bluuebunny/crossref_metadata_2025 huggingface dataset:
Prenatal diagnosis of adult polycystic kidney disease with DNA markers on chromosome 16 and the genetic heterogeneity problem
Authors: Novelli G. , Frontali M. , Baldini D. , Bosman C. , Dallapiccola B. , Pachì A. , Torcia F.
Published: March 2007

A prenatal diagnosis of adult polycystic kidney disease by DNA testing is reported. Evidence showing a linkage between the disease and the 3′HVR and 24.1 restriction fragment length polymorphisms (RFLPs) on chromosome 16 was obtained in the proband's family by linkage analysis of data and homogeneity testing with Italian families of the linked type. Fetal genotype prediction based on both flanking markers was confirmed by histological and ultrastructural findings in fetal kidneys.
Amniotic fluid enzymes in pregnancies with trisomy 21
Authors: Giddy M. J. , Hay D. L. , Horacek I.
Published: March 2007

The activities of a range of microvillous enzymes in amniotic fluid from normal pregnancies (n = 213) and those complicated by trisomy 21 (n = 26) were compared in a prospective study. Using a centrifugal analyser, the activities of leucine aminopeptidase (LAP), gamma glutamyl transferase (GGT), aspartate transferase (AST), and isoenzymes of alkaline phosphate (ALP) were measured in amniotic fluid alongside alpha fetoprotein (AFP) levels. Of the markers studied, LAP was found to be the most reliable indicator of trisomy 21. Using levels below the 5th percentile, LAP showed sensitivity 73 per cent, specificity 94 per cent, and predictive value positive 63 percent. Although these tests would not replace karyotyping in all cases, the measurement of LAP could be useful as a rapid initial screening test, particularly when amniocentesis is performed for indications other than chromosomal abnormalities.
Exophthalmus–prenatal ultrasonic features for diagnosis of Crouzon syndrome
Authors: Menashe Y. , Baruch G. Ben , Rabinovitch O. , Shalev Y. , Katzenlson M. B. M. , Shalev E.
Published: March 2007

Prenatal real‐time ultrasonographic diagnosis of exophthalmus is presented. Diagnosis was made at the 35th week of gestation in a fetus of a patient affected with Crouzon syndrome (craniofacial dysotosis). Recognition of exophthalmus as a part of Crouzon syndrome and the easy visualization of the eye balls and palpebrae in the third trimester made the diagnosis possible.
Measurement of HPRT activity in the human unfertilized oocyte and pre‐embryo
Authors: Braude Peter R. , Monk Marilyn , Pickering Susan J. , Cant Anne , Johnson Martin H.
Published: March 2007

The hypoxanthine phosphoribosyl transferase (HPRT) and adenine phosphoribosyl transferase (APRT) activities in individual non‐fertilized human eggs and in human pre‐embryos (4‐cell to blastocyst stage) have been analysed. A wide spread of activities was observed, the mean values of which decline with time post‐ovulation for both eggs and advancing preembryonic stages. The variation in activities was less in groups of eggs or pre‐embryos recovered from a single ovulatory cycle. The activity of HPRT, but not of APRT, was readily detectable in single 4‐cell and 8‐cell blastomeres. When pre‐embryos at various preimplantation stages were exposed to α‐amanitin, to block transcription of mRNA from the preembryonic genome, no clear effect on HPRT activity was observed. It is concluded that the HPRT and APRT activities measured in the pre‐embryos studied here are likely to be maternally inherited, and that use of a direct assay for HPRT activity for the pre‐implantation diagnosis of Lesch–Nyhan disease would be premature.
A rare case of 68,XX triploidy diagnosed by amniocentesis
Authors: Kaffe Sara , Eliasen Carol , Wan Livia , Charles Norman , Jansen Valerie , Alba Greco M. , Hsu Lillian Y. F.
Published: March 2007

68,XX triploidy was found in the amniotic fluid cell culture of a 40‐year‐old patient. Elective termination of the pregnancy revealed a fetus with multiple congenital anomalies. While this case does show some common features with monosomy X, a greater similarity to the triploidy syndrome is observed.
Fetal skin biopsy in prenatal diagnosis of some genodermatoses
Authors: Bakharev V. A. , Aivazyan A. A. , Karetnikova N. A. , Mordovtsev V. N. , Yantovsky Yu. R.
Published: March 2007

Various methods of obtaining fetal skin for prenatal diagnosis of certain autosomal‐recessive congenital genodermatoses have been assessed. An attempt was made to obtain fetal skin by fetoscopy in 15 patients prior to pregnancy termination for a variety of medical reasons at 18–26 weeks. Specimens were obtained only in five cases (8 successful attempts out of 48). In twelve cases, of which five had a history of a child with junctional (Herlitz type) or dystrophic (Hallopeau‐Siemens type) epidermolysis bullosa or non‐bullous congenital ichthyosiform erythroderma at 16–25 weeks of pregnancy, fetal skin was obtained without fetoscopy under direct ultrasonic control. Specimens were obtained in all cases (33 successful attempts out of 39). In three cases, fetal pathology was diagnosed by the method of semi‐thin and ultra‐thin skin sections, and the respective pregnancies were terminated.
Fetal blood sampling demonstrating chimerism in monozygotic twins discordant for sex and tissue karyotype (46,XY and 45,X)
Authors: Gonsoulin Whitney , Copeland Karen L. , Carpenter Robert J. , Hughes Mark R. , Elder Frederick F. B.
Published: March 2007

Fetal blood sampling has been used in the genetic work‐up of twin gestations for rapid karotyping. We present a case of twins which on ultrasound evaluation revealed hydrops fetalis in one twin and a normal second twin. Fetal blood sampling revealed the presence of mosaicism for 46,XY/45,X in both twins. HLA antigen testing showed the twins to be identical. The patient elected pregnancy termination. Blood chromosomal analysis after delivery revealed both twins to have 46,XY/45,X mosaicism, but the twin with signs of hydrops fetalis had tissue chromosomes of 45,X and the normal twin had tissue chromosomes of 46,XY. Amniotic fluid chromosomal analysis revealed 46,XY in twin A and 45,X in twin B. This represents a case of identical (monozygotic) twins with sex discordance. In this case, there was the probable occurrence of post‐zygotic chromosomal non‐disjunction leading to the discordancy of the sex in this set of twins. With the presence of vascular communication in monozygotic twins, there is the possibility of exchange of blood in monozygotic twins and the result of blood chimerism in twins.
Prenatal diagnosis of thrombocytopenia absent radius syndrome by ultrasound and cordocentesis
Authors: Donnenfeld Alan E. , Wiseman Barbara , Lavi Ehud , Weiner Stuart
Published: March 2007

The prenatal diagnosis of thrombocytopenia absent radius (TAR) syndrome, utilizing ultrasound and cordocentesis, is described. To our knowledge, this represents the first prenatal diagnosis of this condition in an index case. The diagnostic evaluation of a fetus with upper extremity limb reduction defects is discussed.
Familial cystic hygroma with normal karyotype
Authors: Watson William J. , Thorp John M. , Seeds John W.
Published: March 2007

A patient is described who had three consecutive fetuses with cystic hygroma and hydrops, two of which had documentation of normal karyotype. Some twenty percent of fetuses with cystic hygroma have a normal karyotype, and many of these have other major malformations. An autosomal recessive pattern of inheritance has been postulated, but cystic hygroma may also occur is association with a variety of syndromes, some of which have other patterns of inheritance.
Unilateral congenital short femur: A case report
Authors: Ashkenazy M. , Lurie S. , Ben‐Itzhak I. , Appelman Z. , Caspi B.
Published: March 2007

A case of congenital short femur in an otherwise healthy infant is described. Antenatal sonographic diagnosis was made at 26 weeks of gestation. The left femur was shorter than the right (ratio 0·82–0·85). In this case, the occurrence of congenital short femur was sporadic. The diagnosis was confirmed after delivery. This case illustrates the importance of ultrasound as an early detector of certain congenital anomalies and as a useful tool in their follow‐up.
First and early second‐trimester diagnosis of fetal urinary tract anomalies using transvaginal sonography
Authors: Bronshtein M. , Yoffe N. , Brandes J. M. , Blumenfeld Z.
Published: March 2007

Urinary tract anomalies are common. Prenatal diagnosis is important and enables either special obstetric management or termination of pregnancy and probably in the future, intrauterine intervention. Transvaginal sonography (TVS) allows visualization of the normal and anomalous fetal urinary tract at an early stage. One thousand nine hundred and forty women were examined via TVS at an early stage of pregnancy between 10 and 16 weeks from the last menstrual period (LMP) and 35 anomalies (1·8 per cent) were clearly identified: 29 cases of low urinary tract obstruction, 2 cases of multicystic dysplastic kidney, 2 cases of polycystic kidney (infantile type), 1 case of double collecting system, and 1 case of horseshoe kidney. Potter syndrome could be ruled out in three patients who had delivered fetuses suffering from this anomaly in previous pregnancies. The concise and early identification of anomalies makes TVS an important aid in the hands of the obstetrician, ultrasonographer, and neonatologist.
Ring 19 mosaicism detected during prenatal diagnosis
Authors: Gillessen‐Kaesbach Gabriele , Ngo Nhan T. K.
Published: March 2007

A ring chromosome 19 was found in 14 of 20 metaphases (67 per cent) derived from amniotic fluid cell cultures following amniocentesis because of increased maternal age. Elective termination of the pregnancy revealed a hypotrophic female fetus with mild dysmorphic signs, but no congenital malformations. The case is discussed in relation to three reports in the literature of ring chromosome 19 mosaicism in a phenotypically normal girl, a mentally retarded man, and a boy with normal psychomotor development and minor dysmorphic features.
Potential role of the cellular allergen stimulation test (CAST) in diagnosis of allergic bronchopulmonary aspergillosis (ABPA) in cystic fibrosis
Authors: Ringer Stephanie , Hipler Uta‐Christina , Elsner Peter , Zintl Felix , Mainz Jochen
Published: March 2007

Allergic bronchopulmonary aspergillosis (ABPA) is a severe complication in cystic fibrosis (CF), which is difficult to identify because of overlapping unspecific diagnostic features with common CF‐manifestations. The cellular allergen stimulation test (CAST) is used in diagnosis of allergic and pseudoallergic reactions. This assay is based on the determination of sulfidoleukotrienes, which are produced by allergen‐stimulated basophils in vitro. The potential role of CAST in diagnosis of ABPA was evaluated in this study. The CAST assay was applied in 27 CF‐patients including eight subjects with positive clinical and serological signs of ABPA. Additional to the Nelson‐criteria for diagnosis of ABPA specific IgE against recombinant Aspergillus antigens (rAsp f 1, 2, 3, 4, and 6) were assessed. The CAST results were positive in all ABPA‐patients and in five controls without any sign of ABPA except positive specific IgE against Aspergillus fumigatus (sensitivity of 100%, specificity of 74%). Specific IgE against rAsp f 4 and/or f 6 were positive in six of the eight ABPA‐patients, but not in the controls. Positive CAST results, total serum IgE > 500 U/ml and positive IgE antibodies against rAsp f 4 and/or f 6 were only found in ABPA‐patients (specificity of 100%). The CAST assay on its own includes high sensitivity with lower specificity. For the discrimination of ABPA from sensitization to Aspergillus, the CAST, the highly elevated total serum IgE and rAsp in combination are potential auxiliary diagnostic parameters. Pediatr Pulmonol. 2007; 42:314–318. © 2007 Wiley‐Liss, Inc.
Flexible fiberoptic bronchoscopy in children with heart diseases: A twelve years experience
Authors: Cerda Jaime , Chacón Jorge , Reichhard Cristina , Bertrand Pablo , Holmgren Nils L. , Clavería Cristián , Sánchez Ignacio
Published: March 2007

In children, cardiac diseases and respiratory disorders are tightly linked entities whose evaluation should be performed integrally. Flexible fiberoptic bronchoscopy (FB) presents a diagnostic and therapeutic role by assessing the airway anatomically, dynamically, and through the performance of several procedures. The present study describes our experience on FB assessment in children with congenital and acquired cardiac diseases, providing a characterization of the principal demographic and clinical features. Records of 72 patients under 14 years (mean age 21 months) with heart diseases, corresponding to 104 FB performed between January 1993 and October 2004 were reviewed. The principal cardiac diseases were left‐to‐right shunt (51.9%), followed by right‐to‐left shunt (17.3%) and miscellaneous cardiopathies (8.7%). The main indications for FB assessment were study of atelectasis (35%), stridor (14%), and pneumonia (14%). Airway malacias, as a group, were the commonest finding, represented mainly by left main bronchus malacia (24%). The second most common finding was stenosis by extrinsic compression, and among these, 75% corresponded to left main bronchus compression. Sixteen different types of clinically meaningful utilities were obtained. No mortality was reported and in only one procedure was there a major complication, which was easily managed. We concluded that FB is an important and safe diagnostic—therapeutic tool in the health care of neonates, infants, and children with a variety of cardiac diseases. Pediatr Pulmonol. 2007; 42:319–324. © 2007 Wiley‐Liss, Inc.
Effects of amino acid composition, finite size of proteins, and sparse statistics on distance‐dependent statistical pair potentials
Authors: Rykunov Dmitry , Fiser András
Published: March 2007

Statistical distance dependent pair potentials are frequently used in a variety of folding, threading, and modeling studies of proteins. The applicability of these types of potentials is tightly connected to the reliability of statistical observations. We explored the possible origin and extent of false positive signals in statistical potentials by analyzing their distance dependence in a variety of randomized protein‐like models. While on average potentials derived from such models are expected to equal zero at any distance, we demonstrate that systematic and significant distortions exist. These distortions originate from the limited statistical counts in local environments of proteins and from the limited size of protein structures at large distances. We suggest that these systematic errors in statistical potentials are connected to the dependence of amino acid composition on protein size and to variation in protein sizes. Additionally, atom‐based potentials are dominated by a false positive signal that is due to correlation among distances measured from atoms of one residue to atoms of another residue. The significance of residue‐based pairwise potentials at various spatial pair separations was assessed in this study and it was found that as few as ∼50% of potential values were statistically significant at distances below 4 Å, and only at most ∼80% of them were significant at larger pair separations. A new definition for reference state, free of the observed systematic errors, is suggested. It has been demonstrated to generate statistical potentials that compare favorably to other publicly available ones. Proteins 2007 © 2007 Wiley‐Liss, Inc.
Activation loop phosphorylation‐independent kinase activity of human protein kinase C ζ
Authors: Ranganathan Senthil , Wang Yimin , Kern Francis G. , Qu Zhican , Li Rongbao
Published: March 2007

Atypical protein kinase C ζ (PKCζ) plays an important role in cell proliferation and survival. PKCζ and its truncated form containing only the kinase domain, CATζ, have been reported to be activated by the phosphorylation of threonine 410 in the activation loop. We expressed both the full length PKCζ and CATζ in a baculovirus/insect cell over‐expression system and purified the proteins for biochemical characterization. Ion exchange chromatography of CATζ revealed three species with different levels of phosphorylation at Thr‐410 and allowed the isolation of the CATζ protein devoid of phosphorylation at Thr‐410. All three species of CATζ were active and their activity was not correlated with phosphorylation at Thr‐410, indicating that the kinase activity of CATζ did not depend solely on activation loop phosphorylation. Tyrosine phosphorylation was detected in all three species of CATζ and the full length PKCζ. Homology structural modeling of PKCζ revealed a conserved, predicted‐to‐be phosphorylated tyrosine residue, Tyr‐428, in the close proximity of the RD motif of the catalytic loop and of Thr‐410 in the activation loop. The structural analysis indicated that phospho‐Tyr‐428 would interact with two key, positively‐charged residues to form a triad conformation similar to that formed by phospho‐Thr‐410. Based on these observations, it is possible that the Thr‐410 phosphorylation‐independent kinase activity of CATζ is regulated by the phosphorylation of Tyr‐428. This alternative mode of PKCζ activation is supported by the observed stimulation of PKCζ kinase activity upon phosphorylation at the equivalent site by Abl, and may be involved in resistance to drug‐induced apoptosis. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Identifying long‐range structure in the intrinsically unstructured transactivation domain of p53
Authors: Vise Pamela , Baral Bharat , Stancik Amber , Lowry David F. , Daughdrill Gary W.
Published: March 2007

Paramagnetic relaxation enhancement (PRE) was used to identify a compact dynamic structure for the intrinsically unstructured transactivation domain of the tumor suppressor protein, p53. Our results show that p53 residues essential for binding to the ubiquitin ligase, MDM2, and the 70 kDa subunit of replication protein A, RPA70, are separated by an average distance of 10–15 Å. This result suggests that a more extended member of the ensemble must be populated prior to binding either MDM2 or RPA70. We also show that PRE can be used to detect intermolecular distances between p53 and RPA70. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Identification by surface plasmon resonance of the mycobacterial lipomannan and lipoarabinomannan domains involved in binding to CD14 and LPS‐binding protein
Authors: Elass Elisabeth , Coddeville Bernadette , Guérardel Yann , Kremer Laurent , Maes Emmanuel , Mazurier Joël , Legrand Dominique
Published: March 2007

The mycobacterial lipoglycans, lipomannan (LM) and lipoarabinomannan (LAM), regulate host defence mechanisms through their interaction with pattern recognition receptors such as Toll‐like receptors (TLRs). We have developed a surface plasmon resonance assay to analyse the molecular basis for the recognition of Mycobacterium kansasii LM or LAM, by immobilized CD14 and LPS‐binding protein (LBP) both being capable to promote presentation of bacterial glycolipids to TLRs. The affinity of either LM/LAM was higher to CD14 than to LBP. Kinetic and Scatchard analyses were consistent with a model involving a single class of binding sites. These interactions required the lipidic anchor, but not the carbohydrate domains, of LM or LAM. We also provide evidence that addition of recombinant LBP enhanced the stimulatory effect of LM or LAM on matrix metalloproteinase‐9 expression and secretion in macrophages, through a TLR1/TLR2‐dependent mechanism.
DESMOID TUMOUR FOLLOWING A DISTAL RADIUS FRACTURE – A COMPLICATION OR A COINCIDENCE?
Authors: TSAI L. H. C. , THAMBOO T. P. , LIM A. Y. T.
Published: March 2007

We describe a case of a desmoid tumour occurring 15 months following an uncomplicated fracture of the left distal radius. The occurrence of a desmoid tumour after fracture is extremely rare and a Medline search revealed only two previous reports. The correlation between the site of trauma and the tumour and the time interval between trauma and presentation strongly supports a causal role of the fracture in the occurrence of this tumour.
Infantile gastroenteritis in the community:a cost-of-illness study
Authors: LORGELLY P. K. , JOSHI D. , ITURRIZA GÓMARA M. , FLOOD C. , HUGHES C. A. , DALRYMPLE J. , GRAY J. , MUGFORD M.
Published: March 2007

Rotavirus infections are the main cause of gastroenteritis in infants and children and it is expected that by the age of 5 years, nearly every child will have experienced at least one episode of rotavirus gastroenteritis. While severe cases are hospitalized, milder disease is either treated at home or by the GP, and as such the true prevalence of rotavirus infection in the community, and the burden of disease, is unknown. This paper reports the results of a cost-of-illness study which was conducted alongside a structured community surveillance study. Forty-eight percent of our sample was found to have rotavirus acute gastroenteritis; and the average total cost of a child presenting with rotavirus gastroenteritis ranged between £59 and £143 per episode, depending on the perspective. Given the prevalence and severity of the disease, the estimated burden of rotavirus gastroenteritis to society is £11.5 million per year.
Heterologous Protein Expression Affects the Death Kinetics of Baculovirus‐Infected Insect Cell Cultures: A Quantitative Study by Use of n‐Target Theory
Authors: Wu Suh‐Chin , Jarvis Donald L. , Dale Bruce E. , Liao James C.
Published: March 2007

The death of cultured insect cells after baculovirus infection is a time‐dependent event. Without a quantitative model, it is difficult to characterize its kinetics. Our group has shown that the cell survival rate can be characterized by use of the n‐target theory, which involves only two parameters: the number of hypothetical inactivation targets (n) and the first‐order death rate (k). In this study, we used different recombinant viruses to examine the effect of heterologous protein expression on the cell survival rate. The proteins expressed were β‐galactosidase, human T‐cell leukemia virus type I p40x, human interleukin‐2, and human tissue plasminogen activator (tPA). The survival rate was affected by protein expression, but the n value remained constant if the protein expression level was high (above 30 mg/L). Low‐level expression of secreted, glycosylated tPA resulted in a reduced n value, which was restored to the normal value when the tPA signal peptide and prosequence were deleted. In addition, if the n value was normal (10–11), the level of protein expression correlated negatively with the death rate. However, if the n value was reduced by unfavorable culture conditions or foreign protein expression, the expression level correlated positively with the death rate. A dimensionless plot with kt as the dimensionless time shows that alteration of the k value while retaining constant n is equivalent to a rescaling of time. Therefore, the survival curves with constant n reduce to a single curve on the dimensionless plot. Although the underlying mechanisms affecting n and k are still unknown, this study shows that they can serve as convenient phenotypes for investigating virus—host interactions.
Continuous β‐Galactosidase Production in Insect Cells with a p10 Gene Based Baculovirus Vector in a Two‐Stage Bioreactor System
Authors: Van Lier Frank L. J. , Van Duijnhoven C. F. Gerard , De Vaan Miranda M. J. A. C. M. , Vlak Just M. , Tramper Johannes
Published: March 2007

Continuous production of polyhedra or baculovirus‐expressed proteins in insect cell cultures is limited to about 4 weeks. The decrease in production has been ascribed to the interference of defective deletion mutants with wild‐type baculoviruses. The deleted genome sequences include the polyhedrin gene (or the heterologous gene of interest); in the remaining part, the major late p10 gene is always maintained. In the present study, the productivity of a recombinant baculovirus with the lacZ gene from Escherichia coli cloned downstream of the p10 promoter at the p10 locus was investigated. It was hypothesized that this p10 promoter driven gene is preserved over a longer period of time in a continuously operated two‐stage bioreactor system than foreign genes behind the polyhedrin promoter at the polyhedrin locus. In two separate runs, β‐galactosidase production with the p10‐lacZ recombinant reached quasi‐steady‐state levels of 30 and 60 units/cm3. Polyhedron production was about 3 × 106 and 6 × 106 polyhedra/cm3, respectively. However, both polyhedron and β‐galactosidase production decreased after about 30 days of relatively constant production. In the infection reactor, deletion mutants of the virus, which contained both the polyhedrin and lacZ gene, were predominant. Therefore, the presence of the polyhedrin or p10 gene alone in deletion mutants is not sufficient for prolonged expression; other genes involved in major late gene expression and not present in the deleted virus are probably necessary.
Influence of Ammonium on Growth, Metabolism, and Productivity of a Continuous Suspension Chinese Hamster Ovary Cell Culture
Authors: Hansen Henrik A. , Emborg Claus
Published: March 2007

A recombinant DNA Chinese hamster ovary (CHO) cell line which produces tissue‐type plasminogen activator (t‐PA) was cultivated continuously in suspension with a constant dilution rate of 0.5 day−1. The cultivation consisted of four phases with four different ammonium chloride concentrations (0,2.5, 5, and 7.5 mM) in the feed medium, causing a reactor ammonium concentration of up to 8 mM. Cell growth was not inhibited by these high ammonium concentrations, as cell densities of around 2.3 × 106 cells mL−1 were established. In contrast, the production of t‐PA was reduced under high ammonium concentration. The decrease in specific t‐PA production could be due to either a negative ammonium influence on productivity or a limitation of medium components, e.g., amino acids. Cell metabolism was changed under high ammonium concentrations, seen most clearly by a decrease in specific ammonium production by a factor of 8 and an increase in specific alanine production of 30%.
Fermentation Process Monitoring through Measurement of Aerosol Release
Authors: Huang Yu‐Li , Willeke Klaus , Juozaitis Arvydas , Donnelly Jean , Leeson Andrea , Wyza Robert
Published: March 2007

Fermentation involves many complex biological processes, some of which can be difficult to monitor. In this study, aerosol measurement was explored as an additional technique for monitoring a batch aerobic fermentation process using Escherichia coli strain W3110. Using this technique, a small aerosol extraction flow from the fermentor was continuously dried in‐line and analyzed with an aerosol size spectrometer and an aerosol photometer, used to measure the size‐integrated aerosol concentration. The results of the measurements demonstrated that the bacterial growth rate and the aerosol number concentration changed in a similar fashion: the effluent aerosol number concentration increased during the exponential growth phase and subsequently decreased after the bacterial cell concentration had reached a stable level. This aerosol concentration increased sharply approximately 1 h after initiation of growth. Thus, this increase in aerosol concentration suggests that the release of aerosols changes as a function of the microbial product formation activity. The products may change the rheological properties of the liquid, especially if surface‐active compounds are produced. The increase in aerosol concentration corresponds to a decrease in the values of the measured surface tension during the same time frame. Furthermore, the aerosol size spectrometer and the photometer showed similar time traces of the effluent aerosols. The size distributions of the solid residues from the fermentation broth remained relatively constant, while the concentrations changed with the phase of fermentation. As the photometer is inexpensive, it appears promising as a convenient instrument for monitoring fermentation processes.
Variability of Pacific subtropical cells in the 50‐year ECCO assimilation
Authors: Schott Friedrich A. , Wang Weiqiang , Stammer Detlef
Published: March 2007

The Pacific Subtropical Cell (STC) circulation is being analyzed from transport time series across 9°S and 9°N, obtained from the German ECCO (GECCO) assimilation results for the period 1952–2002. In this estimate, the interior Pacific STC convergence shows significantly less decadal slowdown from the 1960's to the 1990's (∼5Sv), than in previous estimates based on hydrographic sections. In the GECCO results, about half of this STC convergence decrease is compensated by an increase in the equatorward transport of the western boundary currents. Overall, the STC varies primarily on interannual time scale, with relatively short time lags between STC convergence and transport variations of the Equatorial Undercurrent at 140°W.
Structure of Mercury's magnetosphere for different pressure of the solar wind: Three dimensional hybrid simulations
Authors: Trávníček Pavel , Hellinger Petr , Schriver David
Published: March 2007

We have carried out a self‐consistent three dimensional global hybrid simulation study examining the interaction of the solar wind with Mercury's magnetosphere. We consider two cases: one with relatively high solar wind pressure, and another with relatively low solar wind pressure. With lower solar wind pressure, the subsolar magnetopause forms at about 1.7 RM (where RM is the planetary radius) and well pronounced cusp regions are formed; also a closed ion ring forms around the planet. In the higher solar wind pressure case the magnetopause is pushed closer to Mercury's surface (∼1.2 RM) and the cusp regions are less pronounced; the ion ring in this case is confined to a region closer to the planet with a smaller radial extent. In both cases reconnection occurs at about ∼2.4 RM down the magnetotail and a plasma sheet is formed. In general the plasma within the magnetosphere is more energetic in the high solar wind pressure case and the ion foreshock contains hotter magnetosheath plasma. Particles originating from the planet disperse through the magnetosphere, with the greatest congregation occurring in the inner magnetospheric drift driven rings in both cases. These planetary particles can also leak upstream into the foreshock region.
Ozone loss driven by nitrogen oxides and triggered by stratospheric warmings can outweigh the effect of halogens
Authors: Konopka Paul , Engel Andreas , Funke Bernd , Müller Rolf , Grooß Jens‐Uwe , Günther Gebhard , Wetter Thomas , Stiller Gabriele , von Clarmann Thomas , Glatthor Norbert , Oelhaf Hermann , Wetzel Gerald , López‐Puertas Manuel , Pirre Michel , Huret Nathalie , Riese Martin
Published: March 2007

Ozone loss in the lower and middle stratosphere in spring and summer, in particular over polar regions, is driven mainly by halogens and nitrogen oxides (NOx). Whereas the stratospheric chlorine levels are expected to decrease in the future, the role of NOx for the O3 budget in a changing climate is not well quantified. Here we combine satellite measurements and model simulations to diagnose the accumulated O3 loss during winter and spring 2002–2003 in the Arctic polar stratosphere. We show that in a winter stratosphere strongly disturbed by warmings, O3 loss processes driven by halogens and NOx can significantly overlap within the polar column and become comparable in magnitude even if a significant, halogen‐induced O3 loss has occurred. Whereas, until the beginning of March 2003, polar column O3 loss was mainly caused by the halogen chemistry within the vortex at an altitude around 18 km, the chemical O3 destruction in March and April was dominated by the NOx chemistry in O3‐rich air masses transported from the subtropics and mixed with the polar air above the region affected by the halogens. This NOx‐related O3 loss started around mid‐December 2002 in subtropical air masses above 30 km that moved poleward after the major warming in January, descended to 22 km with an increasing magnitude of O3 loss and reached surprisingly high values of up to 50% local loss around the end of April. To some extent, the NOx‐driven O3 loss was enhanced by mesospheric air trapped in the vortex at the beginning of the winter as a layer of few km in the vertical and transported downward within the vortex. The effect of NOx transported from the subtropics dominated the O3 loss processes in the polar stratosphere in spring 2003, both relative to the effect of the halogens and relative to the contribution of the mesospheric NOx sources. A comparison with the 1999/2000 Arctic winter and with the Antarctic vortex split event in 2002 shows that wave events triggered by stratospheric warmings may significantly enhance O3 loss driven by NOx when O3‐ and NOx‐rich air masses from the subtropics are transported poleward and are mixed with the vortex air.
A gravity wave climatology for Antarctica compiled from Challenging Minisatellite Payload/Global Positioning System (CHAMP/GPS) radio occultations
Authors: Baumgaertner A. J. G. , McDonald A. J.
Published: March 2007

The seasonal, geographical, and altitudinal dependence of gravity wave activity in the lower stratosphere over Antarctica is presented. Gravity wave activity is estimated by calculating potential energy, Ep, from radio occultation profiles obtained by the Challenging Minisatellite Payload/Global Positioning System (CHAMP/GPS) experiment. Significant seasonal variation of wave activity is observed. Smaller wave activity in summer is attributed to waves with small phase velocities experiencing critical level filtering. At other times of the year, when wave activity is large, less filtering occurs and the strong background wind is likely to cause Doppler shifting of waves to longer vertical wavelengths, which can reach larger amplitudes before saturating. Relationships between gravity wave activity and geographic location indicate that topography is a strong source for wave activity especially over the Antarctic Peninsula. However, wind rotation in this area was found to reduce the wave energy in summer at certain altitudes. A strong enhancement of wave energy is observed at the edge of the polar vortex. Again, reduced critical level filtering and Doppler shifting in the area of the jet are likely to be major causes for this finding. Possible limitations to this study due to observational filtering are discussed.
Conceptualizing lateral preferential flow and flow networks and simulating the effects on gauged and ungauged hillslopes
Authors: Weiler Markus , McDonnell J. J.
Published: March 2007

One of the greatest challenges in the field of hillslope hydrology is conceptualizing and parameterizing the effects of lateral preferential flow. Our current physically based and conceptual models often ignore such behavior. However, for addressing issues of land use change, water quality, and other predictions where flow amount and components of flow are imperative, dominant runoff processes like preferential subsurface flow need to be accounted for in the model structure. This paper provides a new approach to formalize the qualitative yet complex explanation of preferential flow into a numerical model structure. We base our examples on field studies of the well‐studied Maimai watershed (New Zealand). We then use the model as a learning tool for improved clarity into the old water paradox and reasons for the seemingly contradictory findings of lateral preferential flow of old water where applied line sources of tracer appear very quickly in the stream following application. We evaluate the model with multiple criteria, including ability to capture flow, hydrograph composition, and tracer breakthrough. We generate output ensembles with different pipe network geometries for model calibration and validation analysis. Surprisingly, the range of runoff response among the ensembles is narrow, indicating insensitivity to specific pipe placement. Our new model structure shows that high transport velocities for artificial line source tracers can be reconciled with the dominance of preevent water during runoff events even when lateral pipe flow dominates response. The work suggests overall that preferential flow can be parameterized within a process‐based model structure via the structured dialog between experimentalist and modeler.
A numerical approach to large deviations in continuous time
Authors: Lecomte Vivien , Tailleur Julien
Published: March 2007

We present an algorithm to evaluate large deviation functions associated to history-dependent
observables. Instead of relying on a time discretization procedure to approximate the
dynamics, we provide a direct continuous-time algorithm valuable for systems with multiple
timescales, thus extending the work of Giardinà, Kurchan and Peliti (2006 Phys. Rev. Lett.

96   120603).

The procedure is supplemented with a thermodynamic-integration scheme which improves
its efficiency. We also show how the method can be used to probe large deviation
functions in systems with a dynamical phase transition—revealed in our context
through the appearance of a non-analyticity in the large deviation functions.
Critical Strain of Carbon Nanotubes: An Atomic-Scale Finite Element Study
Authors: Guo X. , Leung A. Y. T. , Jiang H. , He X. Q. , Huang Y.
Published: March 2007

This paper employs the atomic-scale finite element method (AFEM) to study critical strain of axial buckling for carbon nanotubes (CNTs). Brenner et al. “second-generation” empirical potential is used to model covalent bonds among atoms. The computed energy curve and critical strain for (8, 0) single-walled CNT (SWNT) agree well with molecular dynamics simulations. Both local and global buckling are achieved, two corresponding buckling zones are obtained, and the global buckling behavior of SWNT with a larger aspect ratio approaches gradually to that of a column described by Euler’s formula. For double-walled CNTs with smaller ratio of length to outer diameter, the local buckling behavior can be explained by conventional shell theory very well. AFEM is an efficient way to study buckling of CNTs.
Impact of ‐based versus CT‐based attenuation correction on PET
Authors: van Dalen Jorn A. , Visser Eric P. , Vogel Wouter V. , Corstens Frans H. M. , Oyen Wim J. G.
Published: March 2007

Transmission (Tx) scans are used in PET for attenuation correction (AC). For standalone PET this is typically done using sources, for PET‐CT using CT. Therefore, standalone PET suffers from emission contamination during Tx scans, PET‐CT does not. Here, we studied the effects of AC across the two systems. With a cylindrical phantom (Jaszczak , Data Spectrum Corp.) with hollow spheres (diameter ) two studies were performed. In the first study the hollow spheres were filled with FDG and the background with . In the second study we used in the spheres and in the background. Both a low and a high object‐to‐background ratio are studied this way. Multiple scans were acquired on a standalone PET and a PET‐CT until 1% of the initial concentration remained. Activity concentration in the spheres and background was measured from the reconstructed images and compared to the actual concentration. For standalone PET, emission scans were reconstructed using hot Tx (emission contaminated) and cold Tx (not contaminated). Uniformity within the spheres was investigated by profile analysis. For PET‐CT, the concentration in the big spheres was recovered. For the smaller spheres, recovery was insufficient due to partial volume effects. For standalone PET the recoveries of the spheres were 20% (first study) and 13% (second study) lower than the actual concentration. Using hot Tx, underestimation of activity concentration was up to . Nonuniformities within the biggest spheres were up to 35%, 12%, and 5% (first study), using standalone PET with hot Tx, cold Tx, and using PET‐CT, respectively. Due to contamination of AC by emission photons, standalone PET results in a bias in the activity concentration and uniformity. Especially when patients get follow‐up PET scans on both standalone PET and PET‐CT, this may lead to misinterpretation.
Considerations When Using Discriminant Function Analysis of Antimicrobial Resistance Profiles To Identify Sources of Fecal Contamination of Surface Water in Michigan
Authors: Kaneene John B. , Miller RoseAnn , Sayah Raida , Johnson Yvette J. , Gilliland Dennis , Gardiner Joseph C.
Published: March 2007

The goals of this study were to (i) identify issues that affect the ability of discriminant function analysis (DA) of antimicrobial resistance profiles to differentiate sources of fecal contamination, (ii) test the accuracy of DA from a known-source library of fecal
Escherichia coli
isolates with isolates from environmental samples, and (iii) apply this DA to classify
E. coli
from surface water. A repeated cross-sectional study was used to collect fecal and environmental samples from Michigan livestock, wild geese, and surface water for bacterial isolation, identification, and antimicrobial susceptibility testing using disk diffusion for 12 agents chosen for their importance in treating
E. coli
infections or for their use as animal feed additives. Nonparametric DA was used to classify
E. coli
by source species individually and by groups according to antimicrobial exposure. A modified backwards model-building approach was applied to create the best decision rules for isolate differentiation with the smallest number of antimicrobial agents. Decision rules were generated from fecal isolates and applied to environmental isolates to determine the effectiveness of DA for identifying sources of contamination. Principal component analysis was applied to describe differences in resistance patterns between species groups. The average rate of correct classification by DA was improved by reducing the numbers of species classifications and antimicrobial agents. DA was able to correctly classify environmental isolates when fewer than four classifications were used. Water sample isolates were classified by livestock type. An evaluation of the performance of DA must take into consideration relative contributions of random chance and the true discriminatory power of the decision rules.
Lack of Control of Nitrite Assimilation by Ammonium in an Oceanic Picocyanobacterium,
Synechococcus
sp. Strain WH 8103
Authors: Wyman Michael , Bird Clare
Published: March 2007

In cyanobacteria, the transcriptional activator NtcA is involved in global nitrogen control and, in the absence of ammonium, regulates the expression of genes involved in the assimilation of alternative nitrogen sources. The oceanic picocyanobacterium
Synechococcus
sp. strain WH 8103 harbors a copy of
ntcA
, but in the present study, we show that unlike other marine cyanobacteria that have been investigated, this strain is capable of coassimilating nitrite when grown in the presence of ammonium. Transcript levels for the genes encoding the nitrate/nitrite-bispecific permease NrtP and nitrate reductase (NarB) were substantially down-regulated by ammonium, whereas the abundances of nitrite reductase (NirA) transcripts were similar in nitrite- and ammonium-grown cells. The growth of
Synechococcus
sp. strain WH 8103 in medium containing both ammonium and nitrite resulted in only minor changes in the expression profile in comparison to that of nitrite-grown cells with the exception that the gene encoding the high-affinity ammonium transporter Amt1 was down-regulated to the levels seen in ammonium-grown cells. Whereas the expression of
nrtP
,
narB
, and
amt1
appears to be NtcA dependent in this marine cyanobacterium, the transcription and expression of
nirA
appear not to be. The ability to coassimilate nitrite and reduced-nitrogen sources like ammonium may be an adaptive trait that enables oceanic strains like
Synechococcus
sp. strain WH 8103 to exploit the low nitrite concentrations found in oceanic surface waters that are not available to their principal and more numerous competitor,
Prochlorococcus
.
Thiols in Nitric Oxide Synthase-Containing
Nocardia
sp. Strain NRRL 5646
Authors: Lee Sungwon , Bergeron Hélène , Lau Peter C. K. , Rosazza John P. N.
Published: March 2007

Mycothiol (MSH) [1-
d
-
myo
-inosityl-2-(
N
-acetyl-
l
-cysteinyl)amido-2-deoxy-α-
d
-glucopyranoside], isolated as the bimane derivative, was established to be the major thiol in
Nocardia
sp. strain NRRL 5646, a species most closely related to
Nocardia brasiliensis
strain DSM 43758
T
. Thiol formation and detection of MSH-dependent formaldehyde dehydrogenase activity in cell extracts are relevant to the possible modulation of nitric oxide toxicity generated by strain NRRL 5646.
HpdR Is a Transcriptional Activator of
Sinorhizobium meliloti hpdA
, Which Encodes a Herbicide-Targeted 4-Hydroxyphenylpyruvate Dioxygenase
Authors: Loprasert Suvit , Whangsuk Wirongrong , Dubbs James M. , Sallabhan Ratiboot , Somsongkul Kumpanart , Mongkolsuk Skorn
Published: March 2007

Sinorhizobium meliloti hpdA
, which encodes the herbicide target 4-hydroxyphenylpyruvate dioxygenase, is positively regulated by HpdR. Gel mobility shift and DNase I footprinting analyses revealed that HpdR binds to a region that spans two conserved direct-repeat sequences within the
hpdR-hpdA
intergenic space. HpdR-dependent
hpdA
transcription occurs in the presence of 4-hydroxyphenylpyruvate, tyrosine, and phenylalanine, as well as during starvation.
Functional Complementation of the Essential Gene
fabG1
of
Mycobacterium tuberculosis
by
Mycobacterium smegmatis fabG
but Not
Escherichia coli fabG
Authors: Parish Tanya , Roberts Gretta , Laval Francoise , Schaeffer Merrill , Daffé Mamadou , Duncan Ken
Published: March 2007

Mycolic acids are a key component of the mycobacterial cell wall, providing structure and forming a major permeability barrier. In
Mycobacterium tuberculosis
mycolic acids are synthesized by type I and type II fatty acid synthases. One of the enzymes of the type II system is encoded by
fabG1
. We demonstrate here that this gene can be deleted from the
M. tuberculosis
chromosome only when another functional copy is provided elsewhere, showing that under normal culture conditions
fabG1
is essential. FabG1 activity can be replaced by the corresponding enzyme from the closely related species
Mycobacterium smegmatis
but not by the enzyme from
Escherichia coli. M. tuberculosis
carrying FabG from
M. smegmatis
showed no phenotypic changes, and both the mycolic acids and cell wall permeability were unchanged. Thus,
M. tuberculosis
and
M. smegmatis
enzymes are interchangeable and do not control the lengths and types of mycolic acids synthesized.
A Pair of Highly Conserved Two-Component Systems Participates in the Regulation of the Hypervariable FIR Proteins in DifferentLegionellaSpecies
Authors: Feldman Michal , Segal Gil
Published: March 2007

Legionella pneumophilaand other pathogenicLegionellaspecies multiply inside protozoa and human macrophages by using the Icm/Dot type IV secretion system. The IcmQ protein, which possesses pore-forming activity, and IcmR, which functions as its chaperone, are two essential components of this system. It was previously shown that in 29Legionellaspecies, a large hypervariable-gene family (firgenes) is located upstream from a conservedicmQgene, but although nonhomologous, the FIR proteins were found to function similarly together with their corresponding IcmQ proteins. Alignment of the regulatory regions of 29firgenes revealed that they can be divided into three regulatory groups; the first group contains a binding site for the CpxR response regulator, which was previously shown to regulate theL. pneumophila firgene (icmR); the second group, which includes most of thefirgenes, contains the CpxR binding site and an additional regulatory element that was identified here as a PmrA binding site; and the third group contains only the PmrA binding site. Analysis of the regulatory region of twofirgenes, which included substitutions in the CpxR and PmrA consensus sequences, a controlled expression system, as well as examination of direct binding with mobility shift assays, revealed that both CpxR and PmrA positively regulate the expression of thefirgenes that contain both regulatory elements. The change in the regulation of thefirgenes that occurred during the course of evolution might be required for the adaptation of the differentLegionellaspecies to their specific environmental hosts.