bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissection of Ramularia Leaf Spot Disease by Integrated Analysis of Barley and Ramularia collo-cygni Transcriptome Responses
Authors: Sjokvist Elisabet , Lemcke Rene , Kamble Manoj , Turner Frances , Blaxter Mark , Havis Neil H. D. , Lyngkjær Michael F. , Radutoiu Simona
Published: December 2018

Ramularia leaf spot disease (RLS), caused by the ascomycete fungus Ramularia collo-cygni, has emerged as a major economic disease of barley. No substantial resistance has been identified, so far, among barley genotypes and, based on the epidemiology of the disease, a quantitative genetic determinacy of RLS has been suggested. The relative contributions of barley and R. collo-cygni genetics to disease infection and epidemiology are practically unknown. Here, we present an integrated genome-wide analysis of host and pathogen transcriptome landscapes identified in a sensitive barley cultivar following infection by an aggressive R. collo-cygni isolate. We compared transcriptional responses in the infected and noninfected leaf samples in order to identify which molecular events are associated with RLS symptom development. We found a large proportion of R. collo-cygni genes to be expressed in planta and that many were also closely associated with the infection stage. The transition from surface to apoplastic colonization was associated with downregulation of cell wall–degrading genes and upregulation of nutrient uptake and resistance to oxidative stresses. Interestingly, the production of secondary metabolites was dynamically regulated within the fungus, indicating that R. collo-cygni produces a diverse panel of toxic compounds according to the infection stage. A defense response against R. collo-cygni was identified in barley at the early, asymptomatic infection and colonization stages. We found activation of ethylene signaling, jasmonic acid signaling, and phenylpropanoid and flavonoid pathways to be highly induced, indicative of a classical response to necrotrophic pathogens. Disease development was found to be associated with gene expression patterns similar to those found at the onset of leaf senescence, when nutrients, possibly, are used by the infecting fungus. These analyses, combining both barley and R. collo-cygni transcript profiles, demonstrate the activation of complex transcriptional programs in both organisms.
Biosynthesis of Coenzyme Q in the Phytopathogen Xanthomonas campestris via a Yeast-Like Pathway
Authors: Zhou Lian , Li Ming , Wang Xing-Yu , Liu Hao , Sun Shuang , Chen Haifeng , Poplawsky Alan , He Ya-Wen
Published: December 2018

Coenzyme Q (CoQ) is a lipid-soluble membrane component found in organisms ranging from bacteria to mammals. The biosynthesis of CoQ has been intensively studied in Escherichia coli, where 12 genes (ubiA, -B, -C, -D, -E, -F, -G, -H, -I, -J, -K, and -X) are involved. In this study, we first investigated the putative genes for CoQ8 biosynthesis in the phytopathogen Xanthomonas campestris pv. campestris using a combination of bioinformatic, genetic, and biochemical methods. We showed that Xc_0489 (coq7Xc) encodes a di-iron carboxylate monooxygenase filling the E. coli UbiF role for hydroxylation at C-6 of the aromatic ring. Xc_0233 (ubiJXc) encodes a novel protein with an E. coli UbiJ-like domain organization and is required for CoQ8 biosynthesis. The X. campestris pv. campestris decarboxylase gene remains unidentified. Further functional analysis showed that ubiB and ubiK homologs ubiBXc and ubiKXc are required for CoQ8 biosynthesis in X. campestris pv. campestris. Deletion of ubiJXc, ubiBXc, and ubiKXc led to the accumulation of an intermediate 3-octaprenyl-4-hydroxybenzoic acid. UbiKXc interacts with UbiJXc and UbiBXc to form a regulatory complex. Deletion analyses of these CoQ8 biosynthetic genes indicated that they are important for virulence in Chinese radish. These results suggest that the X. campestris pv. campestris CoQ8 biosynthetic reactions and regulatory mechanisms are divergent from those of E. coli. The variations provide an opportunity for the design of highly specific inhibitors for the prevention of infection by the phytopathogen X. campestris pv. campestris.
Potential Risks of Poaceous Plants as Infectious Sources of Rice Black-Streaked Dwarf Virus Transmitted by the Small Brown Planthopper, Laodelphax striatellus
Authors: Matsukura Keiichiro , Sanada-Morimura Sachiyo , Fujii Tomohisa , Matsumura Masaya
Published: December 2018

The recent reemergence of rice black-streaked dwarf virus (RBSDV) has caused severe rice yield losses in several areas of East Asia. To identify the most important infectious sources of RBSDV, we compared the susceptibility of major poaceous plants to RBSDV infection and survival and the RBSDV acquisition efficiency of a vector insect, the small brown planthopper Laodelphax striatellus. RBSDV infection and survival rates of L. striatellus were significantly high in wheat (Triticum aestivum ‘Norin61’) and rice (Oryza sativa ‘Reiho’), indicating that these crops can be important sources of RBSDV. Our results also showed that RBSDV can complete its infection cycle between Italian ryegrass (Lolium multiflorum ‘Hataaoba’) and L. striatellus. These results indicate that control of RBSDV and L. striatellus on winter-spring crops of wheat and Italian ryegrass may avoid an RBSDV epidemic on rice during the following summer. In addition to infections of wheat and Italian ryegrass, RBSDV infections were detected in Avena fatua, Avena sterilis subsp. ludoviciana, Cynosurus echinatus, Festuca arundinacea, Festuca pratensis, Lolium perenne, and Vulpia myuros var. megalura, although the infection efficiency varied.
Adherence with a low-FODMAP diet in irritable bowel syndrome: are eating disorders the missing link?
Authors: Mari Amir , Hosadurg Deepash , Martin Lee , Zarate-Lopez Natalia , Passananti Valentina , Emmanuel Anton
Published: December 2018

Objectives

The low-FODMAP diet has emerged as an option for the treatment of irritable bowel syndrome (IBS). This diet is very restrictive, and compliance is usually low. Preliminary findings suggest an association between eating disorders (EDs) and the risk of developing IBS. The aim of this study was to assess the correlation between compliance with a low-FODMAP diet and the risk of ED behaviours among patients with IBS.

Patients and methods

A single-centre prospective study was carried out among 233 IBS patients (79.8% females) at University College London Hospital, who commenced a low FODMAPs group programme for IBS (Rome III or IV). Self-reported diet adherence at the end of the 6-week programme was measured. At baseline, and at the 6-week follow-up visit, participants completed the validated IBS-Symptom Severity Score, the SCOFF ED screening questionnaire and the Hospital Anxiety and Depression Scale.

Results

Adherence with a low-FODMAP diet was found in 95 (41%) patients. Overall, 54 (23%) patients were classified to be at risk for ED behaviour. Adherence was 57% in the ED group (31/54) versus 35% in the non-ED group (64/179);P<0.05. Adherence with a low-FODMAP diet was highest (51%) in the IBS with diarrhoea subtype and lowest (10%) in IBS with constipation. There was no significant correlation between IBS-Symptom Severity Score and either adherence (P=0.39) or ED behaviour (P=0.28).

Conclusion

In this IBS cohort, greater adherence to a low-FODMAP diet is associated with ED behaviour. The implications of our study are important in clinical practice for a clinician to have a high index of suspicion of EDs in IBS patients when a high level of low-FODMAP diet achieved.
Serum alkaline phosphatase levels as a simple and useful test in screening for significant fibrosis in treatment-naive patients with hepatitis B e-antigen negative chronic hepatitis B
Authors: Hu Jianhua , Zhang Xiaoli , Gu Jueqing , Yang Meifang , Zhang Xuan , Zhao Hong , Li Lanjuan
Published: December 2018

Background

Staging of liver fibrosis is critical in guiding the treatment of chronic hepatitis B (CHB) virus. Many efforts have been made toward the research of noninvasive techniques, mostly focusing on hepatitis B e-antigen (HBeAg)-positive [HBeAg(+)] CHB patients, whereas HBeAg(+) and HBeA-negative [HBeAg(−)] represent different stages of hepatitis B virus infection. Thus, in this study, we aimed to search for routinely available clinical noninvasive liver fibrosis markers and separately analysed the markers in HBeAg(+) and HBeAg(−) CHB patients.

Methods

Patients with CHB who were treatment naive and who underwent a liver biopsy at our hospital from 1 January 2016 to 31 April 2017 were enrolled. Liver histology was scored using the Scheuer classification system. The area under the receiver operator curve was used to determine the diagnostic accuracy.

Results

A total of 191 patients, including 104 HBeAg(+) and 87 HBeAg(−) treatment-naive CHB patients, were enrolled in this study. Serum alkaline phosphatase (ALP) levels increased gradually in all patients and separately in HBeAg(−) CHB patients, but not in HBeAg(+) CHB patients. ALP was an independent factors predicting significant fibrosis (S≥2) in all of the patients and separately in HBeAg(−) patients, with area under the receiver operator curves of 0.651 and 0.717, respectively. Further, the optimal cut-off value of ALP (>69.5 IU/l) for distinguishing HBeAg(−) CHB patients with significant fibrosis was determined (S≥2).

Conclusion

Serum ALP levels can identify significant fibrosis (S≥2) in treatment-naive HBeAg(−) CHB patients and could potentially reduce the need for liver biopsies and help to guide the clinical treatment of CHB.
Fit4SurgeryTV At-home Prehabilitation for Frail Older Patients Planned for Colorectal Cancer Surgery
Authors: Bruns Emma R.J. , Argillander Tanja E. , Schuijt Henk Jan , van Duijvendijk Peter , van der Zaag Edwin S. , Wassenaar Eelco B. , Gerhards Michael F. , Consten Esther C. , Buskens Christianne J. , van Munster Barbara C. , Bemelman Willem A.
Published: December 2018

Objective

The preoperative phase is a potential window of opportunity. Although frail elderly patients are known to be more prone to postoperative complications, they are often not considered capable of accomplishing a full prehabilitation program. The aim of this study was to assess the feasibility of Fit4SurgeryTV, an at-home prehabilitation program specifically designed for frail older patients with colorectal cancer.

Design

The Fit4SurgeryTV program consisted of a daily elderly adapted computer-supported strength training workout and two protein-rich meals. Frail patients 70 yrs or older with colorectal cancer were included. The program was considered feasible if 80% of the patients would be able to complete 70% of the program.

Results

Fourteen patients (median age, 79 yrs; 5 males) participated. At baseline, 86% patients were physically impaired and 64% were at risk for malnourishment. The median duration of the program was 26 days. The program was feasible as patients followed the exercises for 6 (86%) of 7 days and prepared the recipes 5 (71%) of 7 d/wk. Patients specifically appreciated at-home exercises.

Conclusions

This study showed that at-home prehabilitation in frail older patients with colorectal cancer is feasible. As a result, patients might be fitter for surgery and might recover faster. The perioperative period could serve as a pivotal time point in reverting complications of immobility.
Comparison of Distraction Osteogenesis and Single-Stage Remodeling for Correction of Unilateral Coronal Craniosynostosis
Authors: Corkum Joseph P. , Burke Emily , Samargandi Osama , Retrouvey Helene , Bezuhly Michael
Published: December 2018

Background:

Unilateral coronal craniosynostosis is a challenging condition in craniofacial surgery. Frontoorbital advancement by single-stage resorbable remodeling and distraction osteogenesis (DO) techniques have known intraoperative differences, but their comparative outcomes are less well characterized.

Methods:

A systematic literature search of the MEDLINE, EMBASE, LILACS, and Web of Science databases was conducted. The search was performed using terms related to craniosynostosis and its operative management. The primary outcome of interest was the Whitaker classification. Secondary outcomes included cranial volume or cranial index change, and infection and reoperation rates.

Results:

A total of 6978 eligible articles were identified of which 26 met inclusion criteria. A total of 292 patients were included in the studies, with 223 undergoing a single-stage remodeling procedure (76.4%) and 69 DO procedures (23.6%). There was a trend toward patients with DO having better Whitaker aesthetic outcomes. Only 2 studies reported volumetric changes. There was a substantial difference in planned and unplanned reoperation rates but not in infection rates.

Conclusion:

The results of this systematic review suggest that the techniques have similar outcomes and complications, although there was a trend toward better Whitaker outcomes with DO procedures. Inherent to the DO technique is the need for multiple operations to both insert and remove internal hardware which may affect the overall cost effectiveness.
Evidence that population increase and range expansion by Eurasian Sparrowhawks has impacted avian prey populations
Authors: Paul Bell Christopher
Published: December 2018

The role of increased predator numbers in the general decline of bird populations in the late 20thcentury remains controversial, particularly in the case of the Eurasian Sparrowhawk, for which there are contradictory results concerning its effect on the abundance of potential prey species. Previous studies of breeding season census data for Sparrowhawks and prey species in Britain have measured predator abundance either as raw presence-absence data or as an estimate derived from spatially explicit modelling, and have found little evidence of association between predator and prey populations. Here, a predator index derived from site-level binary logistic modelling was used in a regression analysis of breeding census data on 42 prey species, with significant effects emerging in 27 species (16 positive, 11 negative). The frequency of significant positive associations may indicate the tracking of prey abundance by Sparrowhawks, which would tend to cancel out any negative predation effect on prey populations, rendering it difficult to detect using census data. If so, the negative effects that have emerged for some species may underestimate the impact of increased Sparrowhawk numbers on the prey populations concerned. Nevertheless, estimates of the effect on national populations of prey species, obtained by combining effect sizes with a measure of the increase in site occupancy by the predator, suggest the possibility of a substantial impact. It cannot, therefore, be ruled out that the increase in abundance and range expansion of Sparrowhawks made a significant contribution to contemporaneous declines in the populations of many of its prey species.
Description and biology of two new egg parasitoid species, Trichogramma chagres and T. soberania (Hymenoptera: Trichogrammatidae) reared from eggs of Heliconiini butterflies (Lepidoptera: Nymphalidae: Heliconiinae) collected in Panama
Authors: Woelke Jozef B. , Viktor Fursov N. , Gumovsky Alex V. , de Rijk Marjolein , Estrada Catalina , Verbaarschoot Patrick , Huigens Martinus E. , Fatouros Nina
Published: December 2018

Two new minute egg parasitoid wasp species belonging to the genus Trichogramma (Hymenoptera: Trichogrammatidae), T. chagres sp. nov. and T. soberania sp. nov., were found in a tropical lowland rainforest in Panama, Central America. In this paper, we describe, illustrate and discuss the biology, morphological and molecular characterization of the two new Trichogramma wasp species. Both species were collected from eggs of passion vine butterflies, Agraulis vanillae vanillae (Lepidoptera: Nymphalidae: Heliconiinae) and unidentified Heliconiini species, laid on different Passiflora species (Malpighiales: Passifloraceae). A female T. soberania sp. nov. wasp was noted on the wings of a female Heliconius hecale melicerta butterfly caught in the wild. This suggests that this species may occasionally hitch a ride on adult female butterflies to find suitable host eggs. Our study adds two more species identifications to the scarce record of Trichogramma wasps from the widespread Heliconiini butterflies in Central America.
Robust Antibacterial Activity of Tungsten Oxide (WO3-X) Nanodots
Authors: Duan Guangxin , Chen Lu , Jing Zhifeng , De Luna Phil , Wen Lin , Zhang Leili , Zhao Lin , Xu Jiaying , Li Zhen , Yang Zaixing , Zhou Ruhong
Published: December 2018

Antibacterial agents are an important tool in the prevention of bacterial infections. Inorganic materials are attractive due to their high stability under a variety of conditions compared to organic antibacterial agents. Herein tungsten oxide nanodots (WO3-X), synthesized by a simple one-pot synthetic approach, was found to exhibit efficient antibacterial capabilities. The analyses with colony-forming units (CFU) showed excellent antibacterial activity of WO3-Xagainst both gram-negativeE. coli(Escherichia coli) and gram-positiveS. aureus (Staphylococcus aureus) strains. The scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed clear damage to the bacterial cell membranes, which was further confirmed by molecular dynamics simulations. Additionally, exposure to simulated sunlight was found to further increase germicidal activity of WO3-Xnanodots – a 30-minute exposure to sunlight (combining 50 μg/mL WO3-Xnanodots) showed a 70% decrease inE. coliviability compared to without exposure. Electron spin resonance spectroscopy (ESR) was used to elucidate the underlying mechanism of this photocatalytic activity through the generation of hydroxyl radical species. Cell counting kit-8 (CCK-8) and the live/dead assay were further employed to evaluate the cytotoxicity of WO3-Xnanodots on eukaryotic cells, which demonstrated their general biocompatibility. In all, our results suggest WO3-Xnanodots have considerable potential in antibacterial applications, while also being biocompatible at large.
Nucleosome positioning stability is a significant modulator of germline mutation rate variation across the human genome
Authors: Li Cai , Luscombe Nicholas M.
Published: December 2018

Understanding the patterns and genesis of germlinede novomutations is important for studying genome evolution and human diseases. Nucleosome organization is suggested to be a contributing factor to mutation rate variation across the genome. However, the small number of publishedde novomutations and the low resolution of earlier nucleosome maps limited our understanding of how nucleosome organization affects germline mutation rates in the human genome. Here, we systematically investigated the relationship between nucleosome organization and fine-scale mutation rate variation by analyzing >300,000de novomutations from whole-genome trio sequencing and high-resolution nucleosome maps in human. We found thatde novomutation rates are elevated around strong, translationally stable nucleosomes, a previously under-appreciated aspect. We confirmed this observation having controlled for local sequence context and other potential confounding factors. Analysis of the underlying mutational processes suggests that the increased mutation rates around strong nucleosomes are shaped by a combination of low-fidelity replication, frequent DNA damage and insufficient/error-prone repair in these regions. Interestingly, strong nucleosomes are preferentially located in young SINE/LINE elements, implying frequent nucleosome re-positioning (i.e. shifting of dyad position) and their contribution to hypermutation at new retrotransposons during evolution. These findings provide novel insights into how chromatin organization affects germline mutation rates and have important implications in human genetics and genome evolution.
Role of Innate-like Lymphocytes in the Pathogenesis of Community Acquired Pneumonia
Authors: Hannaway RF , Wang X , Schneider M , Slow S , Schofield MR , Morgan X , Murdoch DR , Ussher JE
Published: December 2018

Background

Mucosal-associated invariant T (MAIT) cells and Vδ2+γδ T cells are anti-bacterial innate-like lymphocytes (ILLs) that are enriched in blood and mucosa. ILLs have been implicated in control of bacterial infection. However, the role of ILLs in community-acquired pneumonia (CAP) is unknown.

Methods

Using sputum samples from a well-characterised CAP cohort, MAIT cell (Vα7.2-Jα12/20/33) and Vδ2+T cell (Vδ2-Jδ1/2/3/4) abundance was determined by quantitative PCR. Cytokine and chemokine concentrations in sputum were measured. The capacity of bacteria in sputum to produce activating ligands for MAIT cells and Vδ2+T cells was inferred by 16S rRNA sequencing.

Results

MAIT cell abundance in sputum was higher in patients with less severe pneumonia; duration of hospital admission was inversely correlated with both MAIT and Vδ2+T cell abundance. The abundance of both ILLs was higher in patients with a confirmed bacterial aetiology, however there was no correlation with total bacterial load or the predicted capacity of bacteria to produce activating ligands. Sputum MAIT cell abundance was associated with interferon- α, and interferon-γ, and sputum neutrophil abundance, while Vδ2+T cell abundance was associated with CXCL11 and interferon-γ.

Conclusions

Pulmonary MAIT and Vδ2+T cells can be detected in sputum in CAP, where they may contribute to improved clinical outcome.
Utilization of tissue ploidy level variation inde novotranscriptome assembly ofPinus sylvestris
Authors: Ojeda Dario I. , Mattila Tiina , Ruttink Tom , Kujala Sonja , Kärkkäinen Katri , Verta Jukka-Pekka , Pyhäjärvi Tanja
Published: December 2018

Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use ofde novoassembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies, including the utility of haploid (megagametophyte) tissue duringde novoassembly as single-allele guides, for six individuals and five different tissues inPinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as risk factors in a diverse hotspot plant genus
Authors: Dinnage Russell , Skeels Alex , Cardillo Marcel
Published: December 2018

Comparative models used to predict species threat status often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genusHakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology, and spatial data, to calculate latent extinction risk (potential for non-threatened species to become threatened), and estimate the most important drivers of risk for individual species. This could be of value for proactive conservation decision-making that targets species of concern before they become threatened.
Interleukin-36 promotes systemic Type-I IFN responses in severe psoriasis.
Authors: Catapano Marika , Vergnano Marta , Romano Marco , Mahil Satveer K , Choon Siew-Eng , Burden David A , Young Helen S , Carr Ian M , Lachmann Helen J , Lombardi Giovanna , Smith Catherine , Ciccarelli Francesca D , Barker Jonathan N , Capon Francesca
Published: December 2018

Psoriasis is an immune-mediated skin disorder associated with severe systemic co-morbidities. Both chronic and acute forms of the disease are characterised by abnormal interleukin (IL)-36 signalling. While the mechanisms whereby IL-36 promotes cutaneous inflammation are well established, its systemic effects have not been investigated. To address this issue, we initially measured leukocyte gene expression in generalised pustular psoriasis, an acute disease variant caused by mutations of the IL-36 receptor antagonist. By undertaking whole-blood and neutrophil RNA-sequencing in affected individuals, we identified a Type-I IFN signature, which correlated with IL-36 signalling up-regulation. We then validated these observations in patients with chronic plaque psoriasis. Finally, we demonstrated that IL-36 acts directly on plasmacytoid dendritic cells, where it potentiates Toll-like Receptor (TLR)-9 activation and IFN-alpha production. This effect was mediated by the induction of PLSCR1, an endosomal TLR-9 transporter. These results define an IL-36/TLR-9/Type-I IFN axis that could be targeted for the treatment of psoriasis co-morbidities.
Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
Authors: van Eijk Patrick , Nandi Shuvro Prokash , Yu Shirong , Bennett Mark , Leadbitter Matthew , Teng Yumin , Reed Simon H.
Published: December 2018

Repair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that global genome–nucleotide excision repair (GG-NER) in chromatin is organized into domains in relation to open reading frames. Here, we define these domains, identifying the genomic locations from which repair is initiated. By examining DNA damage–induced changes in the linear structure of nucleosomes at these sites, we demonstrate how chromatin remodeling is initiated during GG-NER. In undamaged cells, we show that the GG-NER complex occupies chromatin, establishing the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBSs). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromosomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome–nucleosome interaction. We demonstrate that initiation of GG-NER in chromatin is accompanied by the disruption of dynamic nucleosomes that flank GCBSs by the GG-NER complex.
Automated data collection and real-time data analysis suite for serial synchrotron crystallography
Authors: Basu Shibom , Kaminski Jakub W. , Panepucci Ezequiel , Huang Chia-Ying , Warshamanage Rangana , Wang Meitian , Wojdyla Justyna Aleksandra
Published: December 2018

At the Swiss Light Source macromolecular crystallography (MX) beamlines the collection of serial synchrotron crystallography (SSX) diffraction data is facilitated by the recent DA+ data acquisition and analysis software developments. The SSX suite allows easy, efficient and high-throughput measurements on a large number of crystals. The fast continuous diffraction-based two-dimensional grid scan method allows initial location of microcrystals. The CY+
GUI utility enables efficient assessment of a grid scan's analysis output and subsequent collection of multiple wedges of data (so-called minisets) from automatically selected positions in a serial and automated way. The automated data processing (adp) routines adapted to the SSX data collection mode provide near real time analysis for data in both CBF and HDF5 formats. The automatic data merging (adm) is the latest extension of the DA+ data analysis software routines. It utilizes the sxdm (SSX data merging) package, which provides automatic online scaling and merging of minisets and allows identification of a minisets subset resulting in the best quality of the final merged data. The results of both adp and adm are sent to the MX MongoDB database and displayed in the web-based tracker, which provides the user with on-the-fly feedback about the experiment.
4-Methylanilinium 2-carboxyacetate
Authors: Suresh S. , Pandi P. , Akilan R. , Kumar R. Mohan , Chakkaravarthi G.
Published: December 2018

In the crystal of the title salt, C7H10N+·C3H3O4
−, the cations are linked to the anions via N—H...O and trifurcated N—H...(O,O,O) hydrogen bonds. The anions are linked into [010] chains by O—H...O hydrogen bonds. Taken together, these interactions generate (100) sheets.
An evidence-based training and support course for caregivers of children with foetal alcohol spectrum disorder (FASD) in New Zealand
Authors: Gibbs Anita
Published: December 2018

Purpose

The purpose of this paper is to outline the development of an evidence-based training and support course for caregivers of children with foetal alcohol spectrum disorder (FASD) in New Zealand, and a brief evaluation undertaken. The seven-week caregiver training course takes an empowerment and advocacy orientation, and the aim is to assist caregivers who are caring for children with, or suspected to have FASD, develop greater resilience and strategies to help their families live successfully with impairments in a disabling society.

Design/methodology/approach

A total of 13 parents and caregivers received a seven times two-hour weekly group programme of talks, exercises and case study discussions focused on the following objectives: an increased knowledge of FASD; an increased knowledge of successful strategies and interventions that can be used to help families; and having an opportunity to foster strong peer-support relationships with others who share the lived experience of FASD. A brief interview-based evaluation was undertaken to ascertain caregivers’ views of the course, its benefits and limitations.

Findings

Caregivers valued both the content and process of the training course. They highlighted that strength of the training was the delivery by experienced, professionally trained caregivers of children with FASD. They valued the opportunity to spend time with peers in similar circumstances who understood the challenges of parenting a child with FASD.

Originality/value

A short evidence-based specialist training course for parents and caregivers with an empowerment and peer-support orientation is beneficial to parenting children with FASD.
Lattice Boltzmann simulation of free convection’s hydrothermal aspects in a finned/multi-pipe cavity filled with CuO-water nanofluid
Authors: Rahimi Alireza , Azarikhah Pouria , Kasaeipoor Abbas , Hasani Malekshah Emad , Kolsi Lioua
Published: December 2018

Purpose

This paper aims to investigate the natural convection fluid flow and heat transfer in a finned/multi-pipe cavity.

Design/methodology/approach

The cavity is filled with the CuO-water nanofluid. The Koo–Kleinstreuer–Li model is used to estimate the dynamic viscosity and consider Brownian motion. On the other hand, the effect of the shapes of nanoparticles on the thermal conductivity and related heat transfer rate is presented.

Findings

In the present investigation, the governing parameters are Rayleigh number, CuO nanoparticle concentration in pure water and the thermal arrangements of internal active fins and solid bodies. Impacts of these parameters on the nanofluid flow, heat transfer rate, total/local entropy generation and heatlines are presented. It is concluded that adding nanoparticles to the pure fluid has a significant positive influence on the heat transfer performance. In addition, the average Nusselt number and total entropy generation have direct a relationship with the Rayleigh number. The thermal arrangement of the internal bodies and fins is a good controlling tool to determine the desired magnitude of heat transfer rate.

Originality/value

The originality of this paper is to use the lattice Boltzmann method in simulating the nanofluid flow and heat transfer within a cavity included with internal active bodies and fins.
A new framework to support Lean Six Sigma deployment in SMEs
Authors: Moya Carlos Abraham , Galvez Daniel , Muller Laurent , Camargo Mauricio
Published: December 2018

Purpose

The purpose of this paper is to propose an assessment approach to evaluate the organizational capabilities to deploy a Lean Six Sigma (LSS) strategy.

Design/methodology/approach

Based on a comprehensive literature review, critical success factors required to deploy LSS were defined. These key factors are evaluated by a questionnaire based on maturity grids and structured as a multi-criteria model to compute a potential LSS performance indicator. This approach is illustrated through two case studies.

Findings

To promote a successful implementation of LSS in SMEs, it is necessary to consider five main critical factors. The evaluation of these factors could be achieved thanks to a multi-criterion-based maturity indicator for the LSS implementation. The case studies show that this approach allows SMEs to understand their strengths and weaknesses and thus better prepare the implementation of LSS.

Research limitations/implications

The proposed tool identifies characteristics of companies leading to successful LSS implementation; but is not yet able to provide a detailed strategy to improve them. The case studies were applied to manufacturing companies; therefore, there is no evidence of conclusions in the context of services.

Practical implications

The proposed methodology will help managers and practitioners to evaluate the readiness level of a company to implement LSS. Then, they could estimate the effort required to achieve the LSS deployment.

Originality/value

This paper proposes a new metric of the capacity to implement the LSS successfully in SMEs: the Lean Six Sigma Global Index. This indicator is based on a survey completed by managers and supported by observable phenomena to establish a tailored diagnosis before the LSS implementation.
The dual roles of the government in cloud computing assimilation: an empirical study in China
Authors: Wang Nianxin , Xue Yajiong , Liang Huigang , Wang Zhining , Ge Shilun
Published: December 2018

Purpose

The purpose of this paper is to investigate the government roles in cloud computing assimilation along two dimensions: government regulation and government support.

Design/methodology/approach

A research model was developed to depict the dual roles of government regulation and government support in cloud computing assimilation as well as the mediating effect of top management support (TMS). Using survey data collected from 376 Chinese firms that have already adopted cloud services, the authors tested the research model.

Findings

The impacts of both government regulation and government support on cloud computing assimilation are partially mediated by TMS. Government support exerts stronger impacts on TMS than government regulation.

Research limitations/implications

This study extends the current information systems literature by highlighting the specific mechanisms through which governments influence firms’ assimilation of cloud computing.

Practical implications

Governments in developing countries could actively allocate funds or enact policies to effectively encourage cloud computing assimilation.

Originality/value

This study would complement previous findings about government regulation, and develop a more holistic understanding about the dual roles of governments in information technology innovation assimilation.
Social enterprising informing our concept; exploring informal micro social enterprise
Authors: Anderson Alistair R. , Younis Sohail , Hashim Hina , Air Carol
Published: December 2018

Purpose

The paper investigates an unusual form of social enterprising located in a poor region of Pakistan. The purpose of this paper is to examine a novel form of micro social enterprise. Their form and functions are considered, examining how they conform to what is expected of a social enterprise. The extreme cases are analysed to reflect on what constitutes the explanatory characteristics of a social enterprise.

Design/methodology/approach

Information on examples of micro social entrepreneurship was collected from the troubled context of Khyber Pakhtunkhwa, a very poor region of Pakistan. Using the constant comparison method, explanatory themes of structure and practice are drawn out.

Findings

These enterprising social agents were engaged in opening up an opportunity space for those disadvantaged by the context. Driven by a strong sense of community responsibility, they drew upon limited, but culturally available resources. Relevance, embeddedness and informality were identified as structural characteristics, and bricolage and effectuation, frugality and social responsibility emerged as practices. Not only did context shape what they did and how they did it, but the purpose of these enterprises was also to help reshape context. From this analysis, it is argued that conceptual concerns should be directed towards behaviours; it should be asked how are enterprises agents of social change, and how are they enterprising?

Research limitations/implications

It is argued that a robust indicator for social enterprise is not what they are, but what they do. Consequently, for understanding and theorising, it is suggested that the focus remain on enterprising. This study was limited to unusual cases which may be atypical and ungeneralisable. Nonetheless, the concept – enterprising – may have theoretical applications.

Social implications

In reviewing the analysis and findings, it is noted that the proposals in the paper may comprise the early stages of a theory of social entrepreneurship practice. There may be considerable explanatory power in examining the interplays between the agency of social enterprises and the structures that are constituted in the formal and informal institutions with whom they interact.

Originality/value

Descriptively, the account draws attention to a possibly neglected phenomenon. Moreover, the extreme cases draw out the significance of a localised practice. Conceptually, there may be value in prioritising practice in social enterprise rather than form and structure.
Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov
Authors: Kutsuna Ryo , Miyoshi‐Akiyama Tohru , Mori Koji , Hayashi Masahiro , Tomida Junko , Morita Yuji , Tanaka Kaori , Kawamura Yoshiaki
Published: December 2018

Taxonomic studies of strain PAGU 1678T, an obligately anaerobic, gram‐positive, spore‐forming bacterium isolated from biobreeding rat feces, were performed. This strain has been demonstrated to have the ability to exacerbate pathosis in a mouse model of dextran sulfate sodium‐induced ulcerative colitis. Phylogenetic analysis based on the 16S rRNA gene showed high homology with Paraclostridium bifermentans. To clarify the correct taxonomic position of strain PAGU 1678T, a comparative taxonomic study using P. bifermentans PAGU 2008T (═JCM 1386T) and the closely related bacterial species P. benzoelyticum PAGU 2068T (═LMG 28745T) was carried out. Despite the close similarity of 16S rRNA gene sequences, DNA‐DNA hybridization between strain PAGU 1678T and P. bifermentans PAGU 2008T was 60.03% on average, average nucleotide identity was 96.17%, and it was shown to have different genomic sequences. Biochemically, strain PAGU 1678T could be differentiated from P. bifermentans PAGU 2008T by H2S production. Furthermore, strain PAGU 1678T was characterized by the presence of two phospholipids with different polarity on polar lipid analysis. In addition, strain PAGU 1678T differed from P. bifermentans PAGU 2008T in findings on whole‐cell protein analysis and matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry. On the basis of these biochemical and genetic characteristics, a novel subspecies of P. bifermentans with the name Paraclostridium bifermentans subsp. muricolitidis subsp. nov. is here proposed, with PAGU 1678T (═CCUG 72489T ═NBRC 113386T) as the type strain, which automatically creates P. bifermentans subsp. bifermentans subsp. nov. JCM 1386T (═ATCC 638T ═DSM 14991T).
Identification of a germline‐expression promoter for genome editing in Bombyx mori
Authors: Xu Jun , Chen Rong‐Mei , Chen Shu‐Qing , Chen Kai , Tang Lin‐Meng , Yang De‐Hong , Yang Xu , Zhang Yong , Song Hong‐Sheng , Huang Yong‐Ping
Published: December 2018

Identification of stage‐ and tissue‐specific cis‐regulatory elements will enable more precise genomic editing. In previous studies of the silkworm Bombyx mori, we identified and characterized several tissue‐ and sex‐specific cis‐regulatory elements using transgenic technology, including a female‐ and fat body‐specific promoter, vitellogenin, testis‐specific promoters, Radial spoke head 1 (BmR1) and beta‐tubulin 4 (Bmβ4). Here we report a cis‐regulatory element specific for a somatic and germ cell‐expressed promoter, nanos (Bmnos). We investigated activities of three truncated promoter sequences upstream of the transcriptional initiation site sequences of Bmnos in vitro (nos‐0.6kb, nos‐1kb and nos‐2kb) and in vivo (nos‐2kb). In BmN cultured cells, all three lengths drove expression of the gene encoding enhanced green fluorescence protein (EGFP), although nos‐2kb had the highest fluorescence activity. In transgenic silkworms, nos‐2kb drove EGFP expression at the early embryonic stage, and fluorescence was concentrated in the gonads at later embryonic stages. In addition, this cis‐regulatory element was not sex differentiated. The fluorescence intensity gradually weakened following the larval developmental stage in the gonads and were broadly expressed in the whole body. The nos‐2kb promoter drove the Cas9 system with efficiency comparable to that of the broad‐spectrum strong IE1 promoter. These results indicate that Bmnos is an effective endogenous cis‐regulatory element in the early embryo and in the gonad that can be used in applications involving the clustered, regularly interspaced, short palindromic repeats (CRISPR)/Cas9 system.
Cetuximab‐radiotherapy combination in the management of locally advanced cutaneous squamous cell carcinoma
Authors: Joseph Kurian , Alkaabi Khalifa , Warkentin Heather , Ghosh Sunita , Jha Naresh , Smylie Michael , Walker John
Published: December 2018

Introduction

We report the outcomes of using a combination of cetuximab with radiation therapy (Cetux‐RT) to treat a selected group of patients with locally advanced (unresectable) cutaneous squamous cell carcinoma (LA‐cSCC). This study presents two‐year efficacy and safety data for 8 patients with LA‐cSCC treated within a single institution.

Methods

Between 2014 and 2017 a total of eight patients (seven males, one female) with LA‐cSCC received curative intent treatment with Cetux‐RT. All patients received an initial loading dose of cetuximab at 400 mg/m2 seven days prior to radiotherapy, followed by weekly treatment with 250 mg/m2, continuing through the end of radiotherapy. Radiation doses were 6600 cGy/30 fr (n = 2), 6300 cGy/30fr (n = 2) and 5500 cGy/22 fr (n = 4).

Results

The median age was 81 years (range, 55–87). The ECOG performance status of all patients was between 0 and 2. With a median duration of follow‐up of 25 months (range 10–48 months), five patients remain in a complete response. After a partial response, another patient has relapsed and is receiving palliative chemotherapy, while two patients have died during the period of follow up (one of whom died following progression of disease, the other of an unrelated cause). Treatment in this group of patients was well tolerated, with most toxicities ≤ grade 2, and no toxicities of grade 4/5 reported.

Conclusions

Cetux‐RT was well tolerated and provided durable disease control within this patient sample. Our data support the use of the Cetux‐RT regimen for selected patients with inoperable LA‐cSCC and adequate performance status.
Comparison of methods for measuring antibiotic consumption in an intensive care unit
Authors: Olsen Markus Harboe , Anhøj Jacob , Knudsen Jenny Dahl , Frimodt‐Møller Niels , Møller Kirsten
Published: December 2018

Hospitals worldwide are working on minimizing unnecessary use of antimicrobials. To assess actual changes of antimicrobial usage, correct and precise measurements are necessary. This study aimed to compare data on the purchase of antibiotics from the pharmacy and the administration of antibiotics to patients, respectively, in an intensive care unit (ICU). Data were obtained from the Neurointensive Care Unit (NICU) at Rigshospitalet, Denmark. During a 23‐month period, comprising 10 770 bed‐days (BD), the ward purchased 16 908 defined daily doses (DDD) of antibiotics from the pharmacy, and 15 130 DDD and 41 304 individual doses were administered. Intraclass correlation coefficients (ICCs) were calculated; control and runcharts and a Bland–Altman plot were constructed. Pharmacy sales and drug administration data showed no systematic variation over time with a monthly overestimation of pharmacy sales data of 10% (95% confidence interval (CI), 6.20–14.3%) for all antibiotics, and 7% (95% CI: 1.81–11.1%) for broad‐spectrum antibiotics. The antibiotic consumption, without bed‐days, has a clinically acceptable ICC of >0.70 and no systematic difference is suggested by the Bland–Altman plot. In this study of a large NICU, whose antibiotic consumption varied at random, pharmacy sales data were an acceptable approximation of the actual summarized drug consumption.