bluuebunny/crossref_metadata_2025 huggingface dataset:
Dosimetric investigation of dual energy photon beams with assymmetric collimator jaws
Authors: Varatharaj C. , Ravikumar M. , Supe Sanjay , Sathiyan S. , Ganesh K. , Arunkumar T.
Published: January 2009

Dosimetric investigation of dual energy photon beams with assymmetric collimator jaws

Many modern linear accelerators are equipped with asymmetric collimators or jaws that can be moved independently. Asymmetric jaws have got many clinical applications in radiation therapy. In the present study, the dosimetric characteristics of asymmetric collimators from our linear accelerator with 6 and 18 MV X-rays were carried out. The field size factors (FSF) and half value layer (HVL) were measured in a water phantom using 0.6 cc Farmer chamber for symmetric and asymmetric fields for both 6 and 18 MV X-rays. Measurements of beam penumbra, percentage depth dose (PDD), cross beam profiles and calculated isodose curves were measured by RFA 300 for both asymmetric and symmetric fields. The FSF were found to agree with in 3% for symmetric and asymmetric fields. The HVL in water was found to be 15.8 cm and 14.4 cm for 6 MV photons and 26 cm and 22.9 cm for 18 MV photons at the central axis and at 20 cm off the central axis. At 30 cm depth the percentage depth dose for symmetric and asymmetric fields were found to differ as high as 6% for 6 MV and 4% for 18 MV fields. No observable difference in penumbra was noticed for symmetric and asymmetric fields of same dimensions. The constrictions of isodose curves at the edge nearer to central axis were noticed for asymmetrically placed fields. The observed differences could be due to the passage of primary beam through differential thickness of the flattening filter which alters the beam quality.
Introductory: Reflecting on a Good Life
Authors: Višňovský Emil
Published: January 2009

Introductory: Reflecting on a Good Life
The Good Life, The Examined Life, and the Embodied Life
Authors: Shusterman Richard
Published: January 2009

The Good Life, The Examined Life, and the Embodied Life

The good life and the examined life have long been advocated as key philosophical goals, and they have often been closely linked together. My paper critically examines this linkage by considering arguments both for and against the value of self-examination for achieving the good life. Because somatic self-examination has been viewed as especially problematic for the philosophical project of achieving the good life, this form of self-examination will be given special attention in the paper, and its discussion will be situated within the larger issue of the extent to which the embodied life is central to the good life.
Effect of Perforated Film And Polypropylene Nonwoven Covering On The Marketable Value of Early Potato Yield
Authors: Wadas Wanda , Kosterna Edyta , Sawicki Marek
Published: January 2009

Effect of Perforated Film And Polypropylene Nonwoven Covering On The Marketable Value of Early Potato Yield

The effect of cover material (perforated polyethylene film, polypropylene nonwoven) and date of its removal (2 and 3 weeks after plant emergence) on the marketable value of the yield of early potato cultivar (Aksamitka, Cykada) was investigated. Potatoes were harvested 60 and 75 days after planting, in the second and third decade of June. Plant vegetation forcing by covering resulted in an increase in the marketable tuber yield (diameter >30 mm) and improved marketable value due to a reduced share of small tubers, with the diameter of 31-40 mm, especially at a very early date of potato harvest. In potato cultivation for very early crop, the cover material had a greater effect on the tuber yield and its marketable value than the length of plant covering period. Perforated film was a better kind of cover than polypropylene nonwoven, especially in the year with cold spring. At the delayed date of potato harvest the marketable tuber yield depended, to a higher degree on the date of cover removal. Higher yield was obtained when the cover was removed 2 weeks after plant emergence.
Length of Human Vermiform Appendix in Bangladeshi People
Authors: Rahman Md Mahbubur , Khalil Mohsin , Khalil Mansur , Hussain Anwar , Rahman Habibur Rahman , Mannan Sabina , Sultana Seheli Zannat , Ahamed M Shibbir
Published: January 2009

The study was done to find out the length of human vermiform appendix in Bangladeshi people to magnify the knowledge regarding the diverse length of human vermiform appendix in our population. A total 100 vermiform appendix were measured with different age and sex during routine postmortem examination in the autopsy laboratory of forensic medicine department of Mymensingh Medical College. This cross sectional study was done by convenient sampling technique. For convenience of differentiating the length of vermiform appendix in relation to different age and sex, findings were classified in four groups (up to 20 years, 21 to 35 years, 36 to 55 years and 56 to 70 years). Length of vermiform appendix was 2.6 cm to 14 cm. Mean length was 7.9 cm in female and 7.56 cm in male. The highest mean length of vermiform appendix in group A was 9.17 cm and lowest was 5.93 cm in group D. Key words: Human Vermiform Appendix; Length; Bangladesh   DOI:10.3329/jbsp.v2i0.977 J Bangladesh Soc Physiol. 2007 Dec;(2): 13-16
Mass of the Vermiform Appendix in Bangladeshi People
Authors: Rahman M Mahbubur , Khalil Mohsin , Khalil Mansur , Jahan Mst Khurshida , Shafiquazzaman M , Parvin Bilkis
Published: January 2009

This study was done to measure the weight of vermiform appendix in Bangladeshi people to augment the data regarding variational anatomy in our setting. A total 100 vermiform appendix (male - 60, female - 40) were excised from cadaver of different age and sex during routine post mortem examination in the autopsy laboratory of Forensic Medicine Department of Mymensingh Medical College. This cross-sectional study was done by convenient sampling technique. The weight depended on length and thickness. The weight decreases gradually with advancing age probably decreasing number of lymphatic follicle and that replaced by connective tissue. Lymphatic follicles were examined and estimated by microscope. For convenience of differentiating the weight of vermiform appendix in relation to age and sex, specimens were categorized in four age groups (up to 20 year, 21 - 35 years, 36 - 55 years, 56 - 70 years). Mean weight of vermiform appendix was maximum in group - B (4.07 Â± SE 0.82 gm) and minimum in group D (3.01 Â± SE 0.74 gm). The weight range was from 2 gm (group - D) to 5.50 gm (group - B). Diameter of lymphatic follicle was largest 43.08 micrometer in group-A, and least diameter was 3.08 micrometer in group - D. The range of number of lymphatic follicle was 1 to 6. Mean number of lymphatic follicle in male was 4.48 & in female were 5.40. Key Words: Human Vermiform, Appendix, Weight, Lymphatic, Follicle Â  doi: 10.3329/jbsp.v3i0.1787 J Bangladesh Soc Physiol.2008 Dec;(3):8-12.
Evaluation of Parasympathetic Nerve Function Status in Healthy Elderly Subjects
Authors: Islam T , Begum N , Begum S , Ferdousi S , Ali T
Published: January 2009

Background: Autonomic control on cardiovascular activity is modified with age. Impaired autonomic nerve functions are common features of patients suffering from cardiovascular diseases particularly in old age. Objective: To observe the influence of aging process on parasympathetic nerve function. Study design: This observational study was conducted in the Department of Physiology, BSMMU, Dhaka during the period of July 2005 to June 2006. For this purpose, 60 apparently healthy elderly subjects of both sexes were selected as study group and divided into two groups-one group consisted of 30 elderly subjects with age ranged from 51-60 years and another group consisted of 30 elderly subjects with age ranged from 61-70 years. Thirty sex and BMI matched healthy adults with age ranged from 21-30 years were studied as control. Methods: Parasympathetic nerve function status of all the subjects were assessed by three simple non-invasive cardiovascular reflex tests. These were heart rate response to valsalva maneuver, heart rate response to deep breathing and heart rate response to standing (30th:15th ). For statistical analysis one way ANOVA (Post Hoc Test) and the Pearson's correlation co-efficient tests were done. Results: Mean (Â± SD) of valsalva ratio were 1.50Â±0.23, 1.32Â±0.14 and 1.28Â±0.15; HR response to deep breathing test were 25.36Â±3.90, 18.82Â±3.35 and 15.96Â±3.54 beats/min; 30th:15th ratio in standing test were 1.100.06, 1.05Â±0.03 and 1.04Â±0.02 in 21- 30, 51-60 and 61-70 years age groups respectively. All the 3 parameters were significantly lower in both elderly groups compared to that of control adults (p < 0.001) Again, HR response to deep breathing was significantly lower in 61-70 years age group compared to that of 51-60 years age group. Valsalva ratio and 30th:15th ratio were also lower in 61-70 years age group than that of 51-60 years group but the differences were not statistically significant. All the 3 parameters were negatively correlated with age which were statistically significant. Conclusion: From this study it may concluded that aging process substantially impaired cardiovascular parasympathetic nerve functions. Key words: Cardiovascular reflex test, elderly person. Â Â Â Â Â  doi: 10.3329/jbsp.v3i0.1790 J Bangladesh Soc Physiol.2008 Dec;(3):23-28.
Parasympathetic Nerve Functions in Type 2 Diabetes Mellitus: Relation to Glycemic Status and Duration of Diabetes
Authors: Alam Md Khairul , Begum Noorzahan , Begum Selina
Published: January 2009

Background: Cardiovascular autonomic dysfunction is associated with higher mortality and is a common health problem observed in diabetic patients. Early detection of autonomic dysfunction in diabetic patient is important for prevention of this complication. Objectives: The study has been designed to observe the parasympathetic nerve function status in type 2 diabetic subjects in order to assess the relationship between glycemic status and duration of diabetes and the parasympathetic nerve function. Study Design: This cross section study was carried out in the Department of Physiology, Bangabhandhu Sheikh Mujib Medical University, Dhaka, Bangladesh. Forty seven type 2 diabetic subjects were included in two groups. Group B consisted of 25 recently diagnosed diabetic subjects aged 40-68 years and group C consisted of 22 subjects having duration of diabetes for 10 - 20 years. Twenty five (25) age and BMI matched healthy subjects were included in group A (non diabetic) for control. Methods: Parasympathetic nerve functions were assessed by three simple non invasive cardiovascular reflex tests. These were Valsalva maneuver, Heart rate variation (HRV) to deep breathing, HRV to standing up. Glycemic status was assessed by serum glycosylated hemoglobin (HbA1C) and fasting plasma glucose (FPG). Data were analyzed by ât' test, Pearson's correlation coefficient. Results: Valsalva ratio was significantly lower in group C than that of group A but no significant difference was observed between group B & A and also between B and C. HRV in deep breathing and 30th:15th ratios were significantly lower in both the diabetic groups B and C than those of group A but these values were semilar in group B and C. Values of correlation of fasting plasma glucose with valsalva ratio, HRV in deep breathing and 30th:15th ratios in standing test in all three groups were not statistically significant. But correlation of duration of diabeties with valsalva ratio was stastically significant but with RHV in deep breathing and 30th:15th ratios were not significant. Conclusion: From this study it may be concluded that there was progressive deterioration of parasympathetic function with increase in duration of diabetes in patients suffering from type 2 diabetes. Key Words: Parasympathetic, Nerve, Diabetes, Neuropathy Â  doi: 10.3329/jbsp.v3i0.1793 Â  J Bangladesh Soc Physiol.2008 Dec;(3):42-49.
Engineering of the yeast antioxidant enzyme Mpr1 for enhanced activity and stability
Authors: Iinoya Kaoru , Kotani Tetsuya , Sasano Yu , Takagi Hiroshi
Published: January 2009

The budding yeast Saccharomyces cerevisiae Σ1278b has the MPR1 gene, which confers resistance to the proline analogue azetidine‐2‐carboxylate (AZC). This gene encodes an N‐acetyltransferase Mpr1 that detoxifies AZC, and the homologous genes have been found in many yeasts. Recently, we found that Mpr1 protects yeast cells by reducing the intracellular reactive oxygen species (ROS) levels under oxidative stresses, such as heat‐shock, freezing, or ethanol treatment. Unlike the known antioxidant enzymes, Mpr1 is thought to acetylate toxic metabolite(s) involved in ROS generation via oxidative events. To improve the enzymatic functions of Mpr1, we applied PCR random mutagenesis to MPR1. The mutagenized plasmid library was introduced into the S. cerevisiae S288C strain lacking MPR1, and we successfully isolated two Mpr1 variants with higher AZC resistance (K63R and F65L/L117V). Interestingly, overexpression of the K63R variant was found to increase cell viability or decrease intracellular ROS levels after exposure to H2O2 or ethanol compared with the wild‐type Mpr1. In vitro studies with the recombinant enzymes showed that the catalytic efficiency of the K63R variant for AZC and acetyl‐CoA was higher than that of the wild‐type Mpr1 and that the F65L mutation greatly enhanced the thermal stability. The mutational analysis and molecular modeling suggest that an α‐helix containing Lys63 and Phe65 has important roles in the function of Mpr1. In addition, the wild‐type and K63R variant Mpr1 reduced intracellular ROS levels under ethanol stress conditions on haploid sake yeast cells. These results suggest that engineering Mpr1 might be useful in breeding oxidative stress‐tolerant yeast strains. Biotechnol. Bioeng. 2009;103: 341–352. © 2009 Wiley Periodicals, Inc.
Image guided medialization laryngoplasty
Authors: Jin Ge , Baek Nakhoon , Hahn James K. , Bielamowicz Steven , Mittal Rajat , Walsh Raymond
Published: January 2009

Techniques that originate in computer graphics and computer vision have found prominent applications in the medical domain. In this paper, we have seamlessly developed techniques from computer graphics and computer vision together with domain knowledge from medicine to develop an image guided surgical system for medialization laryngoplasty. The technical focus of this paper is to register the preoperative radiological data to the intraoperative anatomical structure of the patient. With careful analysis of the real‐world surgical environment, we have developed an ICP‐based partial shape matching algorithm to register the partially visible anatomical structure to the preoperative CT data. We extracted distinguishable features from the human thyroid cartilage surface and applied image space template matching to find the initial guess for the shape matching. The experimental result shows that our feature‐based partial shape matching method has better performance and robustness compared with original ICP‐based shape matching method. Although this paper concentrates on the medialization laryngoplasty procedure, its generality makes our methods ideal for future applications in other image guided surgical areas. Copyright © 2009 John Wiley & Sons, Ltd.
Two genetic pathways, t(1;10) and amplification of 3p11–12, in myxoinflammatory fibroblastic sarcoma, haemosiderotic fibrolipomatous tumour, and morphologically similar lesions
Authors: Hallor Karolin H , Sciot Raf , Staaf Johan , Heidenblad Markus , Rydholm Anders , Bauer Henrik CF , Åström Kristina , Domanski Henryk A , Meis Jeanne M , Kindblom Lars‐Gunnar , Panagopoulos Ioannis , Mandahl Nils , Mertens Fredrik
Published: January 2009

Myxoinflammatory fibroblastic sarcoma (MIFS) is a low‐grade malignant neoplasm for which limited genetic information, including a t(1;10)(p22;q24) and amplification of chromosome 3 material, is available. To further characterize these aberrations, we have investigated eight soft tissue sarcomas diagnosed as MIFS, haemosiderotic fibrolipomatous tumour (HFT), myxoid spindle cell/pleomorphic sarcoma with MIFS features, and inflammatory malignant fibrous histiocytoma/undifferentiated pleomorphic sarcoma with prominent inflammation (IMFH) harbouring a t(1;10) or variants thereof and/or ring chromosomes with possible involvement of chromosome 3. Using chromosome banding, fluorescencein situhybridization, array‐based comparative genomic hybridization, global gene expression, and real‐time quantitative PCR analyses, we identified the breakpoint regions on chromosomes 1 and 10, demonstrated and delineated the commonly amplified region on chromosome 3, and assessed the consequences of these alterations for gene expression. The breakpoints in the t(1;10) mapped toTGFBR3in 1p22 and in or nearMGEA5in 10q24, resulting in transcriptional up‐regulation ofNPM3and particularlyFGF8, two consecutive genes located close toMGEA5. The ring chromosomes contained a commonly amplified 1.44 Mb region in 3p11–12, which was associated with increased expression ofVGLL3andCHMP2B. The identified genetic aberrations were not confined to MIFS; an identical t(1;10) was also found in a case of HFT and the amplicon in 3p was seen in an IMFH. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Beta‐catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics
Authors: Fattet Sarah , Haberler Christine , Legoix Patricia , Varlet Pascale , Lellouch‐Tubiana Arielle , Lair Severine , Manie Elodie , Raquin Marie‐Anne , Bours Danielle , Carpentier Sabrina , Barillot Emmanuel , Grill Jacques , Doz Francois , Puget Stephanie , Janoueix‐Lerosey Isabelle , Delattre Olivier
Published: January 2009

Medulloblastoma is the most frequent malignant paediatric brain tumour. The activation of the Wnt/β‐catenin pathway occurs in 10‐15% of medulloblastomas and has been recently described as a marker for favourable patient outcome. We report a series of 72 paediatric medulloblastomas evaluated for β‐catenin protein expression, CTNNB1 mutations, and comparative genomic hybridization. Gene expression profiles were also available in a subset of 40 cases. Immunostaining of β‐catenin showed extensive nuclear staining (>50% of the tumour cells) in six cases and focal nuclear staining (<10% of cells) in three cases. The other cases either exhibited a signal strictly limited to the cytoplasm (58 cases) or were negative (five cases). CTNNB1 mutations were detected in all β‐catenin extensively nucleopositive cases. The expression profiles of these cases documented strong activation of the Wnt/β‐catenin pathway. Remarkably, five out of these six tumours showed a complete loss of chromosome 6. In contrast, cases with focal nuclear β‐catenin staining, as well as tumours with negative or cytoplasmic staining, never demonstrated CTNNB1 mutation, Wnt/β‐catenin pathway activation or chromosome 6 loss. Patients with extensive nuclear staining were significantly older at diagnosis and were in continuous complete remission after a mean follow‐up of 75.7 months (range 27.5–121.2 months) from diagnosis. All three patients with focal nuclear staining of β‐catenin died within 36 months from diagnosis. Altogether, these data confirm and extend previous observations that CTNNB1‐mutated tumours represent a distinct molecular subgroup of medulloblastomas with favourable outcome, indicating that therapy de‐escalation should be considered. International consensus on the definition criteria of this distinct medulloblastoma subgroup should be achieved. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Determinants of response to epidermal growth factor receptor tyrosine kinase inhibition in squamous cell carcinoma of the head and neck
Authors: Rogers Susanne J , Box Carol , Chambers Philip , Barbachano Yolanda , Nutting Christopher M , Rhŷs‐Evans Peter , Workman Paul , Harrington Kevin J , Eccles Suzanne A
Published: January 2009

Dramatic responses to epidermal growth factor receptor (EGFR) tyrosine kinase (TK) inhibitors may be seen in non‐small cell lung cancers (NSCLCs) with a sensitizing mutation of the EGFR TK domain. It is not known how to predict response in patients with squamous cell carcinoma of the head and neck (SCCHN), where EGFR TK mutations are less frequent and where response rates in unselected patients are disappointing. We have characterized the intrinsic sensitivity of a panel of 18 SCCHN cell lines to gefitinib, an EGFR TK inhibitor, and have investigated correlations between putative markers of response and intrinsic sensitivity. Induction of G1 arrest was only seen in cell lines with GI50 < 1 µM. Expression of EGFR, by three techniques, correlated with sensitivity to gefitinib. ERB‐B2 expression appeared to influence sensitivity to gefitinib but ERB‐B3 expression did not. While EGFR tyrosine kinase mutations were not detected, EGFR gene amplification was confirmed by fluorescence in situ hybridization in the most sensitive cell line. The number of cytosine adenine dinucleotide repeats in intron 1 of the EGFR gene did not correlate with sensitivity. E‐cadherin expression was detected in cell lines with a range of sensitivities, whereas amphiregulin was secreted predominantly by sensitive cell lines. MET expression was an independent predictor of sensitivity to gefitinib, although neither expression nor phosphorylation of insulin‐like growth factor 1 receptor correlated with intrinsic resistance. Breast receptor kinase (BRK) was more highly expressed in the sensitive cell lines, but siRNA knockdown of neither BRK nor MET affected sensitivity. Our data suggest that overexpression of EGFR and multiple related cell surface receptors may be associated with sensitivity to gefitinib and that differences between our data and the literature highlight that biomarkers of response are tumour type‐ and cell line‐dependent. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Syndromic and non‐syndromic aneurysms of the human ascending aorta share activation of the Smad2 pathway
Authors: Gomez Delphine , Al Haj Zen Ayman , Borges Luciano F , Philippe Monique , Gutierrez Paulo Sampaio , Jondeau Guillaume , Michel Jean‐Baptiste , Vranckx Roger
Published: January 2009

Common features such as elastic fibre destruction, mucoid accumulation, and smooth muscle cell apoptosis are co‐localized in aneurysms of the ascending aorta of various aetiologies. Recent experimental studies reported an activation of TGF‐β in aneurysms related to Marfan (and Loeys‐Dietz) syndrome. Here we investigate TGF‐β signalling in normal and pathological human ascending aortic wall in syndromic and non‐syndromic aneurysmal disease. Aneurysmal ascending aortic specimens, classified according to aetiology: syndromic MFS (n = 15, including two mutations in TGFBR2), associated with BAV (n = 15) or degenerative forms (n = 19), were examined. We show that the amounts of TGF‐β1 protein retained within and released by aneurysmal tissue were greater than for control aortic tissue, whatever the aetiology, contrasting with an unchanged TGF‐β1 mRNA level. The increase in stored TGF‐β1 was associated with enhanced LTBP‐1 protein and mRNA levels. These dysregulations of the extracellular ligand are associated with higher phosphorylated Smad2 and Smad2 mRNA levels in the ascending aortic wall from all types of aneurysm. This activation correlated with the degree of elastic fibre fragmentation. Surprisingly, there was no consistent association between the nuclear location of pSmad2 and extracellular TGF‐β1 and LTBP‐1 staining and between their respective mRNA expressions. In parallel, decorin was focally increased in aneurysmal media, whereas biglycan was globally decreased in aneurysmal aortas. In conclusion, this study highlights independent dysregulations of TGF‐β retention and Smad2 signalling in syndromic and non‐syndromic aneurysms of the ascending aorta. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Quality of security through triple key scheme in wireless sensor networks
Authors: Zia Tanveer A. , Zomaya Albert Y.
Published: January 2009

Quality and security are two intertwined concepts where quality seeks perfection while security countermeasures the elements which weakens the quality. Wireless sensor networks have emerged as a promising future of many sensitive applications. Due to the wireless media and the deployment nature, sensor networks are more prone to security attacks. Several security solutions have been proposed, mostly adding overheads to already resource limited sensor networks. Delivering security and quality simultaneously is challenging because security mechanism severely affects quality mechanisms in terms of performance, data confidentiality, availability, integrity, and authentication. This paper presents a quality of security (QoSec) concept through a triple key scheme (TKS) which has comparatively low security overheads hence providing a quality security solution against the known attacks in wireless sensor networks. Three metrics; time to transmit, latency overheads, and energy overheads are used to do comparative analysis with other existing solutions. Experimental results show that TKS has low overheads hence delivering a quality security at low computational cost. Copyright © 2009 John Wiley & Sons, Ltd.
Simulation study of IEEE 802.15.4 LR‐WPAN for industrial applications
Authors: Chen Feng , Wang Nan , German Reinhard , Dressler Falko
Published: January 2009

The IEEE 802.15.4 protocol has become the primary solution for many low‐rate wireless personal area network (LR‐WPAN) applications. This is especially the case for industrial sensor network applications such as automation control. We contribute to the better understanding of the protocol behavior by presenting a set of results of simulation experiments. Our results outline the capabilities of this protocol in the selected scenarios but also the limitations. In particular, we investigated the dependency of the protocol on protocol‐inherent parameters such as the beacon order and the superframe order but also to different traffic load. Our results can be used for planning and deploying IEEE 802.15.4‐ based sensor networks with specific performance demands. We put a special focus on application scenarios in industrial sensor network applications. The primary requirements are reduced end‐to‐end latency and energy consumption. Our studies are based on our new implementation of IEEE 802.15.4 developed for the simulation framework OMNeT++. Copyright © 2009 John Wiley & Sons, Ltd.
Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm
Authors: PIRINEN MATTI , KULATHINAL SANGITA , GASBARRA DARIO , SILLANPÄÄ MIKKO J.
Published: January 2009

Recent studies show that the PHASE algorithm is a state-of-the-art method for population-based haplotyping from individually genotyped data. We present a modified version of PHASE for estimating population haplotype frequencies from pooled DNA data. The algorithm is compared with (i) a maximum likelihood estimation under the multinomial model and (ii) a deterministic greedy algorithm, on both simulated and real data sets (HapMap data). Our results suggest that the PHASE algorithm is a method of choice also on pooled DNA data. The main reason for improvement over the other approaches is assumed to be the same as with individually genotyped data: the biologically motivated model of PHASE takes into account correlated genealogical histories of the haplotypes by modelling mutations and recombinations. The important questions of efficiency of DNA pooling as well as influence of the pool size on the accuracy of the estimates are also considered. Our results are in line with the earlier findings in that the pool size should be relatively small, only 2–5 individuals in our examples, in order to provide reliable estimates of population haplotype frequencies.
Inferring genetic values for quantitative traits non-parametrically
Authors: GIANOLA DANIEL , de los CAMPOS GUSTAVO
Published: January 2009

Inferences about genetic values and prediction of phenotypes for a quantitative trait in the presence of complex forms of gene action, issues of importance in animal and plant breeding, and in evolutionary quantitative genetics, are discussed. Current methods for dealing with epistatic variability via variance component models are reviewed. Problems posed by cryptic, non-linear, forms of epistasis are identified and discussed. Alternative statistical procedures are suggested. Non-parametric definitions of additive effects (breeding values), with and without employing molecular information, are proposed, and it is shown how these can be inferred using reproducing kernel Hilbert spaces regression. Two stylized examples are presented to demonstrate the methods numerically. The first example falls in the domain of the infinitesimal model of quantitative genetics, with additive and dominance effects inferred both parametrically and non-parametrically. The second example tackles a non-linear genetic system with two loci, and the predictive ability of several models is evaluated.
From “Linguistic Turn” and Hebrews Scholarship to Anadiplosis Iterata: The Enigma of a Structure
Authors: Gelardini Gabriella
Published: January 2009

In 1963, when the “linguistic turn” had evidently taken hold of New Testament studies, Albert Vanhoye, a linguistically trained Catholic priest, published a monograph entitled La structure littéraire de l'épître aux Hébreux.1 The manifold reactions to his refined literary-rhetorical approach and conclusions in favor of a concentric structure oscillated between euphoric approval and offensive disapproval. Along with its translation into German (1979/1980) and a decade later into English (1989), Vanhoye's study influenced and stimulated Hebrews scholarship like none other in the twentieth century.
The Rapture of the Christ: The “Pre-Ascension Ascension” of Jesus in the Theology of Faustus Socinus (1539—1604)
Authors: Gomes Alan W.
Published: January 2009

In this essay I examine a rather quirky and possibly novel teaching of Faustus Socinus (1539—1604): what George H. Williams calls a “pre-Ascension ascension” (hereafter PAA) of Christ into heaven. Faustus claimed that this bodily ascent into heaven took place before Christ's final visible ascension to heaven some time between his baptism and the commencement of his earthly teaching ministry. The theory states in brief that Christ, “after he was born a human, and before he began to discharge the office entrusted to him by God, his own Father, … was in heaven, and abode there for some time.” Christ took this heavenly sojourn “that he might hear from God himself and … see in his very presence what he was soon to proclaim and reveal to the world in God's own name.”1 In another place Socinus states that Jesus, “after his birth from the virgin, and before he announced the gospel, was raptured into heaven (in caelum raptus fuerit). There he learned from God himself what he was to reveal to the human race.”2
Colorectal cancer screening policy in Hungary
Authors: Gulácsi László , Vas Gábor , Pintér István , Kriszbacher Ildikó
Published: January 2009

We read with great interest the excellent paper of Gutiérrez-Ibarluzea et al. on the review of current policies of screening for colorectal cancer in European countries (12).Colorectal cancer screening has been a hot topic in health technology assessment and medical decision making (13;15;18). The study by Gutiérrez-Ibarluzea and colleagues focused mainly on the “old” fifteen member states of the European Union; however, colorectal cancer represents a large epidemiological (3;11) and economic (4) burden for the society and the healthcare financing agency in Eastern European countries. We would like to highlight some important aspect of colorectal cancer screening in Hungary.
Colorectal cancer screening policy in Europe
Authors: Gutiérrez-Ibarluzea Iñaki , Asua José
Published: January 2009

We agreed with Gulácsi et al. on their perception about our article that did not include those eastern European countries that have recently joined the European Union. It does not mean that we tried to provide partial information or that we wanted to diminish the information with other purposes. In fact, the title of our article when it was sent to be published was: “Screening for colon-rectal cancer in the Europe of fifteen, Norway and Switzerland. So equal, so different. Is it time for a common approach?” and so was the title of the oral communication presented in the Annual Meeting of HTAi held in Montreal last summer (7). Even when we believed that this title was more accurate to the data provided in the article, we finally followed the suggestions of the reviewers to make the title short and comprehensive.
Multivariate analysis of Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) Venus Express nightside and limb observations
Authors: Erard S. , Drossart P. , Piccioni G.
Published: January 2009

Spectral signatures measured by Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) on the nightside and at the limb of Venus are analyzed with Independent Component Analysis. A methodology has been set up to minimize instrumental effects and to interpret the results on the basis of studies of the most common situations in the data set. The main spectral components commonly retrieved on the nightside include the bulk signal modulated by atmospheric opacity variations, photometric variations in the long‐wavelength atmospheric windows, a branching parameter describing particle size variations, and O2 emission at 1.26 and 1.58 μm. Faint atmospheric windows are detected at 1.51, 1.55, 1.78, and 1.82 μm for the first time. The polar vortex structure is outlined, with two main circular areas made of many concentric rings with alternating particle sizes. Discrete clouds about 100 km across are observed in low opacity conditions. High‐altitude, warm clouds are tentatively observed from the polar vortex down to 55°S. At the limb, the two signatures of CO2 nonlocal thermodynamic equilibrium emission are directly mapped, and the thermal structure of the cloud layers and upper atmosphere is apparent. Surface emission is detected with a spatial resolution limited by atmosphere blurring, reaching ∼35 km in exceptional conditions. Horizontal offsets indicate that the radiation propagates mostly vertically, consistent with the large optical depth and vertical extent of the cloud layer. Intense scattering is suspected to take place at the bottom of the atmosphere, at least in the southern plains.
Efficient full‐wave analysis of an open‐ended waveguide radiating through a two‐layer superstrate
Authors: Tan Weihua , Shen Zhongxiang
Published: January 2009

This paper presents an efficient full‐wave analysis of an open‐ended waveguide radiating through a two‐layer superstrate. The spectral dyadic Green's function for a multilayer medium is formulated through cascaded matrices, each of which corresponds to one layer of the superstrate independently. The reflection coefficient matrix is derived by enforcing the field matching condition at the opening of the waveguide. The generalized pencil of function (GPOF) method and Gaussian quadrature are adopted to accelerate the computation. Once the excitation and the Green's function are known, the far‐field radiation pattern and directivity are obtained directly from the spectra of the electric and magnetic fields in the half free space. An open‐ended WR‐90 waveguide radiating through a two‐layer superstrate is considered as an example to verify the proposed efficient full‐wave analysis. The effect of the superstrate on the directivity of open‐ended waveguides is also examined and discussed.
A model for lateral hyporheic flow based on valley slope and channel sinuosity
Authors: Cardenas M. Bayani
Published: January 2009

The meandering of rivers results in head gradients across point bar deposits leading to hyporheic exchange: the flow of groundwater from and back to the stream. Two models for predicting horizontal fluid flux through the hyporheic zone, one based solely on valley slope and another that uses both valley slope and channel sinuosity, are presented in this article. Both models require knowledge of aquifer hydraulic conductivity. The models are developed via a suite of groundwater flow simulations with boundary conditions taking a variety of channel geometries, idealized as sinusoidal, and valley slopes that we assume are similar to that of the water table. Functional predictive models are developed by fitting a line or surface to discrete model output which covers the spectrum of most natural meandering rivers. Since the fitted models only require channel slope and/or sinuosity (plus hydraulic conductivity), they are amenable for regional estimation of hyporheic flux using digital terrain data.
Prevention of human granulocyte colony‐stimulating factor protein aggregation in recombinant Pichia pastoris fed‐batch fermentation using additives
Authors: Bahrami Ali , Shojaosadati Seyed Abbas , Khalilzadeh Rasoul , Mohammadian Jafar , Farahani Ebrahim Vashghani , Masoumian Mohammad Reza
Published: January 2009

rhG‐CSF (recombinant human granulocyte colony‐stimulating factor) was expressed in the yeast Pichia pastoris under the control of the AOX1 (alcohol oxidase 1) promoter. The production of rhG‐CSF was induced by switching from growth on glycerol to growth on methanol. In the induction phase, the methanol feed rate had a significant effect on the specific expression rate of rhG‐CSF. A constant feed rate of 16 ml·h−1·l−1 was found to be optimal for a high specific expression rate of rhG‐CSF (0.058 mg−1·h−1·g DCW−1; DCW is dry cell weight). Under this condition, a maximum concentration of 300 mg/l of rhG‐CSF and the expression yield of 0.6 mg of rhG‐CSF/g of methanol were attained. However, the secreted rhG‐CSF was shown to exist as aggregates in the culture broth, owing to hydrophobic interactions. To prevent undesirable protein aggregation, the presence of additional additives in the P. pastoris culture medium was investigated. Among seven additives tested, Tween 20, Tween 80 and betaine exhibited the best results in respect of preventing the formation of rhG‐CSF protein aggregates.
Nuclear weapons at a crossroads as Obama enters office
Authors: Kramer David
Published: January 2009

Modernized warheads and new production facilities are on hold pending an updated nuclear policy demanded by Congress.
The versatility of nanoscale mechanical resonators
Authors: Cleland Andrew N.
Published: January 2009

The vibrations of tiny “diving boards” enable scientists to view the world one atom at a time and may allow the observation of quantum effects in mechanical systems.
ABA mediation of shoot cytokinin oxidase activity: assessing its impacts on cytokinin status and biomass allocation of nutrient-deprived durum wheat
Authors: Vysotskaya Lidia B. , Korobova Alla V. , Veselov Stanislav Y. , Dodd Ian C. , Kudoyarova Guzel R.
Published: January 2009

Although nutrient deprivation alters the concentrations of several plant hormones, the role of each in decreasing shoot-to-root ratio is not clear. A 10-fold dilution of the nutrient concentration supplied to hydroponically-grown 7-day-old durum wheat (Triticum turgidum L. ssp. durum Desf.) plants decreased shoot growth, shoot-to-root ratio and shoot and root cytokinin concentrations, increased shoot ABA concentration and shoot cytokinin oxidase activity, but had no effect on xylem sap ABA and cytokinin concentrations. Nutrient deprivation also increased xylem concentrations of conjugated ABA. The role of ABA in these responses was addressed by adding 11.4 µm ABA to the nutrient solution of well fertilised plants, or 1.2 mm fluridone (an inhibitor of ABA biosynthesis) to the nutrient solution of nutrient-deprived plants. The former induced similar changes in shoot-to-root ratio (by inhibiting shoot growth), shoot ABA concentration, shoot and root cytokinin concentrations and shoot cytokinin oxidase activity as nutrient deprivation. Conversely, fluridone addition to nutrient-deprived plants restored shoot-to-root ratio (by inhibiting root growth), shoot ABA concentration, shoot and root cytokinin concentrations to levels similar to well fertilised plants. Although root growth maintenance during nutrient deprivation depends on a threshold ABA concentration, shoot growth inhibition is independent of shoot ABA status. Although fluridone decreased shoot cytokinin oxidase activity of nutrient-deprived plants, it was still 1.7-fold greater than well fertilised plants, implying that nutrient deprivation could also activate shoot cytokinin oxidase independently of ABA. These data question the root signal basis of cytokinin action, but demonstrate that changes in ABA status can regulate shoot cytokinin concentrations via altering their metabolism.
The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair
Authors: Fineran Peter C. , Blower Tim R. , Foulds Ian J. , Humphreys David P. , Lilley Kathryn S. , Salmond George P. C.
Published: January 2009

Various mechanisms exist that enable bacteria to resist bacteriophage infection. Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population. A highly effective 2-gene Abi system from the phytopathogen
Erwinia carotovora
subspecies
atroseptica
, designated ToxIN, is described. The ToxIN Abi system also functions as a toxin–antitoxin (TA) pair, with ToxN inhibiting bacterial growth and the tandemly repeated ToxI RNA antitoxin counteracting the toxicity. TA modules are currently divided into 2 classes, protein and RNA antisense. We provide evidence that ToxIN defines an entirely new TA class that functions via a novel protein-RNA mechanism, with analogous systems present in diverse bacteria. Despite the debated role of TA systems, we demonstrate that ToxIN provides viral resistance in a range of bacterial genera against multiple phages. This is the first demonstration of a novel mechanistic class of TA systems and of an Abi system functioning in different bacterial genera, both with implications for the dynamics of phage-bacterial interactions.
Gamma flicker triggers attentional selection without awareness
Authors: Bauer Frank , Cheadle Samuel W. , Parton Andrew , Müller Hermann J. , Usher Marius
Published: January 2009

Gamma band modulations in neural activity have been proposed to mediate attentional processes. To support a causal link between gamma activity and attentional selection, we attempt to evoke gamma oscillations by a 50-Hz subliminal flicker. We find that a subliminal 50-Hz flicker at a target location, before target presentation, speeds up and enhances target detection and discrimination. This effect is specific to the middle of the gamma range because it is not evident at <35-Hz flicker. It requires 300 ms to build up, dissipates within 250 ms of flicker offset, and shows a tendency to invert after 500 ms. The results are discussed in relation to a role for gamma band neural synchrony in the allocation of visual attention.
Progenitor cell proliferation in the retina is dependent on Notch-independent Sonic hedgehog/Hes1 activity
Authors: Wall Dana S. , Mears Alan J. , McNeill Brian , Mazerolle Chantal , Thurig Sherry , Wang Yaping , Kageyama Ryoichiro , Wallace Valerie A.
Published: January 2009

Sonic hedgehog (Shh) is an indispensable, extrinsic cue that regulates progenitor and stem cell behavior in the developing and adult mammalian central nervous system. Here, we investigate the link between the Shh signaling pathway and Hes1, a classical Notch target. We show that Shh-driven stabilization of Hes1 is independent of Notch signaling and requires the Shh effector Gli2. We identify Gli2 as a primary mediator of this response by showing that Gli2 is required for Hh (Hedgehog)-dependent up-regulation of Hes1. We also show using chromatin immunoprecipitation that Gli2 binds to the Hes1 promoter, which suggests that Hes1 is a Hh-dependent direct target of Gli2 signaling. Finally, we show that Shh stimulation of progenitor proliferation and cell diversification requires Gli2 and Hes1 activity. This paper is the first demonstration of the mechanistic and functional link between Shh, Gli, and Hes1 in the regulation of progenitor cell behavior.
Importance of Urinary Tract Infection to Antibiotic Use Among Hospitalized Patients
Authors: Gandhi Tejal , Flanders Scott A. , Markovitz Erica , Saint Sanjay , Kaul Daniel R.
Published: January 2009

Many patients with asymptomatic bacteriuria receive extended courses of broad-spectrum antibiotics. Antibiotic use was analyzed in patients admitted to the hospital with urinary tract infection. Strategies to optimize antibiotic use for such patients are discussed and include implementing a process whereby a urine culture is automatically performed if a urinalysis result suggests infection.
Crystallization Kinetics and Mechanism of Low‐Dielectric, Low‐Temperature, Cofirable CaO‐B2O3‐SiO2 Glass‐Ceramics
Authors: Chang Chia‐Ruey , Jean Jau‐Ho
Published: January 2009

The crystallization kinetics and mechanism of low‐dielectric, low‐temperature, cofirable CaO‐B2O3‐SiO2 glass‐ceramics were investigated. Crystalline phases formed during firing included calcium silicates (CaSiO3, Ca3Si2O7, Ca2SiO4) and calcium borate (CaB2O4), with crystalline wollastonite (CaSiO3) the major phase. The crystallization kinetics of wollastonite followed an Avrami equation. The results of the present study showed an apparent activation energy of 200‐260 kJ/mol. Combined with the results of reduced growth rate (growth rate × viscosity) and thermal analysis, the rate‐controlling mechanism of crystallization appeared to be a two‐dimensional surface nucleation growth. As the amount of crystalline wollastonite increased, the dielectric constant decreased, but the thermal expansion coefficient remained relatively unchanged.
Electromechanical Behavior of PZT‐Brass Unimorphs
Authors: Li Xiaoping , Shih Wan Y. , Aksay Ilhan A. , Shih Wei‐Heng
Published: January 2009

We have examined the static and dynamic electromechanical responses of PZT‐brass (piezoelectric‐nonpiezoelectric) plate unimorphs of various brass/PZT thickness ratios. The study was performed both experimentally and theoretically. The static measurements showed that, given a PZT layer thickness, there exists a brass/PZT thickness ratio that gives the unimorph the highest static displacement under an applied field. The effects of geometric shape and external loading on the displacement of the unimorphs were also examined. The dynamic measurements showed that, given a PZT layer thickness, the bending‐mode resonance frequencies increase with an increasing brass/PZT thickness ratio. These results were in good agreement with the theoretical predictions that were obtained with the plate geometry.