bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheD1‐D2 region of the large subunit ribosomalDNAas barcode for ciliates
Authors: Stoeck T. , Przybos E. , Dunthorn M. 
Published: October 2013

AbstractCiliates are a major evolutionary lineage within the alveolates, which are distributed in nearly all habitats on our planet and are an essential component for ecosystem function, processes and stability. Accurate identification of these unicellular eukaryotes through, for example, microscopy or mating type reactions is reserved to few specialists. To satisfy the demand for aDNAbarcode for ciliates, which meets the standard criteria forDNAbarcodes defined by the Consortium for the Barcode of Life (CBOL), we here evaluated theD1‐D2 region of the ribosomalDNAlarge subunit (LSU‐rDNA). Primer universality for the phylumCiliophora was testedin silicowith available database sequences as well as in the laboratory with 73 ciliate species, which represented nine of 12 ciliate classes. Primers tested in this study were successful for all tested classes. To test the ability of theD1‐D2 region to resolve conspecific and congeneric sequence divergence, 63Parameciumstrains were sampled from 24 mating species. The average conspecificD1‐D2 variation was 0.18%, whereas congeneric sequence divergence averaged 4.83%. In pairwise genetic distance analyses, we identified aD1‐D2 sequence divergence of <0.6% as an ideal threshold to discriminateParameciumspecies. Using this definition, only 3.8% of all conspecific and 3.9% of all congeneric sequence comparisons had the potential of false assignments. Neighbour‐joining analyses inferred monophyly for all taxa but for twoParamecium octaureliastrains. Here, we present a protocol for easyDNAamplification of single cells and voucher deposition. In conclusion, the presented data pinpoint theD1‐D2 region as an excellent candidate for an official CBOL barcode for ciliated protists.
Separating mortality and emigration: modelling space use, dispersal and survival with robust‐design spatial capture–recapture data
Authors: Ergon Torbjørn , Gardner Beth 
Published: October 2013

Summary

Capture–recapture (CR) techniques are commonly used to gain information about population dynamics, demography and life‐history traits of populations. However, traditional CR models cannot separate mortality from emigration. Recently developed spatial–capture–recapture (SCR) models explicitly incorporate spatial information into traditional CR models, thus allowing for individuals' movements to be modelled explicitly.

In this paper, we extend SCR models using robust‐design data to allow for both processes in which individuals can disappear from the population, mortality and dispersal, to be estimated separately. We formulate a general robust‐design spatial capture–recapture (RD‐SCR) model, explore the properties of the model in a simulation study and compare the results to a Cormack–Jolly–Seber model and a non‐spatial robust‐design model with temporary emigration. In the case study, we fit several versions of the general model to data on field voles (Microtus agrestis) and compare the results with those from the non‐spatial models fitted to the same data. We also evaluate assumptions of the fitted models with a series of simulation‐based posterior predictive goodness‐of‐fit checks that are applicable to the SCR models in general and the RD‐SCR model in particular.

The simulation results show that the model preforms well under a wide range of dispersal distances. Our model outperforms the traditional CR models in terms of both accuracy and precision for survival. The case study showed that adult females have an c. 3·5 times higher mortality rate than adult males. Males have larger home ranges and disperse longer distances than females, but both males and females mostly move their activity centres within their previous home range between trapping sessions at 3‐week intervals.

Our RD‐SCR model has several advantages compared to other approaches to estimate ‘true’ survival instead of only ‘apparent’ survival. Additionally, the model extracts information about space use and dispersal distributions that are relevant for behavioural studies as well as studies of life‐history variation, population dynamics and management. The model can be widely applied due to the flexible framework, and other variations of the model could easily be implemented.
Estimating true instead of apparent survival using spatial Cormack–Jolly–Seber models
Authors: Schaub Michael , Royle J. Andrew 
Published: October 2013

Summary

Survival is often estimated from capture–recapture data using Cormack–Jolly–Seber (CJS) models, where mortality and emigration cannot be distinguished, and the estimated apparent survival probability is the product of the probabilities of true survival and of study area fidelity. Consequently, apparent survival is lower than true survival unless study area fidelity equals one. Underestimation of true survival from capture–recapture data is a main limitation of the method.

We develop a spatial version of the CJS model that allows estimation of true survival. Besides the information about whether a specific individual was encountered at a given occasion, it is often recorded where the encounter occurred. Thus, information is available about the fraction of dispersal that occurs within the study area, and we use it to model dispersal and estimate true survival. Our model is formulated hierarchically and consists of survival, dispersal and observation submodels, assuming that encounters are possible anywhere within a study area.

In a simulation study, our new spatial CJS model produced accurate estimates of true survival and dispersal behaviour for various sizes and shapes of the study area, even if emigration is substantial. However, when the information about dispersal is scarce due to low survival, low recapture probabilities and high emigration, the estimators are positively biased. Moreover, survival estimates are sensitive to the assumed dispersal kernel.

We applied the spatial CJS model to a data set of adult red‐backed shrikes (Lanius collurio). Apparent survival of males (c. 0·5) estimated with the CJS model was larger than in females (c. 0·4), but the application of the spatial CJS model revealed that both sexes had similar survival probabilities (c. 0·6). The mean breeding dispersal distance in females was c. 700 m, while males dispersed only c. 250 m between years.

Spatial CJS models enable study of dispersal and survival independent of study design constraints such as imperfect detection and size of the study area provided that some of the dispersing individuals remain in the study area. We discuss possible extensions of our model: alternative dispersal models and the inclusion of covariates and of a habitat suitability map.
Thymic metastasis of breast cancer 22 years after surgery: A case report
Authors: Fujioka Shinji , Nakamura Hiroshige , Miwa Ken , Takagi Yuzo , Yurugi Yohei , Taniguchi Yuji , Ishiguro Kiyosuke 
Published: October 2013

AbstractWe report a rare case of thymic metastasis of breast cancer. A 68‐year‐old woman, who had undergone surgery for cancer in her right breast and had been free of recurrence for 22 years, was noted to have an abnormal shadow on a chest X‐ray at a regular medical checkup. Further workup, including chest CT, revealed a 22 × 18‐mm mass in the anterior mediastinum. Fluorine‐18‐fluorodeoxyglucose‐PET showed increased fluorine‐18‐fluorodeoxyglucose uptake that was highly suggestive of thymoma. Thoracoscopic thymothymectomy was performed. The tumor had invaded the pericardium, which was also resected. A small nodule was found in the right lung, and it was also resected. The intraoperative frozen‐section diagnosis was breast cancer metastasis to the thymus and lung. The pathological diagnosis was luminal A solid tubular carcinoma (strongly estrogen receptor and progesterone receptor positive, HER2 negative) with an MIB‐1 index of less than 5%. After surgery, the patient was treated with an aromatase inhibitor. As of August 2013, she has been free of recurrence for more than 36 months. It is extremely rare for breast cancer to metastasize to the thymus more than 20 years after surgery.
Neuroangiostrongyliasis due to Angiostrongylus cantonensis in gang‐gang cockatoos (Callocephalon fimbriatum)
Authors: Reece RL , Perry RA , Spratt DM 
Published: October 2013

Case reportFour gang‐gang cockatoos from an aviary in Sydney displayed severe neurological signs. Three were necropsied and histopathology of the brains and spinal cords revealed migrating nematodes, which were identified as Angiostrongylus cantonensis. The migrating larval nematodes created tracts of malacia in the brain, but elicited little inflammatory cell infiltration. However, adult nematodes that had emerged onto the meningeal surface of the spinal cord evoked a marked non‐suppurative reaction. Detailed histological examination of other tissues revealed larvae embedded in arterioles in the gastrointestinal serosa, lung and heart, which were associated with a significant granulomatous response. The latter lesions were consistent with our understanding of the pathogenesis of infection with this parasite, but have not been previously described, probably as a result of limited sampling.ConclusionsAngiostrongylus cantonensis is still present in the Sydney area and can cause significant disease in exposed animals, including birds. It also highlights potential human health problems.
Incidence of calf scours and associated risk factors in southernNewSouthWales beef herds
Authors: Lievaart JJ , Charman NR , Scrivener C , Morton A , Allworth MB 
Published: October 2013

ObjectiveThe aim of this study was to identify the incidence of morbidity and mortality associated with calf scours in beef calves between birth and 14 days of age. Farm characteristics, animal factors and management practices were also assessed for any association with calf scours being present on the farm.MethodsA questionnaire and return address envelope were distributed to 721 farms with at least 50 head of beef cattle in theHume area ofNewSouthWales,Australia.ResultsIn total, 147 (20.4%) farmers responded to the survey, of which 76 (51.7%) indicated calf scours did occur on their farm. On average, farmers estimated the morbidity of calf scours was 4.5%, but only 0.2% of all calves died as a result of scours. Affected herds were more likely to have multiple breeds and a higher proportion of cows with mismothering problems or weak calves compared with unaffected herds. These differences were confirmed with regression analysis. A large proportion of farmers with affected herds reported the loss of many calves from ‘unexplained’ or ‘sudden’ death within the first 14 days of life.ConclusionsThe incidence of calf morbidity was lower and mortality was within the same range compared with other studies on beef farms around the world. The high percentage of farms reporting losses from ‘unexplained’ or ‘sudden’ death of calves requires further monitoring and diagnostic and economic investigations.
Maternal Magnesium Sulphate Exposure Predicts Neonatal Magnesium Blood Concentrations
Authors: Sherwin Catherine M.T. , Balch Alfred , Campbell Sarah C. , Fredrickson Jeunesse , Clark Erin A.S. , Varner Michael , Stockmann Chris , Korgenski E. Kent , Bonkowsky Joshua L. , Spigarelli Michael G. 
Published: October 2013

AbstractTocolytic use of magnesium sulphate is associated with excess neonatal mortality and has been proposed to follow a dose–response relationship. This study aimed to define the correlation between maternal and neonatal magnesium blood concentrations. Magnesium blood concentrations were retrospectively obtained for mother–neonate pairs who were cared for at an Intermountain Healthcare facility from January 2009 to October 2011. Complete data were available for 231 mother–neonate pairs. Mean (±SD) maternal and neonatal magnesium concentrations were 5.43 ± 1.69 and 2.98 ± 0.94 mg/dL, respectively. Maternal and neonatal magnesium concentrations were highly correlated (p < 0.001). In univariate analyses, residual unexplained variability was high (r2 = 0.19). However, further multivariate analyses revealed that caesarian section, severe pre‐eclampsia and Apgar score at 5 min. were significantly associated with neonatal magnesium concentrations (p < 0.05 for all). Maternal magnesium concentrations correlate with neonatal exposure. This finding suggests that maternal monitoring deserves further evaluation as a marker of foetal toxicity.
How we manage the haematological aspects of major obstetric haemorrhage
Authors: Allard Shubha , Green Laura , Hunt Beverley J. 
Published: October 2013

SummaryMajor obstetric haemorrhage (MOH) remains an important medical challenge worldwide, contributing to significant maternal morbidity and mortality. Prompt and appropriate management is essential if we are to improve outcomes and reduce substandard care that may result in adverse consequences. This review describes the current understanding of the pathophysiological aspects of MOH together with the principles of transfusion and haemostatic therapy, with emphasis on a coordinated multidisciplinary approach. We also highlight the current lack of evidence available from randomized controlled trials to inform best practice and the need to prioritize research in this key clinical area.
Measuring cereblon as a biomarker of response or resistance to lenalidomide and pomalidomide requires use of standardized reagents and understanding of gene complexity
Authors: Gandhi Anita K. , Mendy Derek , Waldman Michelle , Chen Gengxin , Rychak Emily , Miller Karen , Gaidarova Svetlana , Ren Yan , Wang Maria , Breider Michael , Carmel Gilles , Mahmoudi Afshin , Jackson Pilgrim , Abbasian Mahan , Cathers Brian E. , Schafer Peter H. , Daniel Tom O. , Lopez‐Girona Antonia , Thakurta Anjan , Chopra Rajesh 
Published: October 2013

SummaryCereblon, a member of the cullin 4 ring ligase complex (CRL4), is the molecular target of the immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide and is required for the antiproliferative activity of these agents in multiple myeloma (MM) and immunomodulatory activity in T cells. Cereblon's central role as a target of lenalidomide and pomalidomide suggests potential utility as a predictive biomarker of response or resistance to IMiD therapy. Our studies characterized a cereblon monoclonal antibody CRBN65, with high sensitivity and specificity in Western analysis and immunohistochemistry that is superior to commercially available antibodies. We identified multiple cereblon splice variants in both MM cell lines and primary cells, highlighting challenges with conventional gene expression assays given this gene complexity. Using CRBN65 antibody and TaqMan quantitative reverse transcription polymerase chain reaction assays, we showed lack of correlation between cereblon protein and mRNA levels. Furthermore, lack of correlation between cereblon expression in MM cell lines and sensitivity to lenalidomide was shown. In cell lines made resistant to lenalidomide and pomalidomide, cereblon protein is greatly reduced. These studies show limitations to the current approaches of cereblon measurement that rely on commercial reagents and assays. Standardized reagents and validated assays are needed to accurately assess the role of cereblon as a predictive biomarker.
Prenatal exposure to acid‐suppressive drugs and the risk of allergic diseases in the offspring: a cohort study
Authors: Mulder B. , Schuiling‐Veninga C. C. M. , Bos H. J. , De Vries T. W. , Jick S. S. , Hak E. 
Published: October 2013

SummaryBackgroundRecent studies reported increased risks for the development of asthma in children after prenatal exposure to acid‐suppressive drugs. As a result of common pathogenesis, associations could also be present for other allergic diseases.MethodsUsing the prescription database IADB.nl, we conducted a cohort study amongst 33 536 children in the Netherlands, with a maximum follow‐up of 8 years. Maternal exposure was defined as ≥1 dispensed prescription for proton pump inhibitors (PPIs) and/or Histamine 2‐antagonists (H2As) during pregnancy. Children were considered to have a drug‐treated allergic disease if they received either ≥2 prescriptions for dermal (atopic dermatitis), inhaled (asthma) or nasal (allergic rhinitis) steroids within a 12‐month period. Clustered Cox proportional hazard regression was used to estimate crude and adjusted hazard ratios (aHR) with 95% confidence intervals (95% CI).ResultsThe aHR for the development of any allergic disease was 1.37 (95% CI: 1.14–1.66) for children exposed to PPIs or H2As. Prenatal exposure to PPIs and/or H2As was associated with atopic dermatitis, asthma and allergic rhinitis with aHRs of 1.32 (95% CI 1.06–1.64), 1.57 (95% CI 1.20–2.05) and 2.40 (95% CI 1.42–4.04), respectively. The aHR for the development of two or more (aHR 2.13 95% CI: 1.43–3.19) and three allergic diseases (aHR 5.18 95% CI: 2.16–12.42) were even more elevated after prenatal exposure to PPIs or H2As.ConclusionPrenatal exposure to PPIs and H2As appeared associated with an increased risk for the development of atopic dermatitis, asthma and allergic rhinitis in the offspring, especially with the development of multiple allergic diseases. Because our study has limitations inherent to observational studies, prospective studies are now warranted to confirm our findings.
Incidence of nosocomial pneumonia and risk of recurrence after antimicrobial therapy in critically ill lung and heart–lung transplant patients
Authors: Dudau Daniela , Camous Julien , Marchand Séverine , Pilorge Catherine , Rézaiguia‐Delclaux Saïda , Libert Jean‐Marie , Fadel Elie , Stéphan François 
Published: October 2013

AbstractLittle is known about the resolution of symptoms of nosocomial pneumonia (NosoP) after lung and heart–lung transplantation. The aim of this study was to describe the clinical response to antimicrobial therapy in (ICU) patients with NosoP after lung or heart–lung transplantation. Between January 2008 and August 2010, 79 lung or heart–lung transplantations patients were prospectively studied. NosoPwas confirmed by quantitative cultures of bronchoalveolar lavage or endotracheal aspirates. Clinical variables, sequential organ failure assessment (SOFA) score, and radiologic score were recorded from start of therapy until day 9. Thirty‐five patients (44%) experienced 64 episodes of NosoP in ICU. Fourteen patients (40%) had NosoP recurrence. Most frequently isolated organisms were Enterobacteriaceae (30%), Pseudomonas aeruginosa (25%), and Staphylococcus aureus (20%). Sequential organ failure assessment (SOFA) score improved significantly at day 6 and C‐reactive protein level at day 9. SOFA and radiologic scores differed significantly between patients with and without NosoP recurrence at day 3 and 9. The ICU mortality rate did not differ between patients with and without NosoP recurrence, and free of NosoP (14.3%, 9.5%, 11.4%, respectively) (p = 0.91). Severities of illness and lung injury were the two major risk factors for NosoP recurrence. Occurrence of NosoP has no impact on ICU mortality.
Beyond realism in climate change experiments: gradient approaches identify thresholds and tipping points
Authors: Kreyling Juergen , Jentsch Anke , Beier Claus 
Published: October 2013

AbstractExperimental evidence for impacts of increased climatic variability and extremes on ecosystems is urgently needed. The constraint in our knowledge, however, is not caused by the uncertainty in the applied climate scenarios. We need mechanistic understanding from experiments challenging ecological thresholds coupled with ecosystem models to allow for meaningful up‐scaling.
T‐cell immunoglobulin and mucin domain 2 (TIM‐2) is a target of ADAM10‐mediated ectodomain shedding
Authors: Dewitz Christin , Möller‐Hackbarth Katja , Schweigert Olga , Reiss Karina , Chalaris Athena , Scheller Jürgen , Rose‐John Stefan 
Published: October 2013

T‐cell immunoglobulin and mucin domain (TIM)‐2 is expressed on activated B cells. Here, we provide evidence that murine TIM‐2 is a target of ADAM10‐mediated ectodomain shedding, resulting in the generation of a soluble form of TIM‐2. We identified ADAM10 but not ADAM17 as the major sheddase of TIM‐2, as shown by pharmacological ADAM10 inhibition and with ADAM10‐deficient and ADAM17‐deficient murine embryonic fibroblasts. Ionomycin‐induced or 2′(3′)‐O‐(4‐benzoylbenzoyl) ATP triethylammonium salt‐induced shedding of TIM‐2 was abrogated by deletion of 10 juxtamembrane amino acids from the stalk region but not by deletion of two further N‐terminally located blocks of 10 amino acids, indicating a membrane‐proximal cleavage site. TIM‐2 lacking the intracellular domain was cleaved after ionomycin or 2′ (3′)‐O‐(4‐benzoylbenzoyl) ATP triethylammonium salt treatment, indicating that this domain was not involved in the regulation of ectodomain shedding. Moreover, TIM‐2 shedding was negatively controlled by calmodulin. Shed and soluble TIM‐2 interacted with H‐ferritin. In summary, we describe TIM‐2 as a novel target for ADAM10‐mediated ectodomain shedding, and reveal the involvement of ADAM proteases in cellular iron homeostasis.
The COP9 signalosome is involved in the regulation of lipid metabolism and of transition metals uptake in Saccharomyces cerevisiae
Authors: Licursi Valerio , Salvi Chiara , De Cesare Virginia , Rinaldi Teresa , Mattei Benedetta , Fabbri Claudia , Serino Giovanna , Bramasole Laylan , Zimbler Jacob Z. , Pick Elah , Barnes Brett M. , Bard Martin , Negri Rodolfo 
Published: October 2013

The COP9 signalosome (CSN) is a highly conserved eukaryotic protein complex which regulates the cullin RING family of ubiquitin ligases and carries out a deneddylase activity that resides in subunit 5 (CSN5). Whereas CSN activity is essential for the development of higher eukaryotes, several unicellular fungi including the budding yeast Saccharomyces cerevisiae can survive without a functional CSN. Nevertheless, the budding yeast CSN is biochemically active and deletion mutants of each of its subunits exhibit deficiency in cullins deneddylation, although the biological context of this activity is still unknown in this organism. To further characterize CSN function in budding yeast, we present here a transcriptomic and proteomic analysis of a S. cerevisiae strain deleted in the CSN5/RRI1 gene (hereafter referred to as CSN5), coding for the only canonical subunit of the complex. We show that Csn5 is involved in modulation of the genes controlling amino acid and lipid metabolism and especially ergosterol biosynthesis. These alterations in gene expression correlate with the lower ergosterol levels and increased intracellular zinc content which we observed in csn5 null mutant cells. We show that some of these regulatory effects of Csn5, in particular the control of isoprenoid biosynthesis, are conserved through evolution, since similar transcriptomic and/or proteomic effects of csn5 mutation were previously observed in other eukaryotic organisms such as Aspergillus nidulans, Arabidopsis thaliana and Drosophila melanogaster. Our results suggest that the diverged budding yeast CSN is more conserved than was previously thought.
Use of a modified Gurson model for the failure behaviour of the clinched joint on Al6061 sheet
Authors: Xu F. , Zhao S. D. , Han X. L. 
Published: October 2013

ABSTRACTThis paper discusses the ductile fracture behaviour of the clinched joint on Alloy 6061 sheets. Failure behaviour of the clinched joint is associated with the nucleation, growth and coalescence of voids within the microstructure. Various corrections to the original Gurson model are proposed to allow for instability and final fracture of the material. This paper is concerned with the application of the modified Gurson–Tvergaard–Needleman damage developed by Ken Nahshon and Zhenyu Xue. The results of the tension tests are compared with those of numerical analysis to obtain the initial void volume fraction f0 and the shear damage coefficients kw. The modified Gurson–Tvergaard–Needleman model is used to describe the failure behaviour and the shear strength of the clinched joint. Good agreement is shown between the experiment results and the numerical results on the location of fracture and the maximum failure load.