bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in uranium energy spectra measured by SIMS on slightly hyper‐stoichiometric UO2
Authors: Desgranges L. , Pasquet B. , Roure I. , Bienvenu Ph.
Published: July 2012

The energy spectra of UO2 samples with slight hyper‐stoichiometry were measured. In addition to the regular peak detected at 20 eV, it was observed that another peak at 80 eV would grow with the increasing stoichiometry. The relative intensities of the two peaks were used to determine the surface O/U ratio of the sample. We discuss how it would be possible to determine bulk O/U ratio from these results. Copyright © 2012 John Wiley & Sons, Ltd.
ToF‐SIMS of metal‐complex‐based supramolecular architectures on oxide surfaces
Authors: Spampinato V. , Vitale S. , Quici S. , Torrisi A. , Stepanenko V. , Würthner F. , Licciardello A.
Published: July 2012

Time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) was applied in combination with optical absorption spectroscopy for studying the anchoring of polypyridine‐based supramolecular layers on oxide surfaces, such as quartz or indium tin oxide, by means of a layer‐by‐layer method involving a self‐assembly process relying on coordination interactions that lead to the formation, at the surface, of metal‐complex‐based layers. ToF‐SIMS measurements were crucial in setting up the strategy for the preparation of the above systems, as they allowed a detailed monitoring of each preparation step and provided direct qualitative information on the successful anchoring at the surface. Optical measurements, on the other hand, provided quantitative information on the growth of the multilayers, beyond the thickness sampled by static‐SIMS. Copyright © 2012 John Wiley & Sons, Ltd.
Robust analysis in joint models: an application to a study on muscular dystrophy
Authors: Das Kalyan , Chakraborty Arindom
Published: July 2012

Generalized partial ordinal models occur frequently in biomedical investigations where, along with ordinal longitudinal outcomes, there are time‐dependent covariates that act nonparametrically. In these studies, an association between such outcomes and time to an event is of considerable interest to medical practitioners. The primary objective in the present article is to study the robustness of estimators of the parameters of interest in a joint generalized partial ordinal models and a time‐to‐event model, because in many situations, the estimators in such joint models are sensitive to outliers. A Monte Carlo Metropolis–Hastings Newton Raphson algorithm is proposed for robust estimation. A detailed simulation study was performed to justify the behavior of the proposed estimators. By way of motivation, we consider a data set concerning longitudinal outcomes of children involved in a study on muscular dystrophy. Our analysis revealed some interesting findings that may be useful to medical practitioners. Copyright © 2012 John Wiley & Sons, Ltd.
Bioenergy and land use change—state of the art
Authors: Berndes Göran , Ahlgren Serina , Börjesson Pål , Cowie Annette L.
Published: July 2012

Bioenergy projects can lead to direct and indirect land use change (LUC), which can substantially affect greenhouse gas balances with both beneficial and adverse outcomes for bioenergy's contribution to climate change mitigation. The causes behind LUC are multiple, complex, interlinked, and change over time. This makes quantification uncertain and sensitive to many factors that can develop in different directions—including land use productivity, trade patterns, prices and elasticities, and use of by‐products associated with biofuels production. Quantifications reported so far vary substantially and do not support the ranking of bioenergy options with regard to LUC and associated emissions. There are however several options for mitigating these emissions, which can be implemented despite the uncertainties. Long‐rotation forest management is associated with carbon emissions and sequestration that are not in temporal balance with each other and this leads to mitigation trade‐offs between biomass extraction for energy use and the alternative to leave the biomass in the forest. Bioenergy's contribution to climate change mitigation needs to reflect a balance between near‐term targets and the long‐term objective to hold the increase in global temperature below 2°C (Copenhagen Accord). Although emissions from LUC can be significant in some circumstances, the reality of such emissions is not sufficient reason to exclude bioenergy from the list of worthwhile technologies for climate change mitigation. Policy measures to minimize the negative impacts of LUC should be based on a holistic perspective recognizing the multiple drivers and effects of LUC.

This article is categorized under:

Bioenergy > Economics and Policy

Bioenergy > Climate and Environment
Differences in Fecal Androgen Patterns of Breeding and Nonbreeding Kori Bustards (Ardeotis kori)
Authors: Penfold Linda M. , Hallager Sara , Boylan Jeanette , de Wit Martine , Metrione Lara C. , Oliva Marcie
Published: July 2012

To better understand breeding conditions to promote reproduction in captive kori bustards, fundamental endocrine studies measuring fecal androgen metabolites in male and female kori bustards were conducted. Feces collected weekly from males and females were analyzed for testosterone using enzyme‐linked immunoassay. Results from adult males (n = 5), adult females (n = 10), immature males (n = 10), and immature females (n = 10) revealed seasonally elevated testosterone concentrations in fertile, but not nonfertile adult males and females (P > 0.05). Adult females that were not maintained in a breeding group, or that did not produce eggs, did not demonstrate increases in testosterone compared to egg laying counterparts. In males, but not females, seasonal testosterone increases were accompanied by weight gain. Peaks in male fecal androgen metabolites ranged from 10‐ to 22‐fold higher than nonbreeding season (181.5 ± 19.1 vs. 17.0 ± 0.94 ng/g; P < 0.05). Mean breeding season values for adult males were 83.6 ± 6.1 ng/g vs. nonbreeding season values of 12.3 ± 0.73 ng/g (P < 0.05). In females, average breeding season testosterone concentrations were approximately 4‐fold higher than nonbreeding season (55.9 ± 6.0 vs. 14.5 ± 1.8 ng/g), with peaks 10‐ to 30‐fold higher. Results show that noninvasive fecal androgen metabolite analysis can provide a means of predicting fertility potential of male and female kori bustards and might be utilized to assess effects of modifying captive environments to promote reproduction in this species. Zoo Biol. 32:54‐62, 2013. © 2012 Wiley Periodicals, Inc.
Influence of Young Age on Outcome After Esophagectomy for Cancer
Authors: van Nistelrooij Anna M. J. , Andrinopoulou Elrozy R. , van Lanschot Jan J. B. , Tilanus Hugo W. , Wijnhoven Bas P. L.
Published: July 2012

Background

The incidence of esophageal cancer has risen among all age groups. Controversy exists about the clinical presentation and prognosis of young patients. The aim of this study was to compare the clinicopathologic characteristics and outcomes after surgery between patients with esophageal cancer who were <50 years of age and those ≥50 years of age.

Methods

Patients diagnosed with esophageal carcinoma who underwent esophagectomy between January 1990 and December 2010 in a single institution were selected from a prospective database. Patients aged <50 years at diagnosis (n = 163) were compared with those ≥50 years (n = 1151) with respect to clinicopathologic stage and oncologic outcome.

Results

Younger patients had less co‐morbidity (p < 0.001). There were no significantly differences in tumor localization, histology, differentiation, or TNM stage in the two groups. In both groups, 37 % of the patients underwent neoadjuvant chemo(radio)therapy. One or more nonsurgical complications developed in 53 % of the older group versus 42 % in the younger group (p = 0.012). In‐hospital mortality was 6.3 % for patients ≥50 years compared to 1.8 % for younger patients (p = 0.021). The 5 year overall survival was significantly better for the younger patients than for those ≥50 years (41 vs. 31 %, p < 0.001), but median disease‐specific and disease‐free survival did not differ between the groups (37 vs. 30 months, p = 0.140 and 49 vs. 28 months, p = 0.079, respectively). Multivariate analysis identified moderate, poorly, and undifferentiated tumors; tumor‐positive resection margins (pR1–2); and TNM stage IIB–IV as independent predictors of disease‐specific survival.

Conclusions

A considerable proportion (12 %) of patients diagnosed with resectable esophageal carcinoma were <50 years. Phenotypic tumor characteristics and disease‐specific survival were comparable for the two age groups.
Active aneurysmal bone cysts in children: Possible evolution after biopsy
Authors: Louahem Djamel , Kouyoumdjian Pascal , Ghanem Ismat , Mazeau Philippe , Perrochia Hélène , L'Kaissi Mohamed , Cottalorda Jérôme
Published: July 2012

Purpose

The active or aggressive character in certain localisations of aneurysmal bone cysts in children requires either curettage with a considerable recurrence rate or a radical segmental excision, raising complex reconstructive challenges. Cyst maturation with subsequent ossification may be observed either spontaneously or after incisional biopsy.

Patients

Five new cases of active aneurysmal bone cysts (ABCs) with healing of the cyst after biopsy alone are reported. All patients had no treatment of the cyst after the biopsy.

Results

In two cases, the lesion initially increases in size immediately after the biopsy, and it is only secondarily that the lesion decreases in size. Four out of five cases of the spontaneous healing occurred in pelvic bone. The cysts healed after, respectively, 36, 24, 12, 32 and 12 months.

Conclusions

The emergence of these new cases of spontaneous healing encourages promoting clinical and radiological supervision after biopsy in selected cases. Unfortunately, it is impossible to predict a possible aggressive behaviour in ABCs. Then, if the lesion is quickly aggressive with clinically and radiologically increasing size after biopsy, it would be illogical and dangerous to let this ABC evolve. It would be necessary to treat it without delay. On the other hand, if the lesion moderately increased after the biopsy, it is possible to wait and observe the patient during a period of 5 months for a possible healing, if the ABC localisation is not dangerous. Of course, if the lesion does not increase in size after biopsy, there is no delay to treat it.
Generating pluripotent stem cells: Differential epigenetic changes during cellular reprogramming
Authors: Tobin Stacey C. , Kim Kitai
Published: July 2012

Pluripotent stem cells hold enomous potential for therapuetic applications in tissue replacement therapy. Reprogramming somatic cells from a patient donor to generate pluripotent stem cells involves both ethical concerns inherent in the use of embryonic and oocyte‐derived stem cells, as well as issues of histocompatibility. Among the various pluripotent stem cells, induced pluripotent stem cells (iPSC)—derived by ectopic expression of four reprogramming factors in donor somatic cells—are superior in terms of ethical use, histocompatibility, and derivation method. However, iPSC also show genetic and epigenetic differences that limit their differentiation potential, functionality, safety, and potential clinical utility. Here, we discuss the unique characteristics of iPSC and approaches that are being taken to overcome these limitations.
Life at the dry edge: Microorganisms of the Atacama Desert
Authors: Azua-Bustos Armando , Urrejola Catalina , Vicuña Rafael
Published: July 2012

The Atacama Desert, located in northern Chile, is the driest and oldest Desert on Earth. Research aimed at the understanding of this unique habitat and its diverse microbial ecosystems begun only a few decades ago, mainly driven by NASA's astrobiology program. A milestone in these efforts was a paper published in 2003, when the Atacama was shown to be a proper model of Mars. From then on, studies have been focused to examine every possible niche suitable for microbial life in this extreme environment. Habitats as different as the underside of quartz rocks, fumaroles at the Andes Mountains, the inside of halite evaporates and caves of the Coastal Range, among others, have shown that life has found ingenious ways to adapt to extreme conditions such as low water availability, high salt concentration and intense UV radiation.
Clearance of extracellular misfolded proteins in systemic amyloidosis: Experience with transthyretin
Authors: Almeida Maria Rosário , Saraiva Maria João
Published: July 2012

Increasing evidence indicates that accumulation of misfolded proteins in the form of oligomers, protofibrils or amyloid fibrils, and their consequences in triggering intracellular signaling cascades with toxic consequences represent unifying events in many of slowly progressive neurodegenerative disorders. Studies with small compounds or molecules, known to recognize and disrupt amyloidogenic structures, have proven efficient in promoting clearance of protein aggregates in experimental models of systemic and localized forms of amyloidoses. Doxycycline and EGCG were efficient in removing aggregates in pre‐clinical studies in a transgenic mouse model for transthyretin (TTR) systemic amyloidosis and represent an opportunity to address mechanisms and key players in deposit removal. Extracellular chaperones, such as clusterin and metalloproteinases play an important role in this process.
Immunoregulatory molecules are master regulators of inflammation during the immune response
Authors: de la Fuente Hortensia , Cibrián Danay , Sánchez-Madrid Francisco
Published: July 2012

The balance between pro‐ and anti‐inflammatory signalling is critical to maintain the immune homeostasis under physiological conditions as well as for the control of inflammation in different pathological settings. Recent progress in the signalling pathways that control this balance has led to the development of novel therapeutic agents for diseases characterized by alterations in the activation/suppression of the immune response. Different molecules have a key role in the regulation of the immune system, including the receptors PD‐1 (Programmed cell Death 1), CTLA‐4 (Cytotoxic T‐Lymphocyte Antigen 4) and galectins; or the intracellular enzyme IDO (indoleamine 2,3‐dioxygenase). In addition, other molecules as CD69, AhR (Aryl hydrocarbon Receptor), and GADD45 (Growth Arrest and DNA Damage‐inducible 45) family members, have emerged as potential targets for the regulation of the activation/suppression balance of immune cells. This review offers a perspective on well‐characterized as well as emergent negative immune regulatory molecules in the context of autoimmune inflammatory diseases.
Transformation of the fungus Absidia glauca by complementation of a methionine‐auxotrophic strain affected in the homoserine‐acetyltransferase gene
Authors: Karimi Sedighe , Wetzel Jana , Wöstemeyer Johannes , Burmester Anke
Published: July 2012

Transformation of fungi by complementation of auxotrophs is generally much more reliable than usage of antibiotic resistance markers. In order to establish such a system for the model zygomycete Absidia glauca, a stable methionine auxotrophic mutant was isolated after X‐ray mutagenesis of the minus mating type and characterized at the molecular level. The mutant is disrupted in the coding region of the Met2‐1 gene, encoding homoserine O‐acetyltransferase. The corresponding wild type gene was cloned, sequenced and inserted into appropriate vector plasmids. Transformants are prototrophs and show restored methionine‐independent growth, based on complementation by the autonomously replicating plasmids.
CD248 expression on mesenchymal stromal cells is required for post‐natal and infection‐dependent thymus remodelling and regeneration
Authors: Lax Siân , Ross Ewan A. , White Andrea , Marshall Jennifer L. , Jenkinson William E. , Isacke Clare M. , Huso David L. , Cunningham Adam F. , Anderson Graham , Buckley Christopher D.
Published: July 2012

The role of mesenchymal stromal cells (MSCs) in regulating immune responses in the thymus is currently unclear. Here we report the existence and role of a MSC population in the thymus that expresses the pericyte and MSC marker CD248 (endosialin). We show using a CD248‐deficient mouse model, that CD248 expression on these cells is required for full post‐natal thymus development and regeneration post‐Salmonella infection. In CD248−/− mice the thymus is hypocellular and regeneration is poorer, with significant loss of all thymocyte populations. This identifies the requirement of CD248 to maintain optimal thymic cellularity post‐partum and infection.
Evolution of an inhibitory RNA aptamer against T7 RNA polymerase
Authors: Ohuchi Shoji , Mori Yusuke , Nakamura Yoshikazu
Published: July 2012

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. In this study, we isolated an RNA aptamer that specifically inhibits transcription of T7 RNA polymerase (RNAP). The 38‐nucleotide aptamer, which was a shortened variant of an initial SELEX isolate, showed moderate inhibitory activity. By stepwise doped‐SELEX, we isolated evolved variants with strong inhibitory activity. A 29‐nucleotide variant of a doped‐SELEX isolate showed 50% inhibitory concentration at 11 nM under typical in vitro transcription conditions. Pull‐down experiments revealed that the aptamer inhibited the association of T7 RNAP with T7 promoter DNA.
The Astrobiological Landscape
Authors: Ćirković Milan M.
Published: July 2012

Astrobiology is an expanding, interdisciplinary field investigating the origin, evolution and future of life in the universe. Tackling many of the foundational debates of the subject, from discussions of cosmological evolution to detailed reviews of common concepts such as the 'Rare Earth' hypothesis, this volume is the first systematic survey of the philosophical aspects and conundrums in the study of cosmic life. The author's exploration of the increasing number of cross-over problems highlights the relationship between astrobiology and cosmology and presents some of the challenges of multidisciplinary study. Modern physical theories dealing with the multiverse add a further dimension to the debate. With a selection of beautifully presented illustrations and a strong emphasis on constructing a unified methodology across disciplines, this book will appeal to graduate students and specialists who seek to rectify the fragmented nature of current astrobiological endeavour, as well as curious astrophysicists, biologists and SETI enthusiasts.
Epistemic Game Theory
Authors: Perea Andrés
Published: July 2012

In everyday life we must often reach decisions while knowing that the outcome will not only depend on our own choice, but also on the choices of others. These situations are the focus of epistemic game theory. Unlike classical game theory, it explores how people may reason about their opponents before they make their final choice in a game. Packed with examples and practical problems based on stories from everyday life, this is the first textbook to explain the principles of epistemic game theory. Each chapter is dedicated to one particular, natural way of reasoning. The book then shows how each of these ways of reasoning will affect the final choices that can rationally be made and how these choices can be found by iterative procedures. Moreover, it does so in a way that uses elementary mathematics and does not presuppose any previous knowledge of game theory.
Damage and Failure of Composite Materials
Authors: Talreja Ramesh , Singh Chandra Veer
Published: July 2012

Understanding damage and failure of composite materials is critical for reliable and cost-effective engineering design. Bringing together materials mechanics and modeling, this book provides a complete guide to damage, fatigue and failure of composite materials. Early chapters focus on the underlying principles governing composite damage, reviewing basic equations and mechanics theory, before describing mechanisms of damage such as cracking, breakage and buckling. In subsequent chapters, the physical mechanisms underlying the formation and progression of damage under mechanical loads are described with ample experimental data, and micro- and macro-level damage models are combined. Finally, fatigue of composite materials is discussed using fatigue-life diagrams. While there is a special emphasis on polymer matrix composites, metal and ceramic matrix composites are also described. Outlining methods for more reliable design of composite structures, this is a valuable resource for engineers and materials scientists in industry and academia.
The Acquisition of Creole Languages
Authors: Adone Dany
Published: July 2012

How do children acquire a Creole as their first language? This relatively underexplored question is the starting point for this first book of its kind; it also asks how first language acquisition of a Creole differs from that of a non-Creole language. Dany Adone reveals that in the absence of a conventional language model, Creole children acquire language and go beyond the input they receive. This study discusses the role of input, a hotly debated issue in the field of first language acquisition, and provides support for the nativist approach in the debate between nativism and input-based models. The Acquisition of Creole Languages will be essential reading for those in the fields of First Language Acquisition and Creole Studies. Adone takes an interdisciplinary approach, and uses insights from the acquisition of language in the visual modality, making this of great interest to those in the field of Sign Linguistics.
Mathematical Foundations of Imaging, Tomography and Wavefield Inversion
Authors: Devaney Anthony J.
Published: July 2012

Inverse problems are of interest and importance across many branches of physics, mathematics, engineering and medical imaging. In this text, the foundations of imaging and wavefield inversion are presented in a clear and systematic way. The necessary theory is gradually developed throughout the book, progressing from simple wave equation based models to vector wave models. By combining theory with numerous MATLAB based examples, the author promotes a complete understanding of the material and establishes a basis for real world applications. Key topics of discussion include the derivation of solutions to the inhomogeneous and homogeneous Helmholtz equations using Green function techniques; the propagation and scattering of waves in homogeneous and inhomogeneous backgrounds; and the concept of field time reversal. Bridging the gap between mathematics and physics, this multidisciplinary book will appeal to graduate students and researchers alike. Additional resources including MATLAB codes and solutions are available online at www.cambridge.org/9780521119740.
Toxic effects of dietary hydrolysed lipids: anin vivostudy on fish larvae
Authors: Sæle Øystein , Nordgreen Andreas , Olsvik Pål A. , Hjelle Jan I. , Harboe Torstein , Hamre Kristin
Published: July 2012

We have previously described that fish larvae absorb a larger fraction of dietary monoacylglycerol than TAG. To investigate how dietary hydrolysed lipids affect a vertebrate at early life stages over time, we fed Atlantic cod (Gadus morhua) larvae six diets with different degrees of hydrolysed lipids for 30 d. The different diets had no effect on growth, but there was a positive correlation between the level of hydrolysed lipids in the diets and mortality. Important genes in lipid metabolism, such asPPAR, farnesoid X receptor (FXR) and stearoyl-CoA desaturase (SCD), were regulated by the different diets. Genes involved in the oxidative stress response did not respond to the increased lipid hydrolysation in the diets. However, enterocyte damage was observed in animals fed diets with 2·7 % NEFA (diet 3) or more. It is thus possible that mortality was due to infections and/or osmotic stress due to the exposure of the subepithelial tissue. In contrast to earlier experiments showing a positive effect of dietary hydrolysed lipids, we have demonstrated a toxic effect of dietary NEFA on Atlantic cod larvae. Toxicity is not acute but needs time to accumulate.
Excess mortality associated with the 2009 A(H1N1)v influenza pandemic in Antananarivo, Madagascar
Authors: RAJATONIRINA S. , RAKOTOSOLOFO B. , RAKOTOMANANA F. , RANDRIANASOLO L. , RATSITOHARINA M. , RAHARINANDRASANA H. , HERAUD J.-M. , RICHARD V.
Published: July 2012

It is difficult to assess the mortality burden of influenza epidemics in tropical countries. Until recently, the burden of influenza was believed to be negligible in Africa. We assessed the impact of the 2009 influenza epidemic on mortality in Madagascar by conducting Poisson regression analysis on mortality data from the deaths registry, after the first wave of the 2009 A(H1N1) virus pandemic. There were 20% more human deaths than expected in Antananarivo, Madagascar in November 2009, with excess mortality in the ⩾50 years age group (relative risk 1·41). Furthermore, the number of deaths from pulmonary disease was significantly higher than the number of deaths from other causes during this pandemic period. These results suggest that the A(H1N1) 2009 virus pandemic may have been accompanied by an increase in mortality.
Group B rotavirus infection in patients with acute gastroenteritis from India: 1994–1995 and 2004–2010
Authors: LAHON A. , MANIYA N. H. , TAMBE G. U. , CHINCHOLE P. R. , PURWAR S. , JACOB G. , CHITAMBAR S. D.
Published: July 2012

Faecal specimens collected from 2101 patients with acute gastroenteritis from three cities (Pune, Alappuzha, Belgaum) in India during 1994–1995 and 2004–2010 were tested for group B rotavirus (RVB) by amplification of theNSP2gene using RT–PCR. Seventy-five (3·6%) specimens were shown to contain RVB RNA. The positivity rate in Pune, Alappuzha and Belgaum was 4·1%, 7·3% and 4·1%, respectively, in the 2000s which was not significantly different from the detection rate in the 1990s in Pune (2·5%,P>0·05). RVB infections prevailed in adolescents and adults (62/1082, 5·7%) compared to children (13/1019, 1·3%,P<0·001) and were detected throughout the year. Phylogenetically, all strains clustered in an NSP2 lineage together with Indian-Bangladeshi RVB strains belonging to VP7 genotype G2. The study confirmed the occurrence of RVB infections in western India and reported for the first time circulation of RVB strains in southern India, suggesting that an increased awareness and monitoring for RVB infections is necessary in India.
Prevalence, seasonality, and peak age of infection of enteric adenoviruses in Japan, 1995–2009
Authors: DEY S. K. , HOQ I. , OKITSU S. , HAYAKAWA S. , USHIJIMA H.
Published: July 2012

A total of 7185 faecal specimens collected from infants and children with gastroenteritis in seven different regions of Japan during 1995–2009 were examined for adenovirus by polymerase chain reaction. Adenovirus was detected in 568 (7·9%) patients. The adenovirus activity peak was in winter and spring seasons (December–March) during the study period in the Japanese paediatric population. During the last 15 years, adenovirus 41 was the most predominant strain in Japan.
Association of macrophage migration inhibitory factor and mannose-binding lectin-2 gene polymorphisms in acute rheumatic fever
Authors: Col-Araz Nilgun , Pehlivan Sacide , Baspinar Osman , Sever Tugce , Oguzkan-Balci Sibel , Balat Ayse
Published: July 2012

Background

Macrophage migration inhibitory factor and mannose-binding lectin-2 play important roles in the pathogenesis of several acute and chronic inflammatory/autoimmune disorders. The aim of the study was to investigate any possible association between migration inhibitory factor and mannose-binding lectin-2 gene polymorphisms and acute rheumatic fever in children.

Material and methods

A total of 38 unrelated children with acute rheumatic fever and 40 age- and sex-matched healthy controls were analysed for codon 54 A/B polymorphism in mannose-binding lectin-2 gene and −173 G/C polymorphism in migration inhibitory factor gene by using the polymerase chain reaction method.

Results

Frequency of BB genotype of mannose-binding lectin-2 gene was higher in the patient group. Interestingly, children with acute rheumatic fever with AA genotype tended to have chorea compared with children with BB genotype. There was a statistically significant increase in frequency of the migration inhibitory factor −173 CC genotype in patients compared with the control subjects.

Conclusion

The present study is the first to investigate the mannose-binding lectin-2gene polymorphism in children with acute rheumatic fever. BB genotype of mannose-binding lectin-2 (codon 54) and CC genotype of migration inhibitory factor (−173) may have a role in the immunoinflammatory process of acute rheumatic fever.
A dextrocardia in a foetal Egyptian mummy?
Authors: Séguéla Pierre-Emmanuel , Pierrat-Bonnefois Geneviève , Paul Jean-François
Published: July 2012

Egyptian foetal mummies are rare archaeological artefacts. We report the case of a mummified foetus with a highly probable dextrocardia accurately depicted by computed tomography scan.
Treatment of haemoptysis in pulmonary atresia with tranexamic acid
Authors: Devine Matthew J. , Radford Dorothy J.
Published: July 2012

We report the case of a young woman with continuing haemoptysis, pulmonary atresia, previous shunt surgery, and pulmonary hypertension. She was not suitable for further surgery or for therapeutic embolisation of bronchial vessels. Treatment with tranexamic acid resolved the haemoptysis.
Positive allosteric feedback regulation of the stringent response enzyme RelA by its product
Authors: Shyp Viktoriya , Tankov Stoyan , Ermakov Andrey , Kudrin Pavel , English Brian P , Ehrenberg Måns , Tenson Tanel , Elf Johan , Hauryliuk Vasili
Published: July 2012

During the stringent response, Escherichia coli enzyme RelA produces the ppGpp alarmone, which in turn regulates transcription, translation and replication. We show that ppGpp dramatically increases the turnover rate of its own ribosome‐dependent synthesis by RelA, resulting in direct positive regulation of an enzyme by its product. Positive allosteric regulation therefore constitutes a new mechanism of enzyme activation. By integrating the output of individual RelA molecules and ppGpp degradation pathways, this regulatory circuit contributes to a fast and coordinated transition to stringency.
Sumoylation of transcription factor MYB30 by the small ubiquitin-like modifier E3 ligase SIZ1 mediates abscisic acid response in
Arabidopsis thaliana
Authors: Zheng Yuan , Schumaker Karen S. , Guo Yan
Published: July 2012

The phytohormone abscisic acid (ABA) plays an essential role in plant development and during the response of the plant to abiotic stress. In this study, we report that the R2R3-type transcription factor MYB30 is involved in the regulation of ABA signaling.
Arabidopsis
mutants lacking MYB30 are hypersensitive to ABA during germination and seedling growth. A K283R substitution in MYB30 blocks its SUMO E3 ligase SIZ1-mediated sumoylation in
Arabidopsis
protoplasts, indicating that MYB30 is sumoylated by SIZ1 and that K283 is the principal site for small ubiquitin-like modifier conjugation. Expression of

MYB30
K283R

in
myb30
partially rescues the mutant ABA-hypersensitive phenotype, but expression of wild-type
MYB30
complements the mutant phenotype. Overexpression of
MYB30
in wild-type results in an ABA-insensitive phenotype, whereas overexpression of
MYB30
in the
siz1
mutant does not alter
siz1
hypersensitivity to ABA. The
siz1-2 myb30-2
double-mutant exhibits greater ABA sensitivity than either single mutant, but a mutation in the SIZ1-sumoylated ABI5 transcription factor suppresses the ABA hypersensitivity of
myb30-2
to wild-type levels. Our results suggest that coordination of ABI5 and MYB30 sumoylation by SIZ1 may balance gene expression, which is required for regulation of ABA signaling during seed germination.
Quantifying Cumulative Entrainment Effects for Chinook Salmon in a Heavily Irrigated Watershed
Authors: Walters Annika W. , Holzer Damon M. , Faulkner James R. , Warren Charles D. , Murphy Patrick D. , McClure Michelle M.
Published: July 2012

Pacific salmon Oncorhynchus spp. experience multiple small‐scale disturbances throughout their freshwater habitat, but the cumulative effect of these disturbances is often not known or not easily quantifiable. One such disturbance is water diversions, which can entrain fish and alter streamflow regimes. Threatened Lemhi River (Idaho) Chinook salmon O. tshawytscha smolts encounter 41–71 water diversions during their out‐migration. We used passive integrated transponder tag data to model the entrainment rate of Chinook salmon smolts as a function of the proportion of water removed by an irrigation diversion. Under median‐streamflow conditions with unscreened diversions, the estimated cumulative effect of the diversions was a loss of 71.1% of out‐migrating smolts due to entrainment. This is a large potential source of mortality, but screening is an effective mitigation strategy, as estimated mortality was reduced to 1.9% when all diversions were screened. If resources are limited, targeting the diversions that remove a large amount of water and diversions in locations with high fish encounter rates is most effective. Our modeling approach could be used to quantify the entrainment effects of water diversions and set screening priorities for other watersheds.
Metabolite identification and molecular fingerprint prediction through machine learning
Authors: Heinonen Markus , Shen Huibin , Zamboni Nicola , Rousu Juho
Published: July 2012

Motivation: Metabolite identification from tandem mass spectra is an important problem in metabolomics, underpinning subsequent metabolic modelling and network analysis. Yet, currently this task requires matching the observed spectrum against a database of reference spectra originating from similar equipment and closely matching operating parameters, a condition that is rarely satisfied in public repositories. Furthermore, the computational support for identification of molecules not present in reference databases is lacking. Recent efforts in assembling large public mass spectral databases such as MassBank have opened the door for the development of a new genre of metabolite identification methods.

Results: We introduce a novel framework for prediction of molecular characteristics and identification of metabolites from tandem mass spectra using machine learning with the support vector machine. Our approach is to first predict a large set of molecular properties of the unknown metabolite from salient tandem mass spectral signals, and in the second step to use the predicted properties for matching against large molecule databases, such as PubChem. We demonstrate that several molecular properties can be predicted to high accuracy and that they are useful in de novo metabolite identification, where the reference database does not contain any spectra of the same molecule.

Availability: An Matlab/Python package of the FingerID tool is freely available on the web at http://www.sourceforge.net/p/fingerid.

Contact:  markus.heinonen@cs.helsinki.fi
imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel
Authors: Grapov Dmitry , Newman John W.
Published: July 2012

Summary: Interactive modules for Data Exploration and Visualization (imDEV) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enables interactive and dynamic analyses of large data by interfacing R's multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information-rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal and independent component analyses, partial least squares regression and discriminant analysis, through an intuitive interface for creating high-quality two- and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and correlation networks.

Availability and implementation: Freely available for download at http://sourceforge.net/projects/imdev/. Implemented in R and VBA and supported by Microsoft Excel (2003, 2007 and 2010).

Contact:  John.Newman@ars.usda.gov

Supplementary Information: Installation instructions, tutorials and users manual are available at http://sourceforge.net/projects/imdev/.
Quantifying uniformity of mapped reads
Authors: Hower Valerie , Starfield Richard , Roberts Adam , Pachter Lior
Published: July 2012

Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a P-value that can be used to quantify biases arising from experimental protocols and mapping procedures. Our method is useful for comparing different protocols in experiments such as RNA-Seq.

Availability and implementation: We provide a freely available and open source python script that can be used to analyze raw read data or reads mapped to transcripts in BAM format at http://www.math.miami.edu/~vhower/ReadSpy.html

Contact:  lpachter@math.berkeley.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Marked Hyperglycemia Attenuates Anesthetic Preconditioning in Human-induced Pluripotent Stem Cell-derived Cardiomyocytes
Authors: Canfield Scott G. , Sepac Ana , Sedlic Filip , Muravyeva Maria Y. , Bai Xiaowen , Bosnjak Zeljko J.
Published: July 2012

Introduction

Anesthetic preconditioning protects cardiomyocytes from oxidative stress-induced injury, but it is ineffective in patients with diabetes mellitus. To address the role of hyperglycemia in the inability of diabetic individuals to be preconditioned, we used human cardiomyocytes differentiated from induced pluripotent stem cells generated from patients with or without type 2 diabetes mellitus (DM-iPSC- and N-iPSC-CMs, respectively) to investigate the efficacy of preconditioning in varying glucose conditions (5, 11, and 25 mM).

Methods

Induced pluripotent stem cells were induced to generate cardiomyocytes by directed differentiation. For subsequent studies, cardiomyocytes were identified by genetic labeling with enhanced green fluorescent protein driven by a cardiac-specific promoter. Cell viability was analyzed by lactate dehydrogenase assay. Confocal microscopy was utilized to measure opening of the mitochondrial permeability transition pore and the mitochondrial adenosine 5'-triphosphate-sensitive potassium channels.

Results

Isoflurane (0.5 mM) preconditioning protected N-iPSC- and DM-iPSC-CMs from oxidative stress-induced lactate dehydrogenase release and mitochondrial permeability transition pore opening in 5 mM and 11 mM glucose. Isoflurane triggered mitochondrial adenosine-5'-triphosphate-sensitive potassium channel opening in N-iPSC-CMs in 5 mM and 11 mM glucose and in DM-iPSC-CMs in 5 mM glucose; 25 mM glucose disrupted anesthetic preconditioning-mediated protection in DM-iPSC- and N-iPSC-CMs.

Conclusions

The opening of mitochondrial adenosine 5'-triphosphate-sensitive potassium channels are disrupted in DM-iPSC-CMs in 11 mM and 25 mM glucose and in N-iPSC-CMs in 25 mM glucose. Cardiomyocytes derived from healthy donors and patients with a specific disease, such as diabetes in this study, open possibilities in studying genotype- and phenotype-related pathologies in a human-relevant model.
Sodium Nitrite Mitigates Ventilator-induced Lung Injury in Rats
Authors: Pickerodt Philipp A. , Emery Michael J. , Zarndt Rachel , Martin William , Francis Roland C. E. , Boemke Willehad , Swenson Erik R.
Published: July 2012

Background

Nitrite (NO2) is a physiologic source of nitric oxide and protects against ischemia-reperfusion injuries. We hypothesized that nitrite would be protective in a rat model of ventilator-induced lung injury and sought to determine if nitrite protection is mediated by enzymic catalytic reduction to nitric oxide.

Methods

Rats were anesthetized and mechanically ventilated. Group 1 had low tidal volume ventilation (LVT) (6 ml/kg and 2 cm H2O positive end-expiratory pressure; n=10); group 2 had high tidal volume ventilation (HVT) (2 h of 35 cm H2O inspiratory peak pressure and 0 cm H2O positive end-expiratory pressure; n=14); groups 3-5: HVT with sodium nitrite (NaNO2) pretreatment (0.25, 2.5, 25 μmol/kg IV; n=6-8); group 6: HVT+NaNO2+nitric oxide scavenger 2-(4-carboxyphenyl)-4,5dihydro-4,4,5,5-tetramethyl-1H-imidazolyl-1-oxy-3oxide(n=6); group 7: HVT+NaNO2+nitric oxide synthase inhibitor N-nitro-L-arginine methyl ester (n=7); and group 8: HVT+NaNO2+xanthine oxidoreductase inhibitor allopurinol (n=6). Injury assessment included physiologic measurements (gas exchange, lung compliance, lung edema formation, vascular perfusion pressures) with histologic and biochemical correlates of lung injury and protection.

Results

Injurious ventilation caused statistically significant injury in untreated animals. NaNO2 pretreatment mitigated the gas exchange deterioration, lung edema formation, and histologic injury with maximal protection at 2.5 μmol/kg. Decreasing nitric oxide bioavailability by nitric oxide scavenging, nitric oxide synthase inhibition, or xanthine oxidoreductase inhibition abolished the protection by NaNO2.

Conclusions

Nitrite confers protection against ventilator-induced lung injury in rats. Catalytic reduction to nitric oxide and mitigation of ventilator-induced lung injury is dependent on both xanthine oxidoreductase and nitric oxide synthases.
Roles of Gr-1+Leukocytes in Postincisional Nociceptive Sensitization and Inflammation
Authors: Sahbaie Peyman , Li Xiangqi , Shi Xiaoyou , Clark J. David
Published: July 2012

Background

Neutrophils are one of the predominant immune cells initially migrating to surgical wound edges. They produce mediators both associated with supporting (interleukin [IL]-1β, C5a) and reducing (opioid peptides) pain. Studies demonstrate neutrophil depletion/blockade reduces nociceptive sensitization after nerve injury and carrageenan administration, but enhance sensitization in complete Freund's adjuvant inflammation. This research identifies the contribution of infiltrating neutrophils to incisional pain and inflammation.

Methods

Antibody-mediated Gr1 neutrophil depletion preceded hind paw incisions. Sensitization to mechanical and thermal stimuli, effects on edema and local levels of IL-1β and C5a were measured. Local effects of C5a or IL-1 receptor antagonists PMX-53 and anakinra on sensitization after neutrophil depletion were examined. Groups of 4-8 mice were used.

Results

Anti-Gr1 antibody depleted more than 90% of circulating and infiltrating skin neutrophils after incision. Neutrophil depletion did not change magnitude or duration of mechanical hypersensitivity in incised mice. However, paw edema was significantly reduced and heat hypersensitivity was slightly increased in depleted animals. In depleted animals IL-1β levels were half of controls 24 h after incision, whereas C5a levels were increased in both. Prominent IL-1β immunohistochemical staining of epidermis was seen in both groups. PMX-53 and anakinra reduced incisional mechanical and heat nociceptive sensitization to the same extent, regardless of neutrophil depletion.

Conclusions

Neutrophil-derived IL-1β and C5a do not appear to contribute critically to peri-incisional nociceptive signaling. Other sources of mediators, such as epidermal cells, may need to be considered. Controlling inflammatory activation of resident cells in epidermis/deeper structures may show therapeutic efficacy in reducing pain from surgical incisions.
Age-related declines in the fidelity of newly acquired category representations
Authors: Davis Tyler , Love Bradley C. , Maddox W. Todd
Published: July 2012

We present a theory suggesting that the ability to build category representations that reflect the nuances of category structures in the environment depends upon clustering mechanisms instantiated in an MTL-PFC-based circuit. Because function in this circuit declines with age, we predict that the ability to build category representations will be impaired in older adults. Consistent with this prediction, we find that older adults are impaired relative to younger adults at learning nuanced category structures that contain exceptions to the rule. Model-based analysis reveals that this deficit arises from older adults’ failure to engage clustering mechanisms to separate exception and rule-following items in memory.
9-Allyl-9H-carbazole-3,6-dicarbaldehyde
Authors: Hu Bin Bin , Zeng Xiang Chao , Bian Lei , He Ru
Published: July 2012

In the title molecule, C17H13NO2, the allyl group is almost perpendicular to the carbazole mean plane, with a dihedral angle of 89.0 (2)°. In the crystal, nonclassical C—H...O hydrogen bonds link the molecules into corrugated sheets parallel to thebcplane. Weak intermolecular π–π interactions are observed between the benzene rings [centroid–centroid distance = 3.874 (4) Å] from neighbouring sheets.
Trehalose dihydrate fromTremella fuciformis
Authors: Liu Wei , Yan Jun , Song Qin , Gou Xiao-Jun , Chen Feng-Zheng
Published: July 2012

The title compound, C12H22O11·2H2O {systematic name: 6,6′-oxybis[2-(hydroxymethyl)-3,4,5,6-tetrahydro-2H-pyran-3,4,5-triol] dihydrate}, is a disaccharide, which was isolated fromTremella fuciformis. The molecule contains two six-membered rings, both of which adopt a chair conformation. Extensive O—H...O hydrogen bonds occur in the crystal structure.
1-(6-Bromo-3,4-dihydro-2H-1,4-benzoxazin-4-yl)-2,2-dichloroethanone
Authors: Ye Fei , Li Ying , Fu Ying , Zhao Li-Xia , Gao Shuang
Published: July 2012

The title compound, C10H8BrCl2NO2, is a target molecule in our research on herbicide safeners. The oxazine ring has an envelope conformation, with puckering parameters close to ideal values [Q= 0.498 (3) Å, θ = 53.7 (3)° and φ = 253.4 (4)°]. The crystal structure is stabilized by C—H...O, C—H...Cl and C—H...Br interactions.
(E)-3-Chloro-N-[(2-ethoxynaphthalen-1-yl)methylidene]aniline
Authors: Vesek Hilal , Kazak Canan , Alaman Ağar Ayşen , Macit Mustafa , Soylu Mustafa Serkan
Published: July 2012

In the title compound, C19H16ClNO, the dihedral angle between the naphthalene ring system and the chlorobenzene ring is 61.90 (10)° and the C—N—C—C torsion angle is 174.6 (2)°. The molecular structure is stabilized by an intramolecular C—H...N hydrogen bond. The crystal structure features π–π stacking interactions [centroid–centroid distances = 3.7325 (17) and 3.8150 (17) Å].
4-Cyano-1-methylpyridinium iodide
Authors: Kammer Michael N. , Koplitz Lynn V. , Mague Joel T.
Published: July 2012

In the crystal structure of the title compound, C7H7N2+·I−, the cations form inversion-related dimersviaweak pairwise C—H...N hydrogen bonds. In the dimers, the pyridinium rings are parallel to one another with their mean planes separated by a normal distance ofca0.28 Å. Weak C—H...N interactions between adjacent dimers generate a layer lying parallel to (10-1). The remaining H atoms form C—H...I interactions, which link the layers into a three-dimensional structure.
2,2′-[(E)-3-(4-Nitrophenyl)prop-2-ene-1,1-diyl]bis(3-hydroxy-5,5-dimethylcyclohex-2-en-1-one)
Authors: Cha Joo Hwan , Cho Yong Seo , Lee Jae Kyun , Park Junghwan , Sato Hiroyasu
Published: July 2012

In the title compound, C25H29NO6, each of the cyclohexenone rings adopts a half-chair conformation. The hydroxy and carbonyl O atoms face each other and are oriented to allow for the formation of two intramolecular O—H...O hydrogen bonds. In the crystal, weak C—H...O hydrogen bonds are formed between molecules, generating a two-dimensional supramolecular structure.