bluuebunny/crossref_metadata_2025 huggingface dataset:
Different rates of defense evolution and niche preferences in clonal and nonclonal milkweeds (Asclepias spp.)
Authors: Pellissier Loïc , Litsios Glenn , Fishbein Mark , Salamin Nicolas , Agrawal Anurag A. , Rasmann Sergio
Published: September 2015

Given the dual role of many plant traits to tolerate both herbivore attack and abiotic stress, the climatic niche of a species should be integrated into the study of plant defense strategies.

Here we investigate the impact of plant reproductive strategy and components of species' climatic niche on the rate of chemical defense evolution in the milkweeds using a common garden experiment of 49 species.

We found that across Asclepias species, clonal reproduction repeatedly evolved in lower temperature conditions, in species generally producing low concentrations of a toxic defense (cardenolides). Additionally, we found that rates of cardenolide evolution were lower for clonal than for nonclonal species.

We thus conclude that because the clonal strategy is based on survival, long generation times, and is associated with tolerance of herbivory, it may be an alternative to toxicity in colder ecosystems. Taken together, these results indicate that the rate of chemical defense evolution is influenced by the intersection of life‐history strategy and climatic niches into which plants radiate.
Integrating modelling of biodiversity composition and ecosystem function
Authors: Mokany Karel , Ferrier Simon , Connolly Sean R. , Dunstan Piers K. , Fulton Elizabeth A. , Harfoot Michael B. , Harwood Thomas D. , Richardson Anthony J. , Roxburgh Stephen H. , Scharlemann Jörn P. W. , Tittensor Derek P. , Westcott David A. , Wintle Brendan A.
Published: September 2015

There is increasing reliance on ecological models to improve our understanding of how ecological systems work, to project likely outcomes under alternative global change scenarios and to help develop robust management strategies. Two common types of spatiotemporally explicit ecological models are those focussed on biodiversity composition and those focussed on ecosystem function. These modelling disciplines are largely practiced separately, with separate literature, despite growing evidence that natural systems are shaped by the interaction of composition and function. Here we call for the development of new modelling approaches that integrate composition and function, accounting for the important interactions between these two dimensions, particularly under rapid global change. We examine existing modelling approaches that have begun to combine elements of composition and function, identifying their potential contribution to fully integrated modelling approaches. The development and application of integrated models of composition and function face a number of important challenges, including biological data limitations, system knowledge and computational constraints. We suggest a range of promising avenues that could help researchers overcome these challenges, including the use of virtual species, macroecological relationships and hybrid correlative‐mechanistic modelling. Explicitly accounting for the interactions between composition and function within integrated modelling approaches has the potential to improve our understanding of ecological systems, provide more accurate predictions of their future states and transform their management.

Synthesis

There is increasing attention from researchers and policy makers around the world on both assessing and projecting the state of the planet's biodiversity, its ecosystems and the essential services they provide to society. However, existing modelling approaches largely ignore the interactions between biodiversity composition and ecosystem function. We highlight the key challenges and potential solutions to developing integrated models of composition and function. Such models will require a new effort and focus from ecologists, yet the benefits are likely to be substantial, including better informing the management of natural systems at regional, national and international scales.
Pilot Study of Natural Killer Cells in Chronic Fatigue Syndrome/Myalgic Encephalomyelitis and Multiple Sclerosis
Authors: Huth T. K. , Brenu E. W. , Ramos S. , Nguyen T. , Broadley S. , Staines D. , Marshall‐Gradisnik S.
Published: September 2015

Patients with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) and multiple sclerosis (MS) suffer from debilitating fatigue which is not alleviated by rest. In addition to the fatigue‐related symptoms suffered by patients with CFS/ME and MS, dysfunction of the immune system and, in particular, reduced natural killer (NK) cell cytotoxic activity has also been reported in CFS/ME and MS. The purpose of this pilot study was to compare NK cellular mechanisms in patients with CFS/ME and MS to investigate potential dysfunctions in the NK cell activity pathway. Flow cytometry protocols assessed CD56dimCD16+ and CD56brightCD16+/− NK cell expression of adhesion molecules, NK activating and inhibiting receptors, NK cell maturation and lytic proteins. All participants in this study were female and included 14 patients with CFS/ME, nine patients with MS and 19 non‐fatigued controls. The patient groups and the non‐fatigued controls were not taking any immunosuppressive or immune‐enhancing medications. In the MS cohort, KIR2DL5 was significantly increased on CD56brightCD16+/− NK cells and expression of CD94 was significantly increased on CD56dimCD16+ NK cells in comparison with the controls. Co‐expression of CD57 and perforin was significantly increased on CD56dimCD16+ NK cells from patients with CFS/ME compared to the MS and non‐fatigued control participants. The results from this pilot study suggest that NK cells from patients with CFS/ME and MS may have undergone increased differentiation in response to external stimuli which may affect different mechanisms in the NK cell cytotoxic activity pathway.
Complex Shades of Green: Gradually Changing Notions of the ‘Good Farmer’ in aSwedish Context
Authors: Saunders Fred P.
Published: September 2015

There are ever‐growing demands on farmers to consider the wider environmental implications of production, not least in theBalticSeaRegion where concerns about agricultural‐related eutrophication are significant. InSweden, farmers are being nudged through voluntary agro‐environmental measures, enticed by the market and compelled to make the transition from a productivist agriculture to a multifunctional one. Drawing on the ‘good farmer’ concept, inspired by Bourdieu, this article studiesSwedish conventional and agro‐environmental organic farmers' views and reflections on the changing relationship between farming practices and the environment. The article finds that despite 25 years of agro‐environmental policy inSweden, some conventional farmers are still mired in a narrow productivist mindset. That said, the study concludes that we should be wary of conceiving the ‘good farmer’ too strictly in productivist terms, given that the ‘rules of the agricultural game’ inSweden are leading to a more divergent farmer habitus. Farmers are looking for opportunities within the multifunctional agricultural field, which increasingly demands and expects all farmers to embed social and environmental goals into production considerations.
Sequence variations of the locus‐specific 5′ untranslated regions of SLA class I genes and the development of a comprehensive genomic DNA‐based high‐resolution typing method for SLA‐2
Authors: Choi H. , Le M. T. , Lee H. , Choi M.‐K. , Cho H.‐S. , Nagasundarapandian S. , Kwon O.‐J. , Kim J.‐H. , Seo K. , Park J.‐K. , Lee J.‐H. , Ho C.‐S. , Park C.
Published: September 2015

The genetic diversity of the major histocompatibility complex (MHC) class I molecules of pigs has not been well characterized. Therefore, the influence of MHC genetic diversity on the immune‐related traits of pigs, including disease resistance and other MHC‐dependent traits, is not well understood. Here, we attempted to develop an efficient method for systemic analysis of the polymorphisms in the epitope‐binding region of swine leukocyte antigens (SLA) class I genes. We performed a comparative analysis of the last 92 bp of the 5′ untranslated region (UTR) to the beginning of exon 4 of six SLA classical class I‐related genes, SLA‐1, ‐2, ‐3, ‐4, ‐5, and ‐9, from 36 different sequences. Based on this information, we developed a genomic polymerase chain reaction (PCR) and direct sequencing‐based comprehensive typing method for SLA‐2. We successfully typed SLA‐2 from 400 pigs and 8 cell lines, consisting of 9 different pig breeds, and identified 49 SLA‐2 alleles, including 31 previously reported alleles and 18 new alleles. We observed differences in the composition of SLA‐2 alleles among different breeds. Our method can be used to study other SLA class I loci and to deepen our knowledge of MHC class I genes in pigs.
Characterization of a new human monoclonal antibody directed against the Vel antigen
Authors: Danger Y. , Danard S. , Gringoire V. , Peyrard T. , Riou P. , Semana G. , Vérité F.
Published: September 2015

Background and Objectives

The Vel blood group antigen is a poorly characterized high‐prevalence antigen. Until now, anti‐Vel antibodies have been observed in only alloimmunized Vel‐negative individuals. In this study, we aimed to establish a human hybridoma cell line secreting the first anti‐Vel monoclonal antibody (mAb), clone SpG213Dc.

Materials and Methods

Peripheral blood lymphocytes from a French Vel‐negative woman with anti‐Vel in her plasma were transformed with Epstein–Barr virus and then hybridized with the myeloma cell line Sp2/O‐Ag14 using the polyethylene glycol (PEG) method. A specific anti‐Vel mAb was successfully produced and was extensively characterized by serological, flow cytometry and Western blot analyses.

Results

One human anti‐Vel‐secreting clone was produced and the secreted anti‐Vel mAb (SpG213Dc) was examined. The specificity of the SpG213Dc mAb was assessed by its reactivity against a panel of nine genotyped RBCs including, respectively, three Vel‐negative and six Vel‐positive (three wild‐type homozygous and three heterozygous) samples using flow cytometry method. Vel‐positive RBCs were specifically stained and were subsequently used to perform Western blot and immunoprecipitation analysis of the Vel antigen.

Conclusion

Serological characterization of the new monoclonal anti‐Vel SpG213Dc showed a heterogeneous level of expression of the Vel antigen on the different RBCs. Our results suggest that the mAb SpG213Dc can be reliably used as a blood grouping reagent, thus allowing the mass‐scale phenotyping of blood donors to strengthen rare blood banks with Vel‐negative RBC units.
Xenotransplantation and porcine cytomegalovirus
Authors: Denner Joachim
Published: September 2015

Porcine microorganisms may be transmitted to the human recipient when xenotransplantation with pig cells, tissues, and organs will be performed. Most of such microorganisms can be eliminated from the donor pig by specified or designated pathogen‐free production of the animals. As human cytomegalovirus causes severe transplant rejection in allotransplantation, considerable concern is warranted on the potential pathogenicity of porcine cytomegalovirus (PCMV) in the setting of xenotransplantation. On the other hand, despite having a similar name, PCMV is different from HCMV. The impact of PCMV infection on pigs is known; however, the influence of PCMV on the human transplant recipient is unclear. However, first transplantations of pig organs infected with PCMV into non‐human primates were associated with a significant reduction of the survival time of the transplants. Sensitive detection methods and strategies for elimination of PCMV from donor herds are required.
Impact of donor age and weaning status on pancreatic exocrine and endocrine tissue maturation in pigs
Authors: Krishnan Rahul , Truong Nhat , Gerges Marina , Stiewig Miranda , Neel Nicholas , Ho‐Nguyen KhueTu , Kummerfeld Christina , Alexander Michael , Spizzo Tom , Martin Michael , Foster Clarence E. , Monuki Edwin S. , Lakey Jonathan R. T.
Published: September 2015

Background

During the process of islet isolation, pancreatic enzymes are activated and released, adversely affecting islet survival and function. We hypothesize that the exocrine component of pancreases harvested from pre‐weaned juvenile pigs is immature and hence pancreatic tissue from these donors is protected from injury during isolation and prolonged tissue culture.

Methods

Biopsy specimens taken from pancreases harvested from neonatal (5–10 days), pre‐weaned juvenile (18–22 days), weaned juvenile (45–60 days), and young adult pigs (>90 days) were fixed and stained with hematoxylin and eosin. Sections were examined under a fluorescent microscope to evaluate exocrine zymogen fluorescence intensity (ZFI) and under an electron microscope to evaluate exocrine zymogen granule density (ZGD).

Results

Exocrine content estimation showed significantly lower ZFI and ZGD in juvenile pig pancreases (1.5 ± 0.04 U/μm2, ZFI; 1.03 ± 0.07 × 103/100 μm2, ZGD) compared to young adult pigs (2.4 ± 0.05U/μm2, ZFI; 1.53 ± 0.08 × 103/100 μm2 ZGD). Islets in juvenile pig pancreases were on average smaller (105.2 ± 11.2 μm) than islets in young adult pigs (192 ± 7.7 μm), but their insulin content was comparable (80.9 ± 2.2% juvenile; 84.2 ± 0.3% young adult, P > 0.05). All data expressed as mean ± SEM.

Conclusion

Porcine islet xenotransplantation continues to make strides toward utilization in clinical trials of type 1 diabetes. Porcine donor age and weaning status influence the extent of exocrine maturation of the pancreas. Juvenile porcine pancreases may represent an alternative donor source for islet xenotransplantation as their exocrine component is relatively immature; this preserves islet viability during extended tissue culture following isolation.
Cavitation Phenomena and Performance Implications in Archimedes Flow Turbines
Authors: Riglin Jacob D. , Schleicher William C. , Oztekin Alparslan
Published: September 2015

Cavitation produces undesirable effects within turbines, such as noise, decreases in efficiency, and structural degradation of the device. Two microhydro turbines incorporating Archimedean spiral blade geometries were investigated numerically for cavitation effects using computational fluid dynamics (CFD). Separate blade geometries, one with a uniform blade pitch angle and the other with a 1.5 power pitch, were modeled using the Schnerr–Sauer cavitation model. The method used to determine where cavitation occurs along the blade and within the flow involved varying inlet flow rates and the rotation rate of the blade. Cavitation analysis was conducted locally as well as globally, using both cavitation number and Thoma number. The cavitation number was used to correlate the single-phase to the multiphase results for rotation rates of 250 and 500 rpm, allowing for the single-phase simulations to be used to determine where the onset of cavitation occurs. It was determined that cavitation occurred at the exit of the blade at a flow coefficient of approximately 0.33 for the 1.5 pitch blade geometry, while the uniform blade geometry had a value of 1.35. When the rotation rate was reduced to 250 rpm, cavitation occurred at a flow coefficient of 0.72. From the simulations at both rotation rates, it was determined that both geometry and rotation rate have a significant effect on the onset of cavitation and water vapor inception within the flow field. As the rotation rate of the turbine decreases, the onset of cavitation will be prolonged to larger flow coefficients. As the flow coefficient increased beyond the value at which the onset of cavitation occurs, the intensity of cavitation increases and efficiency drops of up to 20% were experienced by the turbines. Based on the net positive suction head required in the system and the available head in the system, the cavitation results were validated. It was determined that the inception cavitation number, Cai, where the onset of cavitation occurs is approximately −1.51.
Development of Three-Dimensional Streamline Image Velocimetry Using Superimposed Delaunay Triangulation and Geometrical Fitting
Authors: Ezra Elishai , Keinan Eliezer , Liberzon Alex , Nahmias Yaakov
Published: September 2015

Flow behavior in complex three-dimensional (3D) microscale domains is the key in the development of microcirculatory pathologies and the design of 3D microfluidics. While numerical simulations are common practice for the derivation of velocity fields in such domains, they are limited to known geometries. Current experimental methods such as micron-scale particle tracing comprise of intricate algorithmic approaches for the accurate tracing of numerous particles in a dense moving liquid suspension and are fundamentally limited in resolution to the finite size of the interrogated steps. Here, we introduce 3D streamlines image velocimetry (3D-SIV), a method to derive fluid velocity fields in arbitrary resolution for fully developed laminar flow in 3D geometries. Our approach utilizes 3D geometrical fitting and superimposed Delaunay triangulation to reconstruct streamtubes and to trace their volumetric changes. Our algorithm has applications in out-of-plane velocimetries, which we demonstrate in a 3D dilated curved geometry and in an ascending aorta. The 3D-SIV can be applied for high-resolution derivation of velocity fields in microcirculatory pathologies and to 3D microfluidic circuits, extending the potential of out-of-plane velocimetries to complex geometries and arbitrary resolution.
Supersonic Liquid Jets Into Quiescent Gaseous Media: An Adaptive Numerical Study
Authors: Majidi Sahand , Afshari Asghar
Published: September 2015

A computational tool is introduced and applied to the emergence of supersonic liquid jets in quiescent compressible gas. A diffuse interface wave propagation method along with an interface sharpening technique is employed to solve the governing equations of compressible multiphase flows. Adaptive mesh refinement (AMR) strategy is utilized to improve the ability of the solver in better resolving the flow features. The accuracy of our method is benchmarked with four experimental and numerical test problems. Then, the evolution of supersonic liquid jets in compressible gaseous media is simulated; demonstrating a good agreement with experimental observations. Moreover, the impact of physical parameters, such as increment in ambient pressure and inlet velocity on the flow characteristics, is examined. The results indicate that the penetration length of the liquid jet decreases with an increase in the ambient pressure. The values of this parameter compare reasonably well with the experiment-based correlations. Further, with lower ambient pressure the Mach cone generated ahead of the liquid jet has a narrower half angle, situated closer to the jet tip. A similar behavior is demonstrated by the induced shock-front when the inlet Mach number of the liquid jet is increased. The simulations indicate the applicability of our numerical methodology to supersonic liquid jet flows for the analysis of shock waves dynamics and shock–interface interaction.
Vision 20/20: Simultaneous CT‐MRI — Next chapter of multimodality imaging
Authors: Wang Ge , Kalra Mannudeep , Murugan Venkatesh , Xi Yan , Gjesteby Lars , Getzin Matthew , Yang Qingsong , Cong Wenxiang , Vannier Michael
Published: September 2015

Multimodality imaging systems such as positron emission tomography‐computed tomography (PET‐CT) and MRI‐PET are widely available, but a simultaneous CT‐MRI instrument has not been developed. Synergies between independent modalities, e.g., CT, MRI, and PET/SPECT can be realized with image registration, but such postprocessing suffers from registration errors that can be avoided with synchronized data acquisition. The clinical potential of simultaneous CT‐MRI is significant, especially in cardiovascular and oncologic applications where studies of the vulnerable plaque, response to cancer therapy, and kinetic and dynamic mechanisms of targeted agents are limited by current imaging technologies. The rationale, feasibility, and realization of simultaneous CT‐MRI are described in this perspective paper. The enabling technologies include interior tomography, unique gantry designs, open magnet and RF sequences, and source and detector adaptation. Based on the experience with PET‐CT, PET‐MRI, and MRI‐LINAC instrumentation where hardware innovation and performance optimization were instrumental to construct commercial systems, the authors provide top‐level concepts for simultaneous CT‐MRI to meet clinical requirements and new challenges. Simultaneous CT‐MRI fills a major gap of modality coupling and represents a key step toward the so‐called “omnitomography” defined as the integration of all relevant imaging modalities for systems biology and precision medicine.
Interrater Reliability of the ENERGY Photo-Rating Instrument for School Environments Related to Physical Activity and Eating
Authors: Altenburg Teatske , Velde Saskia te , Chiu Kai-Jan , Moschonis George , Manios Yannis , De Bourdeaudhuij Ilse , Vik Frøydis N. , Lien Nanna , Brug Johannes , Chinapaw Mai
Published: September 2015

Background:

The school environment can play an important role in the prevention of childhood overweight and obesity. Photos of the school environment may contribute to more adequate measurement of the school environment, as photos can be rated by different assessors. We aimed to examine the interrater reliability for rating characteristics of primary school environments related to physical activity and eating.

Methods:

Photos taken at 172 primary schools in 7 European countries were rated according to a standardized protocol. Briefly, after categorizing all photos in subsections of physical activity or eating opportunities, 2 researchers independently rated aspects of safety, functionality, aesthetics, type of food/drinks advertised, type/variety of foods provided. Interrater reliability was assessed using the intraclass correlation coefficient (ICC) and Cohen’s kappa.

Results:

Six subsections of the photo-rating instrument showed excellent (ICC or Cohen’s kappa ≥0.81) or good (ICC or Cohen’s kappa 0.61 to 0.80) interrater reliability. Outdoor physical activity facilities (ICC = 0.54) showed moderate, and school canteens (Cohen’s kappa = 0.05) and vending machines showed poor (Cohen’s kappa = 0.16) interrater reliability.

Conclusion:

Interrater reliability of the ENERGY (EuropeaN Energy balance Research to prevent excessive weight Gain among Youth) photo-rating instrument was good-to-excellent for 6 out of 9 characteristics of primary school environment components related to physical activity and eating.
Changes in Leisure-Time Physical Activity From the Prepregnancy to the Postpartum Period: 2004 Pelotas (Brazil) Birth Cohort Study
Authors: Coll Carolina , Domingues Marlos , Santos Iná , Matijasevich Alicia , Horta Bernardo Lessa , Hallal Pedro C.
Published: September 2015

Background:

The aim of this study was to evaluate changes in leisure-time physical activity (LTPA) and its correlates from prepregnancy to the postpartum period in mothers enrolled in a Brazilian birth cohort study. Our hypothesis was that LTPA would decline considerably during pregnancy.

Methods:

Maternal LTPA in the 3 months before pregnancy and during each trimester of pregnancy was assessed soon after delivery. A follow-up visit was conducted 3 months later. Weekly frequency and duration of each session of LTPA in a typical week were assessed for each period and a cut-off point of 150 minutes per week was used to classify women as active or not.

Results:

The proportion of women active in leisure time declined from 11.3% in the prepregnancy to 2.3% in pregnancy and 0.1% in the postpartum period (P for trend <0.001). When considering any LTPA practice, the decline ranged from 15.4% to 4.4% and 7.5% (p for trend <0.001), respectively. Higher income, higher education and lower parity were the main predictors of LTPA practice.

Conclusions:

LTPA declined considerably during pregnancy and did not return to prepregnancy levels at 3 months postpartum. Mothers must be advised on the benefits of LTPA prepregnancy, during, and postpregnancy.
Greenlandic Inuit show genetic signatures of diet and climate adaptation
Authors: Fumagalli Matteo , Moltke Ida , Grarup Niels , Racimo Fernando , Bjerregaard Peter , Jørgensen Marit E. , Korneliussen Thorfinn S. , Gerbault Pascale , Skotte Line , Linneberg Allan , Christensen Cramer , Brandslund Ivan , Jørgensen Torben , Huerta-Sánchez Emilia , Schmidt Erik B. , Pedersen Oluf , Hansen Torben , Albrechtsen Anders , Nielsen Rasmus
Published: September 2015

Greenlanders' genomes signal a fatty diet

The evolutionary consequences of inhabiting a challenging environment can be seen within the genomes of Greenland Inuit. Fumagalli
et al.
have found signs of selection for genetic variants in fat metabolism, not just for promoting heat-producing brown fat cells but also for coping with the large amounts of polyunsaturated fatty acids found in their seafood diet (see the Perspective by Tishkoff). Genes under selection in these populations have a strong effect on height and weight of up to 2 cm and 4 kg, respectively, as well as a protective effect on cholesterol and triglyceride levels.

Science
, this issue p.
1343
; see also p.
1282
X-ray–driven reaction front dynamics at calcite-water interfaces
Authors: Laanait Nouamane , Callagon Erika B. R. , Zhang Zhan , Sturchio Neil C. , Lee Sang Soo , Fenter Paul
Published: September 2015

Driving dissolution with x-rays

Carbonate minerals are important for Earth's carbon cycle. They precipitate directly from solution into diverse materials, depending on their physical or biological source. Whether carbonate minerals grow or dissolve is controlled by the thermodynamic drivers of the mineral/water interface. To control and observe the reactions, Lanaait
et al.
developed a synchrotron x-ray technique that images calcium carbonate surfaces in water and selectively tunes the solution saturation state (see the Perspective by Wolthers). The x-ray beam drives fast-moving reaction fronts far from equilibrium that are more limited by solution-ion transport than by surface processes.

Science
, this issue p.
1330
; see also p.
1288
Dengue viruses cluster antigenically but not as discrete serotypes
Authors: Katzelnick Leah C. , Fonville Judith M. , Gromowski Gregory D. , Arriaga Jose Bustos , Green Angela , James Sarah L. , Lau Louis , Montoya Magelda , Wang Chunling , VanBlargan Laura A. , Russell Colin A. , Thu Hlaing Myat , Pierson Theodore C. , Buchy Philippe , Aaskov John G. , Muñoz-Jordán Jorge L. , Vasilakis Nikos , Gibbons Robert V. , Tesh Robert B. , Osterhaus Albert D.M.E. , Fouchier Ron A.M. , Durbin Anna , Simmons Cameron P. , Holmes Edward C. , Harris Eva , Whitehead Stephen S. , Smith Derek J.
Published: September 2015

The devil in the dengue details

Along with their mosquito vectors, dengue viruses are spreading worldwide to infect millions of people. For a few, subsequent infection results in lethal hemorrhagic disease. Katzelnick
et al.
used antibody-binding data to map structural divergence and antigenic variation among dengue viruses. Comparing results in monkeys and humans, the viruses approximately clustered into the four known groups. However, the four virus groups showed as much antigenic distance within a group as between groups. This finding helps explain why immune responses to dengue are highly variable, and it has complex implications for epidemiology, disease, and vaccine deployment.

Science
, this issue p.
1338
Making contacts count
Networking for Nerds
Find, Access and Land Hidden Game-Changing Career Opportunities Everywhere
Alaina G. Levine
Wiley Blackwell, 2015. 225 pp..
Authors: Magoń Monika S.
Published: September 2015

A scientist's guide to building professional networks
Genome Assemblies for 11 Yersinia pestis Strains Isolated in the Caucasus Region
Authors: Zhgenti Ekaterine , Johnson Shannon L. , Davenport Karen W. , Chanturia Gvantsa , Daligault Hajnalka E. , Chain Patrick S. , Nikolich Mikeljon P.
Published: September 2015

Yersinia pestis
, the causative agent of plague, is endemic to the Caucasus region but few reference strain genome sequences from that region are available. Here, we present the improved draft or finished assembled genomes from 11 strains isolated in the nation of Georgia and surrounding countries.
De Novo
Genome Sequence of Yersinia aleksiciae Y159
T
Authors: Sprague Lisa D. , Neubauer Heinrich
Published: September 2015

We report here on the genome sequence of
Yersinia aleksiciae
Y159
T
, isolated in Finland in 1981. The genome has a size of 4 Mb, a G+C content of 49%, and is predicted to contain 3,423 coding sequences.
Genome Sequence of Bradyrhizobium pachyrhizi Strain PAC48
T
, a Nitrogen-Fixing Symbiont of
Pachyrhizus erosus
(L.) Urb
Authors: Delamuta Jakeline Renata Marçon , Ribeiro Renan Augusto , Gomes Douglas Fabiano , Souza Renata Carolina , Chueire Ligia Maria Oliveira , Hungria Mariangela
Published: September 2015

Bradyrhizobium pachyrhizi
PAC48
T
has been isolated from a jicama nodule in Costa Rica. The draft genome indicates high similarity with that of
Bradyrhizobium elkanii
. Several coding sequences (CDSs) of the stress response might help in survival in the tropics. PAC48
T
carries
nodD1
and
nodK
, similar to
Bradyrhizobium
(
Parasponia
) ANU 289 and a particular
nodD2
gene.
Draft Genome Sequences of Five Clinical Enterococcus cecorum Strains Isolated from Different Poultry Species in Poland
Authors: Dolka Beata , Heidemann Olsen Rikke , Naundrup Thøfner Ida Cecilie , Christensen Jens Peter
Published: September 2015

Here, we report five draft genome sequences of
Enterococcus cecorum
strains that were isolated from different bird species of affected poultry flocks (commercial broilers [CB], broiler breeders [BB], commercial layers [CL], ducks [D], and geese [G]) in Poland.
Uterine size and ovarian size in adolescents with functional hypothalamic amenorrhoea
Authors: Bumbuliene Zana , Klimasenko Jelena , Sragyte Diana , Zakareviciene Jolita , Drasutiene Grazina
Published: September 2015

Introduction

Functional hypothalamic amenorrhoea (FHA) is a condition characterised by the absence of menses due to suppression of the hypothalamic-pituitary-ovarian axis.

Objective

The purpose of the study was to estimate uterine and ovarian sizes in adolescents with FHA and to compare these results with findings in peers having regular menstrual cycles.

Design

Prospective case-controlled study.

Settings

Vilnius University Hospital Santariskiu Klinikos, Lithuania.

Patients

Lithuanian adolescents—45 with FHA and 40 comparison group participants.

Main outcome measures

We assessed ultrasound measurements of internal reproductive organs, levels of luteinising hormone, follicle-stimulating hormone, prolactin, oestradiol and calculated body mass index (BMI).

Results

The mean age of the participants was 16.3±1.2 years, the mean age after menarche—3.6 years. In adolescents with FHA the BMI was 17.8±1.8 kg/m2 and 20.4±1.4 kg/m2 in the comparison group, p<0.001. The uterine volume (14.7±6.3 cm3 vs 31.7±10.6 cm3, p<0.001), cervical length (2.3±0.4 cm vs 2.6±0.5 cm, p=0.03), volume of both ovaries (9.3±3.6 cm3 vs 13.8±4.3 cm3, p<0.001) and levels of LH (2.70±2.59 vs 6.01±2.44, p<0.001) were significantly lower in girls with FHA. A significantly positive correlation between volume of uterus and levels of LH (r=0.415; p<0.001) was found. We identified a positive correlation between uterine volume, uterine corpus length, cervical length, ovarian volume and weight, BMI.

Conclusions

In adolescents with FHA the dimensions of uterus and ovaries were smaller than in girls having regular menstrual cycles. Our study confirmed the influence of oestrogen on uterus size: oestrogen deficiency causes a reduction in uterine size. Uterine size and ovarian size correlate positively with BMI.
Abstracts from international Emergency Medicine journals
Authors: Weber Ellen J
Published: September 2015

Editor's note:EMJhas partnered with the journals of multiple international emergency medicine societies to share from each a highlighted research study, as selected by their editors.
Enhancing a 32-Bit Processor Core with Efficient Cryptographic Instructions
Authors: Benhadjyoussef Noura , Elhadjyoussef Wajih , Machhout Mohsen , Tourki Rached , Torki Kholdoun
Published: September 2015

Embedded processor is often expected to achieve a higher security with good performance and economical use of resource. However, the choice regarding the best solution for how cryptographic algorithms are incorporated in processor core is one of the most challenging assignments a designer has to face. This paper presents an inexpensive instruction set extensions (ISE) of efficient cryptographic algorithms on 32-bit processors assuring various types of instruction (public/private key cryptography, random number generator (RNG) and secure hash function (SHF)). These extensions provide hardware instructions that implement a full algorithm in a single instruction. Our enhanced LEON2 SPARC V8 core with cryptographic ISE is implemented using Xilinx XC5VFX70t FPGA device and an ASIC CMOS 40-nm technology. The total area of the resulting chip is about 1.93 mm2 and the estimated power consumption of the chip is 16.3 mW at 10 MHz. Hardware cost and power consumption evaluation are provided for different clock frequencies and the achieved results show that our circuit is able to be arranged in many security constrained devices.
Design and Analysis of 32-Bit CLA Using Energy Efficient Adiabatic Logic for Ultra-Low-Power Application
Authors: Chanda Manash , De Swapnadip , Sarkar Chandan Kumar
Published: September 2015

This paper shows that a conventional semi-custom design-flow based on a energy efficient adiabatic logic (EEAL) cell library allows any VLSI designer to design and verify complex adiabatic arithmetic units in a simple way, thus, enjoying the energy reduction benefits of adiabatic logic. A family of semi-custom EEAL-based 32-bit carry-lookahead adder (CLA) has been designed in a TSMC 90-nm CMOS process technology and verified by CADENCE Design suite. Differential cascode voltage swing (DCVS) logic has been used to implement the newly proposed EEAL and it uses only a sinusoidal clock supply to ensure correct operation. Post-layout simulations show that semi-custom adiabatic arithmetic units can save significant amount of energy, as compared to the previously reported single clocked adiabatic logic and logically equivalent static CMOS implementation. Extensive CADENCE simulations have been done for the verification of the functionality of the proposed logic structure.
Reconstructing Software High-Level Architecture by Clustering Weighted Directed Class Graph
Authors: Qiu Dehong , Zhang Qifeng , Fang Shaohong
Published: September 2015

Software architecture reconstruction plays an important role in software reuse, evolution and maintenance. Clustering is a promising technique for software architecture reconstruction. However, the representation of software, which serves as clustering input, and the clustering algorithm need to be improved in real applications. The representation should contain appropriate and adequate information of software. Furthermore, the clustering algorithm should be adapted to the particular demands of software architecture reconstruction well. In this paper, we first extract Weighted Directed Class Graph (WDCG) to represent object-oriented software. WDCG is a structural and quantitative representation of software, which contains not only the static information of software source code but also the dynamic information of software execution. Then we propose a WDCG-based Clustering Algorithm (WDCG-CA) to reconstruct high-level software architecture. WDCG-CA makes full use of the structural and quantitative information of WDCG, and avoids wrong compositions and arbitrary partitions successfully in the process of reconstructing software architecture. We introduce four metrics to evaluate the performance of WDCG-CA. The results of the comparative experiments show that WDCG-CA outperforms the comparative approaches in most cases in terms of the four metrics.
Generation of Business Event Data Sets for Testing RFID Information Services
Authors: Kim Gihong , Hong Bonghee
Published: September 2015

The testing of RFID information services requires a test data set of business events comprising object, aggregation, quantity and transaction events. To generate business events, we need to address the performance issues in creating a large volume of event data. This paper proposes a new model for the tag life cycle and a fast generation algorithm for this model. We present the results of experiments with the generation algorithm, showing that it outperforms previous methods.
Dynamics of a planar thin shell at a Taub–FRW junction
Authors: Acuña Jan Tristram , Esguerra Jose Perico
Published: September 2015

We address the problem of stitching together the vacuum, static, planar-symmetric Taub spacetime and the flat Friedmann–Robertson–Walker (FRW) cosmology using the Israel thin shell formalism. The joining of Taub and FRW spacetimes is reminiscent of the Oppenheimer–Snyder collapse used in modeling the formation of a singularity from a collapsing spherical ball of dust. A possible mechanism for the formation of a planar singularity is provided. It is hoped that tackling such example will improve our intuition on planar-symmetric systems in Einstein’s general relativity (GR).
The effect of asthma on the perimeter of the airway basement membrane
Authors: Elliot John G. , Budgeon Charley A. , Harji Salima , Jones Robyn L. , James Alan L. , Green Francis H.
Published: September 2015

When comparing the pathology of airways in individuals with and without asthma, the perimeter of the basement membrane (Pbm) is used as a marker of airway size, as it is independent of airway smooth muscle shortening or airway collapse. The extent to which the Pbm is itself altered in asthma has not been quantified. The aim of this study was to compare the Pbm from the same anatomical sites in postmortem lungs from subjects with ( n = 55) and without ( n = 30) asthma (nonfatal or fatal). Large and small airways were systematically sampled at equidistant “levels” from the apical segment of the left upper lobes and anterior and basal segments of the left lower lobes of lungs fixed in inflation. The length of the Pbm was estimated from cross sections of airway at each relative level. Linear mixed models were used to investigate the relationships between Pbm and sex, age, height, smoking status, airway level, and asthma group. The final model showed significant interactions between Pbm and airway level in small (<3 mm) airways, in subjects having asthma ( P < 0.0001), and by sex ( P < 0.0001). No significant interactions for Pbm between asthma groups were observed for larger airways (equivalent to a diameter of ∼3 mm and greater) or smoking status. Asthma is not associated with remodeling of the Pbm in large airways. In medium and small airways, the decrease in Pbm in asthma (≤20%) would not account for the published differences in wall area or area of smooth muscle observed in cases of severe asthma.
A New Scene Classification Method Based on Local Gabor Features
Authors: Dong Baoyu , Ren Guang
Published: September 2015

A new scene classification method is proposed based on the combination of local Gabor features with a spatial pyramid matching model. First, new local Gabor feature descriptors are extracted from dense sampling patches of scene images. These local feature descriptors are embedded into a bag-of-visual-words (BOVW) model, which is combined with a spatial pyramid matching framework. The new local Gabor feature descriptors have sufficient discrimination abilities for dense regions of scene images. Then the efficient feature vectors of scene images can be obtained byK-means clustering method and visual word statistics. Second, in order to decrease classification time and improve accuracy, an improved kernel principal component analysis (KPCA) method is applied to reduce the dimensionality of pyramid histogram of visual words (PHOW). The principal components with the bigger interclass separability are retained in feature vectors, which are used for scene classification by the linear support vector machine (SVM) method. The proposed method is evaluated on three commonly used scene datasets. Experimental results demonstrate the effectiveness of the method.
Multiplex H. pylori Serology and Risk of Gastric Cardia and Noncardia Adenocarcinomas
Authors: Shakeri Ramin , Malekzadeh Reza , Nasrollahzadeh Dariush , Pawilta Michael , Murphy Gwen , Islami Farhad , Sotoudeh Masoud , Michel Angelika , Etemadi Arash , Waterboer Tim , Poustchi Hossein , Brennan Paul , Boffetta Paolo , Dawsey Sanford M. , Kamangar Farin , Abnet Christian C.
Published: September 2015

The reported associations with gastric adenocarcinoma and seropositivity to different Helicobacter pylori antigens using multiplex serology have not been consistent across studies. We aimed to investigate the association between 15 different multiplex serology antigens and the risk of gastric cardia (GCA) and gastric noncardia (GNCA) adenocarcinomas in northeastern Iran, a population with high rates of gastric adenocarcinoma. We included 272 cases of gastric adenocarcinoma (142 GCA, 103 GNCA, and 27 unspecified) and 524 controls who were individually matched to cases for age, sex, and place of residence in a population-based case–control study. Seropositivity to H. pylori was assessed using both multiplex serology and H. pylori IgG ELISA. Ninety-five percent of controls were seropositive to H. pylori. Of the 15 antibodies in the multiplex assay, 11 showed no significant association with gastric adenocarcinomas. CagA and VacA were associated with a significantly increased risk of all gastric adenocarcinoma and GNCA in multivariate models. Surprisingly, GroEL and NapA were significantly associated with a reduced risk of these tumors. Only CagA antigen was associated with significantly elevated risk of GCA. We found no associations between H. pylori seropositivity overall either by whole-cell ELISA test or multiplex serology, likely due to the high prevalence of seropositivity. Individual antigen testing showed that CagA positivity was associated with increased risk of both noncardia and cardia adenocarcinoma, which is similar to some other Asian populations, whereas two antigens were associated with lower risk of gastric cancer. This latter result was unexpected and should be retested in other populations. Cancer Res; 75(22); 4876–83. ©2015 AACR.
Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid
Authors: Castells Xavier , Karanović Sandra , Ardin Maude , Tomić Karla , Xylinas Evanguelos , Durand Geoffroy , Villar Stephanie , Forey Nathalie , Le Calvez-Kelm Florence , Voegele Catherine , Karlović Krešimir , Mišić Maja , Dittrich Damir , Dolgalev Igor , McKay James , Shariat Shahrokh F. , Sidorenko Viktoria S. , Fernandes Andrea , Heguy Adriana , Dickman Kathleen G. , Olivier Magali , Grollman Arthur P. , Jelaković Bojan , Zavadil Jiri
Published: September 2015

Background: Dietary exposure to cytotoxic and carcinogenic aristolochic acid (AA) causes severe nephropathy typically associated with urologic cancers. Monitoring of AA exposure uses biomarkers such as aristolactam-DNA adducts, detected by mass spectrometry in the kidney cortex, or the somatic A>T transversion pattern characteristic of exposure to AA, as revealed by previous DNA-sequencing studies using fresh-frozen tumors.

Methods: Here, we report a low-coverage whole-exome sequencing method (LC-WES) optimized for multisample detection of the AA mutational signature, and demonstrate its utility in 17 formalin-fixed paraffin-embedded urothelial tumors obtained from 15 patients with endemic nephropathy, an environmental form of AA nephropathy.

Results: LC-WES identified the AA signature, alongside signatures of age and APOBEC enzyme activity, in 15 samples sequenced at the average per-base coverage of approximately 10×. Analysis at 3 to 9× coverage revealed the signature in 91% of the positive samples. The exome-wide distribution of the predominant A>T transversions exhibited a stochastic pattern, whereas 83 cancer driver genes were enriched for recurrent nonsynonymous A>T mutations. In two patients, pairs of tumors from different parts of the urinary tract, including the bladder, harbored overlapping mutation patterns, suggesting tumor dissemination via cell seeding.

Conclusions: LC-WES analysis of archived tumor tissues is a reliable method applicable to investigations of both the exposure to AA and its biologic effects in human carcinomas.

Impact: By detecting cancers associated with AA exposure in high-risk populations, LC-WES can support future molecular epidemiology studies and provide evidence-base for relevant preventive measures. Cancer Epidemiol Biomarkers Prev; 24(12); 1873–81. ©2015 AACR.
Prediagnostic Plasma Adiponectin and Survival among Patients with Colorectal Cancer
Authors: Chong Dawn Q. , Mehta Raaj S. , Song Mingyang , Kedrin Dmitriy , Meyerhardt Jeffrey A. , Ng Kimmie , Wu Kana , Fuchs Charles S. , Giovannucci Edward L. , Ogino Shuji , Chan Andrew T.
Published: September 2015

Circulating adiponectin is inversely related to the risk of colorectal cancer. However, its influence on colorectal cancer survival is unclear. We conducted a prospective study to evaluate the association between prediagnostic plasma levels of adiponectin and mortality in patients with colorectal cancer. We identified 621 incident colorectal cancer cases who provided blood specimens prior to diagnosis within the Nurses' Health Study (NHS) and Health Professionals Follow-up Study (HPFS). Cox proportional hazards models were used to calculate HRs and 95% confidence intervals (CI). After a median follow-up of 9 years, there were 269 (43%) total deaths, of which 181 (67%) were due to colorectal cancer. Compared with participants in the lowest quartile of adiponectin, those in the highest quartile had multivariate HRs of 1.89 (95% CI, 1.21–2.97; Ptrend = 0.01) for colorectal cancer–specific mortality and 1.66 (95% CI, 1.15–2.39; Ptrend = 0.009) for overall mortality. The apparent increased risk in colorectal cancer–specific mortality was more pronounced in patients with metastatic disease (HR, 3.02: 95% CI, 1.50–6.08). Among patients with colorectal cancer, prediagnostic plasma adiponectin is associated with an increased risk of colorectal cancer–specific and overall mortality and is more apparent in patients with metastatic disease. Adiponectin may be a marker for cancers which develop through specific pathways that may be associated with worsened prognosis. Further studies are needed to validate these findings. Cancer Prev Res; 8(12); 1138–45. ©2015 AACR.