bluuebunny/crossref_metadata_2025 huggingface dataset:
PAI‐1, CAIX, and VEGFA expressions as prognosis markers in oral squamous cell carcinoma
Authors: Peterle Gabriela Tonini , Maia Lucas Lima , Trivilin Leonardo Oliveira , de Oliveira Mayara Mota , dos Santos Joaquim Gasparini , Mendes Suzanny Oliveira , Stur Elaine , Agostini Lidiane Pignaton , Rocha Lília Alves , Moysés Raquel Ajub , Cury Patrícia Maluf , Nunes Fábio Daumas , Louro Iúri Drumond , dos Santos Marcelo , da Silva Adriana Madeira Álvares
Published: April 2018

Background

In oral squamous cell carcinoma (OSCC), the HIF‐1 complex promotes the expression of genes involved in specific mechanisms of cell survival under hypoxic conditions, such as plasminogen activator inhibitor‐1 (PAI‐1), carbonic anhydrase 9 (CAIX), and vascular endothelial growth factor A (VEGFA). The study aimed to investigate the presence and prognostic value of PAI‐1, CAIX, and VEGFA in OSCC.

Materials and Methods

Immunohistochemistry was used to analyze the expressions of these proteins in 52 tumoral tissue samples of patients with OSCC, surgically treated and followed by a minimum of 24 months after surgery. The correlations between protein expressions and clinicopathological parameters and prognosis were analyzed.

Results

Positive PAI‐1 membrane expression was significantly associated with local disease relapse (P = .027). Multivariate analysis revealed that the positive PAI‐1 membrane expression is an independent marker for local disease relapse, with approximately 14‐fold increased risk when compared to negative expression (OR = 14.49; CI = 1.40‐150.01, P = .025). Strong PAI‐1 cytoplasmic expression was significantly associated with the less differentiation grade (P = .027). Strong CAIX membrane expression was significantly associated with local disease‐free survival (P = .038). Positive CAIX cytoplasmic expression was significantly associated with lymph node affected (P = .025) and with disease‐specific survival (P = .022). Multivariate analysis revealed that the positive CAIX cytoplasmic expression is an independent risk factor for disease‐related death, increasing their risk approximately 3‐fold when compared to negative expression (HR = 2.84; CI = 1.02‐7.87, P = .045). Positive VEGFA cytoplasmic expression was significantly associated with less differentiation grade (P = .035).

Conclusion

Our results suggest a potential role for these expressions profiles as tumor prognostic markers in OSCC patients.
Pathological categorization of the stem‐pitting and mild strains Citrus tristeza virus in Taiwan and their genomic analysis
Authors: Lin Chun‐Yi , Chen Ying‐Hua , Wu Meng‐Ling , Su Hong‐Ji , Hung Ting‐Hsuan
Published: April 2018

Citrus tristeza virus (CTV), the causal agent of tristeza disease, causes the devastating diseases worldwide. In Taiwan, complex cultivars and long‐term infection by CTV result in more than 90% of infected citrus trees, but local strain identification and classification are still incomplete. Here, six CTV strains were categorized by grafting onto eight citrus cultivars and the pathological characteristics of the stem‐pitting mild strains were identified. After 6 months of inoculation, the pummelo stem‐pitting severe strain (CTV‐Pum/SP/T1) only caused severe symptoms in Wentan pummelo (WP) and the mild strain (CTV‐Pum/M/T5) was symptomless in every cultivar; the sweet orange (SO) stem‐pitting severe strain (CTV‐SwO/SP/T7) affected SO, WP and Ponkan mandarin (PM), and the mild strain (CTV‐SwO/M/T51) caused no symptoms in SO except for WP; the mandarin stem‐pitting severe strain (CTV‐Man/SP/T46) caused severe impacts in PM, WP and Eureka lemon, whereas the mild strain (CTV‐Man/M/T2) only caused severe stem‐pitting in WP. The full‐length sequencing of both pummelo stem‐pitting strains and phylogenetic analysis revealed that CTV‐Pum/SP/T1 and CTV‐Pum/M/T5 were related to the HA18‐9 and HA16‐5 strains from Hawaii, respectively. Moreover, recombination analysis revealed that TCT repeat sequences existed at open reading frame 1a in both the CTV‐Pum/SP/T1 and the T36 strains from the United States, indicating that the possible evolution relationship between two regions. Furthermore, improved universal and specific primer pairs were designed for more specific, sensitive detection to meet the needs for quarantine and early prevention. The understanding of strain pathogenicity and genomic analysis provided further characterization of each strain and enabled practical challenge inoculation against CTV disease.
Effects of fire and grazing on above‐ground biomass and species diversity in recovering grasslands in northeast China
Authors: Huang Yue , Wang Kelin , Deng Bowen , Sun Xuekai , Zeng De‐Hui
Published: April 2018

Questions

Fire and grazing can affect plant communities through different pathways in grasslands. However, little is known about how these disturbances affect plant communities in recovered semi‐arid grasslands. Here we investigated effects of prescribed fire, sheep grazing and their interactions on above‐ground biomass and species diversity in degraded semi‐arid grasslands recovered from cropping agriculture.

Location

Keerqin grasslands, northeast China.

Methods

A short‐term grazing and burning experiment with split‐plot design was conducted, with burning applied at the main plot level and grazing applied at the subplot level. After 1 year of spring burning and 2 years of grazing by sheep, the above‐ground biomass, species diversity, biomass proportion of plant functional groups and soil resource availability of the grasslands were measured and compared between treatments using a split‐plotANOVAmodel.

Results

One‐year of spring fire significantly increased above‐ground biomass, while 2 years of grazing by sheep significantly decreased it. Species diversity was reduced by grazing in the burned plots but enhanced by grazing in the unburned plots. Fire significantly increased the biomass percentage of grasses and reduced that of forbs. Fire also changed soil water content and inorganic N concentration, and grazing enhanced light intensity to the soil surface. Moreover, above‐ground biomass was positively related to soil water content and inorganic N concentration under both disturbances. Species diversity had a positive linear relationship with biomass percentage of grasses and a negative relationship with biomass percentage of forbs under sheep grazing.

Conclusions

Both short‐term fire and grazing are important in determining the above‐ground biomass in degraded semi‐arid grasslands, and their effects are opposite. Grazing coupled with fire has negative effects on species diversity. Thus, we advise that fire and grazing should be carefully applied when used in the same management regime to maintain above‐ground biomass and species diversity in managing this grassland ecosystem.
DNA sequencing to clarify the taxonomical conundrum of the clinical coelomycetes
Authors: Valenzuela‐Lopez Nicomedes , Cano‐Lira José F. , Stchigel Alberto M. , Guarro Josep
Published: April 2018

The taxonomy of the fungi that produce human infections and that develop asexual fruiting bodies in culture has become very complex. Recent molecular studies have produced dramatic changes in their classification. Currently, the coelomycetes traditionally included inSphaeropsidalesandMelanconialesare in fact distributed across at least three different classes of the Phylum Ascomycota. Approximately 1000 genera and 7000 species have been grouped in the classesDothideomycetes,LeotiomycetesandSordariomycetesand their proper identification can only be made by analysing their DNA sequences and comparing them with those corresponding to type strains available in the adequate databases. To facilitate this task for scientists and clinicians involved in the study of these complex, and every day more numerous taxa, we have updated the knowledge about the taxonomy of the commonest coelomycetes of clinical interest with the aim of improving their identification and antifungal treatment.
Performance of serum (1,3)‐ß‐d‐glucan screening for the diagnosis of invasive aspergillosis in neutropenic patients with haematological malignancies
Authors: Furfaro Elisa , Giacobbe Daniele Roberto , Del Bono Valerio , Signori Alessio , Guolo Fabio , Minetto Paola , Clavio Marino , Ballerini Filippo , Gobbi Marco , Viscoli Claudio , Mikulska Malgorzata
Published: April 2018

We report our experience with the use of (1,3)‐ß‐d‐glucan (BDG) screening for the diagnosis of invasive aspergillosis (IA) in neutropenic patients with haematological malignancies. The performance of BDG screening was assessed retrospectively in per patient and per sample analyses. Overall, 20 among 167 patients developed IA (12%). In the per patient analysis, BDG showed 60% sensitivity and 78% specificity when the criterion for positivity was the presence of at least one BDG value ≥80 pg/mL. For 2 consecutive positive results, sensitivity decreased to 40%, while specificity increased to 93% and was similar to that of a positive galactomannan (GM; 90%). The highest specificity (97%) was observed for combined positivity of at least one BDG and at least one GM. In the per sample analysis, the specificity of BDG was 100% in the best scenario, 96% in the median scenario and 89% in the worst scenario. BDG became positive before GM in 33% of IA patients with both markers positive (n = 12). Despite good specificity for 2 consecutive positive results, the BDG test offered unsatisfactory performance for the diagnosis of IA due to low sensitivity. The combination of BDG and GM showed the potential for increasing specificity.
Cutaneous Langerhans cell histiocytosis presenting with hypopigmented lesions: Report of two cases and review of literature
Authors: Mori Shoko , Adar Tony , Kazlouskaya Viktoryia , Alexander Jaime B. , Heilman Edward , Glick Sharon A.
Published: April 2018

Langerhans cell histiocytosis is a rare group of disorders that results from the abnormal proliferation and accumulation of dendritic‐derived cells in various organs of the body, such as the skin and bones. Hypopigmented macules are a rare cutaneous presentation of Langerhans cell histiocytosis that may pose a diagnostic dilemma when no other findings of Langerhans cell histiocytosis are present at the time of examination. We present 2 cases of the hypopigmented variant of Langerhans cell histiocytosis, including a case with histopathologic features of regression, and a review of the literature. These cases highlight the importance of including Langerhans cell histiocytosis in the differential diagnosis of an infant with hypopigmented macules and papules.
Optimal Advertising Budget Allocation in Luxury Fashion Markets with Social Influences: A Mean‐Variance Analysis
Authors: Chiu Chun‐Hung , Choi Tsan‐Ming , Dai Xin , Shen Bin , Zheng Jin‐Hui
Published: April 2018

Optimizing advertising budget allocation in the luxury fashion industry is an important problem. In this study, motivated by real‐world practices, we consider a luxury fashion firm serving a conspicuous market consisting of two groups of consumers who influence one another. We investigate the optimal customer portfolios and budget allocation problem using the mean‐variance (MV) framework. Under the basic model in which all budget must be spent, we identify different scenarios and propose an algorithm to construct the MV efficient frontier for each scenario. Interestingly, different from the classic investment portfolio problem, we reveal that: (i) not all budget allocations between the two groups of consumers are MV efficient, which means that the efficient frontier is not continuous; (ii) in the presence of social influence, diversification of customer portfolio does not always lead to a smaller variance, which counterintuitively means that focusing on a single consumer group can reduce risk. We also prove that to maximize expected profit, the optimal strategy is to allocate all advertising budget to one group of consumers only (i.e., a polarized strategy). We illustrate analytically, the importance of identifying the right scenario for budget planning. Finally, we examine the budget saving strategy in the extended model and uncover that the respective range of efficient solutions is smaller than the one under the all budget spending strategy. This shows that the budget saving strategy offers less flexibility for MV efficient budget allocation than the all budget spending strategy.
Early postnatal growth and neurodevelopment in children born moderately preterm or small for gestational age at term: A systematic review
Authors: Taine Marion , Charles Marie‐Aline , Beltrand Jacques , Rozé Jean Christophe , Léger Juliane , Botton Jérémie , Heude Barbara
Published: April 2018

Background

Clinicians' interest in the long‐term effects of early postnatal growth (EPG) is growing. There is compelling evidence linking rapid EPG with later cardiovascular risk, but its neurodevelopmental benefits still remain hypothetical in individuals born moderately preterm (MP) or small for gestational at term (SGAT).

Methods

The objective was to perform a systematic review of the relationship between EPG before age 3 years and neurodevelopmental outcome for individuals born MP (32‐36 weeks' gestational age) or SGAT. Following Preferred Reporting Items for Systematic Reviews and Meta‐analyses (PRISMA) guidelines, 3 independent investigators searched for articles published on this topic in the Web of Science, EMBASE and PubMed from database inception to July 1, 2017. A detailed quality scale was used to evaluate articles.

Results

We selected 19 articles relying on 12 distinct study populations; 7 articles from 3 study populations were considered at moderate or high quality. The lack of standardisation of growth analysis methods prevented performing a meta‐analysis. Overall, EPG was positively associated with neurodevelopmental outcome, especially Intelligence Quotient (IQ) when available. In this relationship, the first 6 months of life might be a critical period. Analysis of the few articles investigating the shape of the relationships revealed a non‐linear association, with a plateau for IQ with higher weight gain, which suggests a possible ceiling effect.

Conclusions

A positive association was generally found between EPG and neurodevelopmental outcome for individuals born MP or SGAT. Strategies for future epidemiological studies are suggested to improve the characterisation of this relationship.
Relation between respiratory activity and sperm parameters in boar spermatozoa cryopreserved with alpha‐tocopherol and selected by Sephadex
Authors: Satorre MM , Breininger E , Cetica PD , Córdoba M
Published: April 2018

Contents

Our aim was to evaluate the effect of Sephadex filtration on respiratory activity of porcine spermatozoa and its relation with quality and functional sperm parameters. Samples were evaluated regarding oxygen uptake and sperm parameters: motility, plasma and acrosome membrane integrity, capacitation and acrosome reaction induction in vitro, plasma membrane functionality, determined by the hypo‐osmotic swelling test (HOST), and lipid peroxidation assessed by thiobarbituric acid assay. Sephadex filtration improved all routine quality parameters (motility, plasma and acrosome membrane integrity) and functional parameters (HOST, in vitro capacitation and true acrosome reaction levels) and produced a significant decrease in cryocapacitation and lipid peroxidation. Oxygen uptake increased in Sephadex samples (41 ± 7%) respect to single washing. Oxygen addition of carbonyl‐cyanide‐m‐chlorophenylhydrazone (CCCP) confirmed mitochondrial coupling in washed and Sephadex samples; showing an increase of 2.6 and 4.2 times for oxygen consumption in single washing and Sephadex ones, respectively. The increase in oxygen uptake with succinate addition with respect to basal oxygen uptake was significantly lower in Sephadex samples (63 ± 25%) than in the washed ones (183 ± 35%). Sephadex samples showed higher mitochondrial activity measured by oxygen consumption and improved quality and functional parameters. Our study recommends this protocol due to the fact that this filtration method removes dead or damaged spermatozoa allowing to obtain cryopreserved boar spermatozoa with optimized fertilizing capacity.
Red blood cell transfusion and outcomes in acute pulmonary embolism
Authors: Wong Christopher C.Y. , Chow Wallace W.K. , Lau Jerrett K. , Chow Vincent , Ng Austin C.C. , Kritharides Leonard
Published: April 2018

Background and objective

Blood transfusion has been associated with adverse outcomes in certain conditions. This study investigates the prevalence and outcomes of red blood cell (RBC) transfusion in patients with acute pulmonary embolism (PE).

Methods

Retrospective study of consecutive patients from 2000 to 2012 admitted to a tertiary hospital with a primary diagnosis of acute PE. Transfusion status during the hospital admission was ascertained. Mortality was tracked from a state‐wide death database and analysed using multivariable modelling.

Results

A total of 73 patients (5% of all patients admitted with PE) received RBC transfusion during their admission. These patients were significantly older, had more co‐morbidities, worse haemodynamics, higher simplified pulmonary embolism severity index scores, and lower plasma sodium and haemoglobin (Hb) levels at admission. Unadjusted mortality for the transfused group was significantly higher at 30‐day (19% vs 4%, P < 0.001) and 6‐month (40% vs 10%, P < 0.001) follow‐up. Multivariable modelling showed RBC transfusion to be a significant independent predictor of mortality at 30‐day (odds ratio 3.06, 95% CI: 1.17–8.01, P = 0.02) and 6‐month (hazard ratio (HR) 1.97, 95% CI: 1.12–3.46, P = 0.02). Sensitivity analysis confirmed that transfused patients had higher mortality than non‐transfused patients in the subgroup of patients with Hb <100 g/L.

Conclusion

RBC transfusion in patients hospitalized with acute PE is rare and appears to be associated with increased risk of short‐ and long‐term mortality, independent of Hb level on admission. This finding underscores the need for future randomized controlled studies on the impact of RBC transfusion in the management of patients admitted with acute PE. [Correction added on 4 May 2018, after first online publication: the word ‘serum’ was changed to ‘plasma’ throughout the article where appropriate.]
Tiered Approach to Resilience Assessment
Authors: Linkov Igor , Fox‐Lent Cate , Read Laura , Allen Craig R. , Arnott James C. , Bellini Emanuele , Coaffee Jon , Florin Marie‐Valentine , Hatfield Kirk , Hyde Iain , Hynes William , Jovanovic Aleksandar , Kasperson Roger , Katzenberger John , Keys Patrick W. , Lambert James H. , Moss Richard , Murdoch Peter S. , Palma‐Oliveira Jose , Pulwarty Roger S. , Sands Dale , Thomas Edward A. , Tye Mari R. , Woods David
Published: April 2018

Regulatory agencies have long adopted a three‐tier framework for risk assessment. We build on this structure to propose a tiered approach for resilience assessment that can be integrated into the existing regulatory processes. Comprehensive approaches to assessing resilience at appropriate and operational scales, reconciling analytical complexity as needed with stakeholder needs and resources available, and ultimately creating actionable recommendations to enhance resilience are still lacking. Our proposed framework consists of tiers by which analysts can select resilience assessment and decision support tools to inform associated management actions relative to the scope and urgency of the risk and the capacity of resource managers to improve system resilience. The resilience management framework proposed is not intended to supplant either risk management or the many existing efforts of resilience quantification method development, but instead provide a guide to selecting tools that are appropriate for the given analytic need. The goal of this tiered approach is to intentionally parallel the tiered approach used in regulatory contexts so that resilience assessment might be more easily and quickly integrated into existing structures and with existing policies.
Human Dose–Response Data for Francisella tularensis and a Dose‐ and Time‐Dependent Mathematical Model of Early‐Phase Fever Associated with Tularemia After Inhalation Exposure
Authors: McClellan Gene , Coleman Margaret , Crary David , Thurman Alec , Thran Brandolyn
Published: April 2018

Military health risk assessors, medical planners, operational planners, and defense system developers require knowledge of human responses to doses of biothreat agents to support force health protection and chemical, biological, radiological, nuclear (CBRN) defense missions. This article reviews extensive data from 118 human volunteers administered aerosols of the bacterial agent Francisella tularensis, strain Schu S4, which causes tularemia. The data set includes incidence of early‐phase febrile illness following administration of well‐characterized inhaled doses of F. tularensis. Supplemental data on human body temperature profiles over time available from de‐identified case reports is also presented. A unified, logically consistent model of early‐phase febrile illness is described as a lognormal dose–response function for febrile illness linked with a stochastic time profile of fever. Three parameters are estimated from the human data to describe the time profile: incubation period or onset time for fever; rise time of fever; and near‐maximum body temperature. Inhaled dose‐dependence and variability are characterized for each of the three parameters. These parameters enable a stochastic model for the response of an exposed population through incorporation of individual‐by‐individual variability by drawing random samples from the statistical distributions of these three parameters for each individual. This model provides risk assessors and medical decisionmakers reliable representations of the predicted health impacts of early‐phase febrile illness for as long as one week after aerosol exposures of human populations to F. tularensis.
An Integrated Scenario Ensemble‐Based Framework for Hurricane Evacuation Modeling: Part 2—Hazard Modeling
Authors: Blanton Brian , Dresback Kendra , Colle Brian , Kolar Randy , Vergara Humberto , Hong Yang , Leonardo Nicholas , Davidson Rachel , Nozick Linda , Wachtendorf Tricia
Published: April 2018

Hurricane track and intensity can change rapidly in unexpected ways, thus making predictions of hurricanes and related hazards uncertain. This inherent uncertainty often translates into suboptimal decision‐making outcomes, such as unnecessary evacuation. Representing this uncertainty is thus critical in evacuation planning and related activities. We describe a physics‐based hazard modeling approach that (1) dynamically accounts for the physical interactions among hazard components and (2) captures hurricane evolution uncertainty using an ensemble method. This loosely coupled model system provides a framework for probabilistic water inundation and wind speed levels for a new, risk‐based approach to evacuation modeling, described in a companion article in this issue. It combines the Weather Research and Forecasting (WRF) meteorological model, the Coupled Routing and Excess STorage (CREST) hydrologic model, and the ADvanced CIRCulation (ADCIRC) storm surge, tide, and wind‐wave model to compute inundation levels and wind speeds for an ensemble of hurricane predictions. Perturbations to WRF's initial and boundary conditions and different model physics/parameterizations generate an ensemble of storm solutions, which are then used to drive the coupled hydrologic + hydrodynamic models. Hurricane Isabel (2003) is used as a case study to illustrate the ensemble‐based approach. The inundation, river runoff, and wind hazard results are strongly dependent on the accuracy of the mesoscale meteorological simulations, which improves with decreasing lead time to hurricane landfall. The ensemble envelope brackets the observed behavior while providing “best‐case” and “worst‐case” scenarios for the subsequent risk‐based evacuation model.
Correlate of burden and coping ability of caregivers of older adults with chronic illness in Nigeria
Authors: Faronbi Joel Olayiwola
Published: April 2018

Aim

Caring for older adults with chronic illness is associated with enormous physical and psychological stress on the informal caregivers. This study assessed burden experienced by caregivers of older adults with chronic illness, explored coping strategies of caregivers in relation to identified chronic conditions and determined the influence of caregiver's burden, caregiver's characteristics and older adult's characteristics on their coping ability.

Method

This is a cross‐sectional, correlational study, and data were collected among 325 caregivers of older adults living with chronic illness in Osun State, Nigeria, using a checklist, Katz IADL, Zarit Burden Interview and Brief Cope Scale. Data were analysed using descriptive and inferential statistics.

Findings

Results revealed that the age of the caregivers ranged between 19 and 70 years with a mean of 47.79 (±11.94). They were caring for older adults with heart diseases (47.7%), kidney diseases (8.0%), cancer (10.2%), gastrointestinal disorders (5.5%), stroke (18.5%), diabetes mellitus (10.2%) who had partial (60.9%) to total level of dependency (39.1%). Over 59% of caregivers experienced severe burden, which is associated with religion (p < 0.001). Coping strategies used include religion (7.37 ± 0.85), planning (6.70 ± 0.89), positive reframing (6.42 ± 1.01) and emotion‐focused coping (29.97 ± 3.30), which was the most used coping domain. Caregiver's burden was a predictor of emotion‐focused (β = −0.16), problem‐focused (β = −0.15), dysfunctional (β = −0.14) and the total coping score (β = −0.48). In addition, religion predicted emotion‐focused coping (β = 0.69).

Conclusion

This study concluded that caregiving activities impose a severe burden on the caregivers. Religion was the most used, and coping ability is predicted by burden and religion. Therefore, healthcare providers should consider interventions to promote the use of effective coping skills.
Being in a bubble – Childbirth as a potential path towards becoming in health – Lived experiences of mothers during childbirth
Authors: Hemberg Jessica Anne Viveka , Kock Jeanette
Published: April 2018

Background

Childbirth is often seen as an existentially important life event. However, few studies focus on the experience from the woman's perspective.

The aim and research questions

The aim of this study was to explore women's experiences of strength and health during childbirth through an ontological understanding. What enables women to experience strength and health during childbirth?

Research design, participants and research context

A hermeneutical approach was used. The material consists of texts from interviews with eight women who have recently (a few days to some weeks) given birth. The texts were interpreted through latent content analysis.

Ethical considerations

Informed consent was sought from the participants regarding participation in the study and the storage and handling of data for research purposes.

Findings

The overall theme was ‘Childbirth as a movement towards becoming in health’. The three main themes were as follows: ‘The self as a source of strength’, ‘The other as a source of strength in communion’ and ‘Alleviation of suffering as a source of strength’. Seven subthemes were also described.

Conclusion

Childbirth may be seen as a potential path towards becoming in health. The midwife has a central position in supporting women's experiences of health. Family‐centred care may enhance women's experiences of becoming in health during childbirth. Further research in this field should focus on revealing midwives’ perspectives on what gives women health in connection with childbirth.
Linear factor copula models and their properties
Authors: Krupskii Pavel , Genton Marc G.
Published: April 2018

We consider a special case of factor copula models with additive common factors and independent components. These models are flexible and parsimonious with O(d) parameters where d is the dimension. The linear structure allows one to obtain closed form expressions for some copulas and their extreme‐value limits. These copulas can be used to model data with strong tail dependencies, such as extreme data. We study the dependence properties of these linear factor copula models and derive the corresponding limiting extreme‐value copulas with a factor structure. We show how parameter estimates can be obtained for these copulas and apply one of these copulas to analyse a financial data set.
A nonconstraining templated powder grid for measurement of strain
Authors: Brodnik N. R. , Hsueh C.‐J. , Johnson M. T.
Published: April 2018

A method was developed and validated for mounting grid patterns with pitches on the order of tens to hundreds of micrometres onto specimens for the purposes of mechanical characterisation and fracture analysis. The method uses a low stiffness, low‐toughness photopolymer to create a textured pattern of pillars on the sample, and the spaces between these pillars are then filled in with an opaque powder to provide optical contrast. This type of grid is desirable both because of its relatively quick preparation time and because of its minimal influence on the mechanical properties of the sample. The method for mounting this powder‐based grid onto samples is discussed. Then, the accuracy of this new type of grid is validated against current state‐of‐the‐art epoxy‐mounted lithography grids as well as digitally fabricated sinusoidal grids using synthetic digital manipulation. Finally, the experimental performance of the powder‐based grid is assessed in both uniaxial tension on a poly(methyl methacrylate) specimen with a stress concentrator and fracture of stereolithographically printed photopolymer specimens. Synthetic testing shows that the powder grids are of comparable accuracy to lithography grids, but additional processing variability leads to strain errors of about 3% in powder grids compared with the 2.1% seen in lithography grids. In experiments, the powder‐based grids produce deformation patterns comparable with those expected from analytical results, and fracture toughness values for homogeneous stereolithographically printed specimens are uniform and consistent with expected values.
HLA‐DRB1*15:03 and HLA‐DRB1*11: useful predictive alleles for alloantibody production in thalassemia patients
Authors: Darvishi P. , Sharifi Z. , Azarkeivan A. , Akbari A. , Pourfathollah A. A.
Published: April 2018

Background and Objectives

Recently, thalassemia has been introduced as a chronic disease. In spite of prolonging life in thalassemia patients, the quality of their life has not significantly improved. One of the challenges that makes their quality of life poor is alloimmunisation which causes several complications to patients by restricting their options. Some individuals are more susceptible to developing an alloantibody than others. They are categorised as responders and non‐responders. Determining responders before the first transfusion allows transfusion services to provide compatible blood and prevent alloimmunisation. The aim of the present study was to determine the relationship between HLA‐DRB1*15:03, HLA‐DRB1*11 and HLA‐DRB1*09:01 alleles and alloimmunisation in Iranian thalassemia patients.

Materials and Methods

Antibody screening tests were performed by tube method, and HLA‐DRB1 genotyping was determined by Sequence‐Specific Primers (SSP‐PCR) in 59 alloimmunised and 205 non‐alloimmunised patients. HLA‐DRB1 allele frequencies were compared between alloantibody‐positive and ‐negative groups through the χ2 test.

Results

HLA‐DRB1*15:03 allele frequency was significantly different between groups (P = 0·000, odds ratio (OR) = 4·193). There was a correlation between HLA‐DRB1*11 and anti‐K (P = 0·000, OR = 6·643). There was no association between HLA‐DRB1*09:01 and alloimmunisation (P = 0·350).

Conclusions

According to our results, detecting HLA‐DRB1*15:03 and HLA‐DRB1*11 alleles are useful in the pre‐transfusion test and could determine responder patients and improve transfusion safety.
Waking up too early – the consequences of preterm birth on sleep development
Authors: Bennet Laura , Walker David W. , Horne Rosemary S. C.
Published: April 2018

Good quality sleep of sufficient duration is vital for optimal physiological function and our health. Sleep deprivation is associated with impaired neurocognitive function and emotional control, and increases the risk for cardiometabolic diseases, obesity and cancer. Sleep develops during fetal life with the emergence of a recognisable pattern of sleep states in the preterm fetus associated with the development, maturation and connectivity within neural networks in the brain. Despite the physiological importance of sleep, surprisingly little is known about how sleep develops in individuals born preterm. Globally, an estimated 15 million babies are born preterm (<37 weeks gestation) each year, and these babies are at significant risk of neural injury and impaired brain development. This review discusses how sleep develops during fetal and neonatal life, how preterm birth impacts on sleep development to adulthood, and the factors which may contribute to impaired brain and sleep development, leading to altered neurocognitive, behavioural and motor capabilities in the infant and child. Going forward, the challenge is to identify specific risk factors for impaired sleep development in preterm babies to allow for the design of interventions that will improve the quality and quantity of sleep throughout life.

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Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export
Authors: Terahara Naoya , Inoue Yumi , Kodera Noriyuki , Morimoto Yusuke V. , Uchihashi Takayuki , Imada Katsumi , Ando Toshio , Namba Keiichi , Minamino Tohru
Published: April 2018

Cooperative remodeling of the FlhA ring terminates hook assembly and initiates filament assembly at the hook tip.
Observations of biogenic ion-induced cluster formation in the atmosphere
Authors: Rose Clémence , Zha Qiaozhi , Dada Lubna , Yan Chao , Lehtipalo Katrianne , Junninen Heikki , Mazon Stephany Buenrostro , Jokinen Tuija , Sarnela Nina , Sipilä Mikko , Petäjä Tuukka , Kerminen Veli-Matti , Bianchi Federico , Kulmala Markku
Published: April 2018

On the ability of biogenic vapors to initiate ion-induced cluster formation in the boreal forest.
Resistance to Echinocandins in Candida Can Be Detected by Performing the Etest Directly on Blood Culture Samples
Authors: Bordallo-Cardona María Ángeles , Marcos-Zambrano Laura Judith , Sánchez-Carrillo Carlos , Bouza Emilio , Muñoz Patricia , Escribano Pilar , Guinea Jesús
Published: April 2018

We examined the rapid evaluation of susceptibility to echinocandins in
Candida
spp. using the Etest performed directly on positive blood cultures and anidulafungin-containing agar plates. We prospectively collected 80 positive blood cultures (Bactec-FX system, Becton-Dickinson, Cockeysville, MD, USA) with echinocandin-susceptible
Candida
spp. (
n
= 60) and echinocandin-intermediate
Candida parapsilosis
(
n
= 20) from patients with candidemia. Additionally, blood culture bottles of nonfungemic/bacteremic patients were spiked with 35 echinocandin-resistant
Candida
species isolates. A total of 2 to 4 drops of medium from each bottle were stroked directly onto both RPMI 1640 agar plates with micafungin and anidulafungin Etest strips (ET
DIR
) and Sabouraud agar plates containing 2 mg/liter of anidulafungin. The isolates were tested according to the EUCAST method and Etest standard (ET
SD
). Essential and categorical agreement between the methods was calculated. The essential agreement and categorical agreement between the EUCAST method and ET
DIR
and ET
SD
were both >97.4%. The essential agreement between ET
DIR
and the EUCAST method for both echinocandins was >97%. The categorical agreement between the
FKS
sequence and ET
DIR
was 97.4%. The ET
DIR
MICs of anidulafungin and micafungin (≥0.19 mg/liter and ≥0.064 mg/liter, respectively) effectively separated all susceptible
FKS
wild-type isolates from the resistant
FKS
mutant isolates. The categorical agreement (62.6%) between the EUCAST method and growth on anidulafungin-containing plates was poor, with the best agreement observed for
Candida glabrata
(94.2%). When performed directly on positive blood cultures from patients with candidemia, the Etest with micafungin and anidulafungin is a reliable procedure for the rapid testing of susceptibility to echinocandins in
Candida
species isolates.
The Catabolite Repressor/Activator Cra Is a Bridge Connecting Carbon Metabolism and Host Colonization in the Plant Drought Resistance-Promoting Bacterium Pantoea alhagi LTYR-11Z
Authors: Zhang Lei , Li Muhang , Li Qiqi , Chen Chaoqiong , Qu Meng , Li Mengyun , Wang Yao , Shen Xihui
Published: April 2018

Efficient root colonization is a prerequisite for application of plant growth-promoting (PGP) bacteria in improving health and yield of agricultural crops. We have recently identified an endophytic bacterium,
Pantoea alhagi
LTYR-11Z, with multiple PGP properties that effectively colonizes the root system of wheat and improves its growth and drought tolerance. To identify novel regulatory genes required for wheat colonization, we screened an LTYR-11Z transposon (Tn) insertion library and found
cra
to be a colonization-related gene. By using transcriptome (RNA-seq) analysis, we found that transcriptional levels of an
eps
operon, the
ydiV
gene encoding an anti-FlhD
4
C
2
factor, and the
yedQ
gene encoding an enzyme for synthesis of cyclic dimeric GMP (c-di-GMP) were significantly downregulated in the Δ
cra
mutant. Further studies demonstrated that Cra directly binds to the promoters of the
eps
operon,
ydiV
, and
yedQ
and activates their expression, thus inhibiting motility and promoting exopolysaccharide (EPS) production and biofilm formation. Consistent with previous findings that Cra plays a role in transcriptional regulation in response to carbon source availability, the activating effects of Cra were much more pronounced when LTYR-11Z was grown within a gluconeogenic environment than when it was grown within a glycolytic environment. We further demonstrate that the ability of LTYR-11Z to colonize wheat roots is modulated by the availability of carbon sources. Altogether, these results uncover a novel strategy utilized by LTYR-11Z to achieve host colonization in response to carbon nutrition in the environment, in which Cra bridges a connection between carbon metabolism and colonization capacity of LTYR-11Z.

IMPORTANCE
Rapid and appropriate response to environmental signals is crucial for bacteria to adapt to competitive environments and to establish interactions with their hosts. Efficient colonization and persistence within the host are controlled by various regulatory factors that respond to specific environmental cues. The most common is nutrient availability. In this work, we unraveled the pivotal role of Cra in regulation of colonization ability of
Pantoea alhagi
LTYR-11Z in response to carbon source availability. Moreover, we identified three novel members of the Cra regulon involved in EPS synthesis, regulation of flagellar biosynthesis, and synthesis of c-di-GMP and propose a working model to explain the Cra-mediated regulatory mechanism that links carbon metabolism to host colonization. This study elucidates the regulatory role of Cra in bacterial attachment and colonization of plants, which raises the possibility of extending our studies to other bacteria associated with plant and human health.
Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm
Authors: Utomo Condro , Tanjung Zulfikar Achmad , Aditama Redi , Buana Rika Fithri Nurani , Pratomo Antonius Dony Madu , Tryono Reno , Liwang Tony
Published: April 2018

Ganoderma boninense
is the dominant fungal pathogen of basal stem rot (BSR) disease on
Elaeis guineensis
. We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences.
Draft Genome Sequence of Novosphingobium sp. Strain HII-3, a Bacterium Capable of Degrading the Cembranoid α(β)-2,7,11-Cembratriene-4,6-Diol to Farnesal
Authors: Huang Shen , Qian Yumei , Wei Tao , Jia Chunxiao , Yang Pengfei , Mao Duobin
Published: April 2018

Novosphingobium
sp. HII-3, the first bacterium confirmed to degrade the cembranoid α(β)-2,7,11-cembratriene-4,6-diol to farnesal, was isolated from cured tobacco leaf in Henan, China. Here, we report the annotated draft genome sequence of strain HII-3, which has an estimated size of 4.45 Mb and comprises 4,072 coding sequences.
Complete Genome Sequencing of a Novel Type of
Omikronpapillomavirus 1
in Indian River Lagoon Bottlenose Dolphins (Tursiops truncatus)
Authors: Rodrigues Thaís C. S. , Subramaniam Kuttichantran , Cortés-Hinojosa Galaxia , Wellehan James F. X. , Ng Terry Fei Fan , Delwart Eric , McCulloch Stephen D. , Goldstein Juli D. , Schaefer Adam M. , Fair Patricia A. , Reif John S. , Bossart Gregory D. , Waltzek Thomas B.
Published: April 2018

The genome sequence of a papillomavirus was determined from fecal samples collected from bottlenose dolphins in the Indian River Lagoon, FL. The genome was 7,772 bp and displayed a typical papillomavirus genome organization. Phylogenetic analysis supported the bottlenose dolphin papillomavirus as being a novel type of
Omikronpapillomavirus
1
.
Draft Genome Sequence of the First South Korean Clinical Isolate of Burkholderia pseudomallei, H0901
Authors: Shin Yong-Woo , Choi Myung-Min , Chun Jeong-Hoon , Yu Jae-Yon , Kim Dae-Won , Rhie Gi-eun
Published: April 2018

We report here the draft genome sequence of
Burkholderia pseudomallei
H0901. This strain was isolated in 2003 from the first melioidosis patient in South Korea.
Complete Genome Sequence of a Porcine Polyomavirus from Nasal Swabs of Pigs with Respiratory Disease
Authors: Hause Ben M. , Smith Catherine , Bishop Brian , Stewart Chelsea , Simonson Randy
Published: April 2018

Metagenomic sequencing of pooled nasal swabs from pigs with unexplained respiratory disease identified a large number of reads mapping to a previously uncharacterized porcine polyomavirus.
Sus scrofa
polyomavirus 2 was most closely related to betapolyomaviruses frequently detected in mammalian respiratory samples.
Genome Reduction in
Psychromonas
Species within the Gut of an Amphipod from the Ocean’s Deepest Point
Authors: Zhang Weipeng , Tian Ren-Mao , Sun Jin , Bougouffa Salim , Ding Wei , Cai Lin , Lan Yi , Tong Haoya , Li Yongxin , Jamieson Alan J. , Bajic Vladimir B. , Drazen Jeffrey C. , Bartlett Douglas , Qian Pei-Yuan
Published: April 2018

As a unique but poorly investigated habitat within marine ecosystems, hadal trenches have received interest in recent years. This study explores the gut microbial composition and function in hadal amphipods, which are among the dominant carrion feeders in hadal habitats. Further analyses of a dominant strain revealed genomic features that may contribute to its adaptation to the amphipod gut environment. Our findings provide new insights into animal-associated bacteria in the hadal biosphere.
Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets
Authors: Brooks Lauren E. , Ul-Hasan Sabah , Chan Benjamin K. , Sistrom Mark J.
Published: April 2018

Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections; however, no widespread treatments have been developed to date. Our study evaluates an often-underappreciated aspect of resistance—the impact of evolutionary selection. We evaluate selection on all annotated efflux genes in all sequenced ESKAPE pathogens, providing critical context for and insight into current and future development of efflux-targeting treatments for resistant bacterial infections.
Evolution of Bacterial Global Modulators: Role of a Novel H-NS Paralogue in the Enteroaggregative
Escherichia coli
Strain 042
Authors: Prieto A. , Bernabeu M. , Aznar S. , Ruiz-Cruz S. , Bravo A. , Queiroz M. H. , Juárez A.
Published: April 2018

Global regulators such as H-NS play key relevant roles enabling bacterial cells to adapt to a changing environment. H-NS modulates both core and horizontally transferred (HGT) genes, but the mechanism by which H-NS can differentially regulate these genes remains to be elucidated. There are several instances of bacterial cells carrying genes that encode homologues of the global regulators. The question is what the roles of these proteins are. We noticed that the enteroaggregative
E. coli
strain 042 carries a new hitherto uncharacterized copy of the
hns
gene. We decided to investigate why this pathogenic
E. coli
strain requires an extra H-NS paralogue, termed H-NS2. In our work, we show that H-NS2 displays specific expression and regulatory properties. H-NS2 targets a subset of H-NS-specific genes and may help to differentially modulate core and HGT genes by the H-NS cellular pool.
Hypomorphic citrullinaemia due to mutatedASS1with episodic ataxia
Authors: Saini Arushi Gahlot , Attri Savita , Sankhyan N , Singhi Pratibha
Published: April 2018

Children with citrullinaemia commonly present in the neonatal period with life-threatening hyperammonaemia and progressive encephalopathy. Less often, ‘hypomorphic’ or mild late-onset childhood or adult-onset forms may be seen with intermittent neurological symptoms or acute crisis in pregnancy. We describe an 11-year-old boy with late-onset citrullinaemia manifesting as brief episodes of ataxia triggered by minor febrile illnesses, significant citrullinaemia, mild hyperammonaemia, normal neurological examination and mild cerebellar atrophy. Targeted gene sequencing showed a homozygous, missense mutation c.815G>A (p.R272H) in exon 12 ofASS1gene resulting in the amino acid substitution of histidine for arginine at codon 272. Our case highlights the importance of recognising urea cycle defects as a cause of intermittent neurological symptoms such as ataxia. Type-1 citrullinaemia may remain hypomorphic and needs a high index of suspicion.