bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knowledge and valuation of Andean agroforestry species: the role of sex, age, and migration among members of a rural community in Bolivia
Authors: Brandt Regine , Mathez-Stiefel Sarah-Lan , Lachmuth Susanne , Hensen Isabell , Rist Stephan 
Published: December 2013

AbstractBackgroundAgroforestry is a sustainable land use method with a long tradition in the Bolivian Andes. A better understanding of people’s knowledge and valuation of woody species can help to adjust actor-oriented agroforestry systems. In this case study, carried out in a peasant community of the Bolivian Andes, we aimed at calculating the cultural importance of selected agroforestry species, and at analysing the intracultural variation in the cultural importance and knowledge of plants according to peasants’ sex, age, and migration.MethodsData collection was based on semi-structured interviews and freelisting exercises. Two ethnobotanical indices (Composite Salience, Cultural Importance) were used for calculating the cultural importance of plants. Intracultural variation in the cultural importance and knowledge of plants was detected by using linear and generalised linear (mixed) models.Results and discussionThe culturally most important woody species were mainly trees and exotic species (e.g.Schinus molle,Prosopis laevigata,Eucalyptus globulus). We found that knowledge and valuation of plants increased with age but that they were lower for migrants; sex, by contrast, played a minor role. The age effects possibly result from decreasing ecological apparency of valuable native species, and their substitution by exotic marketable trees, loss of traditional plant uses or the use of other materials (e.g. plastic) instead of wood. Decreasing dedication to traditional farming may have led to successive abandonment of traditional tool uses, and the overall transformation of woody plant use is possibly related to diminishing medicinal knowledge.ConclusionsAge and migration affect how people value woody species and what they know about their uses. For this reason, we recommend paying particular attention to the potential of native species, which could open promising perspectives especially for the young migrating peasant generation and draw their interest in agroforestry. These native species should be ecologically sound and selected on their potential to provide subsistence and promising commercial uses. In addition to offering socio-economic and environmental services, agroforestry initiatives using native trees and shrubs can play a crucial role in recovering elements of the lost ancient landscape that still forms part of local people’s collective identity.
RETRACTED ARTICLE: Ferroportin in the progression and prognosis of hepatocellular carcinoma
Authors: Wang Qin , Zhou Jun , Zhong Dewu , Wang Qunwei , Huang Jiangsheng 
Published: December 2013

Abstract

Background
Hepatocellular carcinoma (HCC) is the fifth most common malignant tumor in men and the seventh in women and understanding the molecular mechanisms of HCC and establishing more effective therapies are critical and urgent issues. Our objective was to study the expression of ferroportin in hepatocellular carcinoma (HCC) tissue samples and the relationship between ferroportin expression and HCC characteristics.

Methods
Sixty HCC tissues and their corresponding para-cancer liver tissues (PCLT) were obtained from sixty HCC patients who had undergone hepatectomy in the Second Xiangya Hospital of Central South University. Ten normal liver tissue samples were also obtained as a control. Immunohistochemistry (IHC) was performed to analyze the ferroportin expression in HCC, and the relationship between ferroportin expression and HCC clinical pathological characteristics also was analyzed. For the evaluation of IHC results, the comprehensive scoring criteria were met according to the staining intensity and the number of positive staining cells. Western blotting was performed to detect the expression level of ferroportin in HCC cell lines.

Results
Ferroportin expression in HCC tissue was significantly lower compared to PCLT and normal liver tissue (P <0.05). Moreover, ferroportin expression was related to liver cancer cell de-differentiation, the severity degree in TNM staging, Edmondson-Steiner grading, intrahepatic metastasis and portal vein invasion. In addition, high expression of ferroportin was observed in normal human liver cell lines L02 and HL7702, whereas weak positive expression and even negative expression of ferroportin were observed in HCC cell lines FOCUS, MHCC-97H, HepG2 and SMMC-7721. Furthermore, among the four kinds of HCC cell lines, the expression level of ferroportin was the lowest in MHCC-97H cells.

Conclusions
Ferroportin expression level declines along with the progression of liver cancer, suggesting that the reduction of ferroportin may serve as an important marker for poor HCC prognosis and as a new therapeutic target.
Crystal structures of the A2A adenosine receptor and their use in medicinal chemistry
Authors: Jacobson Kenneth A 
Published: December 2013

AbstractNew insights into drug design are derived from the X-ray crystallographic structures of G protein-coupled receptors (GPCRs), and the adenosine receptors (ARs) are at the forefront of this effort. The 3D knowledge of receptor binding and activation promises to enable drug discovery for GPCRs in general, and specifically for the ARs. The predictability of modeling based on the X-ray structures of the A2AAR has been well demonstrated in the identification, design and modification of both known and novel AR agonists and antagonists. It is expected that structure-based design of drugs acting through ARs will provide new avenues to clinically useful agents.
Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity
Authors: Rosli Hernan G , Zheng Yi , Pombo Marina A , Zhong Silin , Bombarely Aureliano , Fei Zhangjun , Collmer Alan , Martin Gregory B 
Published: December 2013

Abstract
Background
Microbe-associated molecular patterns, such as those present in bacterial flagellin, are powerful inducers of the innate immune response in plants. Successful pathogens deliver virulence proteins, termed effectors, into the plant cell where they can interfere with the immune response and promote disease. Engineering the plant immune system to enhance disease resistance requires a thorough understanding of its components.

Results
We describe a high-throughput screen, using RNA sequencing and virus-induced gene silencing, to identify tomato genes whose expression is enhanced by the flagellin microbe-associated molecular pattern flgII-28, but reduced by activities of the Pseudomonas syringae pv. tomato (Pst) type III effectors AvrPto and AvrPtoB. Gene ontology terms for this category of Flagellin-induced repressed by effectors (FIRE) genes showed enrichment for genes encoding certain subfamilies of protein kinases and transcription factors. At least 25 of the FIRE genes have been implicated previously in plant immunity. Of the 92 protein kinase-encoding FIRE genes, 33 were subjected to virus-induced gene silencing and their involvement in pattern-triggered immunity was tested with a leaf-based assay. Silencing of one FIRE gene, which encodes the cell wall-associated kinase SlWAK1, compromised the plant immune response resulting in increased growth of Pst and enhanced disease symptoms.

Conclusions
Our transcriptomic approach identifies FIRE genes that represent a pathogen-defined core set of immune-related genes. The analysis of this set of candidate genes led to the discovery of a cell wall-associated kinase that participates in plant defense. The FIRE genes will be useful for further elucidation of the plant immune system.
Spatial expression of transcription factors in Drosophilaembryonic organ development
Authors: Hammonds Ann S , Bristow Christopher A , Fisher William W , Weiszmann Richard , Wu Siqi , Hartenstein Volker , Kellis Manolis , Yu Bin , Frise Erwin , Celniker Susan E 
Published: December 2013

Abstract
Background
Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown.

Results
We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study.

Conclusions
We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system.
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes
Authors: Kocher Sarah D , Li Cai , Yang Wei , Tan Hao , Yi Soojin V , Yang Xingyu , Hoekstra Hopi E , Zhang Guojie , Pierce Naomi E , Yu Douglas W 
Published: December 2013

Abstract
Background
Taxa that harbor natural phenotypic variation are ideal for ecological genomic approaches aimed at understanding how the interplay between genetic and environmental factors can lead to the evolution of complex traits. Lasioglossum albipes is a polymorphic halictid bee that expresses variation in social behavior among populations, and common-garden experiments have suggested that this variation is likely to have a genetic component.

Results
We present the L. albipes genome assembly to characterize the genetic and ecological factors associated with the evolution of social behavior. The de novo assembly is comparable to other published social insect genomes, with an N50 scaffold length of 602 kb. Gene families unique to L. albipes are associated with integrin-mediated signaling and DNA-binding domains, and several appear to be expanded in this species, including the glutathione-s-transferases and the inositol monophosphatases. L. albipes has an intact DNA methylation system, and in silico analyses suggest that methylation occurs primarily in exons. Comparisons to other insect genomes indicate that genes associated with metabolism and nucleotide binding undergo accelerated evolution in the halictid lineage. Whole-genome resequencing data from one solitary and one social L. albipes female identify six genes that appear to be rapidly diverging between social forms, including a putative odorant receptor and a cuticular protein.

Conclusions
L. albipes represents a novel genetic model system for understanding the evolution of social behavior. It represents the first published genome sequence of a primitively social insect, thereby facilitating comparative genomic studies across the Hymenoptera as a whole.
The evolution, impact and properties of exonic splice enhancers
Authors: Cáceres Eva Fernández , Hurst Laurence D 
Published: December 2013

Abstract
Background
In humans, much of the information specifying splice sites is not at the splice site. Exonic splice enhancers are one of the principle non-splice site motifs. Four high-throughput studies have provided a compendium of motifs that function as exonic splice enhancers, but only one, RESCUE-ESE, has been generally employed to examine the properties of enhancers. Here we consider these four datasets to ask whether there is any consensus on the properties and impacts of exonic splice enhancers.

Results
While only about 1% of all the identified hexamer motifs are common to all analyses we can define reasonably sized sets that are found in most datasets. These consensus intersection datasets we presume reflect the true properties of exonic splice enhancers. Given prior evidence for the properties of enhancers and splice-associated mutations, we ask for all datasets whether the exonic splice enhancers considered are purine enriched; enriched near exon boundaries; able to predict trends in relative codon usage; slow evolving at synonymous sites; rare in SNPs; associated with weak splice sites; and enriched near longer introns. While the intersect datasets match expectations, only one original dataset, RESCUE-ESE, does. Unexpectedly, a fully experimental dataset identifies motifs that commonly behave opposite to the consensus, for example, being enriched in exon cores where splice-associated mutations are rare.

Conclusions
Prior analyses that used the RESCUE-ESE set of hexamers captured the properties of consensus exonic splice enhancers. We estimate that at least 4% of synonymous mutations are deleterious owing to an effect on enhancer functioning.
Lifetime affect and midlife cognitive function: prospective birth cohort study
Authors: Richards M. , Barnett J. H. , Xu M. K. , Croudace T. J. , Gaysina D. , Kuh D. , Jones P. B. ,   the MRC National Survey of Health and Development scientific and data collection team
Published: December 2013

BackgroundRecurrent affective problems are predictive of cognitive impairment, but the timing and directionality, and the nature of the cognitive impairment, are unclear.AimsTo test prospective associations between life-course affective symptoms and cognitive function in late middle age.MethodA total of 1668 men and women were drawn from the Medical Research Council National Survey of Health and Development (the British 1946 birth cohort). Longitudinal affective symptoms spanning age 13–53 years served as predictors; outcomes consisted of self-reported memory problems at 60–64 years and decline in memory and information processing from age 53 to 60–64 years.ResultsRegression analyses revealed no clear pattern of association between longitudinal affective symptoms and decline in cognitive test scores, after adjusting for gender, childhood cognitive ability, education and midlife socioeconomic status. In contrast, affective symptoms were strongly, diffusely and independently associated with self-reported memory problems.ConclusionsAffective symptoms are more clearly associated with self-reported memory problems in late midlife than with objectively measured cognitive performance.
Cell migration and division in amoeboid-like fission yeast
Authors: Flor-Parra Ignacio , Bernal Manuel , Zhurinsky Jacob , Daga Rafael R. 
Published: December 2013

Summary
Yeast cells are non-motile and are encased in a cell wall that supports high internal turgor pressure. The cell wall is also essential for cellular morphogenesis and cell division. Here, we report unexpected morphogenetic changes in a Schizosaccharomyces pombe mutant defective in cell wall biogenesis. These cells form dynamic cytoplasmic protrusions caused by internal turgor pressure and also exhibit amoeboid-like cell migration resulting from repeated protrusive cycles. The cytokinetic ring responsible for cell division in wild-type yeast often fails in these cells; however, they were still able to divide using a ring-independent alternative mechanism relying on extrusion of the cell body through a hole in the cell wall. This mechanism of cell division may resemble an ancestral mode of division in the absence of cytokinetic machinery. Our findings highlight how a single gene change can lead to the emergence of different modes of cell growth, migration and division.
Mutations in the Drosophila ortholog of the vertebrate Golgi pH regulator (GPHR) protein disturb endoplasmic reticulum and Golgi organization and affect systemic growth
Authors: Charroux Bernard , Royet Julien 
Published: December 2013

Summary
Sorting of secretory cargo and retrieval of components of the biosynthetic pathway occur in organelles such as the Golgi apparatus, the endoplasmic reticulum and the endosomes. In order to perform their functions in protein sorting, these organelles require a weakly acidified lumen. In vitro data have shown that Golgi luminal pH is in part regulated by an anion channel called Golgi pH Regulator (GPHR). Mammalian cells carrying a mutated GPHR version present an increased luminal pH leading to delayed protein transport, impaired glycosylation and Golgi disorganization. Using Drosophila as a model system, we present here the first phenotypic consequences, at the organism level, of a complete lack of GPHR function. We show that, although all individuals carrying complete loss-of-function mutations in the dGPHR gene can go through embryonic development, most of them die at late larval stages. The dGPHR mutations are, however, sublethal and can therefore generate escapers that are smaller than controls. Using cellular and molecular readouts, we demonstrate that the effects of dGPHR mutation on larval growth are not due to Insulin signaling pathway impairment and can be rescued by providing dGPHR in only some of the larval tissues. We reveal that, although functionally exchangeable, the invertebrate and vertebrate GPHRs display not completely overlapping sub-cellular localization. Whereas the mammalian GPHR is a Golgi-only associated protein whose inactivation disturbs the Golgi apparatus, our data suggest that dGPHR is expressed in both the ER and the Golgi and that dGPHR mutant flies have defects in both organelles that lead to a defective secretory pathway.
Zebrafish etv7 regulates red blood cell development through the cholesterol synthesis pathway
Authors: Quintana Anita M. , Picchione Fabrizio , Klein Geltink Ramon I. , Taylor Michael R. , Grosveld Gerard C. 
Published: December 2013

Summary
ETV7 is a human oncoprotein that cooperates with Eμ-MYC to promote pre B-cell leukemia in mice. It is normally expressed in the bone marrow and fetal liver and is up regulated in primary leukemia suggesting that it is involved in proper hematopoiesis and leukemogenesis. ETV7 has been deleted in most rodents, but is conserved in all other vertebrates including the zebrafish, Danio rerio. In this report, we characterize the function of the zebrafish etv7 gene during erythropoiesis. Our results demonstrate that etv7 regulates the expression of the zebrafish lanosterol synthase (lss) gene, an essential gene in the cholesterol synthesis pathway. Furthermore, morpholino knockdown of etv7 leads to loss of hemoglobin containing red blood cells, a phenotype which can be rescued by injection of exogenous cholesterol. We conclude that etv7 is essential for normal red blood cell development through regulation of the lss gene and the cholesterol synthesis pathway.
Catalytic Dehydration of 1,2-Propanediol into Propanal over Ag-Modified Silica–Alumina
Authors: Sun Daolai , Narita Ryosuke , Sato Fumiya , Yamada Yasuhiro , Sato Satoshi 
Published: December 2013

Abstract
Vapor-phase catalytic dehydration of 1,2-propanediol was investigated over several solid acid catalysts, such as alumina, silica–alumina, HY zeolite, and β-zeolite. These acids catalyzed the dehydration of 1,2-propanediol to produce propanal (Figure 1Figure 1. Dehydration of 1,2-propanediol to propanal.), while zeolites were particularly deactivated because of deposition of carbonaceous species. An amorphous silica–alumina was modified with metals such as Ag and Cu to stabilize the catalytic activity under hydrogen flow conditions. Ag-modified silica–alumina is a promising catalyst for the production of propanal from 1,2-propanediol.
Development of a Flow-injection Spin-trapping ESR System for Estimation of Second-order Rate Constants for Reactions of a Superoxide Radical Anion and Selected Phenolic Compounds
Authors: Sakurai Yasuhiro , Yamaguchi Tomoko , Nakajima Akira , Kanaori Kenji , Tajima Kunihiko 
Published: December 2013

Abstract
A flow-injection ESR system was developed for the quantitative detection of a superoxide radical anion (O2•−), which was generated by the riboflavin-dependent photoreduction of oxygen. This system was applied for estimation of second-order rate constants (ks) of the reactions between the O2•− and selected phenolic compounds, such as caffeic acid, chlorogenic acid, rutin, trolox, vanillic acid, and 4-hydroxycinnamic acid.
Inside Debt and the Design of Corporate Debt Contracts
Authors: Anantharaman Divya , Fang Vivian W. , Gong Guojin 
Published: December 2013

Theory posits that managerial holdings of debt (“inside debt”) align managers' incentives with those of outside debtholders. Executive pensions, consisting of rank-and-file (RAF) plans and supplemental executive retirement plans (SERPs), and other deferred compensation (ODC) have debt-like payoffs, and could therefore function as inside debt. However, whereas SERPs are often unfunded and unsecured, RAF plans are funded and secured to some extent, and ODC may be invested in equity and withdrawn flexibly before retirement. Special arrangements in executive debt-like compensation could hence weaken or even nullify any incentive-alignment effect. We find that higher CEO debt-like compensation leads to lower promised yield and fewer covenants in a sample of loans originated in 2006–2008. This effect is driven entirely by benefits accrued under SERPs, consistent with SERPs more closely resembling risky corporate debt; balances accrued under RAF and ODC plans do not provide similar effects. Furthermore, promised yields are lower when debt-like compensation claims can be withdrawn only after outside debt claims are expected to settle. Our findings persist after accounting for endogeneity using state personal income tax rates as an instrument for CEOs' willingness to defer compensation. Overall, the evidence suggests that executive debt-like compensation is only effective at resolving stockholder–debtholder conflicts when its payoffs are truly debt-like and that lenders' perceptions are affected not only by the magnitude of debt-like compensation but also by its seniority. Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2013.1813 . This paper was accepted by Wei Jiang, finance.