bluuebunny/crossref_metadata_2025 huggingface dataset:
EFFECTIVE CLARIFICATION OF POMEGRANATE JUICE USING LACCASE TREATMENT OPTIMIZED BY RESPONSE SURFACE METHODOLOGY FOLLOWED BY ULTRAFILTRATION
Authors: NEIFAR MOHAMED , ELLOUZE‐GHORBEL RAOUDHA , KAMOUN AMEL , BAKLOUTI SEMIA , MOKNI ABIR , JAOUANI ATEF , ELLOUZE‐CHAABOUNI SEMIA
Published: October 2009

Phenolic compounds of pomegranate juice, which are responsible for haze formation and browning during storage, could be selectively removed by combined enzyme‐ultrafiltration process. The pomegranate juice was treated with Fomes fomentarius laccase at various enzyme concentrations (0.5–5 U/mL), temperatures (20–50C) and times (30–300 min). The effect of these enzymatic treatments on total phenol content and clarity of the juice were evaluated using a central composite design. The optimum treatment conditions were: enzyme concentration 5 U/mL; time 300 min; and temperature 20C. Their application led to a 40% reduction of total phenols but induced a threefold decrease of the juice clarity. This drawback was overcome by ultrafiltration of the laccase‐treated juice. The pomegranate juice obtained was clear, stable and characterized by total phenolics = 864 mg/L, clarity (A650 nm × 1,000) = 86 and color (A420 nm × 1,000) = 236 versus 1,681, 127 and 382, respectively, for untreated juice.

PRACTICAL APPLICATIONS

The tendency for hazes to develop in pomegranate juices during storage is a persistent problem in the fruit juice industry. In this work, laccase treatment optimized by response surface methodology followed by ultrafiltration was used to clarify the pomegranate juice. The application of the optimum enzymatic treatment conditions (enzyme concentration 5 U/mL; time 300 min; and temperature 20C) followed by ultrafiltration (cutoff value 15 KDa) decreases the total phenolics of about 50% and the antioxidant capacity of about 20% and, increases the clarity of about 30% versus untreated juice.
Do scattered white spots in the duodenum mark a specific gastrointestinal pathology?
Authors: BIYIKOĞLU İbrahim , BABALI Ayşegül , ÇAKAL Başak , KÖKLÜ Seyfettin , FILIK Levent , ASTARCI Müzeyyen H , ÜSTÜN Hüseyin , ÜSTÜNDAĞ Yücel , AKBAL ERDEM
Published: October 2009

OBJECTIVE:  To discover whether scattered white spots (SWS) in the duodenum are related to a specific kind of disease. We also scrutinized other upper endoscopic findings which might be associated with SWS.

METHODS:  Among the patients who were admitted for upper gastrointestinal system endoscopy, those having the endoscopic appearance of SWS in duodenum were enrolled in this study. In total 107 patients [70 women, 37 men, mean age: 51.6 ± 16.88 years (range: 17–82 years)] were included. At least three duodenal biopsies were taken from each patient and histopathological examinations were done by experienced pathologists.

RESULTS:  The histopathological examination revealed that 39 (36.4%) patients had intestinal lymphangiectasia (IL), 15 (14%) patients had giardiasis (G) and 30 (28.1%) patients had chronic non‐specific duodenitis (CD). Two patients with IL were also found to have G. Twenty patients had both IL and CD. One had both G and CD. G was the least common etiology for SWS in the duodenum. The most common reasons for SWS in the duodenum in this study group were IL and CD, in order of decreasing frequency. There was no significant relationship with the other upper endoscopic findings in all these patients.

CONCLUSION:  Histopathological examinations should be provided for each patient with SWS in the duodenum to assess the etiology.
Clinical features and spiral computed tomography analysis of undifferentiated embryonic liver sarcoma in adults
Authors: YANG Lian , CHEN Li Bo , XIAO Jie , HAN Ping
Published: October 2009

OBJECTIVE:  To summarize the clinical and spiral computed tomography (CT) features of undifferentiated embryonic liver sarcoma (UELS) in adults.

METHODS:  Clinical and CT findings of four adult patients with pathology‐approved UELS were retrospectively analyzed with a literature review. All patients were examined using a plain and enhanced spiral CT scan.

RESULTS:  The participants were two men and two women with a mean age of 36.5 years. The clinical manifestations were the right upper quadrant mass, pain (n= four) and intermittent fever (n= three). Laboratory tests showed a mild elevation of alpha‐fetoprotein in one patient and mildly abnormal liver function in two. Liver cirrhosis was present in one patient coexistent with hepatocellular carcinoma. CT findings indicated a huge well‐defined cystic‐solid mass with varying degrees of enhancement of the solid component. Irregular high‐density lesions showing hemorrhage occurred in three patients and the inferior vena cava was compressed in one.

CONCLUSION:  UELS showed a solitary and predominantly cystic or multicystic appearance on CT imaging compared with ultrasound (US) from the medical literature, which shows a predominantly hypoechoic mass. The laboratory tests were normal or mildly abnormal despite the presence of the large mass. The combination of these clinical features and CT findings together with those of US are helpful in making a prospective diagnosis.
Nonalcoholic fatty liver disease: Quantitative assessment of liver fat content by computed tomography, magnetic resonance imaging and proton magnetic resonance spectroscopy
Authors: ZHONG Liang , CHEN Jie Jun , CHEN Jie , LI Lei , LIN Zhi Qian , WANG Wen Jing , XU Jian Rong
Published: October 2009

OBJECTIVE:  The purpose of this study was to evaluate the clinical application of imaging technology in the quantitative assessment of fatty liver with magnetic resonance imaging (MRI) and proton MR spectroscopy.

METHODS:  Overall 36 patients with diffuse fatty liver who had undertaken the computed tomography (CT) scan, MRI and proton MR spectroscopy (1H MRS) were analyzed. Their body mass index (BMI) was measured and their liver to spleen CT ratio (L/S) calculated on the plain CT scan. MR T1‐weighted imaging (T1WI) was obtained with in‐phase (IP) and out‐of‐phase (OP) images. T2‐weighted imaging (T2WI) was acquired with or without the fat‐suppression technique. The liver fat content (LFC) was quantified as the percentage of relative signal intensity loss on T1WI or T2WI images. The intrahepatic content of lipid (IHCL) was expressed as the percentage of peak value ratio of lipid to water by 1H MRS.

RESULTS:  The results of BMI measurement, CT L/S ratio, LFC calculated from MR T1WI and T2WI images, as well as IHCL measured by 1H MRS were 27.26 ± 3.01 kg/m2, 0.88 ± 0.26, 13.80 ± 9.92%, 40.67 ± 16.04% and 30.98 ± 20.43%, respectively. The LFC calculated from MR T1WI, T2WI images and IHCL measured by 1H MRS correlated significantly with the CT L/S ratio (r=−0.830, P= 0.000; r=−0.736, P= 0.000; r=−0.461, P= 0.005, respectively). BMI correlated significantly only with the liver fat contents measured by T1WI IP/OP and 1H MRS (r=−0.347, P= 0.038; r=−0.374, P= 0.025, respectively).

CONCLUSION:  CT, MR imaging and 1H MRS were effective methods for the quantitative assessment of LFC. The MR imaging, especially 1H MRS, would be used more frequently in the clinical evaluation of fatty liver and 1H MRS could more accurately reflect the severity of fatty liver.
Randomization in the Design of Experiments
Authors: Cox D. R.
Published: October 2009

A general review is given of the role of randomization in experimental design. Three objectives are distinguished, the avoidance of bias, the establishment of a secure base for the estimation of error in traditional designs, and the provision of formally exact tests of significance and confidence limits. The approximate randomization theory associated with analysis of covariance is outlined and conditionality considerations are used to explain the limited role of randomization in experiments with very small numbers of experimental units. The relation between the so‐called design‐based and model‐based analyses is discussed. Corresponding results in sampling theory are mentioned briefly.
The Coverage Properties of Confidence Regions After Model Selection
Authors: Kabaila Paul
Published: October 2009

It is very common in applied frequentist (“classical”) statistics to carry out a preliminary statistical (i.e. data‐based) model selection by, for example, using preliminary hypothesis tests or minimizing AIC. This is usually followed by the inference of interest, using the same data, based on the assumption that the selected model had been given to us a priori. This assumption is false and it can lead to an inaccurate and misleading inference. We consider the important case that the inference of interest is a confidence region. We review the literature that shows that the resulting confidence regions typically have very poor coverage properties. We also briefly review the closely related literature that describes the coverage properties of prediction intervals after preliminary statistical model selection. A possible motivation for preliminary statistical model selection is a wish to utilize uncertain prior information in the inference of interest. We review the literature in which the aim is to utilize uncertain prior information directly in the construction of confidence regions, without requiring the intermediate step of a preliminary statistical model selection. We also point out this aim as a future direction for research.
The Intra‐Cluster Correlation Coefficient in Cluster Randomized Trials: A Review of Definitions
Authors: Eldridge Sandra M. , Ukoumunne Obioha C. , Carlin John B.
Published: October 2009

The intra‐cluster correlation coefficient (ICC) of the primary outcome plays a key role in the design and analysis of cluster randomized trials (CRTs), but the precise definition of this parameter is somewhat elusive, especially in the context of non‐normally distributed outcomes. In this paper, we provide a unified treatment of ICC as used in CRTs. We present a general definition of the ICC that may be expressed in different ways depending on the modelling approach used to describe the data, illustrating how this general definition is applied to continuous and dichotomous outcomes. Greater complexity arises for dichotomous outcomes; in particular, the usual definition of the ICC cannot be related directly to the parameters of the logistic‐normal model that is commonly used for dichotomous outcomes. We show how the definition of the ICC is different when covariates are introduced. Finally, we use our framework and definition of the ICC to draw out implications for those interpreting and choosing values of the ICC when planning CRTs.
The Effects of Resistance Training on Metabolic Health With Weight Regain
Authors: Warner Shana O. , Linden Melissa A. , Liu Ying , Harvey Benjamin R. , Thyfault John P. , Whaley‐Connell Adam T. , Chockalingam Anand , Hinton Pamela S. , Dellsperger Kevin C. , Thomas Tom R.
Published: October 2009

J Clin Hypertens (Greenwich). 2010;12:64–72. ©2009 Wiley Periodicals, Inc.

To determine whether resistance training effectively maintains improvements in cardiometabolic syndrome risk factors during weight regain, 9 individuals lost 4% to 6% of their body weight during an 8‐ to 12‐week diet‐ and aerobic exercise–induced weight loss phase followed by a controlled weight regain phase (8–12 weeks), during which they regained approximately 50% of the lost weight while participating in a supervised resistance training program. Following weight loss (6.0%±0.3%), body mass index, body fat percentage, waist circumference, all abdominal adipose tissue depots, total cholesterol, low‐density lipoprotein cholesterol, insulin, and homeostasis model assessment (HOMA) were significantly reduced, while quantitative insulin‐sensitivity check index (QUICKI) and cardiorespiratory fitness (maximal oxygen consumption) significantly increased. During weight regain (48.3%±3.3% of lost weight), body fat percentage, waist circumference, and maximal oxygen consumption were maintained and muscular strength and lean body mass significantly increased. Abdominal adipose tissue depots, insulin, HOMA, and QUICKI did not significantly change after weight regain. Resistance training was effective in maintaining improvements in metabolic health during weight regain.
Modeling the Hydrology of Climate Change in California’s Sierra Nevada for Subwatershed Scale Adaptation1
Authors: Young Charles A. , Escobar‐Arias Marisa I. , Fernandes Martha , Joyce Brian , Kiparsky Michael , Mount Jeffrey F. , Mehta Vishal K. , Purkey David , Viers Joshua H. , Yates David
Published: October 2009

Young, Charles A., Marisa I. Escobar‐Arias, Martha Fernandes, Brian Joyce, Michael Kiparsky, Jeffrey F. Mount, Vishal K. Mehta, David Purkey, Joshua H. Viers, and David Yates, 2009. Modeling the Hydrology of Climate Change in California’s Sierra Nevada for Subwatershed Scale Adaptation. Journal of the American Water Resources Association (JAWRA) 45(6):1409‐1423.

Abstract:  The rainfall‐runoff model presented in this study represents the hydrology of 15 major watersheds of the Sierra Nevada in California as the backbone of a planning tool for water resources analysis including climate change studies. Our model implementation documents potential changes in hydrologic metrics such as snowpack and the initiation of snowmelt at a finer resolution than previous studies, in accordance with the needs of watershed‐level planning decisions. Calibration was performed with a sequence of steps focusing sequentially on parameters of land cover, snow accumulation and melt, and water capacity and hydraulic conductivity of soil horizons. An assessment of the calibrated streamflows using goodness of fit statistics indicate that the model robustly represents major features of weekly average flows of the historical 1980‐2001 time series. Runs of the model for climate warming scenarios with fixed increases of 2°C, 4°C, and 6°C for the spatial domain were used to analyze changes in snow accumulation and runoff timing. The results indicated a reduction in snowmelt volume that was largest in the 1,750‐2,750 m elevation range. In addition, the runoff center of mass shifted to earlier dates and this shift was non‐uniformly distributed throughout the Sierra Nevada. Because the hydrologic model presented here is nested within a water resources planning system, future research can focus on the management and adaptation of the water resources system in the context of climate change.
Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds
Authors: PATEL SELINA , WAUGH JOHN , MILLAR CRAIG D. , LAMBERT DAVID M.
Published: October 2009

Our ability to DNA barcode the birds of the world is based on the effective amplification and sequencing of a 648 base pair (bp) region of the mitochondrial cytochromecoxidase (COI orcox1) gene. For many geographic regions the large numbers of vouchered specimens necessary for the construction of a DNA barcoding database have already been collected and are available in museums and other institutions. However, many of these specimens are old (>20 years) and are stored as either fixed study skins or dried skeletons. DNA extracted from such historical samples is typically degraded and, generally, only short DNA fragments can be recovered from such specimens making the recovery of the barcoding region as a single fragment difficult. We report two sets of conserved primers that allow the amplification of the entire DNA barcoding region in either three or five overlapping fragments. These primer sets allow the recovery of DNA barcodes from valuable historical specimens that in many cases are unique in that they are unable or unlikely to be collected again. We also report three new primers that in combination allow the effective amplification from modern samples of the entire DNA barcoding region as a single DNA fragment for 17 orders of Southern Hemisphere birds.
Prevalence of major eye diseases and causes of visual impairment in the adult Finnish population: a nationwide population‐based survey
Authors: Laitinen Arja , Laatikainen Leila , Härkänen Tommi , Koskinen Seppo , Reunanen Antti , Aromaa Arpo
Published: October 2009

Purpose:  To estimate the prevalence of cataract, glaucoma, age‐related maculopathy (ARM) and diabetic retinopathy (DR) in the adult Finnish population.

Methods:  A representative cross‐sectional sample of the Finnish population aged 30 years and older. Of the 7979 eligible people, 7413 (93%) were interviewed and/or examined. The interview included self‐reported doctor‐made diagnoses of cataract, glaucoma, degenerative fundus changes (mainly ARM) or DR. Information on self‐reported eye diseases was complemented with data from national registers, and case records were gathered for non‐participants and persons with visual acuity (VA) < 0.5 or reporting difficulties in vision or eye diseases without assessed VA.

Results:  Based on self‐reported and/or register‐based data the estimated total prevalences of cataract, glaucoma, ARM and DR in the study population were 10%, 5%, 4% and 1%, respectively. All these chronic eye diseases increased with age (p < 0.001). The corresponding prevalences for persons aged 65 and older were 34%, 13%, 12% and 2%, respectively. Cataract and glaucoma were more common in women than in men [odds ratio (OR) 1.55, 95% confidence interval (CI) 1.26–1.91; OR 1.57, 95% CI 1.24–1.98, respectively]. The most prevalent eye diseases in people with visual impairment (VA ≤ 0.25) were ARM (37%), unoperated cataract (27%), glaucoma (22%) and DR (7%).

Conclusion:  The high prevalence of these mainly age‐related eye diseases, together with increasing life expectancy, mean that continuous efforts are needed to identify and treat eye diseases in order to maintain patients’ quality of life and to alleviate the social and economic burden of serious eye diseases.
The Differential Importance of Personal and Environmental Resources to Older Canadians
Authors: LOW GAIL , KEATING NORAH , GAO ZHIWEI
Published: October 2009

S'appuyant sur le système social de production et sur la théorie du capital social, les auteurs questionnent l'importance spécifique des ressources personnelles et environnementales sur la satisfaction, en utilisant le temps, la santé, la situation financière et les activités principales comme variables. Les données sur les Canadiens et les Canadiennes âgés de 60 ans et plus (n=5,986) ayant participéà l'Enquête sociale générale — engagement social (cycle 17) ont été analysées. Les personnes âgées canadiennes ont été très satisfaites de l'utilisation de leur temps, mais moins de leur situation financière. Alors que les limitations dues à la santé et le sentiment de maîtrise ont été importants dans les quatre domaines, l'environnement physique et les activités communautaires ont eu de plus en plus d'effets idiosyncrasiques et spécifiques aux domaines. Les auteurs analysent en outre la signification de leurs résultats en se servant de la documentation sur la résilience, de la spécificité fonctionnelle des relations sociales et de l'utilisation maximale des ressources.

Drawing on social productive function and social capital theory, we examine the differential importance of personal and environmental resources to the satisfaction with time use, health, finances, and main activities. Data pertaining to Canadians aged 60 and above (n=5,986) participating in the General Social Survey (Cycle 17) were analyzed. Canadian seniors were most satisfied with their time use and least with their finances. While health limitations and the sense of mastery were important to all four domains, the physical environment and civic activities yielded increasingly idiosyncratic, domain‐specific effects. We further explore the significance of our findings using literature pertaining to resilience, the functional specificity of social relationships, and the maximum utility of resources.
Treatment of aseptic nonunion after intramedullary nailing fixation with locking plate
Authors: Chen Sheng‐bao , Zhang Chang‐qing , Jin Dong‐xu , Cheng Xiang‐guo , Sheng Jia‐gen , Zeng Bing‐fang
Published: October 2009

Objective:  To evaluate the safety and efficacy of locking plate combined with bone grafting in the treatment of aseptic nonunion following intramedullary nailing fixation of fractures of the long bones.

Methods:  Thirty‐eight consecutive patients treated in our hospital between January 2004 and December 2006 were included in this retrospective study. The nonunions included 20 femurs, 15 tibias, and 3 humeri. The duration of non‐union ranged from 6 to 84 months and 21 (55.3%) of them were located around the metaphysis of the affected long bones. There were 12 women and 26 men with a mean age of 39.2 years (range, 9–70 years). Locking plate combined with bone grafting was the procedure chosen to treat every case of nonunion in this series. The clinical outcomes were evaluated.

Results:  All patients were followed up for 6–20 months (average 11.6 months). After locking plate fixation combined with bone grafting, union was achieved in all cases, the average healing time being 5.3 months (range, 4–8 months). Infection of the superficial incision occurred in three cases (7.9%) and delayed healing of the incision in one case, all of which healed with no further complications. The function of the adjacent joints was excellent to good in 30 patients (78.9%), fair in 7 (18.4%) and poor in 1 (2.6%) after follow‐up.

Conclusion:  Locking plate fixation combined with bone grafting is a highly effective treatment for aseptic nonunions of the long bones after intramedullary nailing fixation, especially in the case of metaphyseal nonunion.
Posterolateral transforaminal interbody fusion for thoracic disc herniation: a retrospective study of 38 cases
Authors: Ding Wen‐yuan , Guo Zhao , Zhang Ying‐ze , Shen Yong , Li Bao‐jun , Zhang Wei , Chen Hong‐liang
Published: October 2009

Objective:  To evaluate the clinical results of posterolateral transforaminal interbody fusion (PTIF) for the treatment of thoracic disc herniation (TDH).

Methods:  Thirty‐eight patients with TDH were treated with PTIF in our hospital from November 1999 to November 2003. The mean follow‐up period was 5.8 years (range, 4.2 to 6.5 years). There were 24 men and 14 women, ranging from 30.5 to 67.5 years, with an average of 46.5 years. The interval between onset of symptoms and surgery ranged from 5 to 12 months with an average of 9 months. In this group, the disc herniation involved T9‐10 or T10‐11 in 26 (68.5%) patients, T8‐9 in 4 (10.5%), T11‐12 in 4 (10.5%) and T12L1 in 4 (10.5%). All patients underwent X‐ray and magnetic resonance imaging (MRI) examination. Twenty‐two patients underwent myelography, while 25 patients underwent computer tomography (CT) or CT myelography (CTM) examination. The clinical results were evaluated using the Otani scoring system.

Results:  The outcome according to the Otani scoring system was excellent in 16 patients, good in 18, fair in 2 and poor in 2. No neurological symptoms, wound infection or clinical or radiographic evidence of instability were found; and the fusion rate was 100% by final follow‐up. An excellent or good outcome was achieved in 89.5% of patients.

Conclusion:  PTIF is an effective strategy for the treatment of TDH.
The role of the calcar femorale in stress distribution in the proximal femur
Authors: Zhang Qi , Chen Wei , Liu Huai‐jun , Li Zhi‐yong , Song Zhao‐hui , Pan Jin‐she , Zhang Ying‐ze
Published: October 2009

Objective:  To investigate the role of the calcar femorale in stress distribution in the proximal femur.

Methods:  Twenty‐five specimens of proximal femurs were fixed to simulate single‐limb stance. Strain gauges were applied to record the strain under different loads. Strain values of 27 selected sites in the proximal femur were recorded and analyzed at the level of 100 N, 200 N, 300 N, 400 N, 500 N, 600 N and 700 N, respectively before and after disruption of the calcar femorale.

Results:  When a normal load was being borne, strain values measured in the posterior and medial aspects of the proximal femur were greater than those measured in the anterior and lateral aspects, no matter whether the calcar femorale was disrupted or not. However after disruption of the calcar femorale, strain values in the posterior and medial aspects of the proximal femur increased significantly, whereas those of the anterior and lateral aspects decreased significantly.

Conclusion:  The calcar femorale redistributes stress in the proximal femur by decreasing the load in the posterior and medial aspects and increasing the load in the anterior and lateral aspects.
Analysis of Heat Flow Around Bolted Joints and Variations of Axial Bolt Force
Authors: Fukuoka Toshimichi , Nomura Masataka , Shino Keiichi
Published: October 2009

A bolted joint is widely used for the structures and machines subjected to thermal load, such as pressure vessels, internal combustion engines, brake disks, etc. In order to accurately evaluate the thermal stresses thus produced, the effect of thermal contact resistance at the interface and the heat flow through small gaps, which exist around the objective bolted joint, must be taken into account. In this paper, a numerical approach is proposed to solve the mechanical and thermal behaviors of bolted joints with high accuracy and computation efficiency, where empirical equations for thermal contact coefficient and apparent thermal contact coefficient are incorporated into commercial engineering software. By conducting systematic three-dimensional finite element analyses, it has been quantitatively elucidated how the supplied heat flows through each part of a bolted joint and how the axial bolt stress and bolt bending stress vary with time. It is concluded that bolted joints made of the materials with low thermal conductivity show specific heat flow patterns around the bolted joint and generate a large amount of variations in both axial bolt stress and bolt bending stress.
Evaluation on an Internal Surface Crack in a Compound Tube
Authors: Ali A. A. , Purbolaksono J. , Khinani A. , Rashid A. Z. , Tarlochan F.
Published: October 2009

In this paper stress intensity factors of a longitudinal semielliptical surface crack on the inner surface in a compound tube subjected to internal pressure are presented. Variations of modulus of elasticity and thickness for the inner part of the tube are used in order to evaluate their effects on the normalized stress intensity factors. The boundary element method is used to analyze the problems. The increasing of thickness of the inner region causes decreasing values of the normalized stress intensity factor, as the modulus of elasticity for the inner part is greater than that of the outer part. Conversely, if the modulus of elasticity for the inner region is smaller, the increasing of thickness of the inner part would give increasing values of the normalized stress intensity factor. A larger inner radius and smaller thickness of the tube gives a higher normalized stress intensity factor.
UV detection based on a ZnO∕LiNbO3 layered surface acoustic wave oscillator circuit
Authors: Wei Ching-Liang , Chen Ying-Chung , Fu Jiun-Lin , Kao Kuo-Sheng , Cheng Da-Long , Cheng Chien-Chuan
Published: October 2009

This study elucidates the combination of an oscillator circuit with a high-frequency amplifier, a matching network, and a layered surface acoustic wave device for detecting ultraviolet (UV) light. The oscillator circuit shows an excellent performance with the resonance frequency of 109.34MHz and phase noise of −107.137dB at 100kHz. The frequency shift that is caused by the interaction between the acoustic wave and carriers upon excitation by UV light in the ZnO thin film is discussed. The frequency variation of the oscillator steadily increases with the intensity of the UV light. An extreme frequency shift of 63.75kHz was observed as the UV light intensity reached 1250μW∕cm2.
Transmission electron microscopy specimen preparation perpendicular to the long axis of high aspect ratio features
Authors: Irwin R. B. , Anciso A. , Jones P. J. , Glenn A. L. , Williams B. L. , Sridhar S. , Arshad S.
Published: October 2009

A new variation of transmission electron microscopy (TEM) specimen preparation is introduced. By thinning a tall high aspect ratio structure perpendicular to the long dimension (i.e., from the side) rather than from perpendicular to the short dimension (either the top or the bottom), it is possible to obtain a more uniformly thin TEM specimen over the entire long dimension of the structure. This article will describe the rational for this variation in specimen preparation. The necessary modifications of four different specimen preparation methods (in situ lift-out, traditional H-bar, ex situ lift-out, and tripod polishing) will be discussed and images of specimens obtained by both of these first two methods will be shown. Additional potential advantages and other applications of this specimen preparation method will be covered.
Preferential growth of helium-doped Ti films deposited by magnetron sputtering
Authors: Zhang Lei , Shi L. Q. , He Z. J. , Zhang B. , Wang L. B.
Published: October 2009

The authors present a study on the influence of the bias voltages on the preferred orientation and microstructure of helium-doped Ti films. The films were deposited in a vacuum chamber by both direct-current magnetron sputtering and electron-cyclotron-resonance plasma-aided magnetron sputtering (ECR-PMS) methods. The preferred orientation and microstructure of the films were analyzed by x-ray diffraction (XRD) and transmission electron microscopy. They found that the preferred crystal orientation of helium-doped Ti films was controllably varied from (002) to (100) orientation by increasing the bias voltage (i.e., ion bombardment current and energy). The dominant bombardment effect on the orientation was from the Ar ions of the anode sheath in the magnetron sputtering plasma, and He bombardment also showed a slight influence on the orientation transformation at low trapped-helium content in the crystal. The XRD peak broadening of helium-doped Ti films prepared by ECR-PMS is much more serious than for conventional magnetron sputtering even at low helium concentrations. It is believed that asynchronous bombardment from He ions in the ECR plasma area and Ar ions in the deposition plasma during film growth significantly decreases the mobility of Ti adatoms on the surface and enhances the growth of helium-induced defects, thus increasing the crystal disorder and influencing the crystal orientation transformation. On the contrary, the sequential bombardment of He and Ar particles can decrease helium-dissolution produced defects and improve crystallization.
Clean Air for Megacities
Authors: Parrish David D. , Zhu Tong
Published: October 2009

Air pollution in megacities has severe health impacts, but its control could provide opportunities for climate change mitigation.
A Late Archean Sulfidic Sea Stimulated by Early Oxidative Weathering of the Continents
Authors: Reinhard Christopher T. , Raiswell Rob , Scott Clint , Anbar Ariel D. , Lyons Timothy W.
Published: October 2009

Of Ancient Iron and Oxygen

Finding clues to understand the early evolution of ocean and atmospheric chemistry and its links to the evolution of life remains a daunting task. Often just a few rock samples provide our only evidence of what conditions on Earth were like long ago.

Reinhard
et al.

(p.
713
) combined iron speciation data from a 2.5-billion-year-old shale from Australia with sulfur isotope data from this and nearby formations to conclude that oxygen chemistry predominanty consisted of an anoxic sulfide–rich water column, instead of iron-rich oceans, as previously speculated. Thus, brief pulses of reduced iron from hydrothermal vents may have been responsible for the formation of nearby banded iron formations and may have provided enough buffering to prolong the appearance of atmospheric oxygen generated by the expansion of newly evolved cyanobacteria.
4D Nanoscale Diffraction Observed by Convergent-Beam Ultrafast Electron Microscopy
Authors: Yurtsever Aycan , Zewail Ahmed H.
Published: October 2009

Converging on Dynamics

Electron diffraction is a versatile technique for discerning atomic-level structure, but the data emerge averaged over the micron–scale area sampled by the electrons, and so blur local distinctions in systems that aren't strictly periodic. A recent approach to minimizing this problem has been to focus the electron beam impinging on the sample.
Yurtsever and Zewail
(p.
708
) have now applied convergent focusing to an ultrafast electron diffraction apparatus and were thus able to resolve picosecond structural dynamics in local regions tens of nanometers across. The technique was used to probe heterogeneous temperature changes in laser-heated silicon.
Beyond Climate Science
Authors: Barron Eric J.
Published: October 2009

The United States is moving rapidly into an age of climate-related decisions involving mitigation and adaptation, following decades of focusing on reducing uncertainties in attribution and prediction. But the nation lacks a deliberate approach to generating the “environmental intelligence” needed to support good decisions.
Correspondence in Flux
The Calculus of Friendship
What a Teacher and a Student Learned About Life While Corresponding About Math

by Steven Strogatz

Princeton University Press, Princeton, NJ, 2009. 180 pp. $19.95. ISBN 9780691134932.
Authors: Finegold Brie
Published: October 2009

Wolpert offers lay readers a short, wide-ranging introduction to cell biology.
Study Finds Science Pipeline Strong, But Losing Top Students
Authors: Bhattacharjee Yudhijit
Published: October 2009

A new study finds little evidence for leaks in the U.S. pipeline for producing native-born scientists except for a steep drop in the percentage of the highest performing students taking science and engineering jobs.
Glacier Man
Authors: Vince Gaia
Published: October 2009

A retired civil engineer battles climate change in the Himalayas, building artificial glaciers that provide irrigation water to mountain villages.
Escaping Detection, Finally Caught
Authors: Khidr Lily
Published: October 2009

A magnetic nanosensor yields quantitative, sensitive, and reproducible multiplex protein detection irrespective of sample composition.
Abundance of Multiple High-Risk Human Papillomavirus (HPV) Infections Found in Cervical Cells Analyzed by Use of an Ultrasensitive HPV Genotyping Assay
Authors: Schmitt Markus , Dondog Bolormaa , Waterboer Tim , Pawlita Michael , Tommasino Massimo , Gheit Tarik
Published: October 2009

PCR methods enable the detection of a large variety of human papillomavirus (HPV) genotypes that infect the anogenital tract. However, PCR with consensus primers, general primers, and, to a lesser extent, broad-spectrum primers may underrepresent the true prevalence of HPV, especially the true prevalence of multiple infections. We compared the rate of HPV positivity determined by a broad-spectrum PCR with primers BSGP5+ and BSGP6+ (BS-PCR) coupled to an established bead-based multiplex HPV genotyping (MPG) assay with the rate of HPV positivity determined by a multiplex PCR with type-specific primers (TS-PCR) coupled to a newly developed MPG assay for 735 selected cervical scraping samples. While the primers used for the BS-PCR are located within the L1 region of the HPV genome, the primers used for the TS-PCR target the E7 gene. The overall rates of positivity for the 19 HPV types included in both assays were 60.9% and 72.2% by the BS-PCR and the TS-PCR, respectively, and the two assays found multiple infections in 34.8% and 58.0% of the specimens, respectively. Both HPV detection assays allowed the semiquantitative detection of HPV types and identified the same dominant HPV type in 66.6% of the multiple infections. In conclusion, the TS-PCR-MPG assay significantly increased the rate of detection of HPV DNA and the number of infections with multiple HPV types detected and demonstrated that the prevalence of low-copy-number HPV infections in the anogenital tract may be strongly underestimated by conventional HPV amplification methods, especially in cases of multiple infections. As a consequence, PCR-TS-MPG appears to be highly suited for analysis of the significance of multiple infections in the development of cervical cancer and for the study the natural history and the latency of HPV.
Diversity of Human Parechoviruses Isolated from Stool Samples Collected from Thai Children with Acute Gastroenteritis
Authors: Pham Ngan Thi Kim , Trinh Quang Duy , Khamrin Pattara , Maneekarn Niwat , Shimizu Hideaki , Okitsu Shoko , Mizuguchi Masashi , Ushijima Hiroshi
Published: October 2009

A total of 82 fecal specimens which were known to be negative for rotavirus, adenovirus, norovirus, sapovirus, and astrovirus and which were collected from infants and children with acute gastroenteritis in Chiang Mai, Thailand, from January to December 2005 were screened for human parechovirus (HPeV). HPeV was detected by reverse transcription-PCR with a primer pair that amplified the 5′ untranslated region of its genome and was genotyped by sequencing of the VP1 region. HPeV was detected in 12 of 82 specimens tested, and the detection rate was found to be 14.6%. The capsid VP1 gene was successfully sequenced from nine of the HPeV strains detected. The HPeV strains studied clustered into four different genotypes, HPeV genotype 1 (HPeV1) to HPeV4, and the majority of the strains studied (five strains) belonged to HPeV1. This is the first finding of HPeV from children with acute gastroenteritis in Thailand. In addition, the diversity of the Thai HPeV strains was also noted.
Multiplex PCR-Ligation Detection Reaction Assay for Simultaneous Detection of Drug Resistance and Toxin Genes from
Staphylococcus aureus
,
Enterococcus faecalis
, and
Enterococcus faecium
Authors: Granger K. , Rundell M. S. , Pingle M. R. , Shatsky R. , Larone D. H. , Golightly L. M. , Barany F. , Spitzer E. D.
Published: October 2009

A multiplex PCR-ligation detection reaction (PCR-LDR) assay was developed for rapid detection of methicillin, tetracycline, and vancomycin resistance, as well as toxic shock toxin and Panton-Valentine leukocidin. The assay was tested on 470 positive blood culture bottles containing
Staphylococcus aureus
or enterococci. PCR-LDR exhibited a sensitivity and specificity of ≥98% for all components except tetracycline resistance, which had a sensitivity of 94.7%. Rapid and sensitive detection of antimicrobial resistance and virulence genes could help guide therapy and appropriate infection control measures.
Molecular Epidemiology of Genogroup II-Genotype 4 Noroviruses in the United States between 1994 and 2006
Authors: Zheng Du-Ping , Widdowson Marc-Alain , Glass Roger I. , Vinjé Jan
Published: October 2009

Human noroviruses (NoVs) of genogroup II, genotype 4 (GII.4) are the most common strains detected in outbreaks of acute gastroenteritis worldwide. To gain insight into the epidemiology and genetic variation of GII.4 strains, we analyzed 773 NoV outbreaks reported to the CDC from 1994 to 2006. Of these NoV outbreaks, 629 (81.4%) were caused by GII viruses and 342 (44.2%) were caused by GII.4 strains. The proportion of GII.4 outbreaks increased from 5% in 1994 to 85% in 2006, but distinct annual differences were noted, including sharp increases in 1996, 2003, and 2006 each associated with newly emerging GII.4 strains. Sequence analysis of the full-length VP1 gene of GII.4 strains identified in this study and from GenBank segregated these viruses into at least 9 distinct subclusters which had 1.3 to 3.2% amino acid variation between strains in different subclusters. We propose that GII.4 subclusters be defined as having >5% sequence variation between strains. Our data confirm other studies on the rapid emergence and displacement of highly virulent GII.4 strains.
Comparison of BD GeneOhm Cdiff Real-Time PCR Assay with a Two-Step Algorithm and a Toxin A/B Enzyme-Linked Immunosorbent Assay for Diagnosis of Toxigenic
Clostridium difficile
Infection
Authors: Kvach Elizabeth J. , Ferguson David , Riska Paul F. , Landry Marie L.
Published: October 2009

The BD GeneOhm Cdiff assay, a real-time PCR assay for the detection of the
Clostridium difficile
toxin B (
tcdB
) gene, was compared with the toxin A/B (Tox A/B) II enzyme-linked immunosorbent assay (ELISA) and a two-step algorithm which includes a C. Diff Chek-60 glutamate dehydrogenase (GDH) antigen assay followed by cytotoxin neutralization. Four hundred liquid or semisolid stool samples submitted for diagnostic
C. difficile
testing, 200 GDH antigen positive and 200 GDH antigen negative, were selected for analysis. All samples were tested by the C. Diff Chek-60 GDH antigen and cytotoxin neutralization assays, the Tox A/B II ELISA, and the BD GeneOhm Cdiff assay. Specimens with discrepant results were tested by toxigenic culture as an independent “gold standard.” Of 200 GDH-positive samples, 71 were positive by the Tox A/B II ELISA, 88 were positive by the two-step method, 93 were positive by PCR, and 96 were positive by the GDH antigen assay only. Of 200 GDH-negative samples, 3 were positive by PCR only. Toxigenic culture was performed for 41 samples with discrepant results, and 39 were culture positive. Culture resolution of discrepant results showed the Tox A/B II assay to have detected 70 (66.7%), the two-step method to have detected 87 (82.9%), and PCR to have detected 96 (91.4%) of 105 true positives. The BD GeneOhm Cdiff assay was more sensitive in detecting toxigenic
C. difficile
than the Tox A/B II assay (
P
< 0.0001); however, the difference between PCR and the two-step method was not significant (
P
= 0.1237). Enhanced sensitivity and rapid turnaround time make the BD GeneOhm Cdiff assay an important advance in the diagnosis of toxigenic
C. difficile
infection.
Analysis of Herpes Simplex Virus Type 1 DNA Packaging Signal Mutations in the Context of the Viral Genome
Authors: Tong Lily , Stow Nigel D.
Published: October 2009

The minimal signal required for the cleavage and packaging of replicated concatemeric herpes simplex virus type 1 (HSV-1) DNA corresponds to an approximately 200-bp fragment, Uc-DR1-Ub, spanning the junction of the genomic L and S segments. Uc and Ub occupy positions adjacent to the L and S termini and contain motifs (
pac
2 and
pac
1, respectively) that are conserved near the ends of other herpesvirus genomes. We have used homologous Red/ET recombination in
Escherichia coli
to introduce wild-type and specifically mutated Uc-DR1-Ub fragments into an ectopic site of a cloned HSV-1 genome from which the resident packaging signals had been previously deleted. The resulting constructs were transfected into mammalian cells, and their abilities to replicate and become encapsidated, generate Uc- and Ub-containing terminal fragments, and give rise to progeny virus were assessed. In general, the results obtained agree well with previous observations made using amplicons and confirm roles for the
pac
2 T element in the initiation of DNA packaging and for the GC-rich motifs flanking the
pac
1 T element in termination. In contrast to a previous report, the sequence of the DR1 element was also crucial for DNA packaging. Following repair of the resident packaging signals in mammalian cells, recombination occurred at high frequency in progeny virus between the repaired sequences and mutated Uc-DR1-Ub inserts. This restored the ability of mutated Uc-DR1-Ub inserts to generate terminal fragments, although these were frequently larger than expected from simple repair of the original lesion.
Polymorphisms in the putative micro-RNA-binding sites of mesothelin gene are associated with serum levels of mesothelin-related protein
Authors: Cristaudo Alfonso , Foddis Rudy , Bonotti Alessandra , Simonini Silvia , Vivaldi Agnese , Guglielmi Giovanni , Bruno Rossella , Landi Debora , Gemignani Federica , Landi Stefano
Published: October 2009

Background

Serum mesothelin, also known as soluble mesothelin-related protein (SMRP), reportedly shows increased levels in epithelial-type malignant pleural mesothelioma, but sometimes also arrives at high values in healthy asbestos-exposed subjects.

Objectives

This study aimed to investigate whether single nucleotide polymorphisms in the 3′untranslated region (3′UTR) of the mesothelin-encoded gene (MSLN) are associated with the SMRP levels measured in serum.

Methods

The 3′UTR of the mesothelin gene was genotyped in 59 healthy asbestos-exposed subjects, selected on the basis of their SMRP levels. Direct sequencing did not show any new polymorphism, but enabled us to genotype two known SNPs (rs1057147, rs57272256). Differences in the mean values of SMRP in wild-type and variant heterozygote groups were calculated.

Results

High levels of SMRP in healthy asbestos-exposed subjects were significantly associated with polymorphism rs1057147 (G<A). Regarding rs57272256, there was no statistically significant difference between wild-type and heterozygote groups.

Our study suggests that rs1057147 polymorphism can affect mesothelin expression. Although these data need to be confirmed with a larger number of cases, this study warrants further research in order to better understand the relationship between mesothelin polymorphisms and SMRP.
Changes in methyl mercury concentrations in zooplankton from four experimental reservoirs with differing amounts of carbon in the flooded catchmentsThis paper is part of the series “Forty Years of Aquatic Research at the Experimental Lakes Area”.
Authors: Hall Britt D. , Cherewyk Katharine A. , Paterson Michael J. , Bodaly R. (Drew) A.
Published: October 2009

Methyl mercury (MeHg) concentrations in zooplankton were compared from four experimental reservoirs at the Experimental Lakes Area in northwestern Ontario, Canada, to test the hypothesis that increases in concentrations of MeHg in zooplankton would be proportional to C availability. The experimental reservoirs included three upland reservoirs flooded between 1999 and 2003 that differed in amounts of flooded organic terrestrial C (high, medium, and low C) and an experimental reservoir created over a wetland–peatland complex in 1993. After flooding, MeHg in zooplankton increased from <100 ng·g dry weight–1in inflow source waters to >500 ng·g dry weight–1in all reservoirs. In the first two years of flooding, MeHg in zooplankton was not correlated with amounts of flooded C, but the rates of decline in mean annual concentrations were negatively correlated with the amount of C stored in flooded catchments. Concentrations of MeHg in zooplankton were highly correlated with MeHg concentrations in unfiltered water, with reductions in bioaccumulation associated with increases in dissolved organic C and decreases in pH. Overall, our results suggest that reservoir designs that minimize the amount of flooded terrestrial C should result in shorter periods of elevated MeHg in the food web.