bluuebunny/crossref_metadata_2025 huggingface dataset:
Degradation and half-life of DNA present in biomass from a genetically-modified organism during land application
Authors: Halter Mathew C , Zahn James A
Published: December 2016

White biotechnology has made a positive impact on the chemical industry by providing safer, more efficient chemical manufacturing processes that have reduced the use of toxic chemicals, harsh reaction conditions, and expensive metal catalysts, which has improved alignment with the principles of Green Chemistry. The genetically-modified (GM) biocatalysts that are utilized in these processes are typically separated from high-value products and then recycled, or eliminated. Elimination routes include disposal in sanitary landfills, incineration, use as a fuel, animal feed, or reuse as an agricultural soil amendment or other value-added products. Elimination routes that have the potential to impact the food chain or environment have been more heavily scrutinized for the fate and persistence of biological products. In this study, we developed and optimized a method for monitoring the degradation of strain-specific DNA markers from a genetically-modified organism (GMO) used for the commercial production of 1,3-propanediol. Laboratory and field tests showed that a marker for heterologous DNA in the GM organism was no longer detectable by end-point polymerase chain reaction (PCR) after 14 days. The half-life of heterologous DNA was increased by 17% (from 42.4 to 49.7 h) after sterilization of the soil from a field plot, which indicated that abiotic factors were important in degradation of DNA under field conditions. There was no evidence for horizontal transfer of DNA target sequences from the GMO to viable organisms present in the soil.
Mechanisms and ecological implications of plant‐mediated interactions between belowground and aboveground insect herbivores
Authors: Papadopoulou Galini V. , van Dam Nicole M.
Published: November 2016

Plant‐mediated interactions between belowground (BG) and aboveground (AG) herbivores have received increasing interest recently. However, the molecular mechanisms underlying ecological consequences of BG–AG interactions are not fully clear yet. Herbivore‐induced plant defenses are complex and comprise phytohormonal signaling, gene expression and production of defensive compounds (defined here as response levels), each with their own temporal dynamics. Jointly they shape the response that will be expressed. However, because different induction methods are used in different plant‐herbivore systems, and only one or two response levels are measured in each study, our ability to construct a general framework for BG–AG interactions remains limited. Here we aim to link the mechanisms to the ecological consequences of plant‐mediated interactions between BG and AG insect herbivores. We first outline the molecular mechanisms of herbivore‐induced responses involved in BG–AG interactions. Then we synthesize the literature on BG–AG interactions in two well‐studied plant‐herbivore systems, Brassica spp. and Zea mays, to identify general patterns and specific differences. Based on this comprehensive review, we conclude that phytohormones can only partially mimic induction by real herbivores. BG herbivory induces resistance to AG herbivores in both systems, but only in maize this involves drought stress responses. This may be due to morphological and physiological differences between monocotyledonous (maize) and dicotyledonous (Brassica) species, and differences in the feeding strategies of the herbivores used. Therefore, we strongly recommend that future studies explicitly account for these basic differences in plant morphology and include additional herbivores while investigating all response levels involved in BG–AG interactions.
Azolla — A Model Organism for Plant Genomic Studies
Authors: Qiu Yin-Long , Yu Jun
Published: November 2016

The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.
A Novel Approach for Identifying the Heme-Binding Proteins from Mouse Tissues
Authors: Li Xiaolei , Wang Xiaoshan , Zhao Kang , Zhou Zhengfeng , Zhao Caifeng , Yan Ren , Lin Liang , Lei Tingting , Yin Jianning , Wang Rong , Feng Xiaoli , Liu Siqi
Published: November 2016

Heme is a key cofactor in aerobic life, both in eukaryotes and prokaryotes. Because of the high reactivity of ferrous protoporphyrin IX, the reactions of heme in cells are often carried out through heme-protein complexes. Traditionally studies of heme-binding proteins have been approached on a case by case basis, thus there is a limited global view of the distribution of heme-binding proteins in different cells or tissues. The procedure described here is aimed at profiling heme-binding proteins in mouse tissues sequentially by 1) purification of heme-binding proteins by heme-agarose, an affinity chromatographic resin; 2) isolation of heme-binding proteins by SDS-PAGE or two-dimensional electrophoresis; 3) identification of heme-binding proteins by mass spectrometry. In five mouse tissues, over 600 protein spots were visualized on 2DE gel stained by Commassie blue and 154 proteins were identified by MALDI-TOF, in which most proteins belong to heme related. This methodology makes it possible to globally characterize the heme-binding proteins in a biological system.
The Structural Characterization and Antigenicity of the S Protein of SARS-CoV
Authors: Li Jingxiang , Luo Chunqing , Deng Yajun , Han Yujun , Tang Lin , Wang Jing , Ji Jia , Ye Jia , Jiang Fanbo , Xu Zhao , Tong Wei , Wei Wei , Zhang Qingrun , Li Shengbin , Li Wei , Li Hongyan , Li Yudong , Dong Wei , Wang Jian , Bi Shengli , Yang Huanming
Published: November 2016

The corona-like spikes or peplomers on the surface of the virion under electronic microscope are the most striking features of coronaviruses. The S (spike) protein is the largest structural protein, with 1,255 amino acids, in the viral genome. Its structure can be divided into three regions: a long N-terminal region in the exterior, a characteristic transmembrane (TM) region, and a short C-terminus in the interior of a virion. We detected fifteen substitutions of nucleotides by comparisons with the seventeen published SARS-CoV genome sequences, eight (53.3%) of which are non-synonymous mutations leading to amino acid alternations with predicted physiochemical changes. The possible antigenic determinants of the S protein are predicted, and the result is confirmed by ELISA (enzyme-linked immunosorbent assay) with synthesized peptides. Another profound finding is that three disulfide bonds are defined at the C-terminus with the N-terminus of the E (envelope) protein, based on the typical sequence and positions, thus establishing the structural connection with these two important structural proteins, if confirmed. Phylogenetic analysis reveals several conserved regions that might be potent drug targets.
The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV
Authors: Wang Jingqiang , Ji Jia , Ye Jia , Zhao Xiaoqian , Wen Jie , Li Wei , Hu Jianfei , Li Dawei , Sun Min , Zeng Haipan , Hu Yongwu , Tian Xiangjun , Tan Xuehai , Xu Ningzhi , Zeng Changqing , Wang Jian , Bi Shengli , Yang Huanming
Published: November 2016

The Coronaviridae family is characterized by a nucleocapsid that is composed of the genome RNA molecule in combination with the nucleoprotein (N protein) within a virion. The most striking physiochemical feature of the N protein of SARS-CoV is that it is a typical basic protein with a high predicted pI and high hydrophilicity, which is consistent with its function of binding to the ribophosphate backbone of the RNA molecule. The predicted high extent of phosphorylation of the N protein on multiple candidate phosphorylation sites demonstrates that it would be related to important functions, such as RNA-binding and localization to the nucleolus of host cells. Subsequent study shows that there is an SR-rich region in the N protein and this region might be involved in the protein-protein interaction. The abundant antigenic sites predicted in the N protein, as well as experimental evidence with synthesized polypeptides, indicate that the N protein is one of the major antigens of the SARS-CoV. Compared with other viral structural proteins, the low variation rate of the N protein with regards to its size suggests its importance to the survival of the virus.
Gene Expression Profiling in Porcine Fetal Thymus
Authors: Chen Yanjiong , Li Shengbin , Ye Lin , Geng Jianing , Deng Yajun , Hu Songnian
Published: November 2016

To obtain an initial overview of gene diversity and expression pattern in porcine thymus, 11,712 ESTs (Expressed Sequence Tags) from 100-day-old porcine thymus (FTY) were sequenced and 7,071 cleaned ESTs were used for gene expression analysis. Clustered by the PHRAP program, 959 contigs and 3,074 singlets were obtained. Blast search showed that 806 contigs and 1,669 singlets (totally 5,442 ESTs) had homologues in GenBank and 1,629 ESTs were novel. According to the Gene Ontology classification, 36.99% ESTs were cataloged into the gene expression group, indicating that although the functional gene (18.78% in defense group) of thymus is expressed in a certain degree, the 100-day-old porcine thymus still exists in a developmental stage. Comparative analysis showed that the gene expression pattern of the 100-day-old porcine thymus is similar to that of the human infant thymus.
Functional Genomics of Wood Quality and Properties
Authors: Tang Wei , Luo Xiaoyan , Nelson Aaron , Collver Hilary , Kinken Katherine
Published: November 2016

Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.
SeeDNA: A Visualization Tool for K-String Content of Long DNA Sequences and Their Randomized Counterparts
Authors: Shen Junjie , Zhang Shuyu , Lee Hoong-Chien , Hao Bailin
Published: November 2016

An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK+ package is freely available.
Clustering Gene Expression Data Based on Predicted Differential Effects of GV Interaction
Authors: Pan Hai-Yan , Zhu Jun , Han Dan-Fu
Published: November 2016

Microarray has become a popular biotechnology in biological and medical research. However, systematic and stochastic variabilities in microarray data are expected and unavoidable, resulting in the problem that the raw measurements have inherent “noise” within microarray experiments. Currently, logarithmic ratios are usually analyzed by various clustering methods directly, which may introduce bias interpretation in identifying groups of genes or samples. In this paper, a statistical method based on mixed model approaches was proposed for microarray data cluster analysis. The underlying rationale of this method is to partition the observed total gene expression level into various variations caused by different factors using an ANOVA model, and to predict the differential effects of GV (gene by variety) interaction using the adjusted unbiased prediction (AUP) method. The predicted GV interaction effects can then be used as the inputs of cluster analysis. We illustrated the application of our method with a gene expression dataset and elucidated the utility of our approach using an external validation.
Electrochemical Detection of Single A-G Mismatch Using Biosensing Surface Based on Gold Nanoparticles
Authors: Zhang Ren-Yun , Wang Xue-Mei , Gong Sheng-Jin , He Nong-Yue
Published: November 2016

The study of small drug molecules interacting with nucleic acids is an area of intense research that has particular relevance in our understanding of relative mechanism in chemotherapeutic applications and the association between genetics (including sequence variation) and drug response. In this contribution, we demonstrate how the sequence-specific binding of an anticancer drug Dacarbazine (DTIC) to single base (A-G) mismatch could be sensitively detected by combining electrochemical detection with biosensing surface based on gold nanoparticles.
PoInTree: A Polar and Interactive Phylogenetic Tree
Authors: Marco Carreras , Eleonora Gianti , Luca Sartori , Edward Plyte Simon , Antonella Isacchi , Roberta Bosotti
Published: November 2016

PoInTree (Polar and Interactive Tree) is an application that allows to build, visualize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component (Steema software).
Classifying Genomic Sequences by Sequence Feature Analysis
Authors: Liu Zhi-Hua , Jiao Dian , Sun Xiao
Published: November 2016

Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream, exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.
Characterizing the Microenvironment Surrounding Phosphorylated Protein Sites
Authors: Fan Shi-Cai , Zhang Xue-Gong
Published: November 2016

Protein phosphorylation plays an important role in various cellular processes. Due to its high complexity, the mechanism needs to be further studied. In the last few years, many methods have been contributed to this field, but almost all of them investigated the mechanism based on protein sequences around protein sites. In this study, we implement an exploration by characterizing the microenvironment surrounding phosphorylated protein sites with a modified shell model, and obtain some significant properties by the rank-sum test, such as the lack of some classes of residues, atoms, and secondary structures. Furthermore, we find that the depletion of some properties affects protein phosphorylation remarkably. Our results suggest that it is a meaningful direction to explore the mechanism of protein phosphorylation from microenvironment and we expect further findings along with the increasing size of phosphorylation and protein structure data.
Identifying G-Protein Coupled Receptors Using Weighted Levenshtein Distance and Nearest Neighbor Method
Authors: Xu Jian-Hua
Published: November 2016

G-protein coupled receptors (GPCRs) are a class of seven-helix transmembrane proteins that have been used in bioinformatics as the targets to facilitate drug discovery for human diseases. Although thousands of GPCR sequences have been collected, the ligand specificity of many GPCRs is still unknown and only one crystal structure of the rhodopsin-like family has been solved. Therefore, identifying GPCR types only from sequence data has become an important research issue. In this study, a novel technique for identifying GPCR types based on the weighted Levenshtein distance between two receptor sequences and the nearest neighbor method (NNM) is introduced, which can deal with receptor sequences with different lengths directly. In our experiments for classifying four classes (acetylcholine, adrenoceptor, dopamine, and serotonin) of the rhodopsin-like family of GPCRs, the error rates from the leave-one-out procedure and the leave-half-out procedure were 0.62% and 1.24%, respectively. These results are prior to those of the covariant discriminant algorithm, the support vector machine method, and the NNM with Euclidean distance.
From Anti-Judaism to Anti-Semitism
Authors: Chazan Robert
Published: November 2016

From its earliest days, Christianity has viewed Judaism and Jews ambiguously. Given its roots within the Jewish community of first-century Palestine, there was much in Judaism that demanded Church admiration and praise; however, as Jews continued to resist Christian truth, there was also much that had to be condemned. Major Christian thinkers of antiquity - while disparaging their Jewish contemporaries for rejecting Christian truth - depicted the Jewish past and future in balanced terms, identifying both positives and negatives. Beginning at the end of the first millennium, an increasingly large Jewish community started to coalesce across rapidly developing northern Europe, becoming the object of intense popular animosity and radically negative popular imagery. The portrayals of the broad trajectory of Jewish history offered by major medieval European intellectual leaders became increasingly negative as well. The popular animosity and the negative intellectual formulations were bequeathed to the modern West, which had tragic consequences in the twentieth century. In this book, Robert Chazan traces the path that began as anti-Judaism, evolved into heightened medieval hatred and fear of Jews, and culminated in modern anti-Semitism.
The Politics of Technology in Africa
Authors: Gagliardone Iginio
Published: November 2016

As more Africans get online, information and communication technologies (ICTs) are increasingly hailed for their transformative potential. Yet, the fascination for the possibilities of promoting more inclusive forms of development in the information age have obfuscated the reality of the complex negotiations among political and economic actors who are seeking to use technology in their competition for power. Building on over ten years of research in Ethiopia, Iginio Gagliardone investigates the relationship between politics, development, and technological adoption in Africa's second most populous country and its largest recipient of development aid. The emphasis the book places on the 'technopolitics' of ICTs, and on their ability to embody and enact political goals, offers a strong and empirically grounded counter-argument to prevalent approaches to the study of technology and development that can be applied to other cases in Africa and beyond.
Authenticity, Power, and Pluralism: A Framework for Understanding Stakeholder Evaluations of Corporate Social Responsibility Activities
Authors: Skilton Paul F. , Purdy Jill M.
Published: November 2016

We explore the essential contestedness of corporate social responsibility (CSR) by framing the interplay between CSR activities and stakeholder evaluations as a contest for jurisdiction over what it means to be socially responsible. This contest arises because firms and stakeholders are often guided by incompatible sensemaking systems. To show why context matters we show how stakeholders evaluate the authenticity of CSR activities on the basis of schemas for responsible behavior on one hand and their perceptions of firm identity on the other. This process can generate complex evaluations whose meaning depends on the distribution of power in fields and the extent to which pluralistic sensemaking systems are compatible. By positioning authenticity evaluations within a framework that describes the state of power and pluralism within which they are produced, we are able to present a systematic explanation of how and why stakeholder responses to CSR vary over a range of settings.
A Critical Interpretive Synthesis of the Ways Children's Needs and Capacities are Represented in the Homelessness and Family Violence Literature
Authors: Fairchild Rebecca , McFerran Katrina Skewes , Thompson Grace
Published: November 2016

This paper describes a critical interpretive synthesis (critical review of the literature) exploring the ways children are described and represented in the homelessness and family violence literature regarding programmes. Authors' descriptions of children and their perceived needs are considered from individual, interpersonal and systemic positions, with an inherent focus on the influence of academic language and power in representing children. The articles reviewed here contained an abundance of negative descriptions of children's poor health, educational and developmental outcomes, but very little acknowledgement of children's personal resources and capacities in times of adversity. The programme goals and strengths-based therapeutic intentions described by the authors of these articles were not always congruent with the ways children were being represented in the early stages of the articles. We argue for a better balance in representing children's strengths alongside their challenges when describing their presentation and participation in programmes and research.
Grouped Cases of Pulmonary Pneumocystosis After Solid Organ Transplantation: Advantages of Coordination by an Infectious Diseases Unit for Overall Management and Epidemiological Monitoring
Authors: Wintenberger Claire , Maubon Daniele , Charpentier Elena , Rendu John , Pavese Patricia , Augier Caroline , Malvezzi Paolo , Camara Boubou , Mallaret Marie-Reine , Bouillet Laurence , Epaulard Olivier
Published: November 2016

OBJECTIVE

To determine the origin of grouped cases of Pneumocystis pneumonia in solid-organ transplant recipients at our institution.

DESIGN

A case series with clinical examinations, genotyping, and an epidemiological survey.

SETTING

A university hospital in France.

PATIENTS

We report 12 solid-organ transplant recipients with successive cases of Pneumocystis pneumonia that occurred over 3 years; 10 of these cases occurred in a single year.

METHODS

We used molecular typing of P. jirovecii strains by multilocus sequence typing and clinical epidemiological survey to determine potential dates and places of transmission.

RESULTS

Between May 2014 and March 2015, 10 solid-organ transplant recipients (5 kidney transplants, 4 heart transplants, and 1 lung transplant) presented with Pneumocystis pneumonia. Molecular genotyping revealed the same P. jirovecii strain in at least 6 patients. This Pneumocystis strain was not identified in control patients (ie, nontransplant patients presenting with pulmonary pneumocystosis) during this period. The epidemiological survey guided by sequencing results provided information on the probable or possible dates and places of contamination for 5 of these patients. The mobile infectious diseases unit played a coordination role in the clinical management (adaptation of the local guidelines) and epidemiological survey.

CONCLUSION

Our cardiac and kidney transplant units experienced grouped cases of pulmonary pneumocystosis. Genotyping and epidemiological surveying results suggested interhuman contamination, which was quickly eliminated thanks to multidisciplinary coordination.

Infect Control Hosp Epidemiol 2017;38:179–185
An Evaluation of Antibiotic Prescribing Practices Upon Hospital Discharge
Authors: Scarpato Sarah J. , Timko Daniel R. , Cluzet Valerie C. , Dougherty Jillian P. , Nunez Jonathan J. , Fishman Neil O. , Hamilton Keith W. ,   for the CDC Prevention Epicenters Program
Published: November 2016

We conducted a retrospective study of the appropriateness of antimicrobial agents prescribed on discharge from an acute care hospital. Seventy percent of discharge antibiotics were inappropriate in antibiotic drug choice, dose, or duration. Our findings suggest there is a significant need for antimicrobial stewardship at transitions in care.

Infect Control Hosp Epidemiol 2017;38:353–355
Sport, Educational Engagement and Positive Youth Development: Reflections of Aboriginal Former Youth Sports Participants
Authors: Fitch Nicole , Ma'ayah Fadi , Harms Craig , Guilfoyle Andrew
Published: November 2016

Participation in sport during high school has been linked with a range of educational and developmental benefits. However, there is limited research investigating the benefits of participation in sport from the perspective of Aboriginal former youth sports participants. The purpose of the current research was to investigate how participation in sports impacted on the educational engagement, aspirations and development of Aboriginal former youth sports participants. Interpretive phenomenological analysis of semistructured interviews with six participants was conducted. Analysis was conducted utilising the Positive Youth Development asset framework. Participants reported a positive influence for their participation in youth sport on key education related assets including, achievement motivation, school engagement and relationships with teachers. Participants also reflected upon the role of participation in youth sports in the development of empowerment and positive identity assets. For these participants, involvement in youth sport had clear educational and developmental benefits. It is concluded that youth sports participation is one developmental context with the potential to have a positive influence on the educational and developmental trajectory of Aboriginal youth.
Mission-Driven Adaptability in a Changing National Training System
Authors: Zoellner Don , Stephens Anne , Joseph Victor , Monro Davena
Published: December 2016

This case study of an adult and community education provider based in far north Queensland describes its capacity to balance various iterations of public policy against its vision for the future of Aboriginal and Torres Straits Islanders. Community-controlled organisations wanting to contribute to economic and social development in regional/remote Australia through the use of formally recognised vocational education and training have adjusted to at least three major sociopolitical changes at the national policy level since the early 1990s. These include redefining equity, marketising the delivery of public services and increased centralisation. The contemporary orientation of vocational education and training as part of the Indigenous Advancement Strategy has become a highly prescriptive and heavily centralised mechanism for the establishment of employment outcomes. This has been framed as an obligation and right of Australian citizenship as opposed to the other wellbeing and personal development benefits of education. This registered training organisation has navigated four burdensome (re)definitions of equity that have made planning and delivery of true lifelong training objectives difficult. The provider has embraced the marketisation of the sector and navigated other policy changes in order to provide the services and knowledge set out in the college mission statement.
ON APPROXIMATE SOLUTIONS OF SOME DIFFERENCE EQUATIONS
Authors: BRZDĘK JANUSZ , WÓJCIK PAWEŁ
Published: December 2016

In this paper we present a simple (fixed point) method that yields various results concerning approximate solutions of some difference equations. The results are motivated by the notion of Ulam stability.
Epigenetics in type 1 diabetes:TNFagene promoter methylation status in Chilean patients with type 1 diabetes mellitus
Authors: Arroyo-Jousse Viviana , Garcia-Diaz Diego F. , Codner Ethel , Pérez-Bravo Francisco
Published: November 2016

TNF-αis a pro-inflammatory cytokine that is involved in type 1 diabetes (T1D) pathogenesis. TheTNFagene is subject of epigenetic regulation in which folate and homocysteine are important molecules because they participate in the methionine cycle where the most important methyl group donor (S-adenosylmethionine) is formed. We investigated whetherTNFagene promoter methylation status in T1D patients was related to blood folate, homocysteine and TNF-αin a transversal case–control study. We studied T1D patients (n25, mean=13·7 years) and healthy control subjects (n25, mean=31·1 years), without T1D and/or other autoimmune diseases or direct family history of these diseases. A blood sample was obtained for determination of serum folate, plasma homocysteine and TNF-αconcentrations. Whole blood was used for the extraction of DNA to determine the percentage of methylation by real-time PCR and melting-curve analysis. Results are expressed as means and standard deviations for parametric variables and as median (interquartile range) for non-parametric variables. T1D patients showed a higherTNFagene promoter methylation (39·2 (sd19·5) %) when compared with control subjects (25·4 (sd13·7) %) (P=0·008).TNFagene promoter methylation was positively associated only with homocysteine levels in T1D patients (r0·55,P=0·007), but not in control subjects (r−0·122,P=0·872). To our knowledge, this is the first work that reports the methylation status of theTNFagene promoter and its relationship with homocysteine metabolism in Chilean T1D patients without disease complications.
Fāṭimid gardens: archaeological and historical perspectives
Authors: Pradines Stephane , Khan Sher Rahmat
Published: November 2016

This article is the first systematic investigation on the location, layout, design and functions of Fāṭimid gardens. Our study is based on primary sources and focuses on different elements of the recreational and ceremonial functions of gardens. Very little is known about the layout of the royal Fāṭimid gardens because no garden has survived or been excavated so far as we are aware. However, we collected physical insights on the layout and shape of these Fāṭimid gardens through different archaeological excavations in Cairo and outside of Egypt, including our recent discoveries and the garden that we found in Darrāsa.
Emerging preoccupations, developing lexicon
Authors: Poole Brian
Published: November 2016

‘There is a very close link between the life of a society and the lexicon of the language spoken by it.’ (Wierzbicka, 1997: 1).

A few decades ago it probably seemed, to proficient English language users, that if one was ‘active’ that would be sufficient to win plaudits from one's boss and to impress one's friends. After all, being active implies, amongst other things, that one's behaviour is ‘characterized by busy or lively activity’ (Oxford Dictionaries online). However, more recently it has begun to seem that activeness is not enough: one must be ‘proactive’. Cooley (2016) provides readers with ten ways in which they can be more proactive at work. The promotion of proactiveness (or should that be proactivity?) seems, at least on the evidence of this extract, to require a liberal sprinkling of exclamation marks
X-ray powder diffraction of high-absorption materials at the XRD1 beamline off the best conditions: Application to (Gd, Nd)5Si4 compounds
Authors: Carvalho A. M. G. , Nunes R. S. , Coelho A. A.
Published: November 2016

Representative compounds of the new family of magnetic materials Gd5−xNdxSi4 were analyzed by X-ray diffraction at the XRD1 beamline at Laboratório Nacional de Luz Síncrotron. To reduce X-ray absorption, thin layers of the powder samples were mounted outside the capillaries and measured in Debye–Scherrer geometry as usual. The XRD analyses and the magnetometry results indicate that the behavior of the magnetic transition temperature as a function of Nd content may be directly related to the average of the four smallest interatomic distances between different rare earth sites of the majority phase of each compound. The quality and consistency of the results show that the XRD1 beamline is able to perform satisfactory XRD experiments on high-absorption materials even off the best conditions.
Epidemic host community contribution to mosquito-borne disease transmission: Ross River virus
Authors: KOOLHOF I. S. , CARVER S.
Published: November 2016

Most vector-borne diseases infect multiple host species, but disentangling the relative importance of different host species to transmission can be complex. Here we study how host species’ abundance and competence (duration and titre of parasitaemia) influence host importance during epidemic scenarios. We evaluate this theory using Ross River virus (RRV, family Togaviridae, genus Alphavirus), a multi-host mosquito-borne disease with significant human health impacts across Australia and Papua New Guinea. We used host contribution models to find the importance of key hosts (possums, wallabies, kangaroos, horses, humans) in typical mammal communities around five Australian epidemic centres. We found humans and possums contributed most to epidemic RRV transmission, owing to their high abundances, generally followed by macropods. This supports humans as spillover hosts, and that human–mosquito and possum–mosquito transmission is predominant during epidemics. Sensitivity analyses indicate these findings to be robust across epidemic centres. We emphasize the importance of considering abundance and competence in identifying key hosts (during epidemics in this case), and that competence alone is inadequate. Knowledge of host importance in disease transmission may help to equip health agencies to bring about greater effectiveness of disease mitigation strategies.
War and Global Public Reason
Authors: WILLIAMS JEREMY
Published: November 2016

This article offers a new critical evaluation of the Rawlsian model of global public reason (‘GPR’), focusing on its ability to serve as a normative standard for guiding international diplomacy and deliberation in matters of war. My thesis is that, where war is concerned, the model manifests two fatal weaknesses. First, because it demands extensive neutrality over the moral status of persons – and in particular over whether they possess equal basic worth or value – out of respect for the beliefs of inegalitarian yet ‘decent’ societies, or ‘peoples’, Rawlsian GPR renders calculations of proportionality in war impossible. Second, because its content is provided by a conception of global justice (the so-called ‘Law of Peoples’) whose injunctions are addressed exclusively to peoples, as corporate agents, Rawlsian GPR pushes the moral evaluation of the independent wartime choices of individuals off the agenda of the global public forum altogether.
Competing systems in Philadelphia phonology
Authors: Labov William , Fisher Sabriya , Gylfadottír Duna , Henderson Anita , Sneller Betsy
Published: November 2016

This is a study of the competition of linguistic systems within the speech community, tracing the opposition of distinct phonological configurations. Among younger Philadelphians oriented to higher education, the traditional short-a system is giving way to the nasal system, in which all prenasal vowels are tense. We present evidence that this shift occurs systematically in both the lax and tense allophones. The degree of conformity to each system is measured for 106 subjects by the Pillai statistic; community-wide patterns are revealed by regression modeling and bimodality diagrams. Adherence to the traditional system is greatest for White speakers who graduated from Catholic high schools, while the nasal system is strongest for graduates from elite schools with special admission requirements. African American students show no orientation to the traditional system, but parallel White students in the shift to the nasal system. The histories of students through the educational system show that the speaker's short-a system is largely determined during their middle and high school years, before entering college. Special admission interviews play a special role in this process, as brief speech events that strongly determine the person's linguistic environment for the years that follow.
ON THE TRAIL OF QUETZALCOATL/KUKULCAN: TRACING MYTHIC INTERACTION ROUTES AND NETWORKS IN THE MAYA LOWLANDS
Authors: Folan William J. , Bolles David D. , Ek Jerald D.
Published: November 2016

This paper examines ethnohistoric accounts and oral histories accumulated during the last 50 years concerning the movements of the mythical personage of Quetzalcoatl/Kukulcan (Kukul Can) and the role of these narratives in political ideologies between the Epiclassic and Postclassic periods. These narratives outline the movements of Quetzalcoatl/Kukulcan by way of terrestrial, celestial, and subterranean routes that connected pilgrimage centers across the Maya lowlands in the peninsula of Yucatan. Ethnographic and ethnohistoric data presented in this paper describe linkages between important political, economic, and ritual centers that had roots in pan-Mesoamerican social dynamics originating as early as the Terminal Classic or Epiclassic period. Links between cities included not just the physical intersite connections evidenced by causeways that are so prominent in the archaeological record but also intangible, mythical, and symbolic connections embodied in mythical histories of subterranean passageways and celestial umbilical cords. These accounts and oral histories highlight the importance of migration and founding events in the establishment of new cities during the major political, economic, and social reorganizations that took place after the end of the Late Classic period. As a whole, these linkages comprised a political infrastructure connecting a network of cities within the highly integrated and international Postclassic Mesoamerican world. The indigenous histories outlined in this paper complement archaeological data, reflecting an increase in internationalism, economic integration, and the spread of new religious movements beginning in the Terminal or Epiclassic periods across Mesoamerica.
HUMAN SACRIFICE AND DIVINE NOURISHMENT IN MESOAMERICA: THE ICONOGRAPHY OF CACAO ON THE PACIFIC COAST OF GUATEMALA
Authors: Chinchilla Mazariegos Oswaldo
Published: November 2016

This article explores the sacrificial symbolism of cacao (Theobromasp.) on the Pacific coast of Guatemala, manifest in the iconography of ceramic objects and stone sculptures from the Classic period, in textual references from the colonial period, and in contemporary ethnographic data from the southern highlands. The iconographic and textual metaphors contained in these sources linked cacao pods with dead warriors, captives, and sacrificial victims. As interpreted in this article, the harvest of cacao was equated with the acquisition of sacrificial victims, and both were conceived as precious sources of nourishment for the gods. Changes in artistic representations are discernible from Early Classic Teotihuacan-style censers to Early Postclassic Plumbate ceramic effigies. Cacao and other fruits from the Pacific coastal piedmont are still related to the symbolism of war and sacrifice in contemporary rituals from the Tz'utujil town of Santiago Atitlán. Data from southern Guatemala may be relevant to understand the sacrificial symbolism of cacao throughout Mesoamerica.
THE POLYCHROME CERAMICS OF TUTUTEPEC (YUCU DZAA), OAXACA, MEXICO: ICONOGRAPHY AND IDEOLOGY
Authors: Forde Jamie E.
Published: November 2016

In this article, I present the results of an analysis of codex-style polychrome ceramics recovered from excavations of commoner households at the Late Postclassic center of Tututepec (Yucu Dzaa), Oaxaca, Mexico. In employing a basic semiotic approach, I examine the images depicted on these materials to draw inferences regarding salient themes they expressed, and how these themes related to broader social discourse and political ideology. In short, I argue that the data suggest an articulation between the popular ideologies of commoners and ideals that were promoted by the site's ruling elites, a concordance that likely arose through dialogic social processes, rather than coercion or false consciousness. This state of affairs may have contributed to the success of the polity, which was the center of a powerful territorial empire at the time of Spanish contact.
FILTH AND HEALING IN YUCATAN: INTERPRETING IX HUN AHAU, A MAYA GODDESS
Authors: Knowlton Timothy W.
Published: November 2016

This paper analyzes the roles and attributes of the Maya goddess Ix Hun Ahau, the female manifestation of Hun Ahau that appears in theRitual of the Bacabs. This Colonial Yucatec text is our earliest surviving source for how Maya cosmology provided a framework for healing practices. Although the extant manuscript dates to the late eighteenth century, it is the culmination of centuries of interethnic interaction, including innovations emerging from the intellectual exchange that characterized Mesoamerica during the Late Postclassic period (ca. A.D. 1200–1500). The accoutrements and activities ascribed to this goddess in the incantations identify her as a Maya parallel to Tlazolteotl-Ixcuina, the Nahua goddess of weaving, sexuality, pollution, and its purification. Pollution concepts and purification practices that are otherwise peripheral in theRitual of the Bacabs are specifically related to Ix Hun Ahau, suggesting that early intellectual exchange between Mesoamerican peoples extended to medical cosmologies as well.
A SEVENTH-CENTURY INSCRIBED MINIATURE FLASK FROM COPAN FOUND AT TAZUMAL, EL SALVADOR
Authors: Card Jeb J. , Zender Marc
Published: November 2016

Late Classic interaction between Copan and western El Salvador has been archaeologically recognized in prestige items, monumental influences, and the common use of Copador ceramics. An inscribed flask excavated in 1952 in the main pyramid at Tazumal, El Salvador provides historical evidence for these ties. The flask is dedicated as the property of K'ahk' Uti' Witz' K'awiil (Copan Ruler 12), a long-lived seventh-century ruler who presided over the expansion of Copan's influence far outside of the Copan valley. The flask is the only hieroglyphic text from El Salvador naming a recognizable individual or that can be dated to an absolute calendrical span, one of only a few miniature Classic Maya vessels tagged with an individual's name, and the only one naming anajaw(lord). The vessel's text, iconography, and context brings the political relationship between Copan and western El Salvador into sharper focus.
CASTING MAIZE SEEDS IN AN AYÖÖK COMMUNITY: AN APPROACH TO THE STUDY OF DIVINATION IN MESOAMERICA
Authors: Rojas Araceli
Published: November 2016

Recent investigation among the Ayöök (Mixe) people of Oaxaca showed that the on-going use of a 260-day calendar complements the divinatory technique of casting maize seeds. This paper offers a detailed description of this mantic practice as a means to approach and better understand precolonial divinatory practices and the people who practiced them, such as thetonalopouhqueamong the Nahua. In particular, this new data will also serve to shed light on the use of the pictorial manuscripts that portray the 260-day calendar, such as the so-called Borgia Group Codices. Along these lines, historical and colonial accounts, origin narratives, visual culture, and the archaeology surrounding divination will also be re-examined. This article will show that, similar to the Ayöök contemporary daykeepers and diviners, those that lived in the past were also wise women and men who were specialized in managing the complicated system of symbolism surrounding prognostication and prescription set out over 260 days. Furthermore, they employed divination for medical purposes and aided people with afflictions, curing them of sickness.
Local Conditions for Exponentially Many Subdivisions
Authors: LIU HONG , SHARIFZADEH MARYAM , STADEN KATHERINE
Published: November 2016

Given a graph F, let st(F) be the number of subdivisions of F, each with a different vertex set, which one can guarantee in a graph G in which every edge lies in at least t copies of F. In 1990, Tuza asked for which graphs F and large t, one has that st(F) is exponential in a power of t. We show that, somewhat surprisingly, the only such F are complete graphs, and for every F which is not complete, st(F) is polynomial in t. Further, for a natural strengthening of the local condition above, we also characterize those F for which st(F) is exponential in a power of t.