bluuebunny/crossref_metadata_2025 huggingface dataset:
Block bootstrap methods for the estimation of the intensity of a spatial point process with confidence bounds
Authors: MATTFELDT T. , HÄBEL H. , FLEISCHER F.
Published: May 2013

This paper deals with the estimation of the intensity of a planar point process on the basis of a single point pattern, observed in a rectangular window. If the model assumptions of stationarity and isotropy hold, the method of block bootstrapping can be used to estimate the intensity of the process with confidence bounds. The results of two variants of block bootstrapping are compared with a parametric approximation based on the assumption of a Gaussian distribution of the numbers of points in deterministic subwindows of the original pattern. The studies were performed on patterns obtained by simulation of well‐known point process models (Poisson process, two Matérn cluster processes, Matérn hardcore process, Strauss hardcore process). They were also performed on real histopathological data (point patterns of capillary profiles of 12 cases of prostatic cancer). The methods are presented as worked examples on two cases, where we illustrate their use as a check on stationarity (homogeneity) of a point process with respect to different fields of vision. The paper concludes with various methodological discussions and suggests possible extensions of the block bootstrap approach to other fields of spatial statistics.
Three‐dimensional visualization of dermal skin structure using confocal laser scanning microscopy
Authors: ANTUNES A.P.M. , COVINGTON A.D. , PETFORD N. , MURRAY T. , WERTHEIM D.
Published: May 2013

The properties and performance of collagen‐based materials may be affected by the collagen fibre bundle pattern, orientation and weave. The aim of this study was to develop and apply methods to visualize the dermis using confocal laser scanning microscopy from thin tissue sections stained with haematoxylin and eosin. The data was processed to allow three‐dimensional (3‐D) visualization on a PC and using a 3‐D immersive technology system. The 3‐D visualization of the confocal microscope image stacks allowed the evaluation of the collagen macromolecular structure including the collagen fibre bundles. The methods developed provide a novel way of viewing complex organic structures with further potential applications in the medical field.
Long‐term coeliac disease influences risk of death in patients with type 1 diabetes
Authors: Mollazadegan K. , Sanders D. S. , Ludvigsson J. , Ludvigsson J. F.
Published: May 2013

Aim

The aim of this study was to examine mortality in patients with both type 1 diabetes (T1D) and coeliac disease (CD).

Methods

Between 1969 and 2008, we identified individuals with CD through biopsy reports from all pathology departments (n = 28) in Sweden. T1D was defined as a diagnosis of diabetes recorded in the Swedish National Patient Register between 1964 and 2009 in individuals aged ≤30 years. During follow‐up, we identified 960 patients with both T1D and CD. For each individual with T1D and CD, we selected up to five subjects with T1D alone (i.e. no CD), matched for sex, age and calendar period of diagnosis, as the reference group (n = 4608). Using a stratified Cox regression analysis with CD as a time‐dependent covariate, we estimated the risk of death in patients with both T1D and CD compared with those with T1D alone.

Results

Stratifying for time since CD diagnosis, CD was not a risk factor for death in patients with T1D during the first 5 years after CD diagnosis [hazard ratio (HR) 0.87, 95% confidence interval (CI) 0.43–1.73], but thereafter the HR for mortality increased as a function of follow‐up time (5 to <10 years, HR 1.44, 95% CI 0.74–2.79; 10 to <15 years, HR 1.88, 95% CI 0.81–4.36). Having a CD diagnosis for ≥15 years was associated with a 2.80‐fold increased risk of death in individuals with T1D (95% CI 1.28–6.12).

Conclusion

A diagnosis of CD for ≥15 years increases the risk of death in patients with T1D.
Rhizoctonia Web Blight Development on Azalea in Relation to Leaf Wetness Duration in the Glasshouse
Authors: Copes Warren
Published: May 2013

Moisture variables have not been a consistent predictor of Rhizoctonia web blight development on container‐grown azalea. A vapour pressure deficit <2.5 hPa was the only moisture variable attributed to slow web blight development in one study, yet in another study, frequent rainfall provided a moderately successful decision criterion for applying fungicide. To characterize web blight development in response to leaf wetness, plants were inoculated with two isolates of binucleate Rhizoctonia AG‐U and maintained in a glasshouse in open‐topped, clear plastic chambers with 0‐, 4‐, 8‐, 12‐, 16‐ and 20‐h daily cycles of 20–30 s mist at 30‐min intervals under day and night temperatures of 29 and 22°C, respectively. Leaf wetness duration closely matched misting cycle duration. Disease incidence was measured per chamber as a mean of the number of blighted leaves per total leaves per stem. A mixed model procedure was used to compare area under the disease progress curves (AUDPC) over 4–6 weeks in experiments performed in 2008 to 2010. Isolate response to mist cycle durations was not different (P = 0.4283) in 2008, but was different in 2009 (P = 0.0010) and 2010 (P < 0.0001) due to one isolate becoming less aggressive over time. AUDPC was consistently higher on azaleas under 16‐ and 20‐h mist cycles, which formed a higher disease group not significantly different from each other. AUDPC under 0‐, 4‐, and 8‐h mist cycles mostly formed a lower disease group, while ranking for a 12‐h mist cycle varied across experiments from the higher, intermediate, or lower AUDPC groups. Current data demonstrate an empirical relationship between long daily leaf wetness durations and development of severe web blight symptoms within a temperature range considered favourable for Rhizoctonia web blight development. Additional studies would be required to model Rhizoctonia web blight development under natural temperature fluctuations.
Cognitive milieu therapy and physical activity: experiences of mastery and learning among patients with dual diagnosis
Authors: Borge L. , Røssberg J. I. , Sverdrup S.
Published: May 2013

Accessible summary

Cognitive milieu therapy, including physical activity, promoted mastery and learning in inpatients with dual diagnoses. Physical activity was an important source for personal learning.

The learning climate was created through the proactive attitude of staff, including the application of an educational process, a focus on cooperation on equal terms between patients and staff, and a professional methodological approach through cognitive milieu therapy.

The cognitive method was sometimes experienced as too theoretical and difficult to understand, and it was a challenge to achieve an optimal balance between staff‐induced activities and patient initiatives.

Patients highly appreciated learning from other patients.

During the last decade, there has been a growing interest in implementing cognitive milieu therapy (CMT) in psychiatric institutions. However, there is a lack of systematic evaluations from patients' point of view. The aim of this study was to explore and describe patient perceptions of essential experiences of mastery, learning alternative ways of thinking, and acquiring new skills through CMT and physical activity in an inpatient setting. Qualitative interviews were carried out with 20 patients with dual diagnosis. A hermeneutic – phenomenological approach was used in the data collection and analysis. The results showed that the learning climate in the unit was important. This included a proactive attitude from the staff, focusing on cooperation on equal terms between patients and staff, and a professional methodological approach through CMT. The optimal balance between staff‐induced activities and patient initiatives was not easy to obtain. Patients appreciated both the education provided by the staff and learning from other patients. The cognitive method was sometimes experienced as too theoretical and difficult to understand. Physical activity, however, was experienced as ‘concrete’ and providing practical knowledge. It motivated patients to establish new habits and provided opportunities for the development of mastery together with other patients.
Birth of Kids After Artificial Insemination with Sex‐Sorted, Frozen‐Thawed Goat Spermatozoa
Authors: Bathgate R , Mace N , Heasman K , Evans G , Maxwell WMC , de Graaf SP
Published: May 2013

Contents

Successful sex‐sorting of goat spermatozoa and subsequent birth of pre‐sexed kids have yet to be reported. As such, a series of experiments were conducted to develop protocols for sperm‐sorting (using a modified flow cytometer, MoFlo SX®) and cryopreservation of goat spermatozoa. Saanen goat spermatozoa (n = 2 males) were (i) collected into Salamon's or Tris catch media post‐sorting and (ii) frozen in Tris–citrate–glucose media supplemented with 5, 10 or 20% egg yolk in (iii) 0.25 ml pellets on dry ice or 0.25 ml straws in a controlled‐rate freezer. Post‐sort and post‐thaw sperm quality were assessed by motility (CASA), viability and acrosome integrity (PI/FITC‐PNA). Sex‐sorted goat spermatozoa frozen in pellets displayed significantly higher post‐thaw motility and viability than spermatozoa frozen in straws. Catch media and differing egg yolk concentration had no effect on the sperm parameters tested. The in vitro and in vivo fertility of sex‐sorted goat spermatozoa produced with this optimum protocol were then tested by means of a heterologous ova binding assay and intrauterine artificial insemination of Saanen goat does, respectively. Sex‐sorted goat spermatozoa bound to sheep ova zona pellucidae in similar numbers (p > 0.05) to non‐sorted goat spermatozoa, non‐sorted ram spermatozoa and sex‐sorted ram spermatozoa. Following intrauterine artificial insemination with sex‐sorted spermatozoa, 38% (5/13) of does kidded with 83% (3/5) of kids being of the expected sex. Does inseminated with non‐sorted spermatozoa achieved a 50% (3/6) kidding rate and a sex ratio of 3 : 1 (F : M). This study demonstrates for the first time that goat spermatozoa can be sex‐sorted by flow cytometry, successfully frozen and used to produce pre‐sexed kids.
Technology‐enhanced Interactive Teaching of Marginal, Joint and Conditional Probabilities: The Special Case of Bivariate Normal Distribution
Authors: Dinov Ivo D. , Kamino Scott , Bhakhrani Bilal , Christou Nicolas
Published: May 2013

Data analysis requires subtle probability reasoning to answer questions like What is the chance of event A occurring, given that event B was observed? This generic question arises in discussions of many intriguing scientific questions such as What is the probability that an adolescent weighs between 120 and 140 pounds given that they are of average height? and What is the probability of (monetary) inflation exceeding 4% and housing price index below 110? To address such problems, learning some applied, theoretical or cross‐disciplinary probability concepts is necessary. Teaching such courses can be improved by utilizing modern information technology resources. Students' understanding of multivariate distributions, conditional probabilities, correlation and causation can be significantly strengthened by employing interactive web‐based science educational resources. Independent of the type of a probability course (e.g. majors, minors or service probability course, rigorous measure‐theoretic, applied or statistics course) student motivation, learning experiences and knowledge retention may be enhanced by blending modern technological tools within the classical conceptual pedagogical models.

We have designed, implemented and disseminated a portable open‐source web‐application for teaching multivariate distributions, marginal, joint and conditional probabilities using the special case of bivariate Normal distribution. A real adolescent height and weight dataset is used to demonstrate the classroom utilization of the new web‐application to address problems of parameter estimation, univariate and multivariate inference.
Safety profile comparing azathioprine and mycophenolate in kidney transplant recipients receiving tacrolimus and corticosteroids
Authors: Cristelli M.P. , Tedesco‐Silva H. , Medina‐Pestana J.O. , Franco M.F.
Published: May 2013

Background

Debate is increasing on whether mycophenolic acid (MPA) provides survival benefits comparable to azathioprine (AZA) after renal transplantation.

Methods

This retrospective cohort study compared safety and efficacy of AZA (n = 662) vs. MPA (n = 267) in low‐immunologic‐risk kidney transplant recipients (KTR) receiving tacrolimus (TAC) and steroids between 1998 and 2007. Primary outcomes were treatment discontinuation and infection. Secondary endpoints included survival free from biopsy‐proven acute rejection, graft loss, death, and renal function.

Results

The 5‐year survival free of treatment discontinuation was higher in the MPA compared to the AZA group (74.1% vs. 60.3%, P < 0.001). MPA was discontinued exclusively because of adverse events (16.4%), while AZA was discontinued primarily for lack of efficacy (21.2%). In univariable analysis, MPA was associated with higher incidence of total (561.5 vs. 667.5 episodes/1000 person‐year, P < 0.001), bacterial (167 vs. 158 episodes/1000 person‐years, P = 0.001), and viral infections (83.2 vs. 100.4 episodes/1000 person‐years, P = 0.001), but this association was not confirmed in multivariable analysis. Over 29% of viral infections in the AZA group occurred after conversion to MPA. A high incidence of tuberculosis was observed (2.9 episodes/1000 person‐years) with a higher incidence (but not a statistically significant difference) in the AZA group. No significant differences were found in patient survival (90% vs. 89%, P = 0.78) or graft survival (81% vs. 77.7%, P = 0.08), but infection accounted for >50% of all deaths.

Conclusion

The type of antimetabolite, AZA or MPA, was not independently associated with any safety or efficacy outcome 5 years after transplantation, suggesting that AZA is still a viable option for low‐risk KTR receiving TAC and steroids.
Dedicated removal of immunoglobulin (Ig)A, IgM, and Factor (F)XI/activated FXI from human plasma IgG
Authors: Wu Yu‐Wen , Champagne Jérôme , Toueille Magali , Gantier René , Burnouf Thierry
Published: May 2013

Background

Adverse events can be associated with treating critically ill patients with immunoglobulin (Ig)G. Some adverse events are due to contaminants like IgA and activated Factor (F)XI. Therefore, new purification strategies are needed for dedicated removal of these contaminants without impairing IgG recovery.

Study Design and Methods

An immunoglobulin fraction containing IgG, IgM, and IgA was prepared by caprylic acid precipitation of cryoprecipitate‐poor plasma. The capacities of the cation exchangers (S HyperCel and CM Ceramic HyperD F) and anion exchangers (HyperCel STAR AX and Q HyperCel) to remove IgA, IgM, and spiked FXI were tested following a design of experiment approach using microplates and chromatographic column scale‐up. FXI removal was also evaluated using Mustang S chromatographic membranes. IgG/IgG subclasses, IgA, IgM, and FXI were assessed by enzyme‐linked immunosorbent assay, and caprylic acid, by gas chromatography.

Results

Extensive removal of IgA and IgM, but not FXI, was achieved by a two‐step chromatographic process combining S HyperCel used in the IgG binding and elution mode and HyperCel STAR AX used in the IgG flow‐through mode, providing high IgG and IgG subclass recovery (>85%), high purity (>99.5%), and efficient removal of IgA (<0.5%) and IgM (undetectable). Twenty‐six‐fold FXI removal was achieved by processing the resulting purified IgG fraction through Mustang S cation‐exchanger membranes at pH 6.0 and 12.7 mS/cm. Caprylic acid was removed by S HyperCel.

Conclusions

Combining S HyperCel and HyperCel STAR AX extensively removed IgA and IgM, with good IgG recovery. Mustang® S membranes can be used for dedicated removal of FXI.
Feline ocular tumors following ciliary body ablation with intravitreal gentamicin
Authors: Duke Felicia D. , Strong Travis D. , Bentley Ellison , Dubielzig Richard R.
Published: May 2013

Practitioners approach chemical ciliary body ablation (CBA) in cats with caution. In 1994, an academic letter proposed a potential link between intraocular gentamicin injections for glaucoma and the appearance of ocular tumors in cats (Veterinary and Comparative Ophthalmology, 4, 1994, 166). There is an historic perceived risk for the development of feline ocular post‐traumatic sarcoma following gentamicin ciliary body ablation, and many clinicians refrain from chemical ablation in cats for this reason. A recent study discussed the possibility of a correlation between intravitreal gentamicin and tumor promotion in dogs (Veterinary Ophthalmology, 16, 2013, 159). We searched the Comparative Ocular Pathology Laboratory of Wisconsin (COPLOW) database for cases of cats diagnosed with ocular tumors following ciliary body ablation. Of eight cases with historic gentamicin injection, five had malignant tumors: three post‐traumatic sarcomas and two melanomas.
How does selection of climate variables affect predictions of species distributions? A case study of three new weeds in New Zealand
Authors: Sheppard C S
Published: May 2013

Species distribution models are an important tool to predict potential spread of weeds. While recent progress has improved model performance, there is still concern about the validity of such models, especially when applied to novel geographical regions or climates. This study investigates how different sets of variables influence predicted distributions, considering several measures of model performance and how extrapolation to novel geographical regions may affect results. Potential distributions of three new weeds in New Zealand (Archontophoenix cunninghamiana, Psidium guajava and Schefflera actinophylla) are modelled, by training a model based on global data from native and introduced ranges and projecting it to New Zealand, using Maxent. For each species, four models were calibrated: first with a full set of 19 bioclimatic variables, then with a customised set with selection based on analysis of response curves and finally with two reduced sets of uncorrelated variables. Although AUC across all models was very high (AUC ≥ 0.9), correlations between models ranged between 0.27 and 0.98. Inclusion of all variables predicted larger areas to be suitable in the projected region, with highly unlikely predictions in some areas, especially where bioclimatic variables showed values outside the range of the training data (new environments). Conversely, minimal extrapolation and more realistic predictions of weed distributions were obtained from models including a customised set of variables, and even more so from models including only a reduced set of variables. This study shows that careful selection of variables and investigation into extrapolation are vital in generating more realistic predictions of weed distributions.
Hydraulic Improvement to Eliminate S-Shaped Curve in Pump Turbine
Authors: Yin Jun-lian , Wang De-zhong , Wei Xian-zhu , Wang Le-qin
Published: May 2013

For pump turbines, an S-shaped curve can lead to failures in synchronization. To improve the hydraulic design, the component that is responsible for the formation of the S-shaped curve was identified by a hydraulic loss analysis using previous computational fluid dynamics (CFD) results, which indicates that the formation of the S-shaped curve can be ascribed to the runner. To improve the hydraulic design of the runner, a simple numerical approach for direct problem analysis was proposed, based on the blade-loading distributions of runners with and without an S-shaped curve, and directly analyzed. It was implied from the differences in the blade-loading distributions that, when the meridional passage was broadened, the formation of the S-shaped curve was suppressed. To validate this, two runners with different meridional sections were designed by means of the inverse design method. Through model tests, it was verified that the S-shaped curve was eliminated completely and the performance curve of the modified hydraulic model satisfied the requirements for safe operation in a pumped storage plant.
Mixed Additive/Multiplicative H∞ Model Reduction
Authors: Chow Yin-Lam , Hu Yue-Bing , Li Xianwei , Kominek Andreas , Lam James
Published: May 2013

In this paper, the problem of mixed additive/multiplicative model reduction for stable linear continuous-time systems is studied. To deal with nonsquare or nonminimum phase systems, the multiplicative error bound is constructed using spectral factorization technique. By virtue of the bounded real lemma and the projection lemma, a linear matrix inequality approach is proposed for mixed additive/multiplicative H∞ model reduction, which can be implemented by the well-known cone complementary linearization method. Finally, two numerical examples are provided to demonstrate the effectiveness and advantages of the obtained results.
Futile Protein Folding Cycles in the ER Are Terminated by the Unfolded Protein O-Mannosylation Pathway
Authors: Xu Chengchao , Wang Songyu , Thibault Guillaume , Ng Davis T. W.
Published: May 2013

Folding Too Slow, Off You Go

One of the major questions of chaperone-assisted protein-folding pathways is how substrates that fail to fold avoid futile folding cycles.

Xu
et al.

(p.
978
; see the Perspective by

Kleizen and Braakman

) developed a model to examine a folding-competent protein that nevertheless fails to fold within the endoplasmic reticulum. Under these circumstances, the unfolded protein was subject to an unusual glycosylation, O-mannosylation, which appeared to terminate folding of the unfinished molecules. Eliminating O-mannosylation allowed the protein to fold completely.
Comment on “ApoE-Directed Therapeutics Rapidly Clear β-Amyloid and Reverse Deficits in AD Mouse Models”
Authors: Price Ashleigh R. , Xu Guilian , Siemienski Zoe B. , Smithson Lisa A. , Borchelt David R. , Golde Todd E. , Felsenstein Kevin M.
Published: May 2013

Cramer
et al
. (Reports, 23 March 2012, p. 1503; published online 9 February 2012) demonstrates short-term bexarotene treatment clearing preexisting β-amyloid deposits from the brains of APP/PS1ΔE9 mice with low amyloid burden, providing a rationale for repurposing this anticancer agent as an Alzheimer’s disease (AD) therapeutic. Using a nearly identical treatment regimen, we were unable to detect any evidence of drug efficacy despite demonstration of target engagement.
Culture, Genes, and the Human Revolution
Authors: Fisher Simon E. , Ridley Matt
Published: May 2013

Genetic evolution may have been driven by cultural innovations during the emergence of modern humans.
One Good Measure
Authors: Schreiber M. R.
Published: May 2013

Accurate distances to compact binary stars help establish a clear understanding of accretion disk evolution.

[Also see Report by

Miller-Jones
et al.

]
A Sweet Send-Off
Authors: Kleizen Bertrand , Braakman Ineke
Published: May 2013

Proteins that take too long to fold are tagged with sugar to stop their failed attempts and remove them from the cell's folding compartment.

[Also see Report by

Xu
et al.

]
A Fond Farewell
Authors: Norman Colin
Published: May 2013

Half a century ago, Philip Abelson,
Science
's longtime
Editor-in-Chief
, made a radical move in the world of scholarly publishing. He launched a new section of the journal, News and Comment, and staffed it with journalists, not scientists. His rationale: Fundamental changes were taking place in the funding and organization of research, and it was becoming increasingly important for scientists to know about and understand events shaping the scientific enterprise. A decade later, he added another journalist-written section, Research News, that would report on new findings and trends in research itself. This time, he reasoned that because research was becoming ever more specialized, scientists needed objective reporting on developments in disciplines outside their own. Under the leadership of early News editors such as Daniel S. Greenberg and Allen Hammond, the News sections quickly became among the most widely read parts of a journal that has continued to publish the very best research papers.
Long Noncoding RNAs May Alter Chromosome's 3D Structure
Authors: Pennisi Elizabeth
Published: May 2013

Abundant but mysterious molecules called long noncoding RNAs have long puzzled scientists, but some now think they could be influencing the shape of chromatin.
In Latino Genomes, a Rich Source of History
Authors: Pennisi Elizabeth
Published: May 2013

Analyses of DNA of Latinos in South Florida traced their African, European, and South American ancestries.
Two Proofs Spark a Prime Week for Number Theory
Authors: Mackenzie Dana
Published: May 2013

The most dramatic progress has been made on the twin prime conjecture and Goldbach's conjecture in more than a century and a half of trying.
Good Syndrome, a Rare Cause of Refractory Chronic Diarrhea and Recurrent Pneumonia in a Chinese Patient after Thymectomy
Authors: Qu Junyan , Lü Xiaoju , Gao Qin , Zhang Yan
Published: May 2013

The diagnosis of Good syndrome is very difficult. It has various symptoms, and these symptoms can be present at different periods. In this report we present a patient with refractory chronic diarrhea, recurrent pneumonia, and dysgammaglobulinemia after thymectomy, who was finally then diagnosed with Good syndrome.
Capnocytophaga canimorsus Prosthetic Aortitis in an HIV-Positive Woman
Authors: Rougemont Mathieu , Ratib Osman , Wintsch Joëlle , Schrenzel Jacques , Hirschel Bernard
Published: May 2013

A 49-year-old woman with a 15-year history of HIV-hepatitis C virus coinfection had aortic valve and ascending aorta replacement in 2007. She presented with abdominal pain, episodic diarrhea, and profuse sweating in 2010. Thoracoabdominal positron emission tomography-computed tomography finally suggested infectious aortitis, a diagnosis confirmed by a blood culture positive for
Capnocytophaga canimorsus
.
Identification by 16S rRNA Gene Sequencing of an Actinomyces hongkongensis Isolate Recovered from a Patient with Pelvic Actinomycosis
Authors: Flynn A. N. , Lyndon C. A. , Church D. L.
Published: May 2013

A case ofActinomyces hongkongensispelvic actinomycosis in an adult woman is described. Conventional phenotypic tests failed to identify the Gram-positive bacillus isolated from a fluid aspirate of a pelvic abscess. The bacterium was identified by 16S rRNA gene sequencing and analysis using the SmartGene Integrated Database Network System software.
Renal Abscess Caused by a Providencia stuartii Isolate Biochemically Misidentified as Pasteurella
Authors: Chamberland Robin R. , McElvania TeKippe Erin , Burnham Carey-Ann D. , Kennedy Donald J.
Published: May 2013

Providencia stuartii
is associated with urinary tract infection (UTI) in catheterized patients. Here we report an abscess containing
P. stuartii
in a patient with a history of UTI, renal stones, and stent placement. This organism was identified by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry and 16S rRNA gene sequencing following biochemical identification as
Pasteurella
.
Footprint of APOBEC3 on the Genome of Human Retroelements
Authors: Anwar Firoz , Davenport Miles P. , Ebrahimi Diako
Published: May 2013

Almost half of the human genome is composed of transposable elements. The genomic structures and life cycles of some of these elements suggest they are a result of waves of retroviral infection and transposition over millions of years. The reduction of retrotransposition activity in primates compared to that in nonprimates, such as mice, has been attributed to the positive selection of several antiretroviral factors, such as apolipoprotein B mRNA editing enzymes. Among these, APOBEC3G is known to mutate G to A within the context of
G
G in the genome of endogenous as well as several exogenous retroelements (the underlining marks the G that is mutated). On the other hand, APOBEC3F and to a lesser extent other APOBEC3 members induce G-to-A changes within the nucleotide
G
A. It is known that these enzymes can induce deleterious mutations in the genome of retroviral sequences, but the evolution and/or inactivation of retroelements as a result of mutation by these proteins is not clear. Here, we analyze the mutation signatures of these proteins on large populations of long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and endogenous retrovirus (ERV) families in the human genome to infer possible evolutionary pressure and/or hypermutation events. Sequence context dependency of mutation by APOBEC3 allows investigation of the changes in the genome of retroelements by inspecting the depletion of G and enrichment of A within the APOBEC3 target and product motifs, respectively. Analysis of approximately 22,000 LINE-1 (L1), 24,000 SINE Alu, and 3,000 ERV sequences showed a footprint of GG→AG mutation by APOBEC3G and GA→AA mutation by other members of the APOBEC3 family (e.g., APOBEC3F) on the genome of ERV-K and ERV-1 elements but not on those of ERV-L, LINE, or SINE.
Permissive Replication of Homologous Murine Rotavirus in the Mouse Intestine Is Primarily Regulated by VP4 and NSP1
Authors: Feng Ningguo , Yasukawa Linda L. , Sen Adrish , Greenberg Harry B.
Published: May 2013

Homologous rotaviruses (RV) are, in general, more virulent and replicate more efficiently than heterologous RV in the intestine of the homologous host. The genetic basis for RV host range restriction is not fully understood and is likely to be multigenic. In previous studies, RV genes encoding VP3, VP4, VP7, nonstructural protein 1 (NSP1), and NSP4 have all been implicated in strain- and host species-specific infection. These studies used different RV strains, variable measurements of host range, and different animal hosts, and no clear consensus on the host range restriction determinants emerged. We used a murine model to demonstrate that enteric replication of murine RV EW is 1,000- to 10,000-fold greater than that of a simian rotavirus (RRV) in suckling mice. Intestinal replication of a series of EW × RRV reassortants was used to identify several RV genes that influenced RV replication in the intestine. The role of VP4 (encoded by gene 4) in enteric infection was strain specific. RRV VP4 reduced murine RV infectivity only slightly; however, a reassortant expressing VP4 from a bovine RV strain (UK) severely restricted intestinal replication in the suckling mice. The homologous murine EW NSP1 (encoded by gene 5) was necessary but not sufficient for promoting efficient enteric growth. Efficient enteric replication required a constellation of murine genes encoding VP3, NSP2, and NSP3 along with NSP1.
Improving the Effectiveness of Artificial MicroRNA (amiR)-Mediated Resistance against Turnip Mosaic Virus by Combining Two amiRs or by Targeting Highly Conserved Viral Genomic Regions
Authors: Lafforgue Guillaume , Martínez Fernando , Niu Qi-Wen , Chua Nam-Hai , Daròs José-Antonio , Elena Santiago F.
Published: May 2013

A drawback of recent antiviral therapies based on the transgenic expression of artificial microRNAs (amiRs) is the ease with which viruses generate escape mutations. Here, we show two alternative strategies for improving the effectiveness of resistance in plants. First, we expressed two amiRs complementary to independent targets in the viral genome, and second, we designed amiRs complementary to highly conserved RNA motifs in the viral genome.
Induction of Cross-Reactive Antibodies to Novel H7N9 Influenza Virus by Recombinant Newcastle Disease Virus Expressing a North American Lineage H7 Subtype Hemagglutinin
Authors: Goff Peter H. , Krammer Florian , Hai Rong , Seibert Christopher W. , Margine Irina , García-Sastre Adolfo , Palese Peter
Published: May 2013

Severe human disease caused by the emerging H7N9 influenza virus in China warrants a rapid response. Here, we present a recombinant Newcastle disease virus expressing a North American lineage H7 influenza virus hemagglutinin. Sera from immunized mice were cross-reactive to a broad range of H7 subtype viruses and inhibited hemagglutination by the novel H7 hemagglutinin. Immunized mice were protected against a heterologous H7 subtype challenge, and genetic analysis suggested that cross-protective antibodies recognize conserved antigenic sites.
Epstein-Barr Virus Latent Membrane Protein 2A Contributes to Anoikis Resistance through ERK Activation
Authors: Iwakiri Dai , Minamitani Takeharu , Samanta Mrinal
Published: May 2013

Epstein-Barr virus (EBV) is associated with various malignancies, including epithelial cancers. In this study, we analyzed the effect of EBV infection on epithelial cells by using EBV-converted epithelial cells. In EBV-positive cells, the extracellular signal-regulated kinase (ERK) pathway is constitutively activated. Inhibition of ERK activity leads to reduced anoikis resistance; therefore, EBV-positive cells are more resistant to anoikis, a type of apoptosis induced by cell detachment, than are EBV-negative cells. Among the viral genes expressed in EBV-positive cells, the latent membrane protein 2A (LMP2A) is responsible for induction of ERK-mediated anoikis resistance, although the expression level of LMP2A is much lower in EBV-positive cells than in EBV-transformed B cells. Further analysis demonstrated that LMP2A downregulation of the proanoikis mediator Bim through proteasomal degradation is dependent on the immunoreceptor tyrosine-based activation motif (ITAM). These findings suggest that LMP2A-mediated ERK activation is involved in the generation of EBV-associated epithelial malignancies.
Age and Immune Status of Rhesus Macaques Impact Simian Varicella Virus Gene Expression in Sensory Ganglia
Authors: Meyer Christine , Dewane Jesse , Kerns Amelia , Haberthur Kristen , Barron Alex , Park Byung , Messaoudi Ilhem
Published: May 2013

Simian varicella virus (SVV) infection of rhesus macaques (RMs) recapitulates the hallmarks of varicella-zoster virus (VZV) infection of humans, including the establishment of latency within the sensory ganglia. Various factors, including age and immune fitness, influence the outcome of primary VZV infection, as well as reactivation resulting in herpes zoster (HZ). To increase our understanding of the role of lymphocyte subsets in the establishment of viral latency, we analyzed the latent SVV transcriptome in juvenile RMs depleted of CD4 T, CD8 T, or CD20 B lymphocytes during acute infection. We have previously shown that SVV latency in sensory ganglia of nondepleted juvenile RMs is associated with a limited transcriptional profile. In contrast, CD4 depletion during primary infection resulted in the failure to establish a characteristic latent viral transcription profile in sensory ganglia, where we detected 68 out of 69 SVV-encoded open reading frames (ORFs). CD-depleted RMs displayed a latent transcriptional profile that included additional viral transcripts within the core region of the genome not detected in control RMs. The latent transcriptome of CD20-depleted RMs was comparable to the latent transcription in the sensory ganglia of control RMs. Lastly, we investigated the impact of age on the establishment of SVV latency. SVV gene expression was more active in ganglia from two aged RMs than in ganglia from juvenile RMs, with 25 of 69 SVV transcripts detected. Therefore, immune fitness at the time of infection modulates the establishment and/or maintenance of SVV latency.
The Autographa californica Multiple Nucleopolyhedrovirus ORF78 Is Essential for Budded Virus Production and General Occlusion Body Formation
Authors: Tao Xue Ying , Choi Jae Young , Kim Woo Jin , Lee Joo Hyun , Liu Qin , Kim Song Eun , An Saes Byeol , Lee Seok Hee , Woo Soo Dong , Jin Byung Rae , Je Yeon Ho
Published: May 2013

ORF78 (
ac78
) of
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) is a baculovirus core gene of unknown function. To determine the role of
ac78
in the baculovirus life cycle, an AcMNPV mutant with
ac78
deleted, Ac78KO, was constructed. Quantitative PCR analysis revealed that
ac78
is a late gene in the viral life cycle. After transfection into
Spodoptera frugiperda
cells, Ac78KO produced a single-cell infection phenotype, indicating that no infectious budded viruses (BVs) were produced. The defect in BV production was also confirmed by both viral titration and Western blotting. However, viral DNA replication was unaffected, and occlusion bodies were formed. An analysis of BVs and occlusion-derived viruses (ODVs) revealed that AC78 is associated with both forms of the virions and is an envelope structural protein. Electron microscopy revealed that AC78 also plays an important role in the embedding of ODV into the occlusion body. The results of this study demonstrate that AC78 is a late virion-associated protein and is essential for the viral life cycle.
A deadly combination of AIDS, TB and cardiac tumour
Authors: Sahasrabudhe Tushar Ramesh
Published: May 2013

Immunocompromised status in AIDS makes differential diagnosis of any symptom very difficult for a clinician. Sharp clinical judgement and plenty of investigations may be needed to reach the diagnosis, as in this case. We hereby present a case of AIDS and active tuberculosis (TB) under treatment. The patient developed acute onset multifocal neurological symptoms following an episode of fever and diarrhoea. The MRI scan revealed numerous large cerebral infarcts. On investigations to evaluate brain infarcts, we made a diagnosis of left atrial cardiac tumour. Association of cardiac tumours with AIDS has only been rarely reported. It is uncertain if these can be opportunistic tumours in AIDS. The patient successfully came out of this deadly combination of diseases, viz AIDS, TB and large brain infarcts due to atrial tumour; with almost complete recovery.
A painful thumb
Authors: Chan Yuen
Published: May 2013

Isolated traumatic carpometacarpal (CMC) dislocation of the thumb is a rare injury. There are many different ways to manage a thumb CMC joint dislocation which ranges from closed reduction with or without Kirschner wires and casting to ligament reconstruction. However, it is still up for debate on the best management for this injury. We describe a case of isolated traumatic carpometacarpal dislocation of the first CMC joint in a 22-year-old student and reviewed the evidence on management. Our patient was managed with manipulation under anaesthesia (MUA). She returned to preinjury activities with no difficulties within 2 months. Good outcomes can be achieved with MUA to manage dislocation of the first CMC joint; however, those with high activity of the hand may also benefit from ligament reconstruction.
Multidetector CT findings of calvarial eosinophilic granuloma
Authors: Inci Mehmet Fatih , Inci Rahime , Ozkan Fuat
Published: May 2013

Eosinophilic granuloma (EG) is a well-recognised benign form of Langerhans-cell histiocytosis. The estimated incidence of EG is 3–4 per million of the population. More patients are children and adolescents between the ages of 1 and 15 years. The value of plain films in the diagnosis of the EG is limited and the extent of the disease is better defined by multidetector CT (MDCT) scanning. MDCT scan with multiplanar and three-dimensional reconstruction image of the skull and brain clearly demonstrates bone destruction and soft-tissue involvement of the tumour. In this article we present the MDCT imaging characteristics of EG of the skull and discuss the differential diagnosis of this rare lesion with reference to recent literatures.
Endoscopic resection of the inflamed bicipitoradial bursa extended around the radial neck
Authors: Lui Tun Hing
Published: May 2013

The bicipitoradial bursa lies at the insertion of the biceps tendon on the radial tuberosity. It is an unusual site for chronic bursitis and most often, results from repetitive mechanical trauma or overuse. Other causes include tuberculosis, immunological complications of the rheumatological disease, for example, psoriatic arthropathy, rheumatoid arthritis and synovial chondromatosis. Unlike ganglion cyst arising from the elbow joint, resection of the bursa through the elbow arthroscopy is not possible as the bursa is not communicated with the joint. We reported a patient with rheumatoid arthritis presenting with bicipitoradial bursitis extended around the radial neck which was successfully resected endoscopically.
A space occupying lesion masquerading as pancreatic carcinoma
Authors: Naisbitt Christopher Jon , Filobbos Rafik , Bonington Alec , O'Reilly Derek
Published: May 2013

The coexistence of painless jaundice and a space-occupying lesion in the head of the pancreas usually signifies a diagnosis of pancreatic cancer. We present a case, where the cause of a pancreatic mass turned out to be related to tuberculosis. Tuberculosis affecting abdominal organs in isolation is uncommon, and more often forms part of disseminated disease. Pancreatic tuberculosis is very rare, especially in immunocompetent individuals. While every effort should be made to ensure that potentially operable pancreatic cancers undergo prompt surgical excision, the challenge for the future will be to make a preoperative diagnosis of pancreatic conditions that require medical rather than surgical therapy.
McCOY PROPERTY OF SKEW LAURENT POLYNOMIALS AND POWER SERIES RINGS
Authors: ALHEVAZ A. , KIANI D.
Published: May 2013

One of the important properties of commutative rings, proved by McCoy [Remarks on divisors of zero, Amer. Math. Monthly49(5) (1942) 286–295], is that if two nonzero polynomials annihilate each other over a commutative ring then each polynomial has a nonzero annihilator in the base ring. Nielsen [Semi-commutativity and the McCoy condition, J. Algebra298(1) (2006) 134–141] generalizes this property to non-commutative rings. Let M be a monoid and σ be an automorphism of a ring R. For the continuation of McCoy property of non-commutative rings, in this paper, we extend the McCoy's theorem to skew Laurent power series ring R[[x, x-1; σ]] and skew monoid ring R * M over general non-commutative rings. Constructing various examples, we classify how these skew versions of McCoy property behaves under various ring extensions. Moreover, we investigate relations between these properties and other standard ring-theoretic properties such as zip rings and rings with Property (A). As a consequence we extend and unify several known results related to McCoy rings.
ON CONFIGURATION GRAPH AND PARADOXICAL DECOMPOSITION
Authors: YOUSOFZADEH AKRAM , TAVAKOLI ALI , REJALI ALI
Published: May 2013

In this paper, we introduce the concept of configuration graph and show how one can use this notion to simplify the theorem proved by Rejali and Yousofzadeh [Configuration of groups and paradoxical decompositions, Bull. Belg. Math. Soc. Simon Stevin18 (2011) 157–172].
DETECTING EINSTEIN–PODOLSKY–ROSEN STEERING FOR CONTINUOUS VARIABLE WAVEFUNCTIONS
Authors: SU HONG-YI , CHEN JING-LING , WU CHUNFENG , DENG DONG-LING , OH C. H.
Published: May 2013

By use of Reid's criterion and the entropic criterion, we investigate the Einstein–Podolsky–Rosen (EPR) steering for some entangled continuous variable wavefunctions. We find that some entangled states that violate Bell's inequality will not violate Reid's EPR inequality nor the entropic inequality. This implies that neither criterion gives a necessary and sufficient condition to detect the EPR steering.
Pragmatic assessment of research intensive areas in cloud
Authors: Hasteer Nitasha , Bansal Abhay , Murthy B. K.
Published: May 2013

Cloud computing is a name given to a set of systems for enabling ubiquitous, convenient, on-demand network access to a shared pool of configurable computing resources (e.g., networks, servers, storage, applications, and services) that can be rapidly provisioned and released with minimal management effort or service provider interaction. Cloud computing is aimed at making an organization more agile and cost effective. Due to the rapid evolution of Cloud Computing in the recent past, it is relevant to investigate the key areas of research of this technology. In this paper, we present a systematic review of research intensive areas in the field of cloud computing. Research papers in the period from 2009 to 2012 were gathered. A total of 36 research papers were reviewed systematically and categorized into four broad categories based on the issues addressed by them. We identified that the majority of the research papers focused on Cloud Security. By systematically analyzing the work accomplished so far, the gaps and yet to be explored areas in this field are brought to light.
Nickel and Its Alloys as Perspective Materials for Intermediate Temperature Steam Electrolysers Operating on Proton Conducting Solid Acids as Electrolyte
Authors: Nikiforov Aleksey Valerievich , Petrushina Irina Mikhajlovna , Jensen Jens Oluf , Bjerrum Niels J
Published: May 2013

Several stainless steels, nickel-based alloys, Ta-coated stainless steel, niobium, nickel, platinum and gold were evaluated as possible materials for use in the intermediate temperature water electrolysers. The corrosion resistance was measured in molten KH2PO4 as simulated conditions corresponding to proton-conducting solid acids or transition metal phosphates as electrolytes. It was shown that Au is subject to corrosion in molten KH2PO4 during polarisation. However, Ni and Ta-coated stainless steel (AISI 316L) demonstrated high corrosion stability and can be recommended as a construction material for bipolar plates and cell housing. It was shown, that nickel, high-nickel alloys and austenitic stainless steels containing small amounts of Ti have high corrosion resistance in this media.
The antifibrotic effect of a serine protease inhibitor in the kidney
Authors: Morinaga Jun , Kakizoe Yutaka , Miyoshi Taku , Onoue Tomoaki , Ueda Miki , Mizumoto Teruhiko , Yamazoe Rika , Uchimura Kohei , Hayata Manabu , Shiraishi Naoki , Adachi Masataka , Sakai Yoshiki , Tomita Kimio , Kitamura Kenichiro
Published: May 2013

Interstitial fibrosis is a final common pathway for the progression of chronic kidney diseases. Activated fibroblasts have an extremely important role in the progression of renal fibrosis, and transforming growth factor (TGF)-β1 is a major activator of fibroblasts. Since previous reports have indicated that serine protease inhibitors have a potential to inhibit TGF-β1 signaling in vitro, we hypothesized that a synthetic serine protease inhibitor, camostat mesilate (CM), could slow the progression of renal fibrosis. TGF-β1 markedly increased the phosphorylation of TGF-β type I receptor, ERK 1/2, and Smad2/3 and the levels of profibrotic markers, such as α-smooth muscle actin (α-SMA), connective tissue growth factor (CTGF), and plasminogen activator inhibitor-1, in renal fibroblasts (NRK-49F cells), and they were all significantly reduced by CM. In protocol 1, 8-wk-old male Sprague-Dawley rats were subjected to unilateral ureteral obstruction (UUO) and were concurrently treated with a slow-release pellet of CM or vehicle for 14 days. Protocol 2 was similar to protocol 1 except that CM was administered 7 days after UUO. CM substantially improved renal fibrosis as determined by sirius red staining, collagen expression, and hydroxyproline levels. The phosphorylation of ERK1/2 and Smad2/3 and the levels of α-SMA, CTGF, promatrix metalloproteinase-2, and matrix metalloproteinase-2 were substantially increased by UUO, and they were all significantly attenuated by CM. These antifibrotic effects of CM were also observed in protocol 2. Our present results suggest the possibility that CM might represent a new class of therapeutic drugs for the treatment of renal fibrosis through the suppression of TGF-β1 signaling.