative phosphorylation (OXPHOS) generating self-renewal-deficient cancer cells, CD133hi/ERlo/OXPHOSlo. These cells exit metabolic dormancy via an IL6-driven feed-forward ERlo-IL6hi-Notchhi loop, activating OXPHOS, in the absence of ER activity. The inhibition of IL6R/IL6-Notch pathways switches the self-renewal of CD133hi CSCs, from an IL6/Notch-dependent one to an ER-dependent one, through the re-expression of ER. Thus, HT induces an OXPHOS metabolic editing of luminal breast cancers, paradoxically establishing HT-driven self-renewal of dormant CD133hi/ERlo cells mediating metastatic progression, which is sensitive to dual targeted therapy.
Genomic insights into the Ixodes scapularis tick vector of Lyme disease
Authors: Gulia-Nuss Monika , Nuss Andrew B. , Meyer Jason M. , Sonenshine Daniel E. , Roe R. Michael , Waterhouse Robert M. , Sattelle David B. , de la Fuente José , Ribeiro Jose M. , Megy Karine , Thimmapuram Jyothi , Miller Jason R. , Walenz Brian P. , Koren Sergey , Hostetler Jessica B. , Thiagarajan Mathangi , Joardar Vinita S. , Hannick Linda I. , Bidwell Shelby , Hammond Martin P. , Young Sarah , Zeng Qiandong , Abrudan Jenica L. , Almeida Francisca C. , Ayllón Nieves , Bhide Ketaki , Bissinger Brooke W. , Bonzon-Kulichenko Elena , Buckingham Steven D. , Caffrey Daniel R. , Caimano Melissa J. , Croset Vincent , Driscoll Timothy , Gilbert Don , Gillespie Joseph J. , Giraldo-Calderón Gloria I. , Grabowski Jeffrey M. , Jiang David , Khalil Sayed M. S. , Kim Donghun , Kocan Katherine M. , Koči Juraj , Kuhn Richard J. , Kurtti Timothy J. , Lees Kristin , Lang Emma G. , Kennedy Ryan C. , Kwon Hyeogsun , Perera Rushika , Qi Yumin , Radolf Justin D. , Sakamoto Joyce M. , Sánchez-Gracia Alejandro , Severo Maiara S. , Silverman Neal , Šimo Ladislav , Tojo Marta , Tornador Cristian , Van Zee Janice P. , Vázquez Jesús , Vieira Filipe G. , Villar Margarita , Wespiser Adam R. , Yang Yunlong , Zhu Jiwei , Arensburger Peter , Pietrantonio Patricia V. , Barker Stephen C. , Shao Renfu , Zdobnov Evgeny M. , Hauser Frank , Grimmelikhuijzen Cornelis J. P. , Park Yoonseong , Rozas Julio , Benton Richard , Pedra Joao H. F. , Nelson David R. , Unger Maria F. , Tubio Jose M. C. , Tu Zhijian , Robertson Hugh M. , Shumway Martin , Sutton Granger , Wortman Jennifer R. , Lawson Daniel , Wikel Stephen K. , Nene Vishvanath M. , Fraser Claire M. , Collins Frank H. , Birren Bruce , Nelson Karen E. , Caler Elisabet , Hill Catherine A.
Published: February 2016

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing’, prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
Transition to a Moist Greenhouse with CO2 and solar forcing
Authors: Popp Max , Schmidt Hauke , Marotzke Jochem
Published: February 2016

Water-rich planets such as Earth are expected to become eventually uninhabitable, because liquid water turns unstable at the surface as temperatures increase with solar luminosity. Whether a large increase of atmospheric concentrations of greenhouse gases such as CO2 could also destroy the habitability of water-rich planets has remained unclear. Here we show with three-dimensional aqua-planet simulations that CO2-induced forcing as readily destabilizes the climate as does solar forcing. The climate instability is caused by a positive cloud feedback and leads to a new steady state with global-mean sea-surface temperatures above 330 K. The upper atmosphere is considerably moister in this warm state than in the reference climate, implying that the planet would be subject to substantial loss of water to space. For some elevated CO2 or solar forcings, we find both cold and warm equilibrium states, implying that the climate transition cannot be reversed by removing the additional forcing.
Correction: Corrigendum: Photo-generated metamaterials induce modulation of CW terahertz quantum cascade lasers
Authors: Mezzapesa Francesco P. , Columbo Lorenzo L. , Rizza Carlo , Brambilla Massimo , Ciattoni Alessandro , Dabbicco Maurizio , Vitiello Miriam S. , Scamarcio Gaetano
Published: February 2016

Periodic patterns of photo-excited carriers on a semiconductor surface profoundly modifies its effective permittivity, creating a stationary all-optical quasi-metallic metamaterial. Intriguingly, one can tailor its artificial birefringence to modulate with unprecedented degrees of freedom both the amplitude and phase of a quantum cascade laser (QCL) subject to optical feedback from such an anisotropic reflector. Here, we conceive and devise a reconfigurable photo-designed Terahertz (THz) modulator and exploit it in a proof-of-concept experiment to control the emission properties of THz QCLs. Photo-exciting sub-wavelength metastructures on silicon, we induce polarization-dependent changes in the intra-cavity THz field, that can be probed by monitoring the voltage across the QCL terminals. This inherently flexible approach promises groundbreaking impact on THz photonics applications, including THz phase modulators, fast switches, and active hyperbolic media.
Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations
Authors: Khosravian N. , Kamaraj B. , Neyts E. C. , Bogaerts A.
Published: February 2016

This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.
Bio-Source of di-n-butyl phthalate production by filamentous fungi
Authors: Tian Congkui , Ni Jinren , Chang Fang , Liu Sitong , Xu Nan , Sun Weiling , Xie Yuan , Guo Yongzhao , Ma Yanrong , Yang Zhenxing , Dang Chenyuan , Huang Yuefei , Tian Zhexian , Wang Yiping
Published: February 2016

Although DBP (di-n-butyl phthalate) is commonly encountered as an artificially-synthesized plasticizer with potential to impair fertility, we confirm that it can also be biosynthesized as microbial secondary metabolites from naturally occurring filamentous fungi strains cultured either in an artificial medium or natural water. Using the excreted crude enzyme from the fungi for catalyzing a variety of substrates, we found that the fungal generation of DBP was largely through shikimic acid pathway, which was assembled by phthalic acid with butyl alcohol through esterification. The DBP production ability of the fungi was primarily influenced by fungal spore density and incubation temperature. This study indicates an important alternative natural waterborne source of DBP in addition to artificial synthesis, which implied fungal contribution must be highlighted for future source control and risk management of DBP.