bluuebunny/crossref_metadata_2025 huggingface dataset:
Component‐resolved in vitro diagnosis in carrot allergy: Does the use of recombinant carrot allergens improve the reliability of the diagnostic procedure?
Authors: Ballmer‐Weber B. K. , Wangorsch A. , Bohle B. , Kaul S. , Kündig T. , Fötisch K. , Van Ree R. , Vieths S.
Published: July 2005

Background
In Europe, pollen‐related food allergy is the most frequent form of food allergy in adults. Reliability of current diagnostic procedures, however, is poor and therapeutic options are not available.

Objectives
In the present study, we created a panel of recombinant allergens from carrot and evaluated its potential in component‐resolved in vitro diagnosis of carrot allergy.

Methods
Recombinant (r) Dau c 1.0104, Dau c 1.0201 and Dau c 4 were cloned by a polymerase chain reaction strategy, expressed in Escherichia coli and purified. Carrot lipid transfer protein (LTP) was expressed in the yeast Pichia pastoris. Sera from 40 carrot‐allergic patients were investigated. Twenty‐one birch pollen‐allergic subjects with negative open provocation to carrot and 20 non‐allergic subjects were included as controls. IgE binding to recombinant allergens as well as to cross‐reactive carbohydrate determinants (CCD) was measured by ELISA. Cross‐reactivity between Dau c 1 isoforms and Bet v 1 was assayed by ELISA inhibition.

Biological activity of the recombinant carrot allergens was assessed by histamine release assay and peripheral blood mononuclear cells stimulation.

Results
Ninety‐eight percent of the carrot‐allergic patients were positive to at least one recombinant allergen; 98% reacted to rDau c 1.0104, 65% to rDau c 1.0201, 38% to rDau c 4 and 20% had IgE against CCD. Specificity using the recombinant allergens was high when compared with non‐allergic controls, but low compared with birch‐sensitized subjects without carrot allergy. Sensitization to Dau c 1.0201, however, proved to be highly specific for clinically relevant sensitization. Inhibition assays indicated the absence of LTP in carrot root extract, and epitope diversity between Dau c 1.0104, Dau c 1.0201 and Bet v 1.

Conclusions
Our panel of recombinant allergens from carrot can provide a standardized tool for in vitro diagnosis of carrot allergy, and for epitope studies.
Development of γδ thymocyte subsets during prenatal and postnatal ontogeny
Authors: Šinkora Marek , Šinkorová Jana , Holtmeier Wolfgang
Published: July 2005

In this report, we describe 12 subpopulations of porcine γδ thymocytes based on their expression of CD1, CD2, CD4, CD8‐isoforms and CD45RC. Our data suggest that γδ thymocytes can be divided into two major families: (a) one large family of CD4–γδ thymocytes that could be further subdivided according to the CD2/CD8αα phenotype and (b) a small family of CD4+γδ thymocytes bearing CD8αβ and possessing certain unusual features in comparison with other γδ thymocytes. Maturation of γδ thymocytes within the CD4– family begins with proliferation of the CD2+ CD8– CD1+ CD45RC–γδ common precursor. This developmental stage is followed by diversification into the CD2+ CD8αα+, CD2+ CD8– and CD2– CD8– subsets. Their further maturation is accompanied by a loss of expression of CD1 and by increased expression of CD45RC. Therefore, individual subsets develop from CD1+ CD45RC– through CD1– CD45RC– into CD1– CD45RC+ cells. On the other hand, γδ thymocytes within the CD4+ family bear exclusively CD8αβ, always express CD1, but may coexpress CD45RC. These cells have no counterpart in the periphery. Our observations suggest that all peripheral CD8+γδ T cells express CD8αα and that two subsets of these cells differing in major histocompatibility complex II expression, occur. We propose that one subset acquires CD8αα in the thymus while the second acquires CD8αα as a result of stimulation in the periphery.
Association of calpastatin (CAST/MspI) polymorphism with meat quality parameters of fatteners and its interaction withRYR1genotypes
Authors: Krzęcio E. , Kurył J. , Koćwin‐Podsiadła M. , Monin G.
Published: July 2005

The aim of this study was to analyse the effect of polymorphism of calpastatin (CAST) andRYR1genes for some meat quality traits taking into consideration the group of meatiness and their mutual interactions. Investigations were carried out on a group of 201 fatteners which were crosses of four breeds. The results obtained show thatCAST/MspI genotype has an effect close to the major effect for drip loss from LL muscle tissue at 48 h as well as at 96 h postmortem (0.92 and 0.96 SD respectively). Among the meat quality traits analysed and that were affected byCAST/MspI genotype, the animals withBBgenotype at this locus were characterized by the most profitable values of all these traits. Significant interactions betweenCASTandRYR1genotypes observed indicate that the quality of meat influenced byRYR1genotype may be modified by the simultaneous influence of genotype as regards theCASTlocus.
Responses in residual feed intake in lines of Large White pigs selected for growth rate on restricted feeding (measured on ad libitum individual feeding)
Authors: Nguyen N.H. , McPhee C.P. , Wade C.M.
Published: July 2005

Residual feed intake (RFI) represents the deviation of the actual ad libitum food consumption of each animal from that predicted from combination of growth rate, backfat and metabolic body weight measurements. After 4 years of divergent selection of pigs in lines for either high or low postweaning growth rate on restricted feeding, the high line exhibited a significant reduction in RFI relative to the low line. This indicated, to some extents, a lower energy requirement for maintenance in the high than in the low line, possibly because of reduced physical activity of the animals. Estimates of genetical parameters showed that RFI was moderately heritable and those genetic correlations of RFI with carcass backfat and food conversion ratio were moderate to highly positive.
Acral pseudolymphomatous angiokeratoma of children (APACHE)
Authors: Kim Youngjin , Dawes‐Higgs Elizabeth , Mann Stephen , Cook David K
Published: July 2005

A 13‐year‐old girl presented with a 10‐year history of multiple discrete red firm papules situated on her right upper arm. The histopathology examination revealed a massive subepidermal lymphohistiocytic infiltrate, consistent with acral pseudolymphomatous angiokeratoma of children. Treatment with topical application of mometasone furoate 0.1% cream once daily for 6 months improved the lesions partially. However, these papules returned to their pretreatment appearance and consistency within 6 months after the cessation of the topical corticosteroid. The authors prefer the term ‘papular angiolymphoid hyperplasia’ for this entity, based on the absence of histological angiokeratomatous features, the benign nature of the lesion and the previously reported cases from adults and non‐acral sites.
Cloning and characterization of a phospholipase C‐β isoform from the sea urchin Lytechinus pictus
Authors: Kulisz Andre , Dowal Louisa , Scarlata Suzanne , Shen Sheldon S.
Published: July 2005

Calcium is a ubiquitous intracellular signaling molecule controlling a wide array of cellular processes including fertilization and egg activation. The mechanism for triggering intracellular Ca2+ release in sea urchin eggs during fertilization is the generation of inositol‐1,4,5‐trisphosphate by phospholipase C (PLC) hydrolysis of phosphatidylinositol‐4,5‐bisphosphate. Of the five PLC isoforms identified in mammals (β, γ, δ, ∈ and ζ), only PLCγ and PLCδ have been detected in echinoderms. Here, we provide direct evidence of the presence of a PLCβ isoform, named suPLCβ, within sea urchin eggs. The coding sequence was cloned from eggs of Lytechinus pictus and determined to have the greatest degree of homology and identity with the mammalian PLCβ4. The presence of suPLCβ within the egg was verified using a specifically generated antibody. The majority of the enzyme is localized in the non‐soluble fraction, presumably the plasma membrane of the unfertilized egg. This distribution remains unchanged 1 min postfertilization. Unlike PLCβ4, suPLCβ is activated by G protein βγ subunits, and this activity is Ca2+‐dependent. In contrast to all known PLCβ enzymes, suPLCβ is not activated by Gαq‐GTPγS subunit suggesting other protein regulators may be present in sea urchin eggs.
Incidence of sleep disorders in children with presumed normal variant short stature
Authors: Campbell Thomas A , Papadopoulos Verge Dimitri J, Charles F , Williamson Bruce D , Teng Arthur
Published: July 2005

Objective:  To determine whether unrecognized obstructive sleep apnoea (OSA) is present in some children diagnosed with normal variant short stature.

Methods:  One hundred and fifty‐eight children aged less than 15 years and previously diagnosed with familial short stature or constitutional delay of growth were identified from the endocrine clinic database. A validated, standardized questionnaire designed to screen for symptoms of sleep disorders in children was mailed to the parents of eligible children.

Results:  Fifty‐three questionnaires were returned. Fifteen of these had an abnormal score (greater than the mean + three standard deviations in 1157 normal control children). Of these, 10 agreed to a sleep study. Overnight polysomnography showed no evidence of OSA or other sleep/breathing disorders. However, five (half) children showed frequent periodic leg movements of 6.3, 9.2, 9.4, 10.2 and 15.4 per h (adult normal <5 per h).

Conclusions:  We did not find OSA among a group of children with normal variant short stature. However, we found frequent periodic limb movements during sleep in a large proportion of the subjects, the significance of which remains to be determined.
Antibiotic‐related renal failure and cystic fibrosis
Authors: Kennedy Sean E , Henry Richard L , Rosenberg Andrew R
Published: July 2005

Abstract:  Recently published reports suggest that the combination of aminoglycosides with ceftazidime may increase the risk of renal disease in cystic fibrosis. We describe a case of unusually severe acute tubular necrosis occurring in an adolescent with cystic fibrosis receiving i.v. gentamicin plus ceftazidime and discuss the possible mechanisms.
Use of daytime phototherapy for Crigler–Najjar disease
Authors: Nydegger Andy , Bednarz Andrew , Hardikar Winita
Published: July 2005

Abstract:  Crigler–Najjar syndrome type 1 (CNS1) is characterized by a severe unconjugated hyperbilirubinemia from birth. Intensive blue‐light phototherapy is the standard method for management; however, it imposes severe restrictions on the child and their family's lifestyle. We describe here the use of a novel sit‐up phototherapy unit in a child with CNS1. The unit allowed a 50% reduction in phototherapy time while maintaining efficacy, thus enabling the child to attend school.
Increase in low‐birth‐weight infants in Japan and associated risk factors, 1980–2000
Authors: Takimoto Hidemi , Yokoyama Tetsuji , Yoshiike Nobuo , Fukuoka Hideoki
Published: July 2005

Aim: To investigate possible factors related to the recent rise in prevalence of low‐birth‐weight (LBW) infants in Japan.

Methods: A data set comprising 11 746 infants from the Children and Infant Growth Surveys (1980, 1990, and 2000) was analyzed.

Results: The proportion of LBW infants was 4.2% in 1980, 6.1% in 1990, and 8.3% in 2000. The maternal smoking prevalence increased from 6.5% in 1990 to 10.9% in 2000. When multivariate logistic regression analysis was applied to estimate the risk for LBW from 1990 to 2000, the following were selected as independent factors: preterm delivery, early term delivery, female sex of the infant, maternal primiparity, multiple gestation, maternal short stature, older maternal age (>24 years), and maternal smoking. The population attributable fraction (PAF) of preterm plus early term delivery and multiple gestations to LBW was 85.1% in 1990, and 89.3% in 2000. The PAF of maternal smoking was 6.4% in 1990, and 7.4% in 2000.

Conclusions: The increase in preterm deliveries and multiple gestations were found to be the important factors  with  regard  to  the  increase  in  LBW  infants  in  Japan.  The  increased  prevalence  of  maternal  smoking was not substantially associated with the increase in LBW infants.
Real‐time 3‐D sonographic observation of fetal facial expression
Authors: Hata Toshiyuki , Kanenishi Kenji , Akiyama Masashi , Tanaka Hirokazu , Kimura Kuniko
Published: July 2005

Aim: There have been a few reports about 3‐D sonographic observation of fetal movements using dynamic 3‐D sonography. However, dynamic 3‐D sonography is not real‐time, the frame rate being in the region of 4–6 frames per second depending on the size of the region of interest and the number of lines employed. Recently, a new faster 3‐D sonography, which acquires up to 28 frames per second, has become available. Using this system, we studied a full range of fetal facial expressions during pregnancy.

Methods: A total of 17 normal fetuses in 16 pregnancies (15 singletons and one twin) at 20–38 weeks’ gestation was studied using a transabdominal real‐time 3‐D ultrasound machine. This 3‐D ultrasound machine proved capable of providing continuous 3‐D sonographic images every 0.05 and 0.035 s. The fetal face was monitored for 15 min for each subject.

Results: Fetal eyelid movement (fetal blinking) was observed in three of 17 fetuses (17.6%). Double blinking was identified in one fetus at 38 weeks. Various types of mouth movement (yawning, a little opening, chewing, and subtle lip movement) could be observed in nine of 17 fetuses (52.9%). In the course of yawn‐like opening of the mouth, tongue movements such as tongue thrust and tongue click were clearly shown in three fetuses (17.6%). A lingula movement was also identified in the course of tongue movement.

Conclusion: Real‐time 3‐D sonography provides a novel means for evaluation of fetal movement, particularly fetal facial expression, in the second and third trimesters. Real‐time 3‐D sonography might be an important modality in future fetal behavior research and in evaluation of fetal well‐being.
Expression of the endothelial cell differentiation gene 7 (EDG‐7), a lysophosphatidic acid receptor, in ovarian tumor
Authors: Nakamoto Tsuyoshi , Yasuda Katsuhiko , Yasuhara Masahiro , Yoshimura Tomoo , Kinoshita Teruki , Nakajima Tatsuya , Okada Hidetaka , Ikuta Akiko , Kanzaki Hideharu
Published: July 2005

Aim: Lysophosphatidic acid (LPA) has received attention as a mitogen because the physiologically active lipid stimulates ovarian cancer cell growth by interacting with specific receptors, the endothelial cell differentiation gene (EDG) family. In the present study, we have investigated the expression of EDG‐7 mRNA, part of the EDG family, in both human ovarian cancers and established human ovarian cancer cell lines.

Methods: RNA was extracted from six ovarian cancer cell lines and multiple cancerous and normal ovarian tissues. The expression of EDG‐7 mRNA was measured using reverse transcription–polymerase chain reaction and northern blotting, using reduced glyceraldehyde‐phosphate dehydrogenase and S26 as internal controls.

Results: Of the cell lines tested, EDG‐7 mRNA was expressed most intensely in CRL‐11731 and CRL‐1572 and at a lesser but still substantial level in CRL‐11732. The expression of EDG‐7 mRNA was limited in MCAS, CRL‐11730 and TYKnu. In the ovarian cancer tissues, EDG‐7 mRNA was expressed most highly in endometrioid adenocarcinoma and serous cystadenocarcinoma. The expression of EDG‐7 mRNA was limited in clear cell adenocarcinoma and undetectable in mucinous cystadenocarcinoma.

Conclusions: The intense EDG‐7 expression in ovarian cancers suggests that the relation between LPA and EDG‐7 (an LPA receptor) is involved in cancer cell growth and proliferation in some histologic subtypes of ovarian cancer.
Temporal stability of aquatic food webs: partitioning the effects of species diversity, species composition and enrichment
Authors: Steiner Christopher F. , Long Zachary T. , Krumins Jennifer A. , Morin Peter J.
Published: July 2005

Theory predicts that species diversity can enhance stability of community‐level biomass while simultaneously decreasing population‐level stability. Enrichment can theoretically destabilize communities but effects may become weaker with increasing diversity because of the inclusion of consumer‐resistant prey. Few experiments using direct manipulations of species diversity have tested these predictions. We used laboratory‐based aquatic food webs to examine the effects of species composition, diversity and enrichment on temporal variability of population‐ and community‐level biomass. We found weak effects of enrichment on population‐ and community‐level stability. However, diversity enhanced community‐level stability while species composition had no influence. In contrast, composition effects outweighed diversity effects when stability was measured at the population level. We found no negative effects of diversity on population‐level stability, in opposition to theory. Our results indicate that diversity can enhance stability in multitrophic systems, but effects vary with the scale of biological organization at which stability is measured.
Swarmer cell differentiation in Proteus mirabilis
Authors: Rather Philip N.
Published: July 2005

Under the appropriate environmental conditions, the Gram‐negative bacterium Proteus mirabilis undergoes a remarkable differentiation to form a distinct cell type called a swarmer cell. The swarmer cell is characterized by a 20‐ to 40‐fold increase in both cell length and the number of flagella per cell. Environmental conditions required for swarmer cell differentiation include: surface contact, inhibition of flagellar rotation, a sufficient cell density and cell‐to‐cell signalling. The differentiated swarmer cell is then able to carry out a highly ordered population migration termed swarming. Genetic analysis of the swarming process has revealed that a large variety of distinct loci are required for this differentiation including: genes involved in regulation, lipopolysaccharide and peptidoglycan synthesis, cell division, ATP production, putrescine biosynthesis, proteolysis and cell shape determination. The process of swarming is important medically because the expression of virulence genes and the ability to invade cells are coupled to the differentiated swarmer cell. In this review, the genetic and environmental requirements for swarmer cell differentiation will be outlined. In addition, the role  of  the  differentiated  swarmer  cell  in  virulence and its possible role in biofilm formation will be discussed.
Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities
Authors: Farnleitner Andreas H. , Wilhartitz Ines , Ryzinska Gabriela , Kirschner Alexander K. T. , Stadler Hermann , Burtscher Martina M. , Hornek Romana , Szewzyk Ulrich , Herndl Gerhard , Mach Robert L.
Published: July 2005

Spring water of two alpine karst aquifers differing in hydrogeology but of nearby catchments were investigated for their bacterial population dynamics. Dolomite karst aquifer spring 1 (DKAS 1) represents a dolomitic‐limestone karst aquifer spring showing high average water residence time and relative constant flow. Limestone karst aquifer spring 2 (LKAS 2) constitutes a typical limestone karst aquifer spring with a dynamic hydrological regime and discharge. Dolomite karst aquifer spring 1 yielded constantly lower cell counts and biomasses (median of 15 × 106 cells l−1 and 0.22 µg C l−1) as the LKAS 2 (median of 63 × 106 cells l−1 and 1.1 µg C l−1) and distribution of morphotypes and mean cell volumes was also different between the considered systems, indicating the influence of hydrogeology on microbial spring water quality. Molecular bacterial V3 16S‐rDNA profiles revealed remarkable constancy within each spring water throughout the investigation period. Time course analysis of a flood event in LKAS 2 further supported the trend of the temporal constancy of the microbial community. Except for one case, retrieval of partial and full length 16S rDNA gene sequences from the relative constant DKAS 1 revealed similarities to presently known sequences between 80% to 96%, supporting the discreteness of the microbial populations. The gathered results provide first evidence for the presence of autochthonous microbial endokarst communities (AMEC). Recovery of AMEC may be considered of relevance for the understanding of alpine karst aquifer biogeochemistry and ecology, which is of interest as many alpine and mountainous karst springs are important water resources throughout the world.
Intraocular peripheral nerve sheath tumor in a dog
Authors: Sato Tsuneo , Yamamoto Atsuko , Shibuya Hisashi , Sudo Hiroshi , Shirai Wataru , Amemori Takashi
Published: July 2005

A tumor within the right globe in a 9‐year‐old Shetland sheepdog was examined pathologically. The tumor was composed of spindle or oval cells arranged in interwoven bundles with intervening collagenous or mucinous matrices. Immunohistochemically, the tumor bound antibody directed to S‐100 protein and vimentin, but not to desmin, actin smooth muscle, or neurofilament. Electron microscopy revealed that the tumor cells had poorly developed cytoplasmic processes, desmosomes between closely contiguous cells, and a discontinuous basement membrane‐like material. Based on these findings, the tumor was diagnosed as a peripheral nerve sheath tumor (PNST) histologically. To the authors’ knowledge, this is the first reported case of intraocular PNST in dogs.
Principles of anaesthesia in urological surgery
Authors: Cousins Jonathan , Howard Jeremy , Borra Philippa
Published: July 2005

Anaesthesia for urological surgery poses particular challenges for the anaesthetist related to the patient population and procedure type. The aim of this article is to cover the general principles of anaesthesia, with dedicated sections relevant to practising urological surgeons. This represents vast amounts of knowledge that cannot be covered in one article. We will focus upon preoperative preparation for surgery and anaesthesia, perioperative management including monitoring and analgesia, and postoperative management including fluid balance, critical care and recovery. Significant proportions of urological surgical patients have some degree of renal failure and this may be related to the surgery required. Anaesthetic care of patients with chronic renal impairment and transplant surgery will be covered in a future review.
Serial Evaluation of Atrial Tachyarrhythmia Burden and Frequency After Implantation of a Dual‐Chamber Cardioverter‐Defibrillator
Authors: SCHWARTZMAN DAVID , GOLD MICHAEL , QUESADA AURELIO , KOEHLER JODI L. , MEHRA RAHUL , EULER DAVID E. ,   Worldwide Jewel AF‐Only Investigators
Published: July 2005

Background: We sought to characterize atrial tachyarrhythmia (AT) burden and frequency after implantation of a dual‐chamber implantable cardioverter‐defibrillator (D‐ICD).

Methods and Results: A total of 149 subjects underwent implantation of a D‐ICD (Jewel AF® model 7250, Medtronic, Inc.) for the primary indication of drug‐resistant AT, and were followed for at least 12 months during which device programming was constant. The device employed atrial overdrive pacing as well as shocks to terminate episodes of AT. Arrhythmia burden and frequency were evaluated during the 0‐ to 6‐month follow‐up and and 6‐ to 12‐month follow‐up intervals. A majority of subjects (62%) received a type I/III antiarrhythmic drug during follow‐up. The median arrhythmia burden decreased from 8.2 hours/month during 0–6 months to 3.3 hours/month during 6–12 months (P = 0.004); this result was driven primarily by the subgroup with persistent AT prior to device implantation. There was no significant change in the median AT frequency (2.2 vs 1.0 episodes/month). There was a significant decrease in the median shock frequency (0.32 vs 0.00 shocks/month, P = 0.003) and an increase in shock efficacy (85.5% vs 94.9%, P = 0.01).

Conclusions: Device‐based treatment of AT, in association with antiarrhythmic drugs, yields a significant time‐dependent decrease in AT burden but not frequency.
Predictors of Atrial Antitachycardia Pacing Efficacy in Patients Affected by Brady‐Tachy Form of Sick Sinus Syndrome and Implanted with a DDDRP Device
Authors: BORIANI GIUSEPPE , PADELETTI LUIGI , SANTINI MASSIMO , GULIZIA MICHELE , CAPUCCI ALESSANDRO , BOTTO GIANLUCA , RICCI RENATO , MOLON GIULIO , ACCOGLI MICHELE , VICENTINI ALFREDO , BIFFI MAURO , VIMERCATI MARCO , GRAMMATICO ANDREA
Published: July 2005

Background: Recent options to treat atrial tachyarrhythmias (ATA) include implantable devices delivering antitachycardia pacing therapies (ATP). No prospective study selected patients with higher chances of episode termination by ATP or indicated the most effective ATP use. Our aim was to study ATP efficacy in patients with brady‐tachy form of sinus node disease (SND), identifying clinical factors, ATA characteristics, and device features predicting ATP efficacy.

Methods and Results: Three hundred and sixteen patients (105 M, aged 71.1 ± 8.8 years) received a DDDRP pacemaker and were prospectively followed. Median follow‐up was 18 months: 37,125 ATA episodes occurred in 217 patients; ATP treated 5,536 of them. Overall, ATP efficacy was 50.0%. A multivariate analysis identified longer arrhythmia cycle lengths (OR = 1.25; CI = 1.07‐1.47) and shorter delays to ATP delivery (OR = 0.15; CI = 0.10‐0.22) as independent predictors of ATP efficacy for episodes preceded by ≥5 minutes of sinus rhythm. Additionally, ATP efficacy for all treated episodes was predicted by lower New York Heart Association (NYHA) class (OR = 0.64; CI = 0.42‐0.98), episode classification as nonimmediate recurrence of ATA (non‐IRAT) (OR = 0.07; CI = 0.02‐0.33), absence of overlap in the device detection windows (OR = 0.54; CI = 0.32‐0.91), and flecainide treatment (OR = 2.22; CI = 1.04‐4.71).

Conclusions: In patients paced for SND, multivariate analysis shows that ATP efficacy is associated to longer arrhythmia cycle lengths, shorter ATP delivery delays, NYHA class I, episode classification as non‐IRAT, absence of overlap in the atrial arrhythmia device detection windows, and flecainide treatment.
Continuous Toxicity Monitoring in Phase II Trials in Oncology
Authors: Ivanova Anastasia , Qaqish Bahjat F. , Schell Michael J.
Published: July 2005

Summary The goal of a phase II trial in oncology is to evaluate the efficacy of a new therapy. The dose investigated in a phase II trial is usually an estimate of a maximum‐tolerated dose obtained in a preceding phase I trial. Because this estimate is imprecise, stopping rules for toxicity are used in many phase II trials. We give recommendations on how to construct stopping rules to monitor toxicity continuously. A table is provided from which Pocock stopping boundaries can be easily obtained for a range of toxicity rates and sample sizes. Estimation of the probability of toxicity and response is also discussed.
Use of Principal Component Analysis and the GE‐Biplot for the Graphical Exploration of Gene Expression Data
Authors: Pittelkow Yvonne , Wilson Susan R.
Published: July 2005

Summary This note is in response to Wouters et al. (2003, Biometrics59, 1131–1139) who compared three methods for exploring gene expression data. Contrary to their summary that principal component analysis is not very informative, we show that it is possible to determine principal component analyses that are useful for exploratory analysis of microarray data. We also present another biplot representation, the GE‐biplot (Gene Expression biplot), that is a useful method for exploring gene expression data with the major advantage of being able to aid interpretation of both the samples and the genes relative to each other.
A Likelihood Approach for Quantitative‐Trait‐Locus Mapping with Selected Pedigrees
Authors: Wang K.
Published: July 2005

Summary Selective sampling is a cost‐effective design for mapping quantitative trait loci (QTLs). A unified framework, which naturally combines two complementary sources of linkage information in the data, is proposed for the mapping of QTLs using selected pedigrees. Score statistics for detecting linkage are introduced for single‐locus models (univariate or bivariate phenotypes) and two‐locus epistasis models. A computer implementation of the methods for single‐locus univariate‐phenotype models is provided for nuclear families with arbitrary number of sibs and is freely available.
China, Economics, and FDI Reflections on Selling China
Authors: Shenkar Oded
Published: July 2005

Yasheng Huang presents a detailed and meticulous analysis of foreign
direct investment (FDI) in China during the reform period. The author should
be commended for collecting and analysing descriptive information on
China-based FDI that is useful to practitioners as much as to researchers,
and for arguing a seemingly intriguing thesis about China's economic ascent.
He also presents a number of industry cases, some of which, like that on the
Chinese handicraft industry, are particularly captivating. Yet, at the end
of the day, what this book does best in my mind is illustrate the confines
of traditional academic paradigms when faced with real-life phenomena that
are too broad and complex to be captured by a single lens. This is, it
itself, an important service.
Single-Electron Delocalization in Hybrid Vertical-Lateral Double Quantum Dots
Authors: Hatano T. , Stopa M. , Tarucha S.
Published: July 2005

We used a hybrid vertical-lateral double-dot device, consisting of laterally coupled vertical quantum dots, to measure the interdot tunnel coupling. By using nonlinear transport measurements of “Coulomb diamonds,” we showed that an inherent asymmetry in the capacitances of the component dots influences the diamond slopes, thereby allowing for the determination of the dot through which the electron has passed. We used this technique to prepare a delocalized one-electron state and Heitler-London (HL) two-electron state, and we showed that the interdot tunnel coupling, which determines whether HL is the ground state, is tunable. This implies that our device may be useful for implementing two-electron spin entanglement.
Similarities and Specificities of Fungal Keratinolytic Proteases: Comparison of Keratinases of
Paecilomyces marquandii
and
Doratomyces microsporus
to Some Known Proteases
Authors: Gradišar Helena , Friedrich Jožica , Križaj Igor , Jerala Roman
Published: July 2005

Based on previous screening for keratinolytic nonpathogenic fungi,
Paecilomyces marquandii
and
Doratomyces microsporus
were selected for production of potent keratinases. The enzymes were purified and their main biochemical characteristics were determined (molecular masses, optimal temperature and pH for keratinolytic activity, N-terminal amino acid sequences). Studies of substrate specificity revealed that skin constituents, such as the stratum corneum, and appendages such as nail but not hair, feather, and wool were efficiently hydrolyzed by the
P. marquandii
keratinase and about 40% less by the
D. microsporus
keratinase. Hydrolysis of keratin could be increased by the presence of reducing agents. The catalytic properties of the keratinases were studied and compared to those of some known commercial proteases. The profile of the oxidized insulin B-chain digestion revealed that both keratinases, like proteinase K but not subtilisin, trypsin, or elastase, possess broad cleavage specificity with a preference for aromatic and nonpolar amino acid residues at the P-1 position. Kinetic studies were performed on a synthetic substrate, succinyl-Ala-Ala-Pro-Phe-
p
-nitroanilide. The keratinase of
P. marquandii
exhibited the lowest

K
m

among microbial keratinases reported in the literature, and its catalytic efficiency was high in comparison to that of
D. microsporus
keratinase and proteinase K. All three keratinolytic enzymes, the keratinases of
P. marquandii
and
D. microsporus
as well as proteinase K, were significantly more active on keratin than subtilisin, trypsin, elastase, chymotrypsin, or collagenase.
Characterization of a New Bacteriocin Operon in Sakacin P-ProducingLactobacillus sakei, Showing Strong Translational Coupling between the Bacteriocin and Immunity Genes
Authors: Mathiesen Geir , Huehne Kathrin , Kroeckel Lothar , Axelsson Lars , Eijsink Vincent G. H.
Published: July 2005

Previous studies of genes involved in the production of sakacin P byLactobacillus sakeiLb674 revealed the presence of an inducible promoter downstream of the knownsppgene clusters. We show here that this promoter drives the expression of an operon consisting of a bacteriocin gene (sppQ), a cognate immunity gene (spiQ), another gene with an unknown function (orf4), and a pseudoimmunity gene containing a frameshift mutation (orf5). The leader peptide of the new one-peptide bacteriocin sakacin Q contains consensus elements that are typical for so-called “double-glycine” leader peptides. The mature bacteriocin shows weak similarity to the BrcA peptide of the two-peptide bacteriocin brochocin C. Sakacin Q has an antimicrobial spectrum that differs from that of sakacin P, thus expanding the antimicrobial properties of the producer strain. The genes encoding sakacin Q and its cognate immunity protein showed strong translational coupling, which was investigated in detail by analyzing the properties of a series of β-glucuronidase fusions. Our results provide experimental evidence that production of the bacteriocin and production of the cognate immunity protein are tightly coregulated at the translational level.
Influence of Fluid Shear and Microbubbles on Bacterial Detachment from a Surface
Authors: Sharma Prashant K. , Gibcus Marjon J. , van der Mei Henny C. , Busscher Henk J.
Published: July 2005

Prevention of microbial adhesion and detachment of adhering microorganisms from surfaces is important in many environmental, industrial, and medical applications. Fluid shear is an obvious parameter for stimulating microbial detachment from surfaces, but recently it has been pointed out that a passing air-liquid interface also has potential in stimulating microbial detachment. In the present study, the ability of microbubbles to stimulate detachment of bacterial strains from a glass surface is compared with the effects of fluid flow. Adhesion and detachment of
Actinomyces naeslundii
T14V-J1,
Streptococcus oralis
J22, and their coadhering aggregates were studied on glass, mounted in a parallel plate flow chamber. High fluid wall shear rates (11,000 to 16,000 s
−1
) were established in a laminar flow regime in the absence and presence of microbubbles. Wall shear rates stimulated detachment ranging from 70% to 30% for
S. oralis
and
A. naeslundii
, respectively. Coadhering aggregates were detached up to 54%. The presence of microbubbles in the flow increased the detachment of
A. naeslundii
within 2 min of flow from 40% in the absence of microbubbles to 98%, while detachment of neither
S. oralis
nor coadhering aggregates was affected by the presence of microbubbles. In summary, extremely high fluid flows can be effective in stimulating microbial detachment, depending on the strain involved. The addition of microbubbles to the flow allows the detachment of tenaciously adhering bacteria not detached by flow alone, but not of adhering coaggregates.
Characterization of Citrate Synthase from
Geobacter sulfurreducens
and Evidence for a Family of Citrate Synthases Similar to Those of Eukaryotes throughout the
Geobacteraceae
Authors: Bond Daniel R. , Mester Tünde , Nesbø Camilla L. , Izquierdo-Lopez Andrea V. , Collart Frank L. , Lovley Derek R.
Published: July 2005

Members of the family
Geobacteraceae
are commonly the predominant Fe(III)-reducing microorganisms in sedimentary environments, as well as on the surface of energy-harvesting electrodes, and are able to effectively couple the oxidation of acetate to the reduction of external electron acceptors. Citrate synthase activity of these organisms is of interest due to its key role in acetate metabolism. Prior sequencing of the genome of
Geobacter sulfurreducens
revealed a putative citrate synthase sequence related to the citrate synthases of eukaryotes. All citrate synthase activity in
G. sulfurreducens
could be resolved to a single 49-kDa protein via affinity chromatography. The enzyme was successfully expressed at high levels in
Escherichia coli
with similar properties as the native enzyme, and kinetic parameters were comparable to related citrate synthases (
k
cat
= 8.3 s
−1
;

K
m

= 14.1 and 4.3 μM for acetyl coenzyme A and oxaloacetate, respectively). The enzyme was dimeric and was slightly inhibited by ATP (

K
i

= 1.9 mM for acetyl coenzyme A), which is a known inhibitor for many eukaryotic, dimeric citrate synthases. NADH, an allosteric inhibitor of prokaryotic hexameric citrate synthases, did not affect enzyme activity. Unlike most prokaryotic dimeric citrate synthases, the enzyme did not have any methylcitrate synthase activity. A unique feature of the enzyme, in contrast to citrate synthases from both eukaryotes and prokaryotes, was a lack of stimulation by K
+
ions. Similar citrate synthase sequences were detected in a diversity of other
Geobacteraceae
members. This first characterization of a eukaryotic-like citrate synthase from a prokaryote provides new insight into acetate metabolism in
Geobacteraceae
members and suggests a molecular target for tracking the presence and activity of these organisms in the environment.
Azo Reductase Activity of IntactSaccharomyces cerevisiaeCells Is Dependent on the Fre1p Component of Plasma Membrane Ferric Reductase
Authors: Ramalho Patrícia A. , Paiva Sandra , Cavaco-Paulo A. , Casal Margarida , Cardoso M. Helena , Ramalho M. Teresa
Published: July 2005

Unspecific bacterial reduction of azo dyes is a process widely studied in correlation with the biological treatment of colored wastewaters, but the enzyme system associated with this bacterial capability has never been positively identified. Several ascomycete yeast strains display similar decolorizing behaviors. The yeast-mediated process requires an alternative carbon and energy source and is independent of previous exposure to the dyes. When substrate dyes are polar, their reduction is extracellular, strongly suggesting the involvement of an externally directed plasma membrane redox system. The present work demonstrates that, inSaccharomyces cerevisiae, the ferric reductase system participates in the extracellular reduction of azo dyes. TheS. cerevisiaeΔfre1and Δfre1Δfre2mutant strains, but not the Δfre2strain, showed much-reduced decolorizing capabilities. TheFRE1gene complemented the phenotype ofS. cerevisiaeΔfre1cells, restoring the ability to grow in medium without externally added iron and to decolorize the dye, following a pattern similar to the one observed in the wild-type strain. These results suggest that under the conditions tested, Fre1p is a major component of the azo reductase activity.
Determination of Spatial Distributions of Zinc and Active Biomass in Microbial Biofilms by Two-Photon Laser Scanning Microscopy
Authors: Hu Zhiqiang , Hidalgo Gabriela , Houston Paul L. , Hay Anthony G. , Shuler Michael L. , Abruña Héctor D. , Ghiorse William C. , Lion Leonard W.
Published: July 2005

The spatial distributions of zinc, a representative transition metal, and active biomass in bacterial biofilms were determined using two-photon laser scanning microscopy (2P-LSM). Application of 2P-LSM permits analysis of thicker biofilms than are amenable to observation with confocal laser scanning microscopy and also provides selective excitation of a smaller focal volume with greater depth localization. Thin
Escherichia coli
PHL628 biofilms were grown in a minimal mineral salts medium using pyruvate as the carbon and energy source under batch conditions, and thick biofilms were grown in Luria-Bertani medium using a continuous-flow drip system. The biofilms were visualized by 2P-LSM and shown to have heterogeneous structures with dispersed dense cell clusters, rough surfaces, and void spaces. Contrary to homogeneous biofilm model predictions that active biomass would be located predominantly in the outer regions of the biofilm and inactive or dead biomass (biomass debris) in the inner regions, significant active biomass fractions were observed at all depths in biofilms (up to 350 μm) using live/dead fluorescent stains. The active fractions were dependent on biofilm thickness and are attributed to the heterogeneous characteristics of biofilm structures. A zinc-binding fluorochrome (8-hydroxy-5-dimethylsulfoamidoquinoline) was synthesized and used to visualize the spatial location of added Zn within biofilms. Zn was distributed evenly in a thin (12 μm) biofilm but was located only at the surface of thick biofilms, penetrating less than 20 μm after 1 h of exposure. The relatively slow movement of Zn into deeper biofilm layers provides direct evidence in support of the concept that thick biofilms may confer resistance to toxic metal species by binding metals at the biofilm-bulk liquid interface, thereby retarding metal diffusion into the biofilm (G. M. Teitzel and M. R. Park, Appl. Environ. Microbiol.
69:
2313-2320, 2003).
Genomic Organization and Molecular Analysis of Virulent Bacteriophage 2972 Infecting an Exopolysaccharide-Producing
Streptococcus thermophilus
Strain
Authors: Lévesque Céline , Duplessis Martin , Labonté Jessica , Labrie Steve , Fremaux Christophe , Tremblay Denise , Moineau Sylvain
Published: July 2005

The
Streptococcus thermophilus
virulent
pac
-type phage 2972 was isolated from a yogurt made in France in 1999. It is a representative of several phages that have emerged with the industrial use of the exopolysaccharide-producing
S. thermophilus
strain RD534. The genome of phage 2972 has 34,704 bp with an overall G+C content of 40.15%, making it the shortest
S. thermophilus
phage genome analyzed so far. Forty-four open reading frames (ORFs) encoding putative proteins of 40 or more amino acids were identified, and bioinformatic analyses led to the assignment of putative functions to 23 ORFs. Comparative genomic analysis of phage 2972 with the six other sequenced
S. thermophilus
phage genomes confirmed that the replication module is conserved and that
cos
- and
pac
-type phages have distinct structural and packaging genes. Two group I introns were identified in the genome of 2972. They interrupted the genes coding for the putative endolysin and the terminase large subunit. Phage mRNA splicing was demonstrated for both introns, and the secondary structures were predicted. Eight structural proteins were also identified by N-terminal sequencing and/or matrix-assisted laser desorption ionization—time-of-flight mass spectrometry. Detailed analysis of the putative minor tail proteins ORF19 and ORF21 as well as the putative receptor-binding protein ORF20 showed the following interesting features: (i) ORF19 is a hybrid protein, because it displays significant identity with both
pac
- and
cos
-type phages; (ii) ORF20 is unique; and (iii) a protein similar to ORF21 of 2972 was also found in the structure of the
cos
-type phage DT1, indicating that this structural protein is present in both
S. thermophilus
phage groups. The implications of these findings for phage classification are discussed.
Multiplexed Particle-Based Anti-Granulocyte Macrophage Colony Stimulating Factor Assay Used as Pulmonary Diagnostic Test
Authors: Bonfield Tracey L. , John Nejimol , Barna Barbara P. , Kavuru Mani S. , Thomassen Mary Jane , Yen-Lieberman Belinda
Published: July 2005

Pulmonary alveolar proteinosis (PAP) is characterized by the accumulation of lipoproteinaceous material within the lung alveoli. Recent studies indicate that PAP is an autoimmune disease characterized by a neutralizing anti-granulocyte macrophage colony stimulating factor (GM-CSF) antibody. At present the only definitive diagnostic test for PAP is open lung biopsy. We have previously published that anti-GM-CSF is diagnostic for PAP and correlates with disease pathogenesis using a traditional serial anti-GM-CSF antibody titer format (T. L. Bonfield, M. S. Kavuru, and M. J. Thomassen, Clin. Immunol.
105:
342-350, 2002). Titer analysis is a semiquantitative method, and often subtle changes in antibody titer are not detectable. In this report we present data to support anti-GM-CSF detection by a quantitative highly sensitive multiplexed particle-based assay which has the potential to be a clinical diagnostic test.
Role of the Nfa1 Protein in Pathogenic
Naegleria fowleri
Cocultured with CHO Target Cells
Authors: Kang Su-Yeon , Song Kyoung-Ju , Jeong Seok-Ryoul , Kim Jong-Hyun , Park Sun , Kim Kyongmin , Kwon Myung-Hee , Shin Ho-Joon
Published: July 2005

Naegleria fowleri
, a free-living amoeba, exists as a virulent pathogen which causes fatal primary amoebic meningoencephalitis in experimental animals and humans. Using infected and immune mouse sera, we previously cloned an
nfa1
gene from a cDNA library of
N. fowleri
by immunoscreening. The
nfa1
gene (360 bp) produced a recombinant 13.1-kDa protein, and the Nfa1 protein showed pseudopodium-specific immunolocalization on a trophozoite of
N. fowleri
. In this study, the role of the Nfa1 protein as a cell contact mechanism of
N. fowleri
cocultured with target cells was observed by an immunofluorescence assay with an anti-Nfa1 polyclonal antibody. Using confocal microscopic findings, the Nfa1 protein was located on the pseudopodia of
N. fowleri
trophozoites. The Nfa1 protein in
N. fowleri
trophozoites cocultured with CHO target cells was also located on pseudopodia, as well as in a food cup formed as a phagocytic structure in close contact with target cells. The amount of
nfa1
mRNA of
N. fowleri
was strongly increased 6 h after coculture.
Aspergillus nidulans uvsB
ATR
and
scaA
NBS1
Genes Show Genetic Interactions during Recovery from Replication Stress and DNA Damage
Authors: Fagundes Marcia Regina von Zeska Kress , Semighini Camile P. , Malavazi Iran , Savoldi Marcela , de Lima Joel Fernandes , de Souza Goldman Maria Helena , Harris Steven D. , Goldman Gustavo Henrique
Published: July 2005

The ATM/ATR kinases and the Mre11 (Mre11-Rad50-Nbs1) protein complex are central players in the cellular DNA damage response. Here we characterize possible interactions between
Aspergillus nidulans uvsB
ATR
and the Mre11 complex (
scaA
NBS1
). We demonstrate that there is an epistatic relationship between
uvsB
ATR
, the homolog of the ATR/MEC1 gene, and
scaA
NBS1
, the homolog of the NBS1/XRS2 gene, for both repair and checkpoint functions and that correct ScaA
NBS1
expression during recovery from replication stress depends on
uvsB
ATR
. In addition, we also show that the formation of UvsC foci during recovery from replication stress is dependent on both
uvsB
ATR
and
scaA
NBS1
function. Furthermore, ScaA
NBS1
is also dependent on
uvsB
ATR
for nuclear focus formation upon the induction of DNA double-strand breaks by phleomycin. Our results highlight the extensive genetic interactions between UvsB and the Mre11 complex that are required for S-phase progression and recovery from DNA damage.
EMERGENT CPT VIOLATION FROM THE SPLITTING OF FERMI POINTS
Authors: KLINKHAMER F. R. , VOLOVIK G. E.
Published: July 2005

In a fermionic quantum vacuum, the parameters kμ of a CPT-violating Chern–Simons-like action term induced by CPT-violating parameters of the fermionic sector depend on the universality class of the system. As a concrete example, we consider the Dirac Hamiltonian of a massive fermionic quasiparticle and add a particular term with purely-spacelike CPT-violating parameters bμ = (0, b). A quantum phase transition separates two phases, one with a fully-gapped fermion spectrum and the other with topologically-protected Fermi points (gap nodes). The emergent Chern–Simons "vector" kμ = (0, k) now consists of two parts. The regular part, k reg , is an analytic function of |b| across the quantum phase transition and may be nonzero due to explicit CPT violation at the fundamental level. The anomalous (nonanalytic) part, k anom , comes solely from the Fermi points and is proportional to their splitting. In the context of condensed-matter physics, the quantum phase transition may occur in the region of the BEC–BCS crossover for Cooper pairing in the p-wave channel. For elementary particle physics, the splitting of Fermi points may lead to neutrino oscillations, even if the total electromagnetic Chern–Simons-like term cancels out.