bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of microRNA‐5196 in the pathogenesis of systemic sclerosis
Authors: Ciechomska Marzena , Zarecki Patryk , Merdas Michal , Swierkot Jerzy , Morgiel Ewa , Wiland Piotr , Maslinski Wlodzimierz , Bogunia‐Kubik Katarzyna
Published: June 2017

Background

Systemic sclerosis (SSc) is a chronic autoimmune disease characterised by tissue fibrosis and immune abnormalities. Recent evidence suggests that activated circulating monocytes from patients with SSc play an important role in early stages of SSc pathogenesis due to enhanced expression of tissue inhibitor of metalloproteinases 1 (TIMP‐1), IL‐8 and reactive oxygen species (ROS) induction. However, the exact factors that contribute to chronic inflammation and subsequently fibrosis progression are still unknown.

Materials and methods

The expression pattern of IL‐8, TIMP‐1, AP‐1 transcription factor‐Fra2 and ROS induction in peripheral blood monocytes following DZNep (histone methyltransferase inhibitor) and TLR8 agonist stimulation was investigated. Exogenous microRNA‐5196, which is predicted to bind 3′UTR of Fra2 gene, was delivered to reverse profibrotic phenotype in monocytes. Expression of circulating microRNA‐5196 was correlated with SSc parameters.

Results

DZNep + TLR8 agonist stimulation enhanced profibrotic TIMP‐1, IL‐8 and ROS generation in HC and SSc monocytes. As opposed by the decrease of miRNA‐5196 and antioxidant SOD1 expression in SSc monocytes. Exogenous delivery of microRNA‐5196 reduced Fra2 and TIMP‐1 expression suggesting that it may be used as a potential modulator of fibrogenesis in SSc. Circulating microRNA‐5196 was significantly increased in SSc and positively correlated with CRP level but not with Rodnan skin score or ESR.

Conclusions

These results suggest that microRNA‐5196 can be used as a potential biomarker characterising SSc. Overall, this study may open new possibilities for the development of microRNA‐5196‐based diagnostics and therapy in early phases of SSc.
Effect of microbial activity on penetrometer resistance and elastic modulus of soil at different temperatures
Authors: Gao W. , Muñoz‐Romero V. , Ren T. , Ashton R. W. , Morin M. , Clark I. M. , Powlson D. S. , Whalley W. R.
Published: June 2017

We explore the effect of microbial activity stimulated by root exudates on the penetrometer resistance of soil and its elastic modulus. This is important because it is a measure of the mechanical strength of soil and it correlates closely with the rate of elongation of roots. A sandy soil was incubated with a synthetic root exudate at different temperatures, for different lengths of time and with selective suppression of either fungi or bacteria. The shape of the temperature response of penetrometer resistance in soil incubated with synthetic exudate was typical of a poikilothermic temperature response. Both penetrometer resistance and small strain shear modulus had maximum values between 25 and 30°C. At temperatures of 20°C and less, there was little effect of incubation with synthetic root exudate on the small strain shear modulus, although penetrometer resistance did increase with temperature over this range (4–20°C). This suggests that in this temperature range the increase in penetrometer resistance was related to a greater resistance to plastic deformation. At higher temperatures (> 25°C) penetrometer resistance decreased. Analysis of the DNA sequence data showed that at 25°C the number of Streptomyces (Gram‐positive bacteria) increased, but selective suppression of either fungi or bacteria suggested that fungi have the greater role with respect to penetrometer resistance.

Highlights

Effect of microbial activity stimulated by synthetic root exudates on the mechanical properties.

We compared penetrometer measurements and estimates of elastic modulus with microbial community.

Penetrometer resistance of soil showed a poikilothermic temperature response.

Penetrometer resistance might be affected more by fungi than bacteria.
Impact of frailty and residual subsyndromal delirium on 1‐year functional recovery: A prospective cohort study
Authors: Chew Justin , Lim Wee Shiong , Chong Mei Sian , Ding Yew Yoong , Tay Laura
Published: June 2017

Aim

To investigate the association between frailty and incomplete delirium recovery at discharge (residual subsyndromal delirium [RSSD]), and to examine the mediating role of RSSD in the relationship between frailty and functional recovery at 12 months post‐delirium.

Methods

This was a prospective observational study of 234 individuals aged ≥65 years admitted to a specialized delirium unit. A 20‐item frailty index was derived using items from a comprehensive geriatric assessment. Individuals with frailty index ≥0.25 were defined as being frail. Diagnosis of delirium was in accordance with the Confusion Assessment Method. RSSD was defined by the Delirium Rating Scale‐Revised‐98 severity score of ≥13. We measured functional status (modified Barthel Index) on admission and 12 months post‐delirium. We carried out mediation analysis to elucidate the role of baseline frailty and RSSD on 12‐month functional recovery.

Results

A total of 167 (71%) older adults were available for analysis of 12‐month functional status. Frailty was an independent predictor for RSSD (OR 4.1, 95% CI 2.1–8.2,P < 0.001) and functional recovery at 12 months post‐delirium (β = −13.4, 95% CI –24.9 to –1.8,P = 0.02). RSSD significantly mediated the effect of baseline frailty status on functional recovery at 12 months (coefficient = −0.1, 95% CI –0.2 to –0.02,P = 0.02), with 45% of the total effect mediated by RSSD.

Conclusions

Frailty as a risk factor for poor functional recovery in the year post‐delirium might be attributable in part to its impact on incomplete delirium recovery at discharge (RSSD). Our findings support screening and interventions for frailty at admission, and extended rehabilitation for frail individuals with RSSD.Geriatr Gerontol Int 2017; 17: 2472–2478.
A qualitative study exploring the difficulties influencing decision making at the end of life for people with dementia
Authors: Lamahewa Kethakie , Mathew Rammya , Iliffe Steve , Wilcock Jane , Manthorpe Jill , Sampson Elizabeth L , Davies Nathan
Published: June 2017

Background

Dementia is a progressive neurodegenerative condition characterized by declining functional and cognitive abilities. The quality of end of life care for people with dementia in the UK can be poor. Several difficult decisions may arise at the end of life, relating to the care of the person with dementia, for example management of comorbidities.

Objective

To explore difficulties in decision making for practitioners and family carers at the end of life for people with dementia.

Design

Qualitative methodology using focus groups and semi‐structured interviews and thematic analysis methods.

Settings and participants

Former (n=4) and current (n=6) family carers of people with experience of end of life care for a person with dementia were recruited from an English dementia voluntary group in 2015. A further 24 health and care professionals were purposively sampled to include a broad range of expertise and experience in dementia end of life care.

Results

Four key themes were identified as follows: challenges of delivering coherent care in dynamic systems; uncertainty amongst decision makers; internal and external conflict amongst decision makers; and a lack of preparedness for the end of life. Overarching difficulties such as poor communication, uncertainty and conflict about the needs of the person with dementia as well as the decision maker's own role can characterize decision making at the end of life.

Conclusions

This study suggests that decision making at the end of life for people with dementia has the potential to be improved. More planning earlier in the course of dementia with an on‐going approach to conversation may increase preparedness and family carers’ expectations of end of life.
Phylogeography and population dynamics of Antbirds (Thamnophilidae) from Amazonian fluvial islands
Authors: Choueri Érik L. , Gubili Chrysoula , Borges Sérgio H. , Thom Gregory , Sawakuchi André O. , Soares Emílio A. A. , Ribas Camila C.
Published: June 2017

Aim

To investigate the evolution of the avifauna associated to Amazonian fluvial islands, focusing on the Negro River archipelagos.

Locations

Fluvial islands in the Amazon Basin.

Methods

One generalist floodplain species (Hypocnemoides melanopogon) and three river island specialists (Myrmotherula assimilis, Myrmoborus lugubris and Thamnophilus nigrocinereus) were studied (Thamnophilidae). We sequenced two mitochondrial genes and genotyped eight microsatellite loci. Phylogenetic relationships among intraspecific lineages and divergence times were estimated using Bayesian Inference. Haplotype networks, AMOVA (analysis of molecular variance) and Mantel tests were used to verify the spatial organization of genetic diversity. Gene flow and population structure were evaluated using a dissimilarity index, Bayesian inference and allele frequencies. Historical demography was inferred through neutrality tests and Extended Bayesian skyline plots (EBSP).

Results

River island specialists have evolved distinct lineages in different Amazonian tributaries, but exhibit very weak population structure within the Negro river basin. The generalist floodplain species had no population structure along the Amazon basin or within the Negro river basin. Signals of weak and recent (Pleistocene) population expansion were recovered for all species.

Main conclusions

River islands specialists show stronger population structure within Amazonia than floodplain generalists. They show a common spatial and temporal pattern of divergence between populations from the Negro islands and western Amazonia (upper and middle Solimões), which may be related to Amazonian drainage evolution. Island specialists had low genetic diversity within the Negro basin, while the higher and unstructured diversity pattern found in the floodplain generalist species may be a consequence of higher dispersal caused by the seasonal flooding pulse. River islands populations have a recent and dynamic history of contact and isolation, with small historical fluctuations of population sizes, which is in sharp contrast with the patterns found in upland forest birds.
SNP‐based genetic characterization of the Tulane National Primate Research Center's conventional and specific pathogen‐free rhesus macaque (Macaca mulatta) populations
Authors: Kanthaswamy Sree , Ng Jillian , Oldt Robert F. , Phillippi‐Falkenstein Kathrine , Kubisch H. Michael
Published: June 2017

Background

The rhesus macaque is an important biomedical model organism, and the Tulane National Primate Research Center (TNPRC) has one of the largest rhesus macaque breeding colonies in the United States.

Methods

SNP profiles from 3266 rhesus macaques were used to examine the TNPRC colony genetic composition over time and across conventional or SPF animals of Chinese and Indian ancestry.

Results

Chinese origin animals were the least genetically diverse and the most inbred; however, since their derivation from their conventional forebearers, neither the Chinese nor the Indian SPF animals exhibit any significant loss of genetic diversity or differentiation.

Conclusions

The TNPRC colony managers have successfully minimized loss in genetic variation across generations. Although founder effects and bottlenecks among the Indian animals have been successfully curtailed, the Chinese subpopulation still show some influences from these events.
A systematic review on identifying risk factors associated with early sexual debut and coerced sex among adolescents and young people in communities
Authors: Lee Regina Lai Tong , Yuen Loke Alice , Hung Tommy Tsz Man , Sobel Howard
Published: June 2017

Aims and objectives

To review literature on identifying the risk factors associated with early sexual coerced debut with the aim to facilitate the healthcare workers' planning of relevant health services to improve intervention strategies for delaying of early coerced sexual debut or forced sexual debut (CSD/FSD) in the communities.

Background

Identifying the risk factors associated with coercion at first sex is crucial for developing appropriate sexual and reproductive health information and health promotion in response. However, current knowledge about the risk factors associated with coercion, sexual debut (SD) and delayed SD among young people is limited. Health information programmes are important during adolescence, when young people are developing their values and beliefs about sexual activity and sexual norms. However, little is known about those risk factors on initiation of early sexual debut to plan relevant interventions that can delay SD and prevent CSD/FSD in this population.

Design

A systematic review.

Methods

An extensive literature search using MEDLINE (PubMed), Nursing Journals (PubMed), Web of Science, PsychINFO and CINAHL.

Results

The search generated 39 published studies that met our inclusion and exclusion criteria. Thirty‐two articles passed the quality appraisal and were selected. This review identified six domains of risk factors, categorised as: (1) the individual domain, (2) the family domain, (3) the partner/peer domain, (4) the school domain, (5) the community domain and (6) the cultural domain. These factors highlight the influences on sexual decision‐making among adolescents and young people and the timing of their first sexual intercourse.

Conclusion

It is important to use the outcome of this review's categorisation of identified risk factors to facilitate the healthcare workers and plan relevant sexual and reproductive health programmes more accessible to adolescents, especially young females and their parents. There is a need to evaluate the impact of these programmes that can delay SD and prevent CSD/FSD in this population.

Relevance to clinical practice

The results of this study could provide guidance on the planning of effective interventions for delaying of early CSD/FSD in the communities.
Listening for commissioning: A participatory study exploring young people's experiences, views and preferences of school‐based sexual health and school nursing
Authors: Aranda Kay , Coleman Lester , Sherriff Nigel S , Cocking Chris , Zeeman Laetitia , Cunningham Liz
Published: June 2017

Aims and objectives

To explore the experiences, views and preferences of young people aged 11–19 years regarding school‐based sexual health and school nursing to inform commissioning and delivery for one local authority area in England during 2015.

Background

Promoting sexual health for young people remains a challenging, even controversial, but important public health issue. Concerns regarding accessibility, acceptability and efficacy in school‐based sexual health and school nursing are evident in the literature. Additionally, a complex public health policy context now governs the funding, provision and delivery of sexual health and school nursing, which potentially presents further challenges.

Design

A qualitative, participatory design was used to explore sexual health and school nursing. Data were generated from 15 focus groups (n = 74), with young people aged 11–19 years, in educational‐based settings in one local authority area in England.

Results

The resultant themes of visibility in relation to sexual health education and school nursing revealed both the complex tensions in designing and delivering acceptable and appropriate sexual health services for young people and the significance of participatory approaches.

Conclusion

Our study shows the importance of participatory approaches in working with young people to clearly identify what they want and need in relation to sexual health. The findings also confirm the ways in which school‐based sexual health remains challenging but requires a theoretical and conceptual shift. This we argue must be underpinned by participatory approaches.

Relevance to clinical practice

School nurses have always had a significant role to play in promoting positive sexual health for young people and they are exceptionally well placed to challenge the risk‐based cultures that frequently dominate school‐based sexual health. A shift of debates and practices towards the promotion of positive sexual health cultures though previously argued for now requires the active engagement and involvement of young people.
Prying Eyes: A Dramaturgical Approach to Professional Surveillance
Authors: Visser Laura M. , Bleijenbergh Inge L. , Benschop Yvonne W. M. , van Riel Allard C. R.
Published: June 2017

This study examines how professionals engage with the increased surveillance of their daily work. We develop an understanding of professional surveillance at the micro‐level of interaction by drawing on dramaturgical literature. Based on qualitative interviews and observational data of healthcare professionals using a new technology to communicate simultaneously with each other and individual patients, we analyse how professionals use different elements of the theatre (e.g., stages and scripts) to enact surveillance. The significance of our contribution lies especially in the dramaturgical reconceptualization of surveillance as enacted, making it an integral part of displaying one's professionalism.
Understanding adaptogenic activity: specificity of the pharmacological action of adaptogens and other phytochemicals
Authors: Panossian Alexander
Published: June 2017

Adaptogens are stress‐response modifiers that increase an organism's nonspecific resistance to stress by increasing its ability to adapt and survive. The classical reductionist model is insufficiently complex to explain the mechanistic aspects of the physiological notion of “adaptability” and the adaptogenic activity of adaptogens. Here, I demonstrate that (1) the mechanisms of action of adaptogens are impossible to rationally describe using the reductionist concept of pharmacology, whereas the network pharmacology approach is the most suitable method; and (2) the principles of systems biology and pharmacological networks appear to be more suitable for conceptualizing adaptogen function and are applicable to any phytochemical. Molecular targets, signaling pathways, and networks common to adaptogens have been identified. They are associated with stress hormones and key mediators of the regulation of homeostasis. In this context, the mechanisms of action of adaptogens are specifically related to stress‐protective activity and increased adaptability of the organism. Consequently, adaptogens exhibit polyvalent beneficial effects against chronic inflammation, atherosclerosis, neurodegenerative cognitive impairment, metabolic disorders, cancer, and other aging‐related diseases. Current and potential uses of adaptogens are mainly related to stress‐induced fatigue and cognitive function, mental illness, and behavioral disorders. Their prophylactic use by healthy subjects to ameliorate stress and prevent age‐related diseases appears to be justified. It is very unlikely that the pharmacological activity of any phytochemical is specific and associated only with one type of receptor, particularly adaptogenic compounds, which affect key mediators of the adaptive stress response at intracellular and extracellular levels of communication.
Identifying drivers of breeding success in a long‐distance migrant using structural equation modelling
Authors: Souchay Guillaume , van Wijk Rien E. , Schaub Michael , Bauer Silke
Published: June 2017

In migrant animals, conditions encountered at various times and places throughout their annual cycle may affect breeding success. Yet, most studies so far have only investigated the effect of specific parts of the annual cycle, despite the importance to understand how different stages can interact and how these stages compare to intrinsic quality to properly modulate breeding success. Using a structural equation modelling approach, we investigated drivers of breeding success (migration cycle, individual quality, breeding conditions) in hoopoes Upupa epops, a long‐distant migrant. Our causal framework explained 75% of the variation in breeding success. The effect of the migration schedule was negligible, whereas the previous breeding attempt strongly influenced current breeding success. We suggest that the interplay of individual quality and environmental conditions during both previous and current breeding season may be more important drivers of breeding success than migration schedules, even in a long‐distance migrant. We conclude that structural equation modeling is a promising tool to investigate causal relationships. Applied to hoopoes, we demonstrated that current breeding success is strongly linked to previous breeding success. Complementary analysis integrating weather and climate conditions during migration and the breeding season may provide a deeper and wider overview of the annual cycle of hoopoes and additional insights into the existence of carry‐over effects in breeding success.
Production of human vitronectin in Nicotiana benthamiana using the INPACT hyperexpression platform
Authors: Dugdale Benjamin , Kato Maiko , Deo Pradeep , Plan Manuel , Harrison Mark , Lloyd Robyn , Walsh Terry , Harding Robert , Dale James
Published: June 2017

Human vitronectin (hVN) is a glycoprotein that functions as a cell adhesion molecule and a regulator of coagulation in blood plasma and the extracellular matrix. In vitro, hVN is added to serum‐free media in order to promote the adhesion of animal cells to tissue culture surfaces and the proliferation of undifferentiated stem cells. Here, we report the production of hVN in Nicotiana benthamiana using the inducible In Plant ACTivation (INPACT) hyperexpression platform. N. benthamiana plants were transformed with an INPACT expression cassette encoding hVN, and both the Tobacco yellow dwarf virus Rep/RepA activator and Tomato bushy stunt virus p19 gene under the transcriptional control of the ethanol‐inducible AlcR:alcA gene switch. hVN expression was maximal 4–5 days postactivation of the INPACT platform with a dilute ethanol solution, and crude yields of the recombinant protein reached a maximum of 643 ± 78 mg/kg fresh weight. A three‐stage purification protocol was developed using heparin and polyhistidine tag affinity binding and size exclusion filtration, resulting in a plant‐made hVN product of >90% purity. Storage conditions for plant‐made hVN were identified that maximized the capacity of the recombinant protein to promote cell adhesion. Critically, plant‐made hVN was shown to be functionally equivalent to commercial, plasma‐derived hVN at promoting one‐half maximal attachment of murine fibroblast cells (BALB‐C/3T3) in serum‐free medium at <0.1 μg/cm2 to tissue culture plasticware. The INPACT platform represents an attractive means of producing large quantities of functional, animal‐free hVN for in vitro applications.
Distinct controls of leaf widening and elongation by light and evaporative demand in maize
Authors: Lacube Sebastien , Fournier Christian , Palaffre Carine , Millet Emilie J. , Tardieu François , Parent Boris
Published: June 2017

Leaf expansion depends on both carbon and water availabilities. In cereals, most of experimental effort has focused on leaf elongation, with essentially hydraulic effects. We have tested if evaporative demand and light could have distinct effects on leaf elongation and widening, and if short‐term effects could translate into final leaf dimensions. For that, we have monitored leaf widening and elongation in a field experiment with temporary shading, and in a platform experiment with 15 min temporal resolution and contrasting evaporative demands. Leaf widening showed a strong (positive) sensitivity to whole‐plant intercepted light and no response to evaporative demand. Leaf elongation was (negatively) sensitive to evaporative demand, without effect of intercepted light per se. We have successfully tested resulting equations to predict leaf length and width in an external dataset of 15 field and six platform experiments. These effects also applied to a panel of 251 maize hybrids. Leaf length and width presented quantitative trait loci (QTLs) whose allelic effects largely differed between both dimensions but were consistent in the field and the platform, with high QTL × Environment interaction. It is therefore worthwhile to identify the genetic and environmental controls of leaf width and leaf length for prediction of plant leaf area.
Clinico‐molecular analysis of eleven patients with Hermansky–Pudlak type 5 syndrome, a mild form of HPS
Authors: Michaud Vincent , Lasseaux Eulalie , Plaisant Claudio , Verloes Alain , Perdomo‐Trujillo Yaumara , Hamel Christian , Elcioglu Nursel H. , Leroy Bart , Kaplan Josseline , Jouk Pierre‐Simon , Lacombe Didier , Fergelot Patricia , Morice‐Picard Fanny , Arveiler Benoit
Published: June 2017

Hermansky–Pudlak syndrome (HPS), first described in 1959, is a rare form of syndromic oculocutaneous albinism associated with bleeding diathesis and in some cases pulmonary fibrosis and granulomatous colitis. All 10 HPS types are caused by defects in vesicle trafficking of lysosome‐related organelles (LRO) proteins. The HPS5 protein associates with HPS3 and HPS6 to form the biogenesis of lysosome‐related organelles complex‐2 (BLOC‐2). Here, we report the clinical and genetic data of 11 patients with HPS‐5 analyzed in our laboratory. We report 11 new pathogenic variants. The 11 patients present with ocular features that are typical for albinism, with mild hypopigmentation, and with no other major complication, apart from a tendency to bleed. HPS‐5 therefore appears as a mild form of HPS, which is often clinically undistinguishable from mild oculocutaneous or ocular forms of albinism. Molecular analysis is therefore required to establish the diagnosis of this mild HPS form, which has consequences in terms of prognosis and of clinical management of the patients.
An assessment of differences in costs and health benefits of serology and NAT screening of donations for blood transfusion in different Western countries
Authors: Janssen M. P. , van Hulst M. , Custer B. ,   ABO RBDM Health Economics and Outcomes Working Group & Collaborators
Published: June 2017

Background and Objectives

The cost‐utility of safety interventions is becoming increasingly important as a driver of implementation decisions. The aim of this study was to compare the cost‐utility of different blood screening strategies in various settings, and to analyse the extent and cause of differences in health economic results.

Materials and Methods

For eight Western countries (Australia, Canada, Denmark, Finland, France, The Netherlands, UK and the United States of America), data were collected on donor and recipient populations, blood products, screening tests, and on patient treatment practices and costs. An existing ISBT web‐tool model was used to assess the cost‐utility of various strategies for HIV, HCV and HBV screening.

Results

The cost‐utility ratio of serology screening for these eight countries ranges between −11 000 and 92 000 US$ per QALY, and for NAT between −12 000 and 113 000 US$ per QALY when compared to no screening. Combined serology and NAT ranges between 600 and 217 000 US$ per QALY. The incremental cost‐utility of NAT after implementation of serology screening ranges from 2 231 000 to 15 778 000 US$ per QALY.

Conclusion

There are substantial differences in costs per QALY between countries for various HIV, HBV and HCV screening strategies. These differences are primarily caused by costs of screening tests and infection rates in the donor population. Within each country, similar cost per QALY results for serology and NAT compared to no screening, coupled with evidence of limited value of serology and NAT together prompts the need for further discussion on the acceptability of parallel testing by serology and NAT.
Empirical Study of Loincloth Typology in Custom-based Marriage in Congo-Brazzaville and Socioeconomic Implications
Authors: Nzololo Moyo
Published: June 2017

Traditional or custom-based marriage is a rejoicing moment that links two families: the paternal and maternal sides of the husband, along with the paternal and maternal sides of the wife. However, the husband-to-be must go through several expenses - in kind and cash – to face a set of lists he is handed over by the paternal and maternal sides of the wife-to-be. Those lists include first-stage preliminary requisites, second-stage marriage requisites, and the dowry requisites. The latter is the most expensive one, despite recommendations from the provisions of the Congolese code of family that sets fifty thousand CFA for the dowry. Such a list clearly indicates the number of loincloths, branded Super Wax, a high-quality and very expensive loincloth. It represents a relatively insuperable obstacle for the husband-to-be. This paper proposes a typology of loincloths from the main components analysis and hierarchical ascending classification applied to a data table crossing twenty-three loincloths and five criteria. It results, from this typology, six scenarios that have socioeconomic implications proposed from the category of prime quality loincloths.
Effects of Nonuniform Heating and Wall Conduction on Natural Convection in a Square Porous Cavity Using LTNE Model
Authors: Alsabery A. I. , Chamkha A. J. , Hashim I. , Siddheshwar P. G.
Published: June 2017

The effects of nonuniform heating and a finite wall thickness on natural convection in a square porous cavity based on the local thermal nonequilibrium (LTNE) model are studied numerically using the finite difference method (FDM). The finite-thickness horizontal wall of the cavity is heated either uniformly or nonuniformly, and the vertical walls are maintained at constant cold temperatures. The top horizontal insulated wall allows no heat transfer to the surrounding. The Darcy law is used along with the Boussinesq approximation for the flow. The results of this study are obtained for various parametric values of the Rayleigh number, thermal conductivity ratio, ratio of the wall thickness to its height, and the modified conductivity ratio. Comparisons with previously published work verify good agreement with the proposed method. The effects of the various parameters on the streamlines, isotherms, and the weighted-average heat transfer are shown graphically. It is shown that a thicker bottom solid wall clearly inhibits the temperature gradient which then leads to the thermal equilibrium case. Further, the overall heat transfer is highly affected by the presence of the solid wall. The results have possible applications in the heat-storage fluid-saturated porous systems and the applications of the high power heat transfer.
Aerothermal Performance of Shielded Vane Design
Authors: Aslanidou Ioanna , Rosic Budimir
Published: June 2017

This paper presents an experimental investigation of the concept of using the combustor transition duct wall to shield the nozzle guide vane leading edge. The new vane is tested in a high-speed experimental facility, demonstrating the improved aerodynamic and thermal performance of the shielded vane. The new design is shown to have a lower average total pressure loss than the original vane, and the heat transfer on the vane surface is overall reduced. The peak heat transfer on the vane leading edge–endwall junction is moved further upstream, to a region that can be effectively cooled as shown in previously published numerical studies. Experimental results under engine-representative inlet conditions showed that the better performance of the shielded vane is maintained under a variety of inlet conditions.
Parallel Evaluation of the MALDI Sepsityper and Verigene BC-GN Assays for Rapid Identification of Gram-Negative Bacilli from Positive Blood Cultures
Authors: Arroyo Miguel A. , Denys Gerald A.
Published: June 2017

Rapid identification of microorganisms from positive blood cultures has improved clinical management and antimicrobial stewardship. The advent of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has reduced the time to identification of cultured isolates and is now often the definitive method used in the clinical microbiology laboratory. The commercial
in vitro
diagnostic MALDI Sepsityper (Sepsityper) kit has the potential for standardization and clinical routine use for the rapid identification of a broad range of bacteria from positive blood cultures. In this study, we performed a parallel evaluation of the Sepsityper (Bruker Daltonics, Billerica, MA) and the Verigene BC-GN (BC-GN) assays (Nanosphere, Inc., Northfield, IL) for the identification of Gram-negative bacilli. A total of 210 Bactec bottles demonstrating Gram-negative bacilli were prospectively enrolled for this study. Among these, 200 monomicrobial cultures were included in the comparative analysis. For monomicrobial cultures, the BC-GN detected 85% (170/200) compared to that detected by routine culture while the Sepsityper detected 94% (188/200) and 91% (181/200) to the genus and species levels, respectively. Comparable positive percentage agreement and negative percentage agreement were observed between the Sepsityper (96.5% and 98.8%, respectively) and the BC-GN (99.4% and 99.8%, respectively) when only (
n
= 170, 85%) organisms targeted by the latter test were included in the analysis. In conclusion, the two methods evaluated in this study showed excellent performance characteristics for the identification of Gram-negative bacilli commonly isolated from blood cultures. The Sepsityper showed a broader identification range capability that may further improve clinical management and antimicrobial stewardship in patients with less frequent Gram-negative bacilli bloodstream infections.
Differential Requirement of Human Cytomegalovirus UL112-113 Protein Isoforms for Viral Replication
Authors: Schommartz Tim , Tang Jiajia , Brost Rebekka , Brune Wolfram
Published: June 2017

The UL112-113 gene is one of the few alternatively spliced genes of human cytomegalovirus (HCMV). It codes for four phosphoproteins, p34, p43, p50, and p84, all of which are expressed with early kinetics and accumulate at sites of viral DNA replication within the host cell nucleus. Although these proteins are known to play important, possibly essential, roles in the viral replication cycle, little is known about the contribution of individual UL112-113 protein products. Here we used splice site mutagenesis, intron deletion and substitution, and nonsense mutagenesis to prevent the individual expression of each UL112-113 protein isoform and to investigate the importance of each isoform for viral replication. We show that HCMV mutants lacking p34 or p50 expression replicated to high titers in human fibroblasts and endothelial cells, indicating that these proteins are nonessential for viral replication, while mutant viruses carrying a stop mutation within the p84 coding sequence were severely growth impaired. Viral replication could not be detected upon the inactivation of p43 expression, indicating that this UL112-113 protein is essential for viral replication. We also analyzed the ability of UL112-113 proteins to recruit other viral proteins to intranuclear prereplication compartments. While UL112-113 expression was sufficient to recruit the UL44-encoded viral DNA polymerase processivity factor, it was not sufficient for the recruitment of the viral UL84 and UL117 proteins. Remarkably, both the p43 and p84 isoforms were required for the efficient recruitment of pUL44, which is consistent with their critical role in the viral life cycle.

IMPORTANCE
Human cytomegalovirus requires gene products from 11 genetic loci for the lytic replication of its genome. One of these loci, UL112-113, encodes four proteins with common N termini by alternative splicing. In this study, we inactivated the expression of each of the four UL112-113 proteins individually and determined their requirement for HCMV replication. We found that two of the UL112-113 gene products were dispensable for viral replication in human fibroblasts and endothelial cells. In contrast, viral replication was severely reduced or absent when one of the other two gene products was inactivated, indicating that they are of crucial importance for the viral replication cycle. We further showed that the latter two gene products are involved in the recruitment of pUL44, an essential cofactor of the viral DNA polymerase, to specific sites within the cell nucleus that are thought to serve as starting points for viral DNA replication.
Identification of an Intermediate in Hepatitis B Virus Covalently Closed Circular (CCC) DNA Formation and Sensitive and Selective CCC DNA Detection
Authors: Luo Jun , Cui Xiuji , Gao Lu , Hu Jianming
Published: June 2017

Hepatitis B virus (HBV) covalently closed circular (CCC) DNA functions as the only viral template capable of coding for all the viral RNA species and is thus essential to initiate and sustain viral replication. CCC DNA is converted, in a multistep and ill-understood process, from a relaxed circular (RC) DNA, in which neither of the two DNA strands is covalently closed. To detect putative intermediates during RC DNA to CCC DNA conversion, two 3′ exonucleases, exonuclease I (Exo I) and Exo III, were used in combination to degrade all DNA strands with a free 3′ end, which would nevertheless preserve closed circular DNA in either single-stranded (SS) or double-stranded (DS) form. Indeed, an RC DNA species with a covalently closed minus strand but an open plus strand (closed minus-strand RC DNA [cM-RC DNA]) was detected by this approach. Further analyses indicated that at least some of the plus strands in such a putative intermediate likely still retained the RNA primer that is attached to the 5′ end of the plus strand in RC DNA, suggesting that minus-strand closing can occur before plus-strand processing. Furthermore, the same nuclease treatment proved to be useful for sensitive and specific detection of CCC DNA by removing all DNA species other than closed circular DNA. Application of these and similar approaches may allow the identification of additional intermediates during CCC DNA formation and facilitate specific and sensitive detection of CCC DNA, which should help elucidate the pathways of CCC DNA formation and the factors involved.

IMPORTANCE
The hepatitis B virus (HBV) covalently closed circular (CCC) DNA, by serving as the viral transcriptional template, is the molecular basis of viral persistence. CCC DNA is converted, in a multistep and ill-understood process, from relaxed circular (RC) DNA. Little is currently understood about the pathways or factors involved in CCC DNA formation. We have now detected a likely intermediate during the conversion of RC DNA to CCC DNA, thus providing important clues to the pathways of CCC DNA formation. Furthermore, the same experimental approach that led to the detection of the intermediate could also facilitate specific and sensitive detection of CCC DNA, which has remained challenging. This and similar approaches will help identify additional intermediates during CCC DNA formation and elucidate the pathways and factors involved.
High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia
Authors: Shi Mang , Neville Peter , Nicholson Jay , Eden John-Sebastian , Imrie Allison , Holmes Edward C.
Published: June 2017

Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the
Aedes
genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the
Culex
genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three
Culex
species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses.

IMPORTANCE
Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with
Culex
species harboring more viruses at higher abundance than those from
Aedes
mosquitoes.
Seasonal H3N2 and 2009 Pandemic H1N1 Influenza A Viruses Reassort Efficiently but Produce Attenuated Progeny
Authors: Phipps Kara L. , Marshall Nicolle , Tao Hui , Danzy Shamika , Onuoha Nina , Steel John , Lowen Anice C.
Published: June 2017

Reassortment of gene segments between coinfecting influenza A viruses (IAVs) facilitates viral diversification and has a significant epidemiological impact on seasonal and pandemic influenza. Since 1977, human IAVs of H1N1 and H3N2 subtypes have cocirculated with relatively few documented cases of reassortment. We evaluated the potential for viruses of the 2009 pandemic H1N1 (pH1N1) and seasonal H3N2 lineages to reassort under experimental conditions. Results of heterologous coinfections with pH1N1 and H3N2 viruses were compared to those obtained following coinfection with homologous, genetically tagged, pH1N1 viruses as a control. High genotype diversity was observed among progeny of both coinfections; however, diversity was more limited following heterologous coinfection. Pairwise analysis of genotype patterns revealed that homologous reassortment was random while heterologous reassortment was characterized by specific biases. pH1N1/H3N2 reassortant genotypes produced under single-cycle coinfection conditions showed a strong preference for homologous PB2-PA combinations and general preferences for the H3N2 NA, pH1N1 M, and H3N2 PB2 except when paired with the pH1N1 PA or NP. Multicycle coinfection results corroborated these findings and revealed an additional preference for the H3N2 HA. Segment compatibility was further investigated by measuring chimeric polymerase activity and growth of selected reassortants in human tracheobronchial epithelial cells. In guinea pigs inoculated with a mixture of viruses, parental H3N2 viruses dominated but reassortants also infected and transmitted to cage mates. Taken together, our results indicate that strong intrinsic barriers to reassortment between seasonal H3N2 and pH1N1 viruses are few but that the reassortants formed are attenuated relative to parental strains.

IMPORTANCE
The genome of IAV is relatively simple, comprising eight RNA segments, each of which typically encodes one or two proteins. Each viral protein carries out multiple functions in coordination with other viral components and the machinery of the cell. When two IAVs coinfect a cell, they can exchange genes through reassortment. The resultant progeny viruses often suffer fitness defects due to suboptimal interactions among divergent viral components. The genetic diversity generated through reassortment can facilitate the emergence of novel outbreak strains. Thus, it is important to understand the efficiency of reassortment and the factors that limit its potential. The research described here offers new tools for studying reassortment between two strains of interest and applies those tools to viruses of the 2009 pandemic H1N1 and seasonal H3N2 lineages, which currently cocirculate in humans and therefore have the potential to give rise to novel epidemic strains.
Heparin Mimics Extracellular DNA in Binding to Cell Surface-Localized Proteins and Promoting Staphylococcus aureus Biofilm Formation
Authors: Mishra Surabhi , Horswill Alexander R.
Published: June 2017

Staphylococcus aureus
and coagulase-negative staphylococci (CoNS) are the leading causes of catheter implant infections. Identifying the factors that stimulate catheter infection and the mechanism involved is important for preventing such infections. Heparin, the main component of catheter lock solutions, has been shown previously to stimulate
S. aureus
biofilm formation through an unknown pathway. This work identifies multiple heparin-binding proteins in
S. aureus
, and it reveals a potential mechanism through which heparin enhances biofilm capacity. Understanding the details of the heparin enhancement effect could guide future use of appropriate lock solutions for catheter implants.
Use of RNA-Protein Complexes for Genome Editing in Non-
albicans Candida
Species
Authors: Grahl Nora , Demers Elora G. , Crocker Alex W. , Hogan Deborah A.
Published: June 2017

Existing CRISPR-Cas9 genome modification systems for use in
Candida albicans
, which rely on constructs to endogenously express the Cas9 protein and guide RNA, do not work efficiently in other
Candida
species due to inefficient promoter activity. Here, we present an expression-free method that uses RNA-protein complexes and demonstrate its use in three
Candida
species known for their drug resistance profiles. We propose that this system will aid the genetic analysis of fungi that lack established genetic systems.
Giardia
Colonizes and Encysts in High-Density Foci in the Murine Small Intestine
Authors: Barash N. R. , Nosala C. , Pham J. K. , McInally S. G. , Gourguechon S. , McCarthy-Sinclair B. , Dawson S. C.
Published: June 2017

Giardia
is a single-celled parasite causing significant diarrheal disease in several hundred million people worldwide. Due to limited access to the site of infection in the gastrointestinal tract, our understanding of the dynamics of
Giardia
infections in the host has remained limited and largely inferred from laboratory culture. To better understand
Giardia
physiology and colonization in the host, we developed imaging methods to quantify
Giardia
expressing bioluminescent physiological reporters in two relevant animal models. We discovered that parasites primarily colonize and encyst in the proximal small intestine in discrete, high-density foci. We also show that high parasite density contributes to encystation initiation.