bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leucoagaricus gongylophorus uses leaf-cutting ants to vector proteolytic enzymes towards new plant substrate
Authors: Kooij Pepijn W , Rogowska-Wrzesinska Adelina , Hoffmann Daniel , Roepstorff Peter , Boomsma Jacobus J , Schiøtt Morten 
Published: January 2014

Abstract
The mutualism between leaf-cutting ants and their fungal symbionts revolves around processing and inoculation of fresh leaf pulp in underground fungus gardens, mediated by ant fecal fluid deposited on the newly added plant substrate. As herbivorous feeding often implies that growth is nitrogen limited, we cloned and sequenced six fungal proteases found in the fecal fluid of the leaf-cutting ant Acromyrmex echinatior and identified them as two metalloendoproteases, two serine proteases and two aspartic proteases. The metalloendoproteases and serine proteases showed significant activity in fecal fluid at pH values of 5–7, but the aspartic proteases were inactive across a pH range of 3–10. Protease activity disappeared when the ants were kept on a sugar water diet without fungus. Relative to normal mycelium, both metalloendoproteases, both serine proteases and one aspartic protease were upregulated in the gongylidia, specialized hyphal tips whose only known function is to provide food to the ants. These combined results indicate that the enzymes are derived from the ingested fungal tissues. We infer that the five proteases are likely to accelerate protein extraction from plant cells in the leaf pulp that the ants add to the fungus garden, but regulatory functions such as activation of proenzymes are also possible, particularly for the aspartic proteases that were present but without showing activity. The proteases had high sequence similarities to proteolytic enzymes of phytopathogenic fungi, consistent with previous indications of convergent evolution of decomposition enzymes in attine ant fungal symbionts and phytopathogenic fungi.
Allerdictor: fast allergen prediction using text classification techniques
Authors: Dang Ha X. , Lawrence Christopher B. 
Published: January 2014

Abstract
Motivation: Accurately identifying and eliminating allergens from biotechnology-derived products are important for human health. From a biomedical research perspective, it is also important to identify allergens in sequenced genomes. Many allergen prediction tools have been developed during the past years. Although these tools have achieved certain levels of specificity, when applied to large-scale allergen discovery (e.g. at a whole-genome scale), they still yield many false positives and thus low precision (even at low recall) due to the extreme skewness of the data (allergens are rare). Moreover, the most accurate tools are relatively slow because they use protein sequence alignment to build feature vectors for allergen classifiers. Additionally, only web server implementations of the current allergen prediction tools are publicly available and are without the capability of large batch submission. These weaknesses make large-scale allergen discovery ineffective and inefficient in the public domain.
Results: We developed Allerdictor, a fast and accurate sequence-based allergen prediction tool that models protein sequences as text documents and uses support vector machine in text classification for allergen prediction. Test results on multiple highly skewed datasets demonstrated that Allerdictor predicted allergens with high precision over high recall at fast speed. For example, Allerdictor only took ∼6 min on a single core PC to scan a whole Swiss-Prot database of ∼540 000 sequences and identified &lt;1% of them as allergens.
Availability and implementation: Allerdictor is implemented in Python and available as standalone and web server versions at http://allerdictor.vbi.vt.edu.
Contact: lawrence@vbi.vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Unveiling recurrent jets of the ULX Holmberg II X-1: evidence for a massive stellar-mass black hole?
Authors: Cseh D. , Kaaret P. , Corbel S. , Grisé F. , Lang C. , Körding E. , Falcke H. , Jonker P. G. , Miller-Jones J. C. A. , Farrell S. , Yang Y. J. , Paragi Z. , Frey S. 
Published: January 2014

Abstract
We report on the discovery of an apparent triple radio structure hidden inside the radio bubble of the ultraluminous X-ray source Holmberg II X-1. The morphology is consistent with a collimated jet structure, which is observed to emit optically thin synchrotron radiation. The central component has a steep radio spectrum and is brighter than the outer components indicating a renewed radio activity. We estimate a minimum time-averaged jet power of ∼2 × 1039 erg s−1 that is associated with a time-averaged isotropic X-ray luminosity of at least 4 × 1039 erg s−1. Our results suggest that Holmberg II X-1 is powered by a black hole of MBH ≥ 25 M⊙, that is inferred to be accreting at a high Eddington rate with intermittent radio activity.
Treatment with oral beta‐blockers during pregnancy complicated by maternal heart disease increases the risk of fetal growth restriction
Authors: Ersbøll AS , Hedegaard M , Søndergaard L , Ersbøll M , Johansen M 
Published: January 2014

ObjectiveTo investigate the effect on fetal growth of treatment with oral beta‐blockers during pregnancy in women with congenital or acquired heart disease.DesignHistorical matched cohort study.SettingCentre for Pregnant Women with Heart Disease, Copenhagen University Hospital, Denmark.PopulationA cohort of 175 women with heart disease, grouped according to beta‐blocker treatment, and a cohort of 627 women from the overall population matched on seven birthweight‐determining factors.MethodsDifferences between groups were tested by simple descriptive statistics and assessed using standard hypothesis tests. Associations were estimated by correlational analysis and multivariable regression.Main outcome measureProportion of infants born small for gestational age (SGA).ResultsMore of the infants exposed to beta‐blockers were SGA compared with non‐exposed infants (29.4 versus 15.3%; P < 0.05). After adjustment for birthweight‐determining factors, beta‐blocker treatment and maternal body mass index (BMI) were the only factors independently associated with SGA (the relative difference in expected birthweight was −8.6%; 95% CI −13.3 to −3.9%; P = 0.0004). After adjustment for BMI, beta‐blocker treatment was associated with an increased risk of SGA (OR 2.65; 95% CI 1.15–6.10; P = 0.02). In a subgroup with isolated tachyarrhythmias, SGA infants were more frequent in the beta‐blocker exposed group compared with the non‐exposed group (31 versus 10%; P < 0.005). Beta‐blocker treatment was the only independent predictor of SGA, adjusting for several factors influencing fetal growth (the relative difference in expected birthweight was −12.2%; 95% CI −19.9 to −3.9%; P = 0.001).ConclusionsIn a historical cohort of pregnancies complicated by maternal heart disease, treatment with beta‐blockers was found to be independently associated with an increased risk of delivering an SGA infant.
People United to Sustain Health (PUSH): A Community‐Based Participatory Research Study
Authors: Kennedy Betty M. , Katzmarzyk Peter T. , Johnson William D. , Johnson Glenda S. , McGee Bernestine B. , Champagne Catherine M. , Harsha David W. , Crawford Terri , Ryan Donna H. 
Published: January 2014

AbstractThe prevention of weight gain to address the obesity epidemic rather than weight loss involves promoting small changes in food choices and physical activity. People United to Sustain Health (PUSH) was designed to increase fruit and vegetable consumption, physical activity, and food security to prevent weight gain in rural adults. Forty‐nine participants were randomized into a treatment group which received access to a “Rolling Store,” nutrition education and physical activity, and a control group which received family coping classes. Forty‐one (84%) of participants completed the study. At the end of 6 months, weight for all participants was maintained from baseline to completion with no significant differences between the groups. The mean fruit consumption over 6 months for the treatment group increased and was significantly greater than change in the control group (p = 0.01). This community‐based participatory research study was considered successful because weight gain was prevented.
Cost‐effectiveness of rituximab as maintenance treatment for relapsed follicular lymphoma: results of a population‐based study
Authors: Blommestein Hedwig M. , Issa Djamila E. , Pompen Marjolein , Ten Hoor Gerhard , Hogendoorn Mels , Joosten Peter , Zweegman Sonja , Huijgens Peter C. , Uyl‐de Groot Carin A. 
Published: January 2014

AbstractObjectivesOn the basis of two population‐based registries, our study aims to calculate the real‐world cost‐effectiveness of rituximab maintenance compared with observation in relapsed or refractory follicular lymphoma patients who responded to second‐line chemotherapy.MethodsData were obtained from the EORTC20981 trial, the Netherlands Cancer Registry and two population‐based registries. A Markov model was developed to calculate cost per life year gained (LYG) and quality‐adjusted life years (QALYs) for three scenarios.ResultsOur real‐world patients were (62 years) 6 to 7 years older and had higher complete response rates to second‐line chemotherapy than the trial population. Differences between the real‐world rituximab and observation group were observed for second‐line chemotherapy and disease progression. Groups were more balanced after using propensity matching. Relying entirely on updated trial results (scenario1) in combination with local cost data resulted in ratios of €11 259 per LYG and €12 655 per QALY. For scenario2, consisting of trial efficacy and matched real‐world costs, ratios of €21 202 per LYG and €23 821 per QALY were calculated. Using real‐world matched evidence (scenario3) for both effectiveness and costs showed ratios of €10 591 per LYG and €11 245 per QALY.ConclusionAlthough differences in real‐world and trial population were found, using real‐world data as well as results from long‐term trial follow‐up showed favourable ICERs for rituximab maintenance. Nevertheless, results showed that caution is required with data synthesis, interpretation and generalisability of results. As different scenarios provide answers to different questions, we recommend healthcare decision‐makers to recognise the importance of calculating several cost‐effectiveness scenarios.
Detailed carbon chemistry in charcoals from pre‐European Māori gardens of New Zealand as a tool for understanding biochar stability in soils
Authors: Calvelo Pereira R. , Camps Arbestain M. , Kaal J. , Vazquez Sueiro M. , Sevilla M. , Hindmarsh J. 
Published: January 2014

SummaryThe stability of biochar, a form of charcoal intentionally made to be added to soil to sequester carbon (C) and improve its function, remains unclear. As it is not feasible to perform long‐term (decades, centuries) laboratory experiments to assess biochar evolution after soil amendment, the study of ancient archaeological charcoals can help to identify characteristics (and possibly molecular markers) associated with the decomposition and preservation dynamics of biochar in specific pedoclimatic environments. In this study, the chemical composition of the organic carbon fractions of three charcoals from pre‐European Māori gardens of New Zealand (buried > 25 cm depth) was thoroughly assessed. Complementary short‐term incubations of charcoals in sand were used to (i) evaluate the stability of C in the short‐medium term, (ii) model its mineralization processes and (iii) estimate the C turnover. Elemental analysis, thermogravimetric analysis (TG), X‐ray photoelectron spectroscopy (XPS), solid‐state 13C nuclear magnetic resonance (NMR) and pyrolysis gas chromatography/mass spectroscopy (Py‐GC‐MS) gave consistent results in describing the charring intensity and the degree of polycondensation of these charcoals. The oldest buried deposit (770 ± 50 years BP) still retained un‐charred or weakly charred lignocellulosic material, indicating that such material survived decomposition processes for several centuries. The amount of organic C mineralized in 109 days was < 0.5% of the initial charcoal‐C. No differences in MRT among samples were detected in spite of inferred differences in thermal impact. Longer‐term incubations are needed to obtain better estimates of C turnover rates in charred material.
Pre‐schoolers, parents and supermarkets: co‐shopping as a social practice
Authors: Keller Margit , Ruus Riina 
Published: January 2014

AbstractThe objective of this paper was to examine the co‐shopping practices of children and parents in supermarkets, i.e. the practical enactment of grocery shopping. Our special focus is on how informal consumer training occurs during parent–child interaction. We use observational data collected in spring 2008 in different Estonian supermarkets, post‐shopping interviews with parents and focus group interviews with their children. Our analysis is informed by practice theory, which helps to look in detail at how the activities in a particular situation are coordinated by understandings and procedures, and are guided by the engagement in a particular shopping trip. Co‐shopping interactions mostly revolve around particular material objects, although not exclusively. Product choice is a deeply contested area, where both parents and children face numerous pressures in this situation of two‐way socialization. There are implications for consumer education more broadly. To accomplish lasting and meaningful effects on the everyday lives of families, there has to be a wider range of actors – supermarkets, producers, governmental bodies, schools and families – who care about both formal and informal consumer education.
Molecular, genetic and stem cell‐mediated therapeutic strategies for spinal muscular atrophy (SMA)
Authors: Zanetta Chiara , Riboldi Giulietta , Nizzardo Monica , Simone Chiara , Faravelli Irene , Bresolin Nereo , Comi Giacomo P. , Corti Stefania 
Published: January 2014

AbstractSpinal muscular atrophy (SMA) is an autosomal recessive motor neuron disease. It is the first genetic cause of infant mortality. It is caused by mutations in the survival motor neuron 1 (SMN1) gene, leading to the reduction of SMN protein. The most striking component is the loss of alpha motor neurons in the ventral horn of the spinal cord, resulting in progressive paralysis and eventually premature death. There is no current treatment other than supportive care, although the past decade has seen a striking advancement in understanding of both SMA genetics and molecular mechanisms. A variety of disease modifying interventions are rapidly bridging the translational gap from the laboratory to clinical trials. In this review, we would like to outline the most interesting therapeutic strategies that are currently developing, which are represented by molecular, gene and stem cell‐mediated approaches for the treatment of SMA.
Sequences in the terminal protein and reverse transcriptase domains of the hepatitis B virus polymerase contribute to RNA binding and encapsidation
Authors: Cao F. , Jones S. , Li W. , Cheng X. , Hu Y. , Hu J. , Tavis J. E. 
Published: January 2014

SummaryHepatitis B virus (HBV) antiviral therapy is plagued by limited efficacy and resistance to most nucleos(t)ide analog drugs. We have proposed that the complex RNA binding mechanism of the HBV reverse transcriptase (P) may be a novel target for antivirals. We previously found that RNA binds to the duck HBV (DHBV) P through interactions with the T3 and RT1 motifs in the viral terminal protein and reverse transcriptase domains, respectively. Here, we extended these studies to HBV P. HBV T3 and RT1 synthetic peptides bound RNA in a similar manner as did analogous DHBV peptides. The HBV T3 motif could partially substitute for DHBV T3 during RNA binding and DNA priming by DHBV P, whereas replacing RT1 supported substantial RNA binding but not priming. Substituting both the HBV T3 and RT1 motifs restored near wild‐type levels of RNA binding but supported very little priming. Alanine‐scanning mutations to the HBV T3 and RT1 motifs blocked HBV ε RNA binding in vitro and pgRNA encapsidation in cells. These data indicate that both the HBV T3 and RT1 motifs contain sequences essential for HBV ε RNA binding and encapsidation of the RNA pregenome, which is similar to their functions in DHBV. Small molecules that bind to T3 and/or RT1 would therefore inhibit encapsidation of the viral RNA and block genomic replication. Such drugs would target a novel viral function and would be good candidates for use in combination with the nucleoside analogs to improve efficacy of antiviral therapy.
Intensive care units in Turkish hospitals: do they meet the minimum standards?
Authors: Türkmen Emine , Sevinç Selvet , İlhan Marziye 
Published: January 2014

ABSTRACTBackgroundInternational and national standards for ICUs have been developed to ensure patient safety and provide effective and efficient service in these units. However, global economic crises along with shortages in professional health care staff affect the ability of ICUs to meet and maintain these standards.Aims and objectivesThe aim of this study was to ascertain whether the equipment and workforce in intensive care units (ICUs) in Turkish hospitals meet current ICU standards.DesignThis is a descriptive study based on the results of a survey questionnaire.MethodsIn total, 145 ICUs in university and private hospitals in Turkey participated in this survey. Data collection was done by means of a survey questionnaire that assessed the current equipment and workforce in these ICUs.ResultsWe found that 97·0% of the occupied beds in the ICUs had a cardiac monitor. Crash‐carts were present in every ICU. Transport monitors and transport ventilators were available in two of three and in one of two ICUs, respectively. In 82·8% of the ICUs, a physician (as a trainee level) was present at all times, while only a few ICUs had ICU‐care team members such as respiratory‐ and physiotherapist, clinical pharmacists and dieticians available. There was a general shortage of nursing staff in ICUs.ConclusionCurrently, ICUs in Turkish hospitals meet the majority of standards for ICU equipment, but they fail to meet both the international and national standards for ICU workforce requirement.Clinical relevanceHospital and ICU managers could use our findings to compare their facilities with others or to identify areas in need of improvement.
Time Trials Predict the Competitive Performance Capacity of Junior Cross-Country Skiers
Authors: Carlsson Magnus , Carlsson Tomas , Hammarström Daniel , Malm Christer , Tonkonogi Michail 
Published: January 2014

Purpose:This study investigated whether there is a correlation between time-trial performance and competitive performance capacity of male and female junior cross-country skiers and sought to explain sex-specific competitive performance capacity through multiple-regression modeling.Methods:The International Ski Federation’s (FIS) junior ranking points for distance (FISdist) and sprint (FISsprint) competitions were used as performance parameters. A total of 38 elite junior (age 18.5 ± 1.0 y) cross-country skiers (24 men and 14 women) completed 3 time-trial tests: a 3-km level-running time trial (TTRun), a 2-km moderate uphill (1.2° slope) roller-skiing time trial using the double-poling technique (TTDP), and a 2-km uphill (2.8° slope) roller-skiing time trial using the diagonal-stride technique (TTDiag). The correlations were investigated using Pearson correlation analysis, and regression models were created using multiple-linear-regression analysis.Results:For men, FISsprint and FISdist were correlated with the times for TTRun, TTDP, and TTDiag (all P < .001). For women, FISsprint was correlated with the times for TTRun (P < .05), TTDP (P < .01), and TTDiag (P < .01), whereas FISdist was correlated only with the times for TTDP (P < .01) and TTDiag (P < .05). The models developed for FISdist and FISsprint explained 73.9–82.3% of the variance in the performance capacity of male junior cross-country skiers. No statistically valid regression model was found for the women.Conclusions:Running and roller-skiing time trials are useful tests for accurately predicting the performance capacity of junior cross-country skiers.
Molecular Events Accompanying Rous Sarcoma Virus Rescue from Rodent Cells and the Role of Viral Gene Complementation
Authors: Lounková Anna , Dráberová Eduarda , Šenigl Filip , Trejbalová Kateřina , Geryk Josef , Hejnar Jiří , Svoboda Jan 
Published: January 2014

ABSTRACT

Transformation of rodent cells with avian Rous sarcoma virus (RSV) opened new ways to studying virus integration and expression in nonpermissive cells. We were interested in (i) the molecular changes accompanying fusion of RSV-transformed mammalian cells with avian cells leading to virus rescue and (ii) enhancement of this process by retroviral gene products. The RSV-transformed hamster RSCh cell line was characterized as producing only a marginal amount of
env
mRNA, no envelope glycoprotein, and a small amount of unprocessed Gag protein. Egress of viral unspliced genomic RNA from the nucleus was hampered, and its stability decreased. Cell fusion of the chicken DF-1 cell line with RSCh cells led to production of
env
mRNA, envelope glycoprotein, and processed Gag and virus-like particle formation. Proteosynthesis inhibition in DF-1 cells suppressed steps leading to virus rescue. Furthermore, new aberrantly spliced
env
mRNA species were found in the RSCh cells. Finally, we demonstrated that virus rescue efficiency can be significantly increased by complementation with the
env
gene and the highly expressed
gag
gene and can be increased the most by a helper virus infection. In summary, Env and Gag synthesis is increased after RSV-transformed hamster cell fusion with chicken fibroblasts, and both proteins provided in
trans
enhance RSV rescue. We conclude that the chicken fibroblast yields some factor(s) needed for RSV replication, particularly Env and Gag synthesis, in nonpermissive rodent cells.

IMPORTANCE
One of the important issues in retrovirus heterotransmission is related to cellular factors that prevent virus replication. Rous sarcoma virus (RSV), a member of the avian sarcoma and leukosis family of retroviruses, is able to infect and transform mammalian cells; however, such transformed cells do not produce infectious virus particles. Using the well-defined model of RSV-transformed rodent cells, we established that the lack of virus replication is due to the absence of chicken factor(s), which can be supplemented by cell fusion. Cell fusion with permissive chicken cells led to an increase in RNA splicing and nuclear export of specific viral mRNAs, as well as synthesis of respective viral proteins and production of virus-like particles. RSV rescue by cell fusion can be potentiated by in
trans
expression of viral genes in chicken cells. We conclude that rodent cells lack some chicken factor(s) required for proper viral RNA processing and viral protein synthesis.