bluuebunny/crossref_metadata_2025 huggingface dataset:
Opportunities and constraints for biochar technology in Australian agriculture: looking beyond carbon sequestration
Authors: Singh Balwant , Macdonald Lynne M. , Kookana Rai S. , van Zwieten Lukas , Butler Greg , Joseph Stephen , Weatherley Anthony , Kaudal Bhawana B. , Regan Andrew , Cattle Julie , Dijkstra Feike , Boersma Mark , Kimber Stephen , Keith Alexander , Esfandbod Maryam
Published: November 2014

The application of biochar technology for soil amendment is largely based on evidence about soil fertility and crop productivity gains made in the Amazonian Black Earth (terra preta). However, the uncertainty of production gains at realistic application rates of biochars and lack of knowledge about other benefits and other concerns may have resulted in poor uptake of biochar technology in Australia so far. In this review, we identify important opportunities as well as challenges in the adoption of biochar technology for broadacre farming and other sectors in Australia. The paper highlights that for biochar technology to be cost-effective and successful, we need to look beyond carbon sequestration and explore other opportunities to value-add to biochar. Therefore, some emerging and novel applications of biochar are identified. We also suggest some priority research areas that need immediate attention in order to realise the full potential of biochar technology in agriculture and other sectors in Australia.
Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles
Authors: Tasinkevych Mykola , Campbell Michael G. , Smalyukh Ivan I.
Published: November 2014

Significance

There are few theoretical predictions of knotted, linked, solitonic, and other topologically nontrivial field configurations, which can be tested by experiments, due to the lack of experimentally accessible systems and techniques. This work presents an experimental realization and thorough theoretical analysis of interplay between topologies of the nematic field and closed confining surfaces with systematically varied genus. Handlebody-shaped nematic drops with normal boundary conditions reveal a large diversity of controlled field configurations, including ones with linked and knotted half-integer defect lines that are topologically distinct from predictions of mathematical theorems and that can exist only in nonpolar media. Our model system may become a testbed for probing a scale-invariant interplay of topologies of confining surfaces, fields, and defects.
Signaling pathways activated by a protease allergen in basophils
Authors: Rosenstein Rachel K. , Bezbradica Jelena S. , Yu Shuang , Medzhitov Ruslan
Published: November 2014

Significance

Helminths and allergens stimulate type 2 immune responses by largely unknown mechanisms. Proteolytic activity is a common feature of many helminths and allergens and can promote activation of the immune system. Signaling pathways activated by these proteases remain poorly characterized and are the focus of this study. Using basophils as model type 2 immune cells, we identified roles for the immunoreceptor tyrosine-based activation motif (ITAM)-containing adaptor Fc receptor γ-chain and calcium signaling in protease-stimulated basophil activation. We suggest models to explain how protease sensing, ITAM signaling, and nuclear factor of activated T cells pathways contribute to produce allergic type 2 responses. Elucidation of these signaling pathways and ultimately the identity of protease allergen sensors will be important for the development of pharmacologic strategies to target the initiation of allergic responses.
Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats
Authors: Brower Christopher S. , Rosen Connor E. , Jones Richard H. , Wadas Brandon C. , Piatkov Konstantin I. , Varshavsky Alexander
Published: November 2014

Significance

We describe the discovery and analyses of a previously uncharacterized protein, termed Liat1 (ligand of Ate1), which has been identified because of its interactions with the Ate1 arginyltransferase, a component of the N-end rule pathway of protein degradation. All vertebrates contain proteins similar to mouse Liat1. Remarkably, Liat1 proteins of some primates contain tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif. Quantities of these repeats are, in general, different in Liat1 of different primates. For example, there are 4, 13, 13, and 17 repeats in the gorilla, orangutan, bonobo, and human Liat1, respectively, suggesting that repeat number changes in this previously uncharacterized protein may contribute to evolution of primates.
From Tobacco Revolt to Youth Rebellion: A Social History of the Cigarette in Iran
Authors: Batmanghelidj Esfandyar
Published: November 2014

Focusing on the cultural influence of the cigarette, this paper synthesizes a wide range of evidence to argue that the cigarette was a fundamental primer for Iran's encounter with modernity, especially as understood in the context of western influence. Applying the dramaturgical theories of sociologist Erving Goffman, it is argued that the cigarette is an instantiation of the “sign-equipment” of modernization used to refashion the identity and subjectivity of Iranian men and women. This refashioning has occurred in three distinct periods. In the first period (1860–1930), cigarette smoking was a habit adopted by the Persian elite in an attempt to mediate the encounter with European colonial figures. In the second period (1930–70), cigarettes were leveraged by Iranians who wished to be seen as upwardly mobile. In the final and contemporary period (1970–present), cigarettes have become ubiquitous among the adult population, but smoking itself has become the act of youth rebellion as experimentation occurs at increasingly young ages.
Methicillin-ResistantStaphylococcus aureus:Site of Acquisition and Strain Variation in High-Risk Nursing Home Residents with Indwelling Devices
Authors: Gibson Kristen E. , McNamara Sara E. , Cassone Marco , Perri Mary Beth , Zervos Marcus , Mody Lona ,   on behalf of the Targeted Infection Prevention (TIP) Study Team, Ann Arbor, Michigan
Published: November 2014

Objective.

Characterize the clinical and molecular epidemiology of new methicillin-resistantStaphylococcus aureus(MRSA) acquisitions at nasal and extranasal sites among high-risk nursing home (NH) residents.

Design.

Multicenter prospective observational study.

Setting.

Six NHs in southeast Michigan.

Participants.

A total of 120 NH residents with an indwelling device (feeding tube and/or urinary catheter).

Methods.

Active surveillance cultures from the nares, oropharynx, groin, perianal area, wounds (if present), and device insertion site(s) were collected upon enrollment, at day 14, and monthly thereafter. Pulsed-field gel electrophoresis and polymerase chain reaction for SCCmec, agr, and Panton-Valentine leukocidin were performed.

Results.

Of 120 participants observed for 16,290 device-days, 50 acquired MRSA (78% transiently, 22% persistently). New MRSA acquisitions were common in extranasal sites, particularly at device insertion, groin, and perianal areas (27%, 23%, and 17.6% of all acquisitions, respectively). Screening extranasal sites greatly increases the detection of MRSA colonization (100% of persistent carriers and 97.4% of transient carriers detected with nares, groin, perianal, and device site sampling vs 54.5% and 25.6%, respectively, for nares samples alone). Colonization at suprapubic urinary catheter sites generally persisted. Healthcare-associated MRSA (USA100 and USA100 variants) were the dominant strains (79.3% of all new acquisition isolates). Strain diversity was more common in transient carriers, including acquisition of USA500 and USA300 strains.

Conclusion.

Indwelling device insertion sites as well as the groin and perianal area are important sites of new MRSA acquisitions in NH residents and play a role in the persistency of MRSA carriage. Clonal types differ among persistent and transient colonizers.
Impact of Vaginal-Rectal Ultrasound Examinations with Covered and Low-Level Disinfected Transducers on Infectious Transmissions in France
Authors: Leroy Sandrine , M’Zali Fatima , Kann Michael , Weber David J. , Smith David D.
Published: November 2014

Background.

The risk of cross-infection from shared ultrasound probes in endorectal and vaginal ultrasonography due to low-level disinfection (LLD) is difficult to estimate because potential infections are also sexually transmitted diseases, and route of contamination is often difficult to establish. In France, the widely used standard for prevention of infections is through the use of probe covers and LLD of the ultrasound transducer by disinfectant wipes. We performed an in silico simulation based on a systematic review to estimate the number of patients infected after endorectal or vaginal ultrasonography examination using LLD for probes.

Study design.

We performed a stochastic Monte Carlo computer simulation to produce hypothetical cohorts for a population of 4 million annual ultrasound examinations performed in France, and we estimated the number of infected patients for human immunodeficiency virus (HIV), herpes simplex virus, hepatitis B virus, hepatitis C virus, human papilloma virus, cytomegalovirus, and Chlamydia trachomatis. Modeling parameters were estimated by meta-analysis when possible.

Results.

The probability of infection from a contaminated probe ranged from 1% to 6%, depending on the pathogen. For cases of HIV infection, this would result in approximately 60 infected patients per year. For other common viral infections, the number of new cases ranged from 1,600 to 15,000 per year that could be attributable directly to ultrasound and LLD procedures.

Conclusions.

Our simulation results showed that, despite cumulative use of probe cover and LLD, there were still some cases of de novo infection that may be attributable to ultrasound procedures. These cases are preventable by reviewing the currently used LLD and/or upgrading LLD to high-level disinfection, as recommended by the US Centers for Disease Control and Prevention.
Detecting differential peaks in ChIP-seq signals with ODIN
Authors: Allhoff Manuel , Seré Kristin , Chauvistré Heike , Lin Qiong , Zenke Martin , Costa Ivan G.
Published: November 2014

Motivation: Detection of changes in deoxyribonucleic acid (DNA)–protein interactions from ChIP-seq data is a crucial step in unraveling the regulatory networks behind biological processes. The simplest variation of this problem is the differential peak calling (DPC) problem. Here, one has to find genomic regions with ChIP-seq signal changes between two cellular conditions in the interaction of a protein with DNA. The great majority of peak calling methods can only analyze one ChIP-seq signal at a time and are unable to perform DPC. Recently, a few approaches based on the combination of these peak callers with statistical tests for detecting differential digital expression have been proposed. However, these methods fail to detect detailed changes of protein–DNA interactions.

Results: We propose an One-stage DIffereNtial peak caller (ODIN); an Hidden Markov Model-based approach to detect and analyze differential peaks (DPs) in pairs of ChIP-seq data. ODIN performs genomic signal processing, peak calling and p-value calculation in an integrated framework. We also propose an evaluation methodology to compare ODIN with competing methods. The evaluation method is based on the association of DPs with expression changes in the same cellular conditions. Our empirical study based on several ChIP-seq experiments from transcription factors, histone modifications and simulated data shows that ODIN outperforms considered competing methods in most scenarios.

Availability and implementation:  http://costalab.org/wp/odin .

Contact:  ivan.costa@rwth-aachen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
The great escape? The contribution of the empire to Portugal's economic growth, 1500–1800
Authors: Costa Leonor Freire , Palma Nuno , Reis Jaime
Published: November 2014

Newly assembled macroeconomic statistics for early modern Portugal reveal one of Europe's most vigorous colonial traders but one of its least successful growth records. Was the empire a blessing or a drag to the economy? Using an estimated dynamic model, we conclude that intercontinental trade had a substantial and increasingly positive impact on economic growth. In the heyday of colonial expansion, eliminating the economic links to empire would have reduced Portugal's per capita income by at least a fifth. While the empire helped the domestic economy, it was not sufficient to annul the tendency of the latter toward decline in relation to Europe's advanced core, which began to set in from the seventeenth century onward, but only became definite after 1800. We conclude that the explanation for Portugal's long-term backwardness must be sought primarily in domestic conditions.
Functional Analyses of the Diels-Alderase Gene sol5 of Ascochyta rabiei and Alternaria solani Indicate that the Solanapyrone Phytotoxins Are Not Required for Pathogenicity
Authors: Kim Wonyong , Park Chung-Min , Park Jeong-Jin , Akamatsu Hajime O. , Peever Tobin L. , Xian Ming , Gang David R. , Vandemark George , Chen Weidong
Published: November 2014

Ascochyta rabiei and Alternaria solani, the causal agents of Ascochyta blight of chickpea (Cicer arietinum) and early blight of potato (Solanum tuberosum), respectively, produce a set of phytotoxic compounds including solanapyrones A, B, and C. Although both the phytotoxicity of solanapyrones and their universal production among field isolates have been documented, the role of solanapyrones in pathogenicity is not well understood. Here, we report the functional characterization of the sol5 gene, which encodes a Diels-Alderase that catalyzes the final step of solanapyrone biosynthesis. Deletion of sol5 in both Ascochyta rabiei and Alternaria solani completely prevented production of solanapyrones and led to accumulation of the immediate precursor compound, prosolanapyrone II-diol, which is not toxic to plants. Deletion of sol5 did not negatively affect growth rate or spore production in vitro, and led to overexpression of the other solanapyrone biosynthesis genes, suggesting a possible feedback regulation mechanism. Phytotoxicity tests showed that solanapyrone A is highly toxic to several legume species and Arabidopsis thaliana. Despite the apparent phytotoxicity of solanapyrone A, pathogenicity tests showed that solanapyrone-minus mutants of Ascochyta rabiei and Alternaria solani were equally virulent as their corresponding wild-type progenitors, suggesting that solanapyrones are not required for pathogenicity.
Identification of a 12-Gene Fusaric Acid Biosynthetic Gene Cluster in Fusarium Species Through Comparative and Functional Genomics
Authors: Brown Daren W. , Lee Seung-Ho , Kim Lee-Han , Ryu Jae-Gee , Lee Soohyung , Seo Yunhee , Kim Young Ho , Busman Mark , Yun Sung-Hwan , Proctor Robert H. , Lee Theresa
Published: November 2014

In fungi, genes involved in biosynthesis of a secondary metabolite (SM) are often located adjacent to one another in the genome and are coordinately regulated. These SM biosynthetic gene clusters typically encode enzymes, one or more transcription factors, and a transport protein. Fusaric acid is a polyketide-derived SM produced by multiple species of the fungal genus Fusarium. This SM is of concern because it is toxic to animals and, therefore, is considered a mycotoxin and may contribute to plant pathogenesis. Preliminary descriptions of the fusaric acid (FA) biosynthetic gene (FUB) cluster have been reported in two Fusarium species, the maize pathogen F. verticillioides and the rice pathogen F. fujikuroi. The cluster consisted of five genes and did not include a transcription factor or transporter gene. Here, analysis of the FUB region in F. verticillioides, F. fujikuroi, and F. oxysporum, a plant pathogen with multiple hosts, indicates the FUB cluster consists of at least 12 genes (FUB1 to FUB12). Deletion analysis confirmed that nine FUB genes, including two Zn(II)2Cys6 transcription factor genes, are required for production of wild-type levels of FA. Comparisons of FUB cluster homologs across multiple Fusarium isolates and species revealed insertion of non-FUB genes at one or two locations in some homologs. Although the ability to produce FA contributed to the phytotoxicity of F. oxysporum culture extracts, lack of production did not affect virulence of F. oxysporum on cactus or F. verticillioides on maize seedlings. These findings provide new insights into the genetic and biochemical processes required for FA production.
Differences in Virulence and Sporulation of Phytophthora kernoviae Isolates Originating From Two Distinct Geographical Regions
Authors: Widmer T. L.
Published: November 2014

Phytophthora kernoviae has only been isolated from the United Kingdom and New Zealand. To understand what differences may exist between isolates from these two distinct geographical regions, virulence studies on three host plants and sporulation on host leaves were conducted on select isolates. Three host plant species (Rhododendron ponticum, Magnolia stellata, and Annona cherimola) were inoculated individually with sporangia of six different isolates from each geographical region. Results showed an overall higher virulence on all three hosts from isolates originating from the United Kingdom. After inoculation, P. kernoviae sporangia and oospore formation on different host leaves were observed and compared with P. cactorum and P. syringae. Results were host dependent, with P. kernoviae producing generally similar or higher amounts of both propagules compared with the other U.S. indigenous species. These results have implications for regulatory agencies and scientists who are interested in preventing its entrance into the United States and learning more about its potential spread.
How well do Radiologic Assessments of Truncal and Shoulder Balance Correlate With Cosmetic Assessment Indices in Lenke 1C Adolescent Idiopathic Scoliosis?
Authors: Sharma Shallu , Andersen Thomas , Wu Chunsen , Sun Haolin , Wang Yu , Hansen Ebbe S. , Bünger Cody E.
Published: November 2014

Study Design:

A correlation study.

Objective:

The primary objective was to determine the correlation between radiologic and cosmetic indices of trunk and shoulder balance before and after scoliosis surgery in Lenke 1C adolescent idiopathic scoliosis and to determine whether postoperative trunk shift is affiliated with worsening of the patients’ cosmesis.

Summary of Background Data:

Achieving a symmetrical appearance with truncal and shoulder balance is of prime importance to adolescent idiopathic scoliosis patients and their surgeons. However, surgeons prefer radiographic indices rather than measures of patients’ clinical appearance. If radiographic indices are to be considered accurate depictions of the patient’s cosmesis, radiologic and cosmetic indices must necessarily exhibit high association.

Methods:

Radiographic and cosmetic indices of trunk and shoulder balance, along with posterior trunk symmetry index, were measured preoperatively and 3 months postoperatively in 33 Lenke 1C scoliosis patients. Pearson correlation analysis was performed. Paired t test was used to determine significant changes in radiographic and cosmetic indices after surgery. Independent-sample t test was used for all intergroup analyses in trunk shift and no-trunk-shift groups.

Results:

Correlation coefficients between radiologic and cosmetic indices ranged between −0.63 and 0.70 with thoracic apical vertebra-central sacral vertical line (AV-CSVL) distance and first rib angle showing consistent correlations with cosmetic trunk and cosmetic shoulder balance indices. Trunk shift, a postoperative iatrogenic phenomenon, was seen in 19 (58%) patients. These patients had higher preoperative thoracic AV-CSVL translation, thoracic apical vertebra-first thoracic vertebra (AV-T1) translation, thoracic deformity correction rate, AV-T1 correction rates, and shorter fusions compared with the no-trunk-shift group. Posterior trunk symmetry index worsened in trunk shift group and improved significantly (−7.94 vs. 16.53) in no-trunk-shift group. Significant association (P=0.004) was seen between radiographic and cosmetic trunk shift.

Conclusions:

Radiographic indices can only minisculely (r≤0.7) reflect cosmetic deformity in Lenke 1C scoliosis, which emphasizes not only the vulnerability of overreliance on radiographic indices but also the vital importance of clinical cosmetic evaluations. In particular, cosmetic shoulder height and angle are not represented by radiographic indices. However, radiograph trunk shift was significantly associated with cosmetic trunk shift in cosmetic pictures.
Oral Propranolol as an Alternative Therapy for Orbital Angiolymphoid Hyperplasia With Eosinophilia
Authors: McClintic Elysa A. , Ting Andrew , Yeatts R. Patrick
Published: November 2014

An 8-year-old female patient presented with left upper eyelid swelling and erythema. Magnetic resonance imaging revealed an orbital mass involving the left lacrimal gland with subsequent incisional biopsy leading to the diagnosis of angiolymphoid hyperplasia with eosinophilia. Initially prescribed an oral corticosteroid, alternative management was sought after 4 months due to unwanted side effects of steroid therapy. Oral propranolol (2 mg/kg/day) was initiated with concurrent steroid taper. Interval decrease in lesion size was observed on subsequent magnetic resonance imaging with complete resolution of subjective symptoms (Fig. 1). She remains stable 14 months after starting beta-blocker therapy. To our knowledge, our case is the second case report suggesting oral beta-blocker may be an alternative therapy for orbital angiolymphoid hyperplasia with eosinophilia.
Distinct behavioral effects of prefrontal and parietal cortex inactivations on an accumulation of evidence task in the rat
Authors: Erlich Jeffrey C , Brunton Bingni W , Duan Chunyu A , Hanks Timothy D , Brody Carlos D
Published: November 2014

Numerous brain regions have been shown to have neural correlates of gradually accumulating evidence for decision-making, but the causal roles of these regions in decisions driven by accumulation of evi- dence have yet to be determined. Here, in rats performing an auditory evidence accumulation task, we inactivated the frontal orienting fields (FOF) and posterior parietal cortex (PPC), two rat cortical regions that have neural correlates of accumulating evidence and that have been proposed as central to decision-making. We used a detailed model of the decision process to analyze the effect of inactivations. Inactivation of the FOF induced substantial performance impairments that were quantitatively best de- scribed as an impairment in the output pathway of an evidence accumulator with a long integration time constant (>240ms). In contrast, we found a minimal role for PPC in decisions guided by accumulating auditory evidence, even while finding a strong role for PPC in internally-guided decisions.
The genetic architecture of local adaptation I: The genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map
Authors: Friedline Christopher J , Lind Brandon M , Hobson Erin M , Harwood Douglas E , Delfino Mix Annette , Maloney Patricia E , Eckert Andrew J
Published: November 2014

Explaining the origin and evolutionary dynamics of the genetic architecture of adaptation is a major research goal of evolutionary genetics. Despite controversy surrounding success of the attempts to accomplish this goal, a full understanding of adaptive genetic variation necessitates knowledge about the genomic location and patterns of dispersion for the genetic components affecting fitness-related phenotypic traits. Even with advances in next generation sequencing technologies, the production of full genome sequences for non-model species is often cost prohibitive, especially for tree species such as pines where genome size often exceeds 20 to 30 Gbp. We address this need by constructing a dense linkage map for fox- tail pine (Pinus balfouriana Grev. & Balf.), with the ultimate goal of uncovering and explaining the origin and evolutionary dynamics of adaptive genetic variation in natural populations of this forest tree species. We utilized megagametophyte arrays (n = 76?95 megagametophytes/tree) from four maternal trees in combination with double-digestion restriction site associated DNA sequencing (ddRADseq) to produce a consensus linkage map covering 98.58% of the foxtail pine genome, which was estimated to be 1276 cM in length (95% CI: 1174cM to 1378cM). A novel bioinformatic approach using iterative rounds of marker ordering and imputation was employed to produce single-tree linkage maps (507?17066 contigs/map; lengths: 1037.40?1572.80 cM). These linkage maps were collinear across maternal trees, with highly correlated marker orderings (Spearman's ρ > 0.95). A consensus linkage map derived from these single-tree linkage maps contained 12 linkage groups along which 20 655 contigs were non-randomly distributed across 901 unique positions (n = 23 contigs/position), with an average spacing of 1.34 cM between adjacent positions. Of the 20 655 contigs positioned on the consensus linkage map, 5627 had enough sequence similarity to contigs contained within the most recent build of the loblolly pine (P. taeda L.) genome to identify them as putative homologs containing both genic and non-genic loci. Importantly, all 901 unique positions on the consensus linkage map had at least one contig with putative homology to loblolly pine. When combined with the other biological signals that predominate in our data (e.g., correlations of recombination fractions across single trees), we show that dense linkage maps for non-model forest tree species can be efficiently constructed using next generation sequencing technologies. We subsequently discuss the usefulness of these maps as community-wide resources and as tools with which to test hypotheses about the genetic architecture of adaptation.
Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
Authors: Zhao Han-Qing , Zhang Pan , Gao Hua , He Xiandong , Dou Yanmei , Huang August Y. , Liu Xi-Ming , Ye Adam Y. , Dong Meng-Qiu , Wei Liping
Published: November 2014

RNA editing increases transcriptome diversity through post-transcriptional modifications of RNA. Adenosine deaminases that act on RNA (ADARs) catalyze the adenosine-to-inosine (A-to-I) conversion, the most common type of RNA editing in higher eukaryotes. Caenorhabditis elegans has two ADARs, ADR-1 and ADR-2, but their functions remain unclear. Here, we profiled the RNA editomes of C. elegans at different developmental stages of wild-type and ADAR mutants. We developed a new computational pipeline with a “bisulfite-seq-mapping-like” step and achieved a threefold increase in identification sensitivity. A total of 99.5% of the 47,660 A-to-I editing sites were found in clusters. Of the 3080 editing clusters, 65.7% overlapped with DNA transposons in noncoding regions and 73.7% could form hairpin structures. The numbers of editing sites and clusters were highest at the L1 and embryonic stages. The editing frequency of a cluster positively correlated with the number of editing sites within it. Intriguingly, for 80% of the clusters with 10 or more editing sites, almost all expressed transcripts were edited. Deletion of adr-1 reduced the editing frequency but not the number of editing clusters, whereas deletion of adr-2 nearly abolished RNA editing, indicating a modulating role of ADR-1 and an essential role of ADR-2 in A-to-I editing. Quantitative proteomics analysis showed that adr-2 mutant worms altered the abundance of proteins involved in aging and lifespan regulation. Consistent with this finding, we observed that worms lacking RNA editing were short-lived. Taken together, our results reveal a sophisticated landscape of RNA editing and distinct modes of action of different ADARs.
Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line
Authors: Essletzbichler Patrick , Konopka Tomasz , Santoro Federica , Chen Doris , Gapp Bianca V. , Kralovics Robert , Brummelkamp Thijn R. , Nijman Sebastian M.B. , Bürckstümmer Tilmann
Published: November 2014

Near-haploid human cell lines are instrumental for genetic screens and genome engineering as gene inactivation is greatly facilitated by the absence of a second gene copy. However, no completely haploid human cell line has been described, hampering the genetic accessibility of a subset of genes. The near-haploid human cell line HAP1 contains a single copy of all chromosomes except for a heterozygous 30-megabase fragment of Chromosome 15. This large fragment encompasses 330 genes and is integrated on the long arm of Chromosome 19. Here, we employ a CRISPR/Cas9-based genome engineering strategy to excise this sizeable chromosomal fragment and to efficiently and reproducibly derive clones that retain their haploid state. Importantly, spectral karyotyping and single-nucleotide polymorphism (SNP) genotyping revealed that engineered-HAPloid (eHAP) cells are fully haploid with no gross chromosomal aberrations induced by Cas9. Furthermore, whole-genome sequence and transcriptome analysis of the parental HAP1 and an eHAP cell line showed that transcriptional changes are limited to the excised Chromosome 15 fragment. Together, we demonstrate the feasibility of efficiently engineering megabase deletions with the CRISPR/Cas9 technology and report the first fully haploid human cell line.
Genome accessibility is widely preserved and locally modulated during mitosis
Authors: Hsiung Chris C.-S. , Morrissey Christapher S. , Udugama Maheshi , Frank Christopher L. , Keller Cheryl A. , Baek Songjoon , Giardine Belinda , Crawford Gregory E. , Sung Myong-Hee , Hardison Ross C. , Blobel Gerd A.
Published: November 2014

Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that such mitotically retained molecular signatures could provide transcriptional memory through mitosis. To understand the role of chromatin structure in mitotic memory, we performed the first genome-wide comparison of DNase I sensitivity of chromatin in mitosis and interphase, using a murine erythroblast model. Despite chromosome condensation during mitosis visible by microscopy, the landscape of chromatin accessibility at the macromolecular level is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly DNase hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility more strongly, whereas distal regulatory elements tend to lose accessibility. Large domains of DNA hypomethylation mark a subset of promoters that retain accessibility during mitosis and across many cell types in interphase. Erythroid transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but has little influence on mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis, but are modulated at the level of individual genes and regulatory elements.
High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction betweenTheobroma cacaoand the Fungal PathogenMoniliophthora perniciosa
Authors: Teixeira Paulo José Pereira Lima , Thomazella Daniela Paula de Toledo , Reis Osvaldo , do Prado Paula Favoretti Vital , do Rio Maria Carolina Scatolin , Fiorin Gabriel Lorencini , José Juliana , Costa Gustavo Gilson Lacerda , Negri Victor Augusti , Mondego Jorge Maurício Costa , Mieczkowski Piotr , Pereira Gonçalo Amarante Guimarães
Published: November 2014

Witches’ broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. We analyzed the pathogen's transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors. Interestingly, M. perniciosa biotrophic mycelia develop as long-term parasites that orchestrate changes in plant metabolism to increase the availability of soluble nutrients before plant death. Collectively, our results provide unique insight into an intriguing tropical disease and advance our understanding of the development of (hemi)biotrophic plant-pathogen interactions.
Two complexes of PtIVand AuIIIwith 2,2′-dipyridylamine and 2,2′-dipyridylaminide ligands
Authors: Chernyshev Alexander N. , Kukushkin Vadim Yu. , Haukka Matti
Published: November 2014

Two noble metal complexes involving ancillary chloride ligands and chelating 2,2′-bipyridylamine (Hdpa) or its deprotonated derivative (dpa), namely [bis(pyridin-2-yl-κN)amine]tetrachloridoplatinum(IV), [PtCl4(C10H9N3)], and [bis(pyridin-2-yl-κN)aminido]dichloridogold(III), [AuCl2(C10H8N3)], are presented and structurally characterized. The metal atom in the former has a slightly distorted octahedral coordination environment, formed by four chloride ligands and two pyridyl N atoms of Hdpa, while the metal atom in the latter has a slightly distorted square-planar coordination environment, formed by two chloride ligands and two pyridyl N atoms of dpa. The difference in conjugation between the pyridine rings in normal and deprotonated 2,2′-dipyridylamine is discussed on the basis of the structural features of these complexes. The influence of weak interactions on the supramolecular structures of the complexes, providing one-dimensional chains of [PtCl4(C10H9N3)] and dimers of [AuCl2(C10H8N3)], are discussed.
The effects of σC—Se–π hyperconjugation in 1-methoxy- and 1-nitro-4-[(phenylselanyl)methyl]benzene
Authors: White Jonathan Michael , Blanc Paul
Published: November 2014

The structures of 1-methoxy-4-[(phenylselanyl)methyl]benzene, C14H14OSe, (1), and 1-nitro-4-[(phenylselanyl)methyl]benzene, C13H11NO2Se, (2), were determined at 130 K. The two structures, which differ in that (1) contains an electron-rich aromatic ring and (2) contains an electron-deficient aromatic ring, both adopt conformations which allow for σC—Se–π hyperconjugation. However, although there are significant differences in the77Se chemical shifts for these two compounds, they do not display significantly different H2C—Se or H2C—Carbond lengths, suggesting that the effects of σC—Se–π hyperconjugation in (1) and (2) are not strong enough to be manifested in measurable differences in the structural parameters.
A two-dimensional coordination polymer: poly[diaqua(μ4-4,4′-oxydibenzoato)(μ2-4,4′-oxydibenzoato)dilead(II)]
Authors: Xu Xiao-Juan
Published: November 2014

In a new two-dimensional coordination polymer, [Pb(C14H8O5)(H2O)]n, the asymmetric unit consists of a PbIIcation, two halves of two crystallographically distinct fully deprotonated 4,4′-oxydibenzoate ligands and one aqua ligand. Single-crystal X-ray diffraction analysis reveals that the compound is a coordination polymer with the point symbol {53}2{54.82}. In addition, it exhibits a strong fluorescence emission in the solid state at room temperature.
The effects of ERP systems implementation on management accounting in Iranian organizations
Authors: Abbasi Solmaz , Zamani Mahmoud , Valmohammadi Changiz
Published: November 2014

Purpose

– The aim of this paper is to study the effects of enterprise resource planning (ERP) on management accounting in Iranian organizations. Preparing and offering different reports and budgets remain important activities for accountants, and directly implementing ERP systems improves the quality of these reports through real-time data transfer.

Design/methodology/approach

– The research methods used in this paper are descriptive surveys with questionnaires and interviews as the main data collection tools. Statistical population comprises every organization which has implemented an ERP system with financial/accounting modules. The participating 12 organizations were selected based on consultation with experts, and a seven-item Likert questionnaire was prepared and its validity approved and used to collect data. The t-test and Friedman test were applied to assess the hypotheses and rank parameters.

Findings

– Results revealed that the highest effects of implementing an ERP in surveyed Iranian organizations are improving standard levels and the quality of reports, creating more organizational integration and empowering personnel.

Research limitations/implications

– As the implementation of ERP in Iran is still in its initial phases and the sample is restricted to only four organizations, when considering the generalizability of the obtained results, caution should be taken.

Originality/value

– This research is among the few studies on the effects of ERP implementation on accounting management departments, particularly in the context of Iran.
Grey clustering evaluation based on triangular whitenization weight function of enterprise's management innovation performance
Authors: Li Tianbo , Qi Ershi , Huang Yimin
Published: November 2014

Purpose

– The purpose of this paper is to attempt to establish a grey clustering evaluation model of center-point triangular whitenization weight function to measure the performance of enterprise's management innovation (MI). The author intends to provide some theory basis and tool support for enterprise's managers and other researchers who are engaged in performance measuring.

Design/methodology/approach

– The study uses questionnaire survey and expert interviews to determine the index weight of enterprise's MI performance (MIP), classifies the grey clusters based on center-point triangular whitenization weight function, calculates the membership of performance criteria and ranks the performance level of all dimensions.

Findings

– The survey data of case company shows that production performance is in superior level, employee and society influence performance are in satisfied level, finance and market performance are in intermediate level, total MIP is in satisfied level.

Practical implications

– MI is the fundamental way to keep enterprise's core competitiveness and achieve its strategic objectives. Performance is an effective tool to measure the MI. Therefore, based on the practices of MI in China, the study systematically clarifies the performance level of MI from five dimensions.

Originality/value

– The evaluation index of enterprise's MIP is built with five dimensions which contain production, market, finance, employee and social influence. The grey clustering evaluation model based on triangular whitenization weight function is applied to assess the performance criteria. This paper presents a new research idea for enterprise's performance evaluation.
Grey dominance variable precision rough set model based on grey dominance relationship
Authors: Liu Yong , Qian Wu-yong , Forrest Jeffrey
Published: November 2014

Purpose

– The purpose of this paper is to construct a novel grey dominance variable precision rough model.

Design/methodology/approach

– To deal with the problems that the attribute values of the decision-making object are often not exact numbers but interval grey numbers, and the decision-making attributes satisfy a certain preference relationship in the decision-making information because of the complexity and uncertainty of the real world, the authors take advantage of the theoretical thinking of the grey systems, dominance rough set theory and variable precision rough set theory, and construct a novel dominance variable precision rough set model. On the basis of the thinking logic of grey systems, the authors first define the concepts of balance degree, dominance degree and inferior degree, and then the grey dominance relationship based on the comparison of interval grey numbers. Then the authors use the grey dominance relationship to substitute for the indiscernibility relationship of the variable precision rough set so that the grey dominance variable precision rough model is naturally utilized to reduce the system's attributes in order to derive the needed decision rules. At the end, the authors use a decision-making example of the radar target selection to demonstrate the feasibility and effectiveness of the novel model.

Findings

– The results show that the proposed model possesses certain fault tolerance ability and can well-realize decision rule extraction and knowledge discovery out of a given incomplete information system.

Practical implications

– The method exposed in the paper can be used to deal with the decision-making problems with the grey information, preference information and noise data.

Originality/value

– The paper succeeds in realizing both the grey decision-making information with preference information and noise data and the extraction of decision-making rules.
The portfolio models of contained grey profit under uncertainty
Authors: Yan Xi-zu , Song Zhong-min
Published: November 2014

Purpose

– The purpose of this paper is to establish the portfolio models of contained grey profit under uncertainty, and the results are applied to solve uncertain investment problem.

Design/methodology/approach

– In investment problems, uncertainties may exist in model parameters and input data. For the investment problems contained grey profit and incomplete information about natural world state, according to the portfolio theory, the grey systems theory and the uncertainty decision theory, the paper puts forward portfolio models and the methods.

Findings

– Traditional uncertainty decision is researched for incomplete information about natural world state, in reality, investment problems are not only uncertain state information, but income are uncertain.

Practical implications

– Because the investment problems have been widely used in economic analysis, decision analysis and economic management, examples are provided at the end to verify its feasibility.

Originality/value

– The paper successfully combined the portfolio theory, the gray system theory and uncertainty decision theory and new uncertainty investment decision-making models and methods are presented.
Banking the unbanked: the Mzansi intervention in South Africa
Authors: Kostov Philip , Arun Thankom , Annim Samuel
Published: November 2014

Purpose

– This paper aims to understand household’s latent behaviour decision-making in accessing financial services. In this analysis, the determinants of the choice of the pre-entry Mzansi account by consumers in South Africa is looked at.

Design/methodology/approach

– In this study, 102 variables, grouped in the following categories: basic literacy, understanding financial terms, targets for financial advice, desired financial education and financial perception. Using a computationally efficient variable selection algorithm, variables that can satisfactorily explain the choice of a Mzansi account were studied.

Findings

– The Mzansi intervention is appealing to individuals with basic but insufficient financial education. Aspirations seem to be very influential in revealing the choice of financial services, and, to this end, Mzansi is perceived as a pre-entry account not meeting the aspirations of individuals aiming to climb up the financial services ladder. It was found that Mzansi holders view the account mainly as a vehicle for receiving payments, but, on the other hand, are debt-averse and inclined to save. Hence, although there is at present no concrete evidence that the Mzansi intervention increases access to finance via diversification (i.e. by recruiting customers into higher-level accounts and services), this analysis shows that this is very likely to be the case.

Originality/value

– The issue of demand-side constraints on access to finance have been largely been ignored in the theoretical and empirical literature. This paper undertakes some preliminary steps in addressing this gap.
Augmented reality and motion capture apparel e-shopping values and usage intention
Authors: M. Kang Ju-Young
Published: November 2014

Purpose

– The purpose of this paper is to examine: whether monetary, convenience, emotional, and social values were related to utilitarian and hedonic performance expectancies, which were then related to usage intention of augmented reality and motion capture (ARMC) e-shopping via a webcam and whether ego involvement and cognitive effort moderated the links between performance expectancies and usage intention.

Design/methodology/approach

– The proposed model was based on Prospect Theory and the Value-Attitude-Behavior hierarchy consumer decision model. The participants were US online apparel shoppers (n=806) and were drawn from an online consumer panel. Structural equation modeling was employed to test the proposed model and research hypotheses.

Findings

– This study identified that utilitarian performance expectancy was positively related to usage intention. However, hedonic performance expectancy was not positively related to usage intention. Monetary, convenience, emotional, and social values had an indirect influence on usage intention, mediated by utilitarian performance expectancy. Ego involvement and cognitive effort moderated the link between utilitarian performance expectancy and usage intention. Managerial implications were discussed.

Originality/value

– The results not only verify theoretical conceptions regarding usage intention of ARMC e-shopping but also provide beneficial insights into the implementation and development of ARMC e-shopping applications that use webcams and motion capture technology.