bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial activity during pre-maturational culture in in vitro-grown bovine oocytes is related to maturational and developmental competences
Authors: Huang Weiping , Kang Sung-Sik , Nagai Katsuhisa , Yanagawa Yojiro , Takahashi Yoshiyuki , Nagano Masashi
Published: July 2014

The objective of this study was to investigate the dynamics of mitochondrial activity in in vitro-grown (IVG) bovine oocytes during pre-maturational culture (pre-IVM) and its relationship to their developmental competence upon being subjected to different pre-IVM durations. After 12-day IVG culture, oocytes were cultured for 0, 10 or 20 h with 3-isobutyl-1-methylxanthine (IBMX) as pre-IVM. Mitochondrial activity in IVG oocytes after 10 h pre-IVM was the highest among all the pre-IVM durations (P < 0.05). In addition, cleavage (79.4%) and blastocyst rates (38.9%) of embryos derived from IVG oocytes with 10 h pre-IVM were higher than those with 20 h pre-IVM (63.0 and 25.8%, respectively; P < 0.05) and similar to those of in vivo-grown oocytes (82.7 and 36.7%, respectively). To confirm the developmental ability of IVG oocytes with 10 h pre-IVM beyond the blastocyst stage in vivo, embryo transfer was attempted. Transferred embryos developed to the elongated embryonic stage (63.6%, 7/11) in the recipient uterus at Day 16 of oestrus, and a male calf was delivered (50%, 1/2). In conclusion, it was indicated that the mitochondrial activity of bovine IVG oocytes peaked at 10 h pre-IVM and was closely correlated with the nuclear maturation and developmental competences of IVG oocytes.
Comparative proteomic study reveals 17β-HSD13 as a pathogenic protein in nonalcoholic fatty liver disease
Authors: Su Wen , Wang Yang , Jia Xiao , Wu Wenhan , Li Linghai , Tian Xiaodong , Li Sha , Wang Chunjiong , Xu Huamin , Cao Jiaqi , Han Qifei , Xu Shimeng , Chen Yong , Zhong Yanfeng , Zhang Xiaoyan , Liu Pingsheng , Gustafsson Jan-Åke , Guan Youfei
Published: July 2014

Significance

Nonalcoholic fatty liver disease (NAFLD) is a common chronic hepatic disease affecting up to 25% of subjects in the developed world, and represents a progressive illness eventually leading to liver fibrosis and cirrhosis. This study reports an extensive set of human liver lipid droplet (LD)-associated proteins and an array of proteins differentially expressed in human NAFLD. We also uncover 17β-hydroxysteroid dehydrogenase-13, a newly identified LD-associated protein, as a pathogenic molecule in the development of NAFLD. The present study provides a potential link between LD proteins and the pathogenesis of hepatic steatosis.
Insulin-like peptide 5 is an orexigenic gastrointestinal hormone
Authors: Grosse Johannes , Heffron Helen , Burling Keith , Akhter Hossain Mohammed , Habib Abdella M. , Rogers Gareth J. , Richards Paul , Larder Rachel , Rimmington Debra , Adriaenssens Alice A. , Parton Laura , Powell Justin , Binda Matteo , Colledge William H. , Doran Joanne , Toyoda Yukio , Wade John D. , Aparicio Samuel , Carlton Mark B. L. , Coll Anthony P. , Reimann Frank , O’Rahilly Stephen , Gribble Fiona M.
Published: July 2014

Significance

Hormonal factors from specialized enteroendocrine cells in the gut epithelium link the availability of dietary nutrients to energy utilization and storage. Many gut hormones also affect behaviors such as appetite and foraging, conveying for example the satiating effects of food consumption. Here we identify insulin-like peptide 5 (Insl5) as a product of colonic endocrine L-cells, and show that levels were elevated in calorie-restricted mice and reduced after feeding. Consistent with this profile Insl5 administration stimulated food intake in mice, indicating it should join ghrelin as only the second identified gut hormone that enhances appetite. Modulating the Insl5 axis presents a new strategy for the treatment of metabolic disease and obesity.
Analysis of benzo[c]phenanthridine alkaloids inEschscholtzia californicacell culture using HPLC-DAD and HPLC-ESI-MS/MS
Authors: Son Seok Young , Rhee Hong Soon , Lee Min Woo , Park Jong Moon
Published: July 2014

Effective HPLC-DAD and HPLC-ESI-MS/MS methods have been developed for the analysis of eight benzo[c]phenanthridine alkaloids (sanguinarine, chelirubine, macarpine, chelerythrine, dihydrosanguinarine, dihydrochelirubine, dihydromacarpine and dihydrochelerythrine), which are important metabolites in Eschscholtzia californica cell culture. By adopting a ternary gradient pump system, the dihydro-form alkaloids hardly separable from each other could be successfully separated, and all the target alkaloids could be simultaneously quantified with the LOD values of 0.01–0.79 μg/mL and the LOQ values of 0.03–3.59 μg/mL. This HPLC-DAD method was further confirmed by HPLC-ESI-MS/MS system in multiple reaction monitoring mode. Each separated HPLC peak was identified as the target alkaloid, showing its relevant ionized molecule and selected fragment ion. By applying the established method, alkaloid production during the E. californica cell culture could be successfully monitored and some valuable information on its metabolism could be deduced.
Configurations and invariant nets for amenable hypergroups and related algebras
Authors: Willson Benjamin
Published: July 2014

Let

H
H

be a hypergroup with left Haar measure. The amenability of

H
H

can be characterized by the existence of nets of positive, norm one functions in

L
1

(
H
)

L^1(H)

which tend to left invariance in any of several ways. In this paper we present a characterization of the amenability of

H
H

using configuration equations. Extending work of Rosenblatt and Willis, we construct, for a certain class of hypergroups, nets in

L
1

(
H
)

L^1(H)

which tend to left invariance weakly, but not in norm.

We define the semidirect product of

H
H

with a locally compact group. We show that the semidirect product of an amenable hypergroup and an amenable locally compact group is an amenable hypergroup and show how to construct Reiter nets for this semidirect product.

These results are generalized to Lau algebras, providing a new characterization of left amenability of a Lau algebra and a notion of a semidirect product of a Lau algebra with a locally compact group. The semidirect product of a left amenable Lau algebra with an amenable locally compact group is shown to be a left amenable Lau algebra.
Resolving complex tandem repeats with long reads
Authors: Ummat Ajay , Bashir Ali
Published: July 2014

Motivation : Resolving tandemly repeated genomic sequences is a necessary step in improving our understanding of the human genome. Short tandem repeats (TRs), or microsatellites, are often used as molecular markers in genetics, and clinically, variation in microsatellites can lead to genetic disorders like Huntington’s diseases. Accurately resolving repeats, and in particular TRs, remains a challenging task in genome alignment, assembly and variation calling. Though tools have been developed for detecting microsatellites in short-read sequencing data, these are limited in the size and types of events they can resolve. Single-molecule sequencing technologies may potentially resolve a broader spectrum of TRs given their increased length, but require new approaches given their significantly higher raw error profiles. However, due to inherent error profiles of the single-molecule technologies, these reads presents a unique challenge in terms of accurately identifying and estimating the TRs.

Results : Here we present P acmon STR, a reference-based probabilistic approach, to identify the TR region and estimate the number of these TR elements in long DNA reads. We present a multistep approach that requires as input, a reference region and the reference TR element. Initially, the TR region is identified from the long DNA reads via a 3-stage modified Smith–Waterman approach and then, expected number of TR elements is calculated using a pair-Hidden Markov Models –based method. Finally, TR-based genotype selection (or clustering: homozygous/heterozygous) is performed with Gaussian mixture models , using the Akaike information criteria , and coverage expectations.

Availability and implementation:  https://github.com/alibashir/pacmonstr

Contact:  ajayummat@gmail.com or ali.bashir@mssm.edu
Journaled string tree—a scalable data structure for analyzing thousands of similar genomes on your laptop
Authors: Rahn René , Weese David , Reinert Knut
Published: July 2014

Motivation : Next-generation sequencing (NGS) has revolutionized biomedical research in the past decade and led to a continuous stream of developments in bioinformatics, addressing the need for fast and space-efficient solutions for analyzing NGS data. Often researchers need to analyze a set of genomic sequences that stem from closely related species or are indeed individuals of the same species. Hence, the analyzed sequences are similar. For analyses where local changes in the examined sequence induce only local changes in the results, it is obviously desirable to examine identical or similar regions not repeatedly.

Results : In this work, we provide a datatype that exploits data parallelism inherent in a set of similar sequences by analyzing shared regions only once. In real-world experiments, we show that algorithms that otherwise would scan each reference sequentially can be speeded up by a factor of 115.

Availability : The data structure and associated tools are publicly available at http://www.seqan.de/projects/jst and are part of SeqAn, the C ++ template library for sequence analysis.

Contact : rene.rahn@fu-berlin.de
Greek Theater Production
Authors: Meineck Peter
Published: July 2014

Greek theater production means the physical manner in which ancient Greek (mainly Athenian) drama was realized in the theater. This includes the use of masks, costumes, props; set, machinery, and vehicles; the way in which the architectural form of the theater affected the staging (such as entrances and exits); the stage movements (blocking) of the performers; the financial elements that enabled the production of the plays; and the wider cultural environment of the religious festivals within which ancient Greek drama was performed. Although tragedy, comedy and satyrlike performances are attested to elsewhere in the Greek world, most of our evidence for drama in the Classical period comes from Athens. We know of 6th- and early-5th-century performance spaces in Sparta, Argos, Sicily, Athens, and the demes of Attica: although apart from Athens we do not know if narrative drama was performed there or if they were choral dance or ritual spaces. Apart from fragments of plays by Aeschylus possibly produced in Sicily, all of the extant plays of Aeschylus, Sophocles, Euripides, Aristophanes, and Menander were intended for production in Athens. It is also likely that the fragments of the plays of other dramatists from this period were also intended for the Athenian theater, although they may have been re-performed elsewhere. As theater spread throughout the Hellenistic period we find much more material-culture evidence of drama, although less textual evidence. It is important to note that the Greek theater stagecraft developed rapidly and underwent a number of significant changes. The theater also changed architecturally from a temporary wooden stand overlooking a level dancing space (orchestra) at a sanctuary or in a marketplace to a large stone edifice capable of accommodating thousands of people. The texts of ancient plays have come down to us without stage directions. Scholars have attempted to reconstruct Greek theater production techniques from evidence derived from the plays themselves, the material-culture evidence of architectural remains of theater spaces, the iconography of vase painting and sculpture, epigraphic records, and later scholia and commentaries from Hellenistic, Roman, and medieval scholars. As a result there are many controversial issues such as the shape and size of the theater space, the use of scenery and scene painting (or not), the introduction of the scene building and the entrances, exits, and stage movements of the performers.
Edmund Husserl
Authors: Zahavi Dan
Published: July 2014

Edmund Husserl (b. 1859–d. 1938) is a central figure in 20th-century philosophy. A student of Brentano (b. 1838–d. 1917) and a contemporary of Frege (b. 1848–d. 1925), he is the founding father of phenomenology and thereby a figure with a decisive impact not only on thinkers like Heidegger (b. 1889–d. 1976), Edith Stein (b. 1891–d. 1942), Merleau-Ponty (b. 1908–d. 1961), and Sartre (b. 1905–d. 1980), but also on subsequent theory formations in German and French philosophy. More recently, many of Husserl’s ideas have also been taken up and discussed by analytic philosophers. Husserl is primarily known for his analyses of intentionality, perception, temporality, embodiment, and intersubjectivity, for his rehabilitation of the lifeworld and his commitment to a form of transcendental idealism and for his criticism of reductionism, objectivism, and scientism. Most of Husserl’s writings have been published posthumously and they continue to disclose aspects of his thinking that it would have been difficult to anticipate through the study of the works originally published by Husserl himself. Many of these volumes have not yet been translated into English, and the same holds true for much of the research literature.
Neo-Confucianism
Authors: Angle Stephen
Published: July 2014

“Neo-Confucianism” refers to the broad revival of Confucian thinking that emerged in the early Song dynasty (960–1279 ce). At the core of this revival was the movement known to its adherents as the “Learning of the Way” (daoxue), but the new directions in which Confucians took their shared tradition are not limited to the texts and terminology of the Learning of the Way movement, and so it makes sense to use the Western neologism “Neo-Confucianism” as a capacious term to cover the whole Confucian revival. When we include both proponents of the Learning of the Way and their critics—the latter of whose views would not have been possible without the Learning of the Way innovations against which to react—it becomes clear that Neo-Confucianism extends temporally from the early Song all the way into the Qing dynasty (1644–1911) and extends spatially into Korea, Japan, and Vietnam. Although there are certainly themes and debates that extend across dynastic or national boundaries, these borders still serve as useful demarcations and are used here as a primary means of organization. The origins of Neo-Confucianism and its ongoing interactions with Daoist and Chinese Buddhist traditions are related because even if the old idea that Neo-Confucianism is a reaction against Buddhism is too simple, there nonetheless are clear resonances between certain Daoist and (especially) Buddhist views and those at the center of the Learning of the Way. Among the many key concepts of Neo-Confucianism, two have occasioned significant independent scholarly attention, so a separate section of the article focuses on li (pattern, coherence, principle) and xing (nature). Finally, this article follows the existing literature in being broadly interdisciplinary. The most common approach to be found here is intellectual history—especially intellectual biography and history of ideas—but particularly in the more recent scholarship, we see philosophy, cultural history, and methods from religious studies. In each of these latter areas, there is substantial room for further development. One promising area has been the degree to which anglophone scholars are engaging with Sinophone scholarship, and vice versa; with this in mind, the article includes some of the best and most influential Chinese-language materials where appropriate.
Intersectionalities
Authors: Howard Judith A.
Published: July 2014

Individuals are shaped by the multiple categories to which they are perceived to belong and the social structures that undergird systems of categorization. Systems of social categorization are virtually always associated with differential, unequal resources. Intersectionality is a concept fundamental to understanding these societal inequalities; the key assertion of intersectionality is that the various systems of societal oppression do not act independently of each other. Different systems of inequality are transformed in their intersections, the fundamental principle of intersectionality. The phrase “race, class, and gender,” still in use, is a precursor of the concept of intersectionality. The preferred use of the latter term reflects in part the awareness that there are more than three intersecting systems of societal inequalities. The metaphors noted in the section Metaphors of Intersectionality below have been powerful visualizations of this complexity. Further, some identities may be privileged categories, others marginalized. Thus oppression and privilege may be experienced simultaneously, complicating the analysis of inequality. These issues are addressed in the section Critiques of Intersectionality below. Intersectionality crosses levels of analysis, from the micro-level experiences of individual actors to the macro-level structural, organizational, and institutional contexts in which human interactions and experiences are formed. Intersectionality is an analytic approach, a way of thinking about social categories that articulates similarity and difference, always inflected by relations of power. Research adopting an intersectional lens falls into several not entirely distinct groups: theoretical and methodological debates, evident in the sections Organizational Frameworks of Intersectionality and Methodologies, and applications of intersectional dynamics and political interventions, evident in the sections Intersectional Praxis and Transnational Intersectionalities. Intersectionality is also a deeply interdisciplinary concept, an analytic approach that can be found in almost all of the social sciences as well as the humanities; examples here are drawn from political science and psychology, in addition to the sociological examples appropriate to this series.
Sidney Poitier
Authors: Knight Arthur
Published: July 2014

Sidney Poitier (b. 1927–d. 2022) was the first African American to be, inarguably, a movie star and, beyond that, an “institution” of Hollywood film and American culture. Poitier’s stature is such that in his autobiography Barack Obama recalls his mother holding Poitier up as a model alongside Martin Luther King Jr.; that in 2008 the New York Times’s film critics felt Poitier’s acting helped Americans prepare to elect a Black president; and that Quentin Tarantino sought his advice before making Django Unchained (2012), his controversial, violent action film about an ex-slave turned bounty hunter. Poitier was the first African American to win a major Academy Award (Best Actor, 1963; awarded 1964) and the first African American box-office top earner (1967–1968). His many other honors include an honorary British Knighthood (KBE, 1974), honorary Academy Award (2002), and the Presidential Medal of Freedom (2009). That Poitier would achieve such renown was improbable. Poitier’s first Hollywood role was in a social problem film, No Way Out (1950), which featured a brutal interracial melee and a jaundiced view of American race and class relations. But Poitier’s character—a young, aspiring, and dignified doctor—served to provide a glimmer of hope. Poitier’s portrayal made it clear that though his character was angry and had suffered from white prejudice, he would rise above past injustices and work toward a better future. With many variations, this is a character type Poitier repeated over the next two decades in films such as The Defiant Ones (1958), Lilies of the Field (1963), In the Heat of the Night (1967), and Guess Who’s Coming to Dinner (1967). These roles proved influential and led to great success but also to criticism of Poitier as an overly safe and de-sexualized “ebony saint.” In the 1970s Poitier increasingly turned to directing and producing. Never lauded for his directing style, he nonetheless made some influential and successful movies, including the Black western Buck and the Preacher (1972), a trio of comedies that spoofed “blaxploitation” films, and Stir Crazy (1980), a breakthrough film for Richard Pryor and the first movie directed by an African American to earn more than 100 million dollars. After the 1980s, Poitier continued to act, often in character roles or in roles portraying civil rights icons—for example, Nelson Mandela in Mandela and de Klerk (1997), a made-for-television movie. In the twenty-first century, Poitier turned his attention to penning popular, introspective autobiographies and, in 2013, a novel. Poitier was a dual citizen of the United States and the Bahamas and served as the Bahamian ambassador to Japan (1997–2007) and to UNESCO (2002–2007). At his death in January 2022, he was recognized for his accomplishments in obituaries and tributes worldwide.
Material Culture
Authors: Gerritsen Anne
Published: July 2014

Material culture is a broad and interdisciplinary field that explores the cultural meanings objects acquire in context. It does not impose a hierarchy on what is included; anything that is made from a particular material can be seen as material culture. The implication, however, is that raw materials and natural commodities are, on the whole, excluded, and that there is a certain emphasis on the ways in which things have been made. In the case of tea, for example, the plant itself is perhaps not seen as part of material culture, but its methods of cultivation, the ways in which tea is brewed, the various attributes required in the preparation and consumption of the beverage, and all practices surrounding tea are all part of the material culture. There are fruitful overlaps with numerous other fields: with art history, where that discipline explores the so-called decorative arts; with history, where objects form a supplement and/or alternative to written documentation; with anthropology, where objects are part of social practice; and with (prehistoric) archaeology, where objects often are the only available source in the absence of written materials. The emphasis on objects has been useful in a number of areas, especially where written sources are difficult to access. In the field of women and gender, for example, the study of material culture has allowed a different kind of access to the experiences that shaped the lives of men and women who did not leave documentation in writing. In global history, material culture and the use of objects provide ways of overcoming the challenges of materials written in different languages. While material culture has become an important part of numerous academic fields in Europe and North America, in Asia the transition has been slower. The main developments in this area have come from Taiwan, where a number of scholars have made important contributions in this field. This bibliography includes not only materials conceived specifically from within a material culture context, but also work produced within disciplines such as archaeology and art history. Methodologically, they may differ from the study of material culture, but in terms of the source materials they present for the scholar interested in material culture, they are indispensable.
Maternal food quantity affects offspring feeding rate in
Daphnia magna
Authors: Garbutt Jennie S. , Little Tom J.
Published: July 2014

Maternal effects have wide-ranging effects on life-history traits. Here, using the crustacean
Daphnia magna
, we document a new effect: maternal food quantity affects offspring feeding rate, with low quantities of food triggering mothers to produce slow-feeding offspring. Such a change in the rate of resource acquisition has broad implications for population growth or dynamics and for interactions with, for instance, predators and parasites. This maternal effect can also explain the previously puzzling situation that the offspring of well-fed mothers, despite being smaller, grow and reproduce better than the offspring of food-starved mothers. As an additional source of variation in resource acquisition, this maternal effect may also influence relationships between life-history traits, i.e. trade-offs, and thus constraints on adaptation. Maternal nutrition has long-lasting effects on health and particularly diet-related traits in humans; finding an effect of maternal nutrition on offspring feeding rate in
Daphnia
highlights the utility of this organism as a powerful experimental model for exploring the relationship between maternal diet and offspring fitness.
Composition and substrate-dependent strength of the silken attachment discs in spiders
Authors: Grawe Ingo , Wolff Jonas O. , Gorb Stanislav N.
Published: July 2014

Araneomorph spiders have evolved different silks with dissimilar material properties, serving different purposes. The two-compound pyriform secretion is used to glue silk threads to substrates or to other threads. It is applied in distinct patterns, called attachment discs. Although ubiquitously found in spider silk applications and hypothesized to be strong and versatile at low material consumption, the performance of attachment discs on different substrates remains unknown. Here, we analyse the detachment forces and fracture mechanics of the attachment discs spun by five different species on three different substrates, by pulling on the upstream part of the attached thread. Results show that although the adhesion of the pyriform glue is heavily affected by the substrate, even on Teflon it is frequently strong enough to hold the spider's weight. As plant surfaces are often difficult to wet, they are hypothesized to be the major driving force for evolution of the pyriform secretion.
Fast, high-throughput measurement of collective behaviour in a bacterial population
Authors: Colin R. , Zhang R. , Wilson L. G.
Published: July 2014

Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards ‘a better life’. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for bacterial survival and virulence. Both single-cell and macroscopic assays have investigated bacterial behaviours. However, theories that relate the two scales have previously been difficult to test directly. We present an image analysis method, inspired by light scattering, which measures the average collective motion of thousands of bacteria simultaneously. Using this method, a time-varying collective drift as small as 50 nm s
−1
can be measured. The method, validated using simulations, was applied to chemotactic
Escherichia coli
bacteria in linear gradients of the attractant α-methylaspartate. This enabled us to test a coarse-grained minimal model of chemotaxis. Our results clearly map the onset of receptor methylation, and the transition from linear to logarithmic sensing in the bacterial response to an external chemoeffector. Our method is broadly applicable to problems involving the measurement of collective drift with high time resolution, such as cell migration and fluid flows measurements, and enables fast screening of tactic behaviours.
Stochastically driven adult–recruit associations of tree species on Barro Colorado Island
Authors: Getzin Stephan , Wiegand Thorsten , Hubbell Stephen P.
Published: July 2014

The spatial placement of recruits around adult conspecifics represents the accumulated outcome of several pattern-forming processes and mechanisms such as primary and secondary seed dispersal, habitat associations or Janzen–Connell effects. Studying the adult–recruit relationship should therefore allow the derivation of specific hypotheses on the processes shaping population and community dynamics. We analysed adult–recruit associations for 65 tree species taken from six censuses of the 50 ha neotropical forest plot on Barro Colorado Island (BCI), Panama. We used point pattern analysis to test, at a range of neighbourhood scales, for spatial independence between recruits and adults, to assess the strength and type of departure from independence, and its relationship with species properties. Positive associations expected to prevail due to dispersal limitation occurred only in 16% of all cases; instead a majority of species showed spatial independence (≈73%). Independence described the placement of recruits around conspecific adults in good approximation, although we found weak and noisy signals of species properties related to seed dispersal. We hypothesize that spatial mechanisms with strong stochastic components such as animal seed dispersal overpower the pattern-forming effects of dispersal limitation, density dependence and habitat association, or that some of the pattern-forming processes cancel out each other.
Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts
Authors: Sobrinho Roberto Ramos , Xavier César Augusto Diniz , Pereira Hermano Monteiro de Barros , Lima Gaus Silvestre de Andrade , Assunção Iraíldes Pereira , Mizubuti Eduardo Seiti Gomide , Duffy Siobain , Zerbini Francisco Murilo
Published: July 2014

Begomoviruses are whitefly-transmitted, ssDNA plant viruses and are among the most damaging pathogens causing epidemics in economically important crops worldwide. Wild/non-cultivated plants play a crucial epidemiological role, acting as begomovirus reservoirs and as ‘mixing vessels' where recombination can occur. Previous work suggests a higher degree of genetic variability in begomovirus populations from non-cultivated hosts compared with cultivated hosts. To assess this supposed host effect on the genetic variability of begomovirus populations, cultivated (common bean, Phaseolus vulgaris, and lima bean, Phaseolus lunatus) and non-cultivated (Macroptilium lathyroides) legume hosts were sampled from two regions of Brazil. A total of 212 full-length DNA-A genome segments were sequenced from samples collected between 2005 and 2012, and populations of the begomoviruses Bean golden mosaic virus (BGMV) and Macroptilium yellow spot virus (MaYSV) were obtained. We found, for each begomovirus species, similar genetic variation between populations infecting cultivated and non-cultivated hosts, indicating that the presumed genetic variability of the host did not a priori affect viral variability. We observed a higher degree of genetic variation in isolates from MaYSV populations than BGMV populations, which was explained by numerous recombination events in MaYSV. MaYSV and BGMV showed distinct distributions of genetic variation, with the BGMV population (but not MaYSV) being structured by both host and geography.
Massively calcified endosomal death (MCED) of endothelial cells
Authors: Weisenthal L.
Published: July 2014

We have discovered a novel and specific mechanism of endothelial cell death. We refer to this novel death mechanism as massively calcified endosomal death, or MCED. Exposure of endothelial cells to non-specific toxins or other physical stresses induces death by traditional apoptotic and non-apoptotic mechanisms, common to most different types of cells. In contrast, exposure of endothelial cells (but not other types of nucleated cells) to specific insults, such as oxidized pathogenic lipids (e.g. 7-ketocholesterol) or agents with known anti-angiogenic activity (e.g. bevacizumab, certain tyrosine kinase inhibitors, etc.) triggers cell death via a novel pathway, which involves the formation of massively calcified endosomes, which, in turn, escape from the dying endothelial cells as massively calcified exosomes. These endosomes/exosomes appear capable of provoking an inflammatory response, characterized by physical association of calcified microparticles with inflammatory cells (monocytes, lymphocytes, neutrophils) with resulting increased release of an inflammatory mediator (TNF) into the culture medium. Traditional media for the culture of endothelial cells are profoundly inhibitory to MCED, as are some mammalian sera and many human sera, explaining why MCED had not been previously discovered and reported. The present discovery of MCED was accidental, resulting from work with primary cultures of fresh human tumor cell clusters, which invariably contain microcapillary cells. Our culture media are optimized for the tumor cells and not for the endothelial cells and, thus, are permissive of MCED. I propose MCED as the central mechanism underlying both intimal calcification and vascular inflammation in atherosclerosis.
The Genetic Landscape of Transcriptional Networks in a Combined Haploid/Diploid Plant System
Authors: Verta J.-P. , Landry C.R. , MacKay J.
Published: July 2014

Heritable variation in gene expression is a source of evolutionary change and our understanding of the genetic basis of expression variation remains incomplete. Here, we dissected the genetic basis of transcriptional variation in a wild, outbreeding gymnosperm (Picea glauca) according to linked and unlinked genetic variants, their allele-specific (cis) and allele non-specific (trans) effects, and their phenotypic additivity. We used a novel plant system that is based on the analysis of segregating alleles of a single self-fertilized plant in haploid and diploid seed tissues. We measured transcript abundance and identified transcribed SNPs in 66 seeds with RNA-seq. Linked and unlinked genetic effects that influenced expression levels were abundant in the haploid megagametophyte tissue, influencing 48% and 38% of analyzed genes, respectively. Analysis of these effects in diploid embryos revealed that while distant effects were acting intransconsistent with their hypothesized diffusible nature, local effects were associated with a complex mix ofcis,transand compensatory effects. Mostciseffects were additive irrespective of their effect sizes, consistent with a hypothesis that they represent rate-limiting factors in transcript accumulation. We show thattranseffects fulfilled a key prediction of Wright s physiological theory, in which variants with small effects tend to be additive and those with large effects tend to be dominant/recessive. Our haploid/diploid approach allows a comprehensive genetic dissection of expression variation and can be applied to a large number of wild plant species.
The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages
Authors: Daniel Bence , Nagy Gergely , Hah Nasun , Horvath Attila , Czimmerer Zsolt , Poliska Szilard , Gyuris Tibor , Keirsse Jiri , Gysemans Conny , Van Ginderachter Jo A. , Balint Balint L. , Evans Ronald M. , Barta Endre , Nagy Laszlo
Published: July 2014

RXR signaling is predicted to have a major impact in macrophages, but neither the biological consequence nor the genomic basis of its ligand activation is known. Comprehensive genome-wide studies were carried out to map liganded RXR-mediated transcriptional changes, active binding sites, and cistromic interactions in the context of the macrophage genome architecture. The macrophage RXR cistrome has 5200 genomic binding sites, which are not impacted by ligand. Active enhancers are characterized by PU.1 binding, an increase of enhancer RNA, and P300 recruitment. Using these features, 387 liganded RXR-bound enhancers were linked to 226 genes, which predominantly reside in CTCF/cohesin-limited functional domains. These findings were molecularly validated using chromosome conformation capture (3C) and 3C combined with sequencing (3C-seq), and we show that selected long-range enhancers communicate with promoters via stable or RXR-induced loops and that some of the enhancers interact with each other, forming an interchromosomal network. A set of angiogenic genes, including Vegfa, has liganded RXR-controlled enhancers and provides the macrophage with a novel inducible program.
Two waves of de novo methylation during mouse germ cell development
Authors: Molaro Antoine , Falciatori Ilaria , Hodges Emily , Aravin Alexei A. , Marran Krista , Rafii Shahin , McCombie W. Richard , Smith Andrew D. , Hannon Gregory J.
Published: July 2014

During development, mammalian germ cells reprogram their epigenomes via a genome-wide erasure and de novo rewriting of DNA methylation marks. We know little of how methylation patterns are specifically determined. The piRNA pathway is thought to target the bulk of retrotransposon methylation. Here we show that most retrotransposon sequences are modified by default de novo methylation. However, potentially active retrotransposon copies evade this initial wave, likely mimicking features of protein-coding genes. These elements remain transcriptionally active and become targets of piRNA-mediated methylation. Thus, we posit that these two waves play essential roles in resetting germ cell epigenomes at each generation.
Wnt some lose some: transcriptional governance of stem cells by Wnt/β-catenin signaling
Authors: Lien Wen-Hui , Fuchs Elaine
Published: July 2014

In mammals, Wnt/β-catenin signaling features prominently in stem cells and cancers, but how and for what purposes have been matters of much debate. In this review, we summarize our current knowledge of Wnt/β-catenin signaling and its downstream transcriptional regulators in normal and malignant stem cells. We centered this review largely on three types of stem cells—embryonic stem cells, hair follicle stem cells, and intestinal epithelial stem cells—in which the roles of Wnt/β-catenin have been extensively studied. Using these models, we unravel how many controversial issues surrounding Wnt signaling have been resolved by dissecting the diversity of its downstream circuitry and effectors, often leading to opposite outcomes of Wnt/β-catenin-mediated regulation and differences rooted in stage- and context-dependent effects.
Contralateral disconnection of the rat prelimbic cortex and dorsomedial striatum impairs cue-guided behavioral switching
Authors: Baker Phillip M. , Ragozzino Michael E.
Published: July 2014

Switches in reward outcomes or reward-predictive cues are two fundamental ways in which information is used to flexibly shift response patterns. The rat prelimbic cortex and dorsomedial striatum support behavioral flexibility based on a change in outcomes. The present experiments investigated whether these two brain regions are necessary for conditional discrimination performance in which a switch in reward-predictive cues occurs every three to six trials. The GABA agonists baclofen and muscimol infused into the prelimbic cortex significantly impaired performance leading rats to adopt an inappropriate turn strategy. The NMDA receptor antagonist D-AP5 infused into the dorsomedial striatum or prelimbic cortex and dorsomedial striatum contralateral disconnection impaired performance due to a rat failing to switch a response choice for an entire trial block in about two out of 13 test blocks. In an additional study, contralateral disconnection did not affect nonswitch discrimination performance. The results suggest that the prelimbic cortex and dorsomedial striatum are necessary to support cue-guided behavioral switching. The prelimbic cortex may be critical for generating alternative response patterns while the dorsomedial striatum supports the selection of an appropriate response when cue information must be used to flexibly switch response patterns.
(2E)-2-Benzylidene-9-phenyl-3,4-dihydroacridin-1(2H)-one
Authors: Vinuchakkaravarthy T. , Sankaran M. , Mohan P. S. , Velmurugan D.
Published: July 2014

In the title compound, C26H19NO, the plane of the aromatic heterocycle makes a dihedral angle of 75.22 (4)° with that of the attached phenyl ring. In the crystal, molecules are connected by C—H...O interactions, generatingR22(12) dimers. These dimers are further connected by C—H...π interactions, linking the molecules into chains running along thea-axis direction.
A case of mucocutaneous leishmaniasis diagnosed by serology
Authors: Okumura Yoko , Yamauchi Asako , Nagano Isao , Itoh Makoto , Hagiwara Keisuke , Takahashi Kenzo , Uezato Hiroshi , Maeda Manabu , Seishima Mariko
Published: July 2014

A 43‐year‐old Japanese Bolivian male had been suffering from a right leg ulcer after an insect bite during his residence in Bolivia. The ulcer healed after herbal medicine treatment. Ten years later, the patient had symptoms of nasal obstruction, nasal bleeding, and pharyngodynia, which were accompanied by a destructive ulcer with surrounding erythema involving the right nostril apex and columella. Papillary, irregular mucosal lesions were seen on the soft palate. Giemsa staining and polymerase chain reaction (PCR) using biopsy specimens of the papillary mucosal lesions on the soft palate failed to identify Leishmania parasites. However, the IgG antibody test was positive for Leishmania (Leishmania) donovani, and the dot enzyme‐linked immunosorbent assay (dot‐ELISA) using five Leishmania antigens L. (L.) mexicana, L. (L.) amazonensis, Leishmania (Viannia) guyanensis, L. (V.) braziliensis, and L. (V.) panamensis was positive. Combined, the findings suggested mucocutaneous leishmaniasis. Treatment with liposomal amphotericin B was started but was soon terminated because of palpitation, epigastralgia and facial flushing. It is sometimes difficult to identify the parasites in lesions of mucocutaneous leishmaniasis and serological tests are useful for such occasions.
Clinical features of 58 Japanese patients with mosaic neurofibromatosis 1
Authors: Tanito Katsumi , Ota Arihito , Kamide Ryoichi , Nakagawa Hidemi , Niimura Michihito
Published: July 2014

Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder caused by mutation in the NF1 tumor‐suppressor gene, and may sometimes manifest in a mosaic form. “Segmental NF1” is generally assumed to be the result of somatic mosaicism for a NF1 mutation, and patients with mosaic NF1 have typical features of NF1 limited to specific body segments. The clinical features of 58 patients (42 females and 16 males; aged 1–69 years; mean age, 23.4 years) with mosaic NF1 seen at the Jikei University Hospital during 2004–2007 and at the Jikei University Daisan Hospital during 2007–2011, were retrospectively studied. Somatic or gonosomal mosaicism was not investigated. Patients were classified into four groups: (i) pigmentary changes (café‐au‐lait spots and freckling) only (n = 32); (ii) neurofibromas only (n = 5); (iii) neurofibromas and pigmentary changes (n = 13); and (iv) solitary plexiform neurofibromas (n = 8). The area of involvement was variable. The majority of patients were asymptomatic, except patients with plexiform neurofibromas who presented most commonly with pain or tenderness. Lisch nodules were rarely seen. Only four of our 58 patients (6.9%) had specific NF1 complications, including language delay (n = 1) and bone deformity (n = 3). Two patients were ascertained through their children with generalized NF1. Patients with mosaic NF1 are at low risk of developing disease‐associated complications, except patients with plexiform neurofibromas. However, they need to be aware of the small risk of having a child with generalized NF1.
Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management
Authors: Walker Anne‐Sophie , Gladieux Pierre , Decognet Véronique , Fermaud Marc , Confais Johann , Roudet Jean , Bardin Marc , Bout Alexandre , C. Nicot Philippe , Poncet Christine , Fournier Elisabeth
Published: July 2014

Understanding the causes of population subdivision is of fundamental importance, as studying barriers to gene flow between populations may reveal key aspects of the process of adaptive divergence and, for pathogens, may help forecasting disease emergence and implementing sound management strategies. Here, we investigated population subdivision in the multihost fungus Botrytis cinerea based on comprehensive multiyear sampling on different hosts in three French regions. Analyses revealed a weak association between population structure and geography, but a clear differentiation according to the host plant of origin. This was consistent with adaptation to hosts, but the distribution of inferred genetic clusters and the frequency of admixed individuals indicated a lack of strict host specificity. Differentiation between individuals collected in the greenhouse (on Solanum) and outdoor (on Vitis and Rubus) was stronger than that observed between individuals from the two outdoor hosts, probably reflecting an additional isolating effect associated with the cropping system. Three genetic clusters coexisted on Vitis but did not persist over time. Linkage disequilibrium analysis indicated that outdoor populations were regularly recombining, whereas clonality was predominant in the greenhouse. Our findings open up new perspectives for disease control by managing plant debris in outdoor conditions and reinforcing prophylactic measures indoor.
High spatial resolution of distribution and interconnections between Fe‐ and N‐redox processes in profundal lake sediments
Authors: Melton Emily D. , Stief Peter , Behrens Sebastian , Kappler Andreas , Schmidt Caroline
Published: July 2014

The Fe and N biogeochemical cycles play key roles in freshwater environments. We aimed to determine the spatial positioning and interconnections of the N and Fe cycles in profundal lake sediments. The gradients of O2, NO3−, NH4+, pH, Eh, Fe(II) and Fe(III) were determined and the distribution of microorganisms was assessed by most probable numbers and quantitative polymerase chain reaction. The redox zones could be divided into an oxic zone (0–8 mm), where microaerophiles (Gallionellaceae) were most abundant at a depth of 7 mm. This was followed by a denitrification zone (6–12 mm), where NO3−‐dependent Fe(II) oxidizers and organoheterotrophic denitrifiers both reduce nitrate. Lastly, an iron redox transition zone was identified at 12.5–22.5 mm. Fe(III) was most abundant above this zone while Fe(II) was most abundant beneath. The high abundance of poorly crystalline iron suggested iron cycling. The Fe and N cycles are biologically connected through nitrate‐reducing Fe(II) oxidizers and chemically by NOx− species formed during denitrification, which can chemically oxidize Fe(II). This study combines high resolution chemical, molecular and microbiological data to pinpoint sedimentary redox zones in which Fe is cycled between Fe(II) and Fe(III) and where Fe and N‐redox processes interact.
The prevalence of pre‐eclampsia in migrant relative to native Norwegian women: a population‐based study
Authors: Naimy Z , Grytten J , Monkerud L , Eskild A
Published: July 2014

Objective

To compare the prevalence of pre‐eclampsia in migrant women with Norwegian women, and to study the prevalence of pre‐eclampsia by length of residence in Norway.

Design

Observational study.

Setting

The Medical Birth Registry of Norway.

Population

All Norwegian, Pakistani, Vietnamese, Somali, Sri Lankan, Filipino, Iraqi, Thai and Afghan women who gave birth after 20 weeks of gestation during the period 1986–2005 in Norway.

Methods

The prevalence of pre‐eclampsia was calculated by country of birth. The association of country of birth and length of residence in Norway with pre‐eclampsia was estimated as the odds ratio (OR) with 95% confidence interval (CI), using Norwegian women as a reference. We made adjustments for maternal age, parity, multifetal pregnancy, year of delivery and maternal diabetes in multivariable analysis.

Main outcome measure

Pre‐eclampsia.

Results

Migrant women had a lower prevalence of pre‐eclampsia than Norwegian women (2.7% versus 3.7%, P < 0.001). Vietnamese (OR, 0.36; CI, 0.29–0.45), Afghan (OR, 0.52; CI, 0.30–0.90) and Thai (OR, 0.57; CI, 0.45–0.73) women had the lowest risk of pre‐eclampsia relative to Norwegian women. Adjustment for the variables above or separate analyses for nulliparous women did not change the estimates notably. Using Norwegian women as the reference, the risk of pre‐eclampsia increased by length of residence for migrant women: adjusted OR of 0.64 (0.59–0.70) at <5 years and 0.91 (0.84–0.99) at ≥5 years of residence.

Conclusions

The risk of pre‐eclampsia was lower in migrants relative to Norwegian women, but increased by length of residence in Norway.