bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predator–prey population models of migrant insects with phase change
Authors: Cheke Robert A. , Tang Sanyi , Tratalos Jamie A. 
Published: September 2013

Abstract
Locusts and some noctuid moths exhibit polyphenism whereby they can change their “phase” from a solitary (“solitarious”) condition to a gregarious one. Gregarious phase insects are often migratory travelling from recession areas into larger invasion zones and, among locusts, occur in swarms. Difference equation models of the population dynamics of insects that take account of such changes between solitarious or gregarious phases in relation to predation, both with and without time delays, are described. Solutions of the models are non-linear. Chaotic solutions are obtainable under some circumstances even with very low values for the intrinsic rate of increase in the prey population, in contrast to previous conclusions from models without predation. Comparisons with the results obtained for single species with those obtained in this paper show that predation can reduce (i) the average density of the prey, (ii) durations of periods when the populations stay in the gregarious phase, and (iii) the frequency of their shifts from the solitarious state to the gregarious form. Similar results are obtained if a time delay is introduced to mimic a transient phase. With a wide range of parameter values, models including predation with or without random perturbation reveal several stable attractors for phase diagrams of the populations, which are biologically meaningful compared with empirical datasets and which were unobtainable without predation, suggesting that inclusion of predation and time delays improved the realism of the models. However, comparisons between autocorrelation analyses of locust time-series, but of swarms only, with those of model outputs suggest that inclusion of the time delay leads to less, not more, realism. The prediction of non-linearity in the dynamics of migrant insects with phase changes and its significance for forecasting to aid control is briefly discussed in relation to published data on the desert locust Schistocerca gregaria.
DNA polymerase δ stalls on telomeric lagging strand templates independently from G-quadruplex formation
Authors: Lormand Justin D. , Buncher Noah , Murphy Connor T. , Kaur Parminder , Lee Marietta Y. , Burgers Peter , Wang Hong , Kunkel Thomas A. , Opresko Patricia L. 
Published: September 2013

Abstract
Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and progression by the replicative DNA polymerase δ/proliferating cell nuclear antigen/replication factor C complex on telomeric templates that mimic the leading C-rich and lagging G-rich strands. Increased polymerase stalling occurred on the G-rich template, compared with the C-rich and nontelomeric templates. Suppression of G4 formation by substituting Li+ for K+ as the cation, or by using templates with 7-deaza-G residues, did not alleviate Pol δ pause sites within the G residues. Furthermore, we provide evidence that G4 folding is less stable on single-stranded circular TTAGGG templates where ends are constrained, compared with linear oligonucleotides. Artificially stabilizing G4 structures on the circular templates with the G4 ligand BRACO-19 inhibited Pol δ progression into the G-rich repeats. Similar results were obtained for yeast and human Pol δ complexes. Our data indicate that G4 formation is not required for polymerase stalling on telomeric lagging strands and suggest that an alternative mechanism, in addition to stable G4s, contributes to replication stalling at telomeres.
A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1
Authors: Kennedy Jessica A. , Daughdrill Gary W. , Schmidt Kristina H. 
Published: September 2013

Abstract
The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9–17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins.
Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features
Authors: Lv Jie , Liu Hongbo , Huang Zhijun , Su Jianzhong , He Hongjuan , Xiu Youcheng , Zhang Yan , Wu Qiong 
Published: September 2013

Abstract
In silico prediction of genomic long non-coding RNAs (lncRNAs) is prerequisite to the construction and elucidation of non-coding regulatory network. Chromatin modifications marked by chromatin regulators are important epigenetic features, which can be captured by prevailing high-throughput approaches such as ChIP sequencing. We demonstrate that the accuracy of lncRNA predictions can be greatly improved when incorporating high-throughput chromatin modifications over mouse embryonic stem differentiation toward adult Cerebellum by logistic regression with LASSO regularization. The discriminating features include H3K9me3, H3K27ac, H3K4me1, open reading frames and several repeat elements. Importantly, chromatin information is suggested to be complementary to genomic sequence information, highlighting the importance of an integrated model. Applying integrated model, we obtain a list of putative lncRNAs based on uncharacterized fragments from transcriptome assembly. We demonstrate that the putative lncRNAs have regulatory roles in vicinity of known gene loci by expression and Gene Ontology enrichment analysis. We also show that the lncRNA expression specificity can be efficiently modeled by the chromatin data with same developmental stage. The study not only supports the biological hypothesis that chromatin can regulate expression of tissue-specific or developmental stage-specific lncRNAs but also reveals the discriminating features between lncRNA and coding genes, which would guide further lncRNA identifications and characterizations.
Structural insights into Paf1 complex assembly and histone binding
Authors: Chu Xinlei , Qin Xiaohong , Xu Huisha , Li Lei , Wang Zheng , Li Fengzhi , Xie Xingqiao , Zhou Hao , Shen Yuequan , Long Jiafu 
Published: September 2013

Abstract
The highly conserved Paf1 complex (PAF1C) plays critical roles in RNA polymerase II transcription elongation and in the regulation of histone modifications. It has also been implicated in other diverse cellular activities, including posttranscriptional events, embryonic development and cell survival and maintenance of embryonic stem cell identity. Here, we report the structure of the human Paf1/Leo1 subcomplex within PAF1C. The overall structure reveals that the Paf1 and Leo1 subunits form a tightly associated heterodimer through antiparallel beta-sheet interactions. Detailed biochemical experiments indicate that Leo1 binds to PAF1C through Paf1 and that the Ctr9 subunit is the key scaffold protein in assembling PAF1C. Furthermore, we show that the Paf1/Leo1 heterodimer is necessary for its binding to histone H3, the histone octamer, and nucleosome in vitro. Our results shed light on the PAF1C assembly process and substrate recognition during various PAF1C-coordinated histone modifications.
Self-duplexing CUG repeats selectively inhibit mutant huntingtin expression
Authors: Fiszer Agnieszka , Olejniczak Marta , Galka-Marciniak Paulina , Mykowska Agnieszka , Krzyzosiak Wlodzimierz J. 
Published: September 2013

Abstract
Huntington’s disease (HD) is a neurodegenerative genetic disorder caused by the expansion of the CAG repeat in the translated sequence of the HTT gene. This expansion generates a mutant huntingtin protein that contains an abnormally elongated polyglutamine tract, which, together with mutant transcript, causes cellular dysfunction. Currently, there is no curative treatment available to patients suffering from HD; however, the selective inhibition of the mutant allele expression is a promising therapeutic option. In this study, we developed a new class of CAG repeat-targeting silencing reagents that consist of self-duplexing CUG repeats. Self-duplex formation was induced through one or several U-base substitutions. A number of self-duplexing guide-strand-only short interfering RNAs have been tested through transfection into cells derived from HD patients, showing distinct activity profiles. The best reagents were highly discriminatory between the normal and mutant HTT alleles (allele selectivity) and the HTT transcript and other transcripts containing shorter CAG repeats (gene selectivity). We also demonstrated that the self-duplexing CUG repeat short interfering RNAs use the RNA interference pathway to elicit silencing, and repeat-targeting reagents showed similar activity and selectivity when expressed from short hairpin RNA vectors to achieve more durable silencing effects.
On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs
Authors: Wu Chyuan-Chuan , Li Yi-Ching , Wang Ying-Ren , Li Tsai-Kun , Chan Nei-Li 
Published: September 2013

Abstract
Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme–DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically active anticancer drugs whose trapping of Top2-mediated DNA breakage effectively induces genome fragmentation and cell death. To understand the structural basis of this drug action, we previously determined the structure of human Top2 β-isoform forming a cleavage complex with the drug etoposide and DNA, and described the insertion of drug into DNA cleavage site and drug-induced decoupling of catalytic groups. By developing a post-crystallization drug replacement procedure that simplifies structural characterization of drug-stabilized cleavage complexes, we have extended the analysis toward other structurally distinct drugs, m-AMSA and mitoxantrone. Besides the expected drug intercalation, a switch in ribose puckering in the 3′-nucleotide of the cleavage site was robustly observed in the new structures, representing a new mechanism for trapping the Top2 cleavage complex. Analysis of drug-binding modes and the conformational landscapes of the drug-binding pockets provide rationalization of the drugs’ structural-activity relationships and explain why Top2 mutants exhibit differential effects toward each drug. Drug design guidelines were proposed to facilitate the development of isoform-specific Top2-targeting anticancer agents.
ATR kinase activation in G1 phase facilitates the repair of ionizing radiation-induced DNA damage
Authors: Gamper Armin M. , Rofougaran Reza , Watkins Simon C. , Greenberger Joel S. , Beumer Jan H. , Bakkenist Christopher J. 
Published: September 2013

Abstract
The kinase ATR is activated by RPA-coated single-stranded DNA generated at aberrant replicative structures and resected double strand breaks. While many hundred candidate ATR substrates have been identified, the essential role of ATR in the replicative stress response has impeded the study of ATR kinase-dependent signalling. Using recently developed selective drugs, we show that ATR inhibition has a significantly more potent effect than ATM inhibition on ionizing radiation (IR)-mediated cell killing. Transient ATR inhibition for a short interval after IR has long-term consequences that include an accumulation of RPA foci and a total abrogation of Chk1 S345 phosphorylation. We show that ATR kinase activity in G1 phase cells is important for survival after IR and that ATR colocalizes with RPA in the absence of detectable RPA S4/8 phosphorylation. Our data reveal that, unexpectedly, ATR kinase inhibitors may be more potent cellular radiosensitizers than ATM kinase inhibitors, and that this is associated with a novel role for ATR in G1 phase cells.
Spotted Wilt Disease Evaluation Among High-Oleic Peanut Cultivars
Authors: Branch W. D. , Culbreath A. K. 
Published: September 2013

The release of high-oleic, United States runner and virginia market type peanut (Arachis hypogaea L.) cultivars has been steadily increasing during the past several years. Two planting dates were utilized for disease evaluation and agronomic performance among these newer high-oleic cultivars. The first planting date test was in mid-April to allow for increased incidence of spotted wilt disease caused by Tomato spotted wilt virus (TSWV). The second planting date test was in mid-May to allow for less TSWV and provide more of an optimum time by comparison. Significant differences (P ≤ 0.05) were found within each of the three (3-year) averages among cultivars for TSWV and total disease (TD) incidence, pod yield, and dollar values. Among the virginia-types, Georgia Hi-O/L, Georgia-05E, and Georgia-08V, and runner-types, Georgia-02C and Georgia-09B, consistently had the lowest TSWV and TD incidence and the highest pod yield and dollar values in both the mid-April and mid-May planting date tests. No significant differences were found between the mid-April and the mid-May planting dates when averaged across this 5-year study for TSWV and TD incidence, pod yield, and dollar values. This suggests that the high-level of TSWV-resistance among these newer high-oleic cultivars should have a greater influence than planting dates on agronomic performance. Accepted for publication 8 June 2013. Published 12 August 2013.
Identification of the G143A Mutation in Cytochrome b Associated with QoI Resistance in Cercospora beticola Isolates from the Red River Valley
Authors: Bolton Melvin D. , Rivera-Varas Viviana , Secor Gary A. , Cattanach Allan W. , Metzger Michael S. 
Published: September 2013

Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is the most important foliar disease of sugarbeet. The disease is managed in part by timely applications of quinone outside inhibitor (QoI) fungicides. However, pathogen resistance to QoI fungicides is associated with the exchange of glycine to alanine at amino acid position 143 (G143A) in the C. beticola cytochrome b gene. To assess whether QoI resistance has developed in C. beticola in the Red River Valley (RRV) of Minnesota and North Dakota, a real-time PCR procedure was used to determine whether the G143A mutation could be identified in samples harvested from 922 fields across the RRV. In total, 12 fields located in diverse locations within the RRV contained the G143A mutation, suggesting that QoI resistance arose independently at each location and in several genetic backgrounds. This is the first report of QoI resistance in the RRV. Careful monitoring of the G143A mutation will be necessary to ensure that QoI fungicides remain efficacious for CLS management in the RRV region. Accepted for publication 31 May 2013. Published 12 August 2013.
Identification of Poinsettia mosaic virus Associated with a Virus-like Mottle Symptom on Poinsettia in Ohio
Authors: Fisher John R. , Bell John 
Published: September 2013

These results represent the first confirmed report of Poinsettia mosaic virus (PnMV) in poinsettia in Ohio. They also serve to increase awareness of the virus among poinsettia growers so they may more effectively scout nursery stock for infected plants. Accepted for publication 22 May 2013. Published 13 August 2013.
Field and Growth Chamber Inoculations Demonstrate Persea indica as a Newly Recognized Host for the Laurel Wilt Pathogen, Raffaelea laurciola
Authors: Hughes Marc A. , Brar Gurpreet , Ploetz Randy C. , Smith Jason A. 
Published: September 2013

In order to assess the susceptibility of the tree species P. indica to the laurel wilt fungus, Raffaelea lauricola, field and growth chamber experiments were conducted. Accepted for publication 3 June 2013. Published 14 August 2013.
Effect of Snow Removal on Typhula Blight Development at High Elevation Golf Courses in Colorado
Authors: Blunt Tamla , Koski Tony , Tisserat Ned 
Published: September 2013

Golf course superintendents at high elevations in Colorado apply fungicides in late October before permanent snow cover to suppress Typhula blight development. Many remove snow from putting greens in late winter or early spring assuming this practice helps suppress Typhula blight late into the snow season. They also remove snow to prevent ice formation and freeze damage to turfgrass during snowmelt. However, the benefits of spring snow removal in disease suppression and freeze avoidance have not been demonstrated in Colorado. We compared Typhula blight severity and turfgrass health in Kentucky bluegrass and annual bluegrass fairways where snow was removed weekly from late October through mid-November, from early- to mid-March until the end of the snow period, or not removed. Fall snow removal did not reduce Typhula blight severity compared to no snow removal, but it did result in freeze damage to annual, but not Kentucky bluegrass. Spring snow removal had no effect on Typhula blight severity or freeze damage. Thus the practice of snow removal was of no apparent benefit in our studies. Accepted for publication 3 June 2013. Published 21 August 2013.
Quality care perceptions in private Syrian hospitals
Authors: Alasadi Rami , Al Sabbagh Hicham 
Published: September 2013

Purpose
– The paper aims to spotlight the level of patient satisfaction with quality of care in a private hospitals setting.

Design/methodology/approach
– This study was carried out at three private hospitals in Syria. The study used written survey (interview-type questionnaire) assessing patient's perception of the quality of the services offered by the hospitals. The total of 108 patients participated in the study making the response rate 60.3 percent.

Findings
– On the basis of this study, several interesting findings were found. There was a general patient satisfaction with most of the facilities and services provided by the hospitals. Although the focus of the study was not on the medical services, patients were satisfied with the medical treatment. The hotel aspects of the services were found to be evidently poor as indicated by patients.

Research limitations/implications
– The perception of management about the services provided was not studied in detail to find out if there was a perceptual gap between the two parties. The findings of this study can only be generalized to other private hospitals in Syria not public hospitals.

Originality/value
– This paper satisfies the needs of the managers of private hospitals in Damascus/Syria who lack knowledge about what affects the overall patient satisfaction especially with regard to the hotel aspects of services offered by private hospitals as patients generally want more than just a cure of ill health.
Investigating critical success factors of knowledge management in research organizations
Authors: Ramezani Abdollah , Fathain Mohammad , Tajdin Ali 
Published: September 2013

Purpose
– The purpose of this paper is to examine the status of knowledge management (KM) in an Iranian Research Organisation in order to identify and classify the most relevant KM critical success factors.

Design/methodology/approach
– Based on extensive review of KM literature, broad ranges of general KM critical success factors are identified. Then, through field studies and employing factor analysis techniques and Friedman test, the degree of the relevance of each particular KM critical success factors is determined. The research procedure finally led to the identification of KM critical success factors prevailing in the research organization.

Findings
– Eight distinct KM factors including 22 different elements are found to be relevant and critical in the course of KM implementation in the research organization. These factors are “The presence of appropriate organizational culture”, “The existing system for knowledge documentation, recording and registration”, “The presence of motivational system for workforces”, “Appropriate management and planning for KM realization”, “The existing hardware and software infrastructures and standard executive processes in KM field”, “The presence of specialized teams including expert and skillful personnel”, “The existing appropriate organizational architecture of KM and evaluation system for realization of KM” and “The existing systematic relationship with beneficiaries of the research organization”.

Originality/value
– The paper should be of value to researchers of KM in general, and to implementers of KM programs. It presents a range of issues critical to the adoption of KM initiatives.
Exploring quality of e-Government services in Oman
Authors: Kumar Sharma Sujeet , Al-Shihi Hafedh , Madhumohan Govindaluri Srikrishna 
Published: September 2013

Purpose
– The purpose of this paper is to understand the customer perception of service quality with respect to the e-Government services in Oman and conduct an investigation in order to determine the key factors that affect the quality of e-Government services in Oman.

Design/methodology/approach
– Primary data relating to the variables affecting quality of e-Government services and demographic profile data are collected using a questionnaire survey. The questionnaire was designed based on literature review and focus groups. Factor analysis method is employed to identify and rank the important factors affecting service quality.

Findings
– The study found that the four factors listed in the descending order of importance, reliability, responsiveness, efficiency, and security are primary determinants of the quality of e-Government services in Oman.

Practical implications
– This research enables government organizations to enhance their understanding of customer perception of e-Government services. The customer preference information can provide useful direction to the design, implementation, and management of e-Government services.

Social implications
– Improved service quality of e-Government systems can enhance public participation in these systems that have been established with huge investments. The improved participation can result in increased levels of efficiency, convenience, public awareness, transparency, engagement, and information for decision-making.

Originality/value
– The paper addresses quality of e-Government services for the first time in Oman and in the gulf region using a carefully designed research study. The paper is of value to researchers in the area of service quality of e-Government, Government of Oman, and governments in the gulf region and other developing countries that are involved in designing and managing e-Government service systems.