bluuebunny/crossref_metadata_2025 huggingface dataset:
Familial Occurrence of Febrile Seizures and Epilepsy in Severe Myoclonic Epilepsy of Infancy (SMEI) Patients withSCN1AMutations
Authors: Margherita Mancardi Maria , Striano Pasquale , Gennaro Elena , Madia Francesca , Paravidino Roberta , Scapolan Sara , Dalla Bernardina Bernardo , Bertini Enrico , Bianchi Amedeo , Capovilla Giuseppe , Darra Francesca , Elia Maurizio , Freri Elena , Gobbi Giuseppe , Granata Tiziana , Guerrini Renzo , Pantaleoni Chiara , Parmeggiani Antonia , Romeo Antonino , Santucci Margherita , Vecchi Marilena , Veggiotti Pierangelo , Vigevano Federico , Pistorio Angela , Gaggero Roberto , Zara Federico
Published: October 2006

Summary: Purpose:The role of the familial background in severe myoclonic epilepsy of infancy (SMEI) has been traditionally emphasized in literature, with 25–70% of the patients having a family history of febrile seizures (FS) or epilepsy. We explored the genetic background of SMEI patients carryingSCN1Amutations to further shed light on the genetics of this disorder.

Methods:We analyzed the occurrence of FS and epilepsy among first‐ and second‐degree relatives (N = 867) of 74 SMEI probands withSCN1Amutations (70 de novo, four inherited) and compared data with age‐matched and ethnically matched control families. Familial clustering and syndromic concordance within the affected relatives in both groups were investigated.

Results: The frequency of FS or epilepsy in relatives of SMEI patients did not significantly differ from that in controls (FS: 13 of 867 vs. 12 of 674, p = 0.66; epilepsy: 15 of 867 vs. six of 674, p = 0.16). Different forms of epilepsy were identified in both relatives of SMEI probands and controls. Twenty‐eight relatives with FS and epilepsy were distributed in 20 (27%) of 74 SMEI families; among the controls, 18 affected relatives were clustered in 13 (18.5%) of 70 families. No pedigree showed several affected members, including the four with inherited mutations.

Conclusions:A substantial epileptic family background is not present in our SMEI patients withSCN1Amutations. These data do not confirm previous observations and would not support polygenic inheritance in SMEI. The investigation of the family background in additional series of SMEI patients will further shed light on the genetics of this syndrome.
Trachipleistophora extenrec n. sp. a New Microsporidian (Fungi: Microsporidia) Infecting Mammals
Authors: VÁVRA JIŘÍ , HORÁK ALEŠ , MODRÝ DAVID , LUKEŠ JULIUS , KOUDELA BŘETISLAV
Published: October 2006

ABSTRACT. A new microsporidian Trachipleistophora extenrec n. sp. was isolated from a muscle lesion of the streaked tenrec Hemicentetes semispinosus Cuvier, 1798 (Mammalia, Tenrecidae), an insectivore endemic to Madagascar. The spores isolated from the tenrec were infectious to
severe combined immunodeficient (SCID) mice by intramuscular injection. Material obtained from muscular lesions in mice was used for the parasite description. All developmental stages of the microsporidian were covered by a dense coat, which during sporogony changed into the sporophorous vesicle wall. Eight, 16, 32, or more spores were formed inside the sporophorous vesicle as the result of the division by plasmotomy and sequential fission of a multinucleate sporogonial plasmodium. Spores were ovoid, 4.7 × 2.8 μm in size, had a large posterior vacuole, and had an isofilar polar tube with 15–16 coils. Although the fine structure and the developmental pattern of the organism were in some respects similar to the genus Vavraia, molecular phylogeny based on the gene sequences of the small subunit rRNA and RNA polymerase subunit II indicated that the organism belongs to the genus Trachipleistophora. The diagnostic characters of the genera Trachipleistophora and Vavraia are discussed as well as the discrepancies between the phylogenies of these two microsporidian genera based on morphology and molecules.
Analysis of the β‐Tubulin Genes from Enterocytozoon bieneusi Isolates from a Human and Rhesus Macaque
Authors: AKIYOSHI DONNA E. , WEISS LOUIS M. , FENG XIAOCHUAN , WILLIAMS BRYONY A. P. , KEELING PATRICK J. , ZHANG QUANSHUN , TZIPORI SAUL
Published: October 2006

ABSTRACT. Enterocytozoon bieneusi is the most common and clinically significant microsporidium associated with chronic diarrhea and wasting in immunocompromised humans. Albendazole, which is effective against several helminths, protozoa, and microsporidia, is relatively ineffective against infections due to E. bieneusi. A likely explanation for the observed clinical resistance to albendazole was discovered from sequence analysis of the E. bieneusiβ‐tubulin from isolates from an infected human and a naturally infected rhesus macaque. The β‐tubulin of E. bieneusi has a substitution at Glu198, which is one of six amino acids reported to be associated with benzimidazole sensitivity.
Transcriptional Analysis of Three Major Putative Phosphatidylinositol Kinase Genes in a Parasitic Protozoan, Giardia lamblia
Authors: HERNANDEZ YUNUEN , ZAMORA GUS , RAY SUPARNA , CHAPOY JAIME , CHAVEZ EDNA , VALVARDE ROBERT , WILLIAMS EBONYE , ALEY STEPHEN B. , DAS SIDDHARTHA
Published: October 2006

ABSTRACT. The current investigation evaluates the expression of phosphatidylinositol kinase (PIK) genes in the parasitic protozoan, Giardia lamblia. The G. lamblia Genome Database revealed the presence of two putative phosphatidylinositol‐3‐kinase (gPI3K) and one phosphatidylinositol‐4‐kinase (gPI4K) genes resembling the catalytic subunit of eukaryotic PIKs. Primers, designed to amplify mRNA of these three genes, were used to measure transcription by quantitative reverse‐transcriptase polymerase chain reactions. Results suggest that all three PIK genes are expressed in non‐encysting and encysting trophozoites. The relative levels of the mRNA were highest in parasites cultured in pre‐encysting medium that contained no bile. Two inhibitors of PI3K, LY 294002 and wortmannin were found to inhibit the growth of the trophozoite in culture. However, wortmannin was more effective than LY294002. Altogether, the present study indicates that Giardia is capable of expressing PIKs that are necessary for the growth and differentiation of this pathogen.
Sarcomatoid eccrine porocarcinoma: report of two cases and a review of the literature
Authors: Goh Seng Geok Nicholas , Dayrit Johannes F. , Calonje Eduardo
Published: October 2006

Abstract:  Eccrine porocarcinoma is an uncommon sweat gland malignancy. To the best of our knowledge, there has been no report in the English literature of porocarcinoma with predominantly undifferentiated sarcomatous change. We present two cases of sarcomatoid eccrine porocarcinoma associated with a benign poroma. Case 1 pertained to an 82‐year‐old woman with an ulcerated chest wall tumor, and Case 2 was that of a 74‐year‐old woman who presented with an ulcerated plaque in the lower leg. Case 1 showed an unusual pseudo‐angiosarcomatous morphology with spindle cells dissecting through collagen bundles and forming vascular like channels. Case 2 revealed high‐grade malignant spindle cells with focal evidence of ductal differentiation. In both the cases, benign poromatous elements were histologically evident. Immunohistochemistry performed showed pancytokeratin positivity in spindle cells of both lesions. Epithelial membrane antigen and carcino‐embryonic antigen positivity in the malignant ductal elements and focal smooth muscle actin staining of the spindle cells were demonstrated in Case 2. A brief review of relevant literature is presented.
Use of p63 expression in distinguishing primary and metastatic cutaneous adnexal neoplasms from metastatic adenocarcinoma to skin
Authors: Ivan Doina , Nash Jason W. , Prieto Victor G. , Calonje Eduardo , Lyle Stephen , Diwan A. Hafeez , Lazar Alexander J. F.
Published: October 2006

Absract:  p63, a recently identified homologue of the p53 gene, is mainly expressed by basal and myoepithelial cells in skin. Others and we have shown the value of p63 in distinguishing primary adnexal tumors from visceral adenocarcinomas metastatic to skin. We now investigate the pattern of p63 expression in metastases from skin adnexal carcinomas and their cognate primaries and evaluate p63 expression in a larger case series of malignant cutaneous adnexal neoplasms. Immunohistochemical analysis for p63 was performed on 13 metastases of adnexal carcinomas and their corresponding primary tumors. Twenty visceral metastatic adenocarcinomas to the skin and 7 primary mucinous carcinomas with cutaneous or visceral origin were compared. The majority (90.9%) of primary adnexal tumors strongly expressed p63 and their metastases labeled similar to their cognate primary tumors. With one exception, primary or metastatic mucinous carcinomas did not express p63. Metastases from two apocrine carcinomas lacked p63 expression. All other cutaneous metastases from internal adenocarcinomas were negative for p63. Analysis of p63 expression may assist in the differential diagnosis of primary adnexal carcinomas versus metastatic visceral adenocarcinomas to the skin. Metastases from adnexal carcinomas generally retain p63 expression similar to their associated primary tumors.
Low tolerance and high toxicity of thalidomide as maintenance therapy after double autologous stem cell transplant in multiple myeloma patients
Authors: Martino Massimo , Console Giuseppe , Callea Vincenzo , Stelitano Caterina , Massara Elisabetta , Irrera Giuseppe , Messina Giuseppe , Morabito Fortunato , Iacopino Pasquale
Published: October 2006

Although a double autologous peripheral blood stem cell transplant (APBSCT) is an effective therapy for patients (pts) with multiple myeloma and extends progression‐free survival and overall survival, pts show a continued pattern of recurrent disease. The feasibility and tolerability of thalidomide (Thal) administered in the post‐transplantation period as maintenance therapy was tested in 17 pts at a dose of 100 mg/d starting between 3 and 5 months after the second transplantation and continuing either until toxicity precluded further therapy or until pts had disease progression. After a median administration of 13 months (range: 3–26), 76.5% (13 pts) failed to tolerate Thal because of: transiet ischemic attack (three pts), severe fatigue (two), neutropenia (one), piastrinopenia (one), severe opportunistic infectious (two), erectile impotence (one), gastointestinal toxicity (anorexia with weight loss one), peripheral neuropathy (two). After a median follow‐up of 36 months (range: 10–59) from the second transplant, 13 patients attained a CR + near CR (with a conversion rate from 47.1% to 76.5%). In conclusion, Thal as maintenance therapy after double ASCT is associated with low feasibility and high toxicity and could prevent a lengthy use of this antineoplastic agent.
Analysis of a Japanese Black Cattle‐rearing system utilizing a bahiagrass (Paspalum notatum Flügge) pasture: 3. Intake from pasture
Authors: Higashiyama Masakazu , Hirata Masahiko
Published: October 2006

A Japanese Black Cattle‐rearing system utilizing a bahiagrass (Paspalum notatum Flügge) pasture in coastal Miyazaki, southern Japan, was analyzed in terms of intake from pasture. In a field approach, herbage intake by grazing cattle was measured for nine periods (1–5 days) during a grazing season (May–October) along with some other variables (e.g. air temperature, herbage mass, digestibility of grazed herbage), under varying levels of supplementary feeding. The intake from the pasture was most closely related to the intake of supplement, showing a negative linear response at a substitution rate of 0.736–0.750. The intake under no supplementation, i.e. a maximum intake from the pasture, was lower than the voluntary intake predicted with feeding standards. In a modeling approach, a semi‐mechanistic model for predicting grazing intake was developed using information from the literature as well as the field data. The performance of the model was acceptable. The model showed similar substitution rates (0.64–0.69), and considerable intake restriction (nearly 30%) that is not attributable to limitations by herbage mass, herbage allowance, diet digestibility or air temperature. The results indicate that a low maximal intake by the animals due to low grazing motivation is a major characteristic of the system where supplementation is a usual management practice.
Ranking acidity tolerance and growth potential of Austrodanthonia accessions
Authors: Islam M. Anowarul , Dowling Peter M. , Milham Paul J. , Campbell Lindsay C. , Jacobs Brent C. , Garden Denys L.
Published: October 2006

Some Australian native perennial grasses that evolved on acidic soils are useful pasture species such as the 25 species of Austrodanthonia. We evaluated the range of acidity tolerance and growth potential in the field of 9 species of Austrodanthonia, comprising 18 accessions collected from southern temperate New South Wales (NSW) as well as the commercial cultivars Taranna and Bunderra. The soil had natural differences in pH in 10 mM calcium chloride (pHCa) and was classified as a brown chromosol to kurosol (yellow/red podsolic). After germination and growth in pots for 9 weeks, seedlings were transplanted into plots with pH differences (mean 4.3 or mean 4.9). Plant growth was scored for 116 days after transplanting and survival monitored for a further 361 days. Visual scoring of plant growth was highly correlated with dry weights (r2 = 0.99). Survival and shoot dry weight were greater at pHCa 4.9 than at pHCa 4.3. For example, survival was 74% at the higher pH and 47% at the lower pH after 116 days and declined very slowly subsequently. Dry weight and survival at pHCa 4.9 were separately and linearly related to dry weight and survival at pHCa 4.3, respectively. Austrodanthonia accessions/cultivars exhibited about a threefold range of acidity tolerance and dry matter production. When acidity tolerance was ranked using either dry weight or survival, the rankings were similar; however, dry weight data had a greater dispersion, thus dry weight may be the more sensitive tolerance index. On the other hand, survival may be the more cost‐effective indicator of acidity tolerance. It is likely that tolerance of acidity may be attributed to tolerance of aluminum rather than of the hydrogen ion. Some accessions produced more dry matter, had higher survival and greater acidity tolerance than the commercial cultivars and thus show potential as useful pasture components.
Floristic composition and plant biomass of the grasslands in the vicinity of Pavlodar, Kazakhstan
Authors: Hayashi Ichiroku , Kawada Kiyokazu , Akimova Aigul , Nakamura Toru
Published: October 2006

This article deals with the species composition and above‐ground plant biomass of grasslands in the vicinity of Pavlodar, Kazakhstan. The abandoned croplands, an initial stand of secondary succession were recolonized by Agropyron cristatum. In the second stage of the succession, Artemisia absinthium, Agropyron cristatum and Erigeron canadensis appeared. The developed stand, which had been abandoned for 11 years since 1993, was dominated by Stipa capillata including Artemisia austriaca and Medicago falcata, Kochia prostrata and Leymus ramosus. The vegetation of the stand used for grazing was sparse due to overgrazing and the soil was compacted due to trampling by livestock. The lichen, Parmeria vegans, grew in the bare areas of the stand. The average plant height and vegetation coverage of the stand were 44.1 cm and 25–50%, respectively. The dry weights were 73.4 g m−2 in plant biomass including 14.4 g m−2 of Parmeria vegans and 15.2 g m−2 in litter.
Direct Numerical Simulations of Planar and Cylindrical Density Currents
Authors: Cantero Mariano I. , Balachandar S. , García Marcelo H. , Ferry James P.
Published: October 2006

The collapse of a heavy fluid column in a lighter environment is studied by direct numerical simulation of the Navier-Stokes equations using the Boussinesq approximation for small density difference. Such phenomenon occurs in many engineering and environmental problems resulting in a density current spreading over a no-slip boundary. In this work, density currents corresponding to two Grashof (Gr) numbers are investigated (105 and 1.5×106) for two very different geometrical configurations, namely, planar and cylindrical, with the goal of identifying differences and similarities in the flow structure and dynamics. The numerical model is capable of reproducing most of the two- and three-dimensional flow structures previously observed in the laboratory and in the field. Soon after the release of the heavier fluid into the quiescent environment, a density current forms exhibiting a well-defined head with a hanging nose followed by a shallower body and tail. In the case of large Gr, the flow evolves in a three-dimensional fashion featuring a pattern of lobes and clefts in the intruding front and substantial three-dimensionality in the trailing body. For the case of the lower Gr, the flow is completely two dimensional. The dynamics of the current is visualized and explained in terms of the mean flow for different phases of spreading. The initial phase, known as slumping phase, is characterized by a nearly constant spreading velocity and strong vortex shedding from the front of the current. Our numerical results show that this spreading velocity is influenced by Gr as well as the geometrical configuration. The slumping phase is followed by a decelerating phase in which the vortices move into the body of the current, pair, stretch and decay as viscous effects become important. The simulated dynamics of the flow during this phase is in very good agreement with previously reported experiments.
Microstructural Simulation of Solidification Process of Spheroidal-Graphite Cast Iron
Authors: Dardati Patricia M. , Godoy Luis A. , Celentano Diego J.
Published: October 2006

This paper presents a new micro-macro approach for the thermo-microstructural behavior of the solidification process of an eutectic ductile cast iron. The thermal balance is written at a macroscopic level and can take into account both the structural component being cast and its mold. Models of nucleation and growth represent the evolution of the microstructure, following a multinodular solidification theory with independent nucleation of graphite and austenite and a dendritic growth of austenite. The resulting formulation is solved using a finite element discretization of the macro domain, in which the evolution of the microstructure is taken into account at the Gauss integration points. The quantitative agreement between experimental and computational values in terms of cooling curves is acceptable.
Online Multichannel Forging Tonnage Monitoring and Fault Pattern Discrimination Using Principal Curve
Authors: Kim Jihyun , Huang Qiang , Shi Jianjun , Chang Tzyy-Shuh
Published: October 2006

Due to the late response to process condition changes, forging processes are normally exposed to a large number of defective products. To achieve online process monitoring, multichannel tonnage signals are often collected from the forging press. The tonnage signals contain significant amount of real time information regarding the product and the process conditions. In this paper, a methodology is developed to detect profile changes of multichannel tonnage signals for forging process monitoring and to classify fault patterns. The changes include global or local profile deviations, which correspond to deviations of a whole process cycle or process segment(s) within a cycle, respectively. The principal curve method is used to conduct feature extraction and discrimination of tonnage signals. The developed methodology is demonstrated with industry data from a crankshaft forging processes.
Data Mining in Manufacturing: A Review
Authors: Harding J. A. , Shahbaz M. , Srinivas  , Kusiak A.
Published: October 2006

The paper reviews applications of data mining in manufacturing engineering, in particular production processes, operations, fault detection, maintenance, decision support, and product quality improvement. Customer relationship management, information integration aspects, and standardization are also briefly discussed. This review is focused on demonstrating the relevancy of data mining to manufacturing industry, rather than discussing the data mining domain in general. The volume of general data mining literature makes it difficult to gain a precise view of a target area such as manufacturing engineering, which has its own particular needs and requirements for mining applications. This review reveals progressive applications in addition to existing gaps and less considered areas such as manufacturing planning and shop floor control.
A New Configuration for Equal Channel Angular Extrusion Dies
Authors: Luri R. , Luis C. J. , León J. , Sebastian M. A.
Published: October 2006

Equal channel angular extrusion or pressing (ECAE or ECAP) is a process used in order to impart severe plastic deformations to processed materials with the aim of improving their mechanical properties by reducing the grain size. The grain size reduction leads to mechanical properties improvement. In the present study, a new die configuration is proposed for the ECAE process. The advantage of this die geometry is that it allows us to obtain higher plastic strain in each ECAE passage than traditional ECAE dies. It is important to optimize the die geometry, as the main aim of the ECAE process is to impart severe plastic deformations to the processed materials. Consequently, the higher the deformation, the better the improvement on the mechanical properties of the processed materials. In order to determine how variations on geometry affect the plastic strain of the processed materials finite element modeling (FEM) is used. Both analytical and FEM methods will allow us to affirm that by using this new die configuration it is possible to achieve higher deformation values per ECAE passage.
New Mass-Conserving Algorithm for Level Set Redistancing on Unstructured Meshes
Authors: Mut Fernando , Buscaglia Gustavo C. , Dari Enzo A.
Published: October 2006

The level set method is becoming increasingly popular for the simulation of several problems that involve interfaces. The level set function is advected by some velocity field, with the zero-level set of the function defining the position of the interface. The advection distorts the initial shape of the level set function, which needs to be re-initialized to a smooth function preserving the position of the zero-level set. Many algorithms re-initialize the level set function to (some approximation of) the signed distance from the interface. Efficient algorithms for level set redistancing on Cartesian meshes have become available over the last years, but unstructured meshes have received little attention. This presentation concerns algorithms for construction of a distance function from the zero-level set, in such a way that mass is conserved on arbitrary unstructured meshes. The algorithm is consistent with the hyperbolic character of the distance equation (‖∇d‖=1) and can be localized on a narrow band close to the interface, saving computing effort. The mass-correction step is weighted according to local mass differences, an improvement over usual global rebalancing techniques.
Numerical Simulation of Transient Free Surface Flows Using a Moving Mesh Technique
Authors: Battaglia Laura , D’Elía Jorge , Storti Mario , Nigro Norberto
Published: October 2006

In this work, transient free surface flows of a viscous incompressible fluid are numerically solved through parallel computation. Transient free surface flows are boundary-value problems of the moving type that involve geometrical nonlinearities. In contrast to more conventional computational fluid dynamics problems, the computational flow domain is partially bounded by a free surface which is not known a priori, since its shape must be computed as part of the solution. In steady flow the free surface is obtained by an iterative process, but when the free surface evolves with time the problem is more difficult as it generates large distortions in the computational flow domain. The incompressible Navier-Stokes numerical solver is based on the finite element method with equal order elements for pressure and velocity (linear elements), and it uses a streamline upwind/Petrov-Galerkin (SUPG) scheme (Hughes, T. J. R., and Brooks, A. N., 1979, “A Multidimensional Upwind Scheme With no Crosswind Diffusion,” in Finite Element Methods for Convection Dominated Flows, ASME ed., 34. AMD, New York, pp. 19–35, and Brooks, A. N., and Hughes, T. J. R., 1982, “Streamline Upwind/Petrov-Galerkin Formulations for Convection Dominated Flows With Particular Emphasis on the Incompressible Navier-Stokes Equations,” Comput. Methods Appl. Mech. Eng., 32, pp. 199–259) combined with a Pressure-Stabilizing/Petrov-Galerkin (PSPG) one (Tezduyar, T. E., 1992, “Stablized Finite Element Formulations for Incompressible Flow Computations,” Adv. Appl. Mech., 28, pp. 1–44, and Tezduyar, T. E., Mittal, S., Ray, S. E., and Shih, R., 1992, “Incompressible Flow Computations With Stabilized Bilinear and Linear Equal Order Interpolation Velocity-Pressure Elements,” Comput. Methods Appl. Mech. Eng., 95, pp. 221–242). At each time step, the fluid equations are solved with constant pressure and null viscous traction conditions at the free surface and the velocities obtained in this way are used for updating the positions of the surface nodes. Then, a pseudo elastic problem is solved in the fluid domain in order to relocate the interior nodes so as to keep mesh distortion controlled. This has been implemented in the PETSc-FEM code (PETSc-FEM: a general purpose, parallel, multi-physics FEM program. GNU general public license (GPL), http://www.cimec.org.ar/petscfem) by running two parallel instances of the code and exchanging information between them. Some numerical examples are presented.
Investigation of the Dynamics of Microend Milling—Part II: Model Validation and Interpretation
Authors: Jun Martin B. G. , DeVor Richard E. , Kapoor Shiv G.
Published: October 2006

In Part II of this paper, experimental and analytical methods have been developed to estimate the values of the process faults defined in Part I of this paper. The additional faults introduced by the microend mill design are shown to have a significant influence on the total net runout of the microend mill. The dynamic model has been validated through microend milling experiments. Using the dynamic model, the effects of minimum chip thickness and elastic recovery on microend milling stability have been studied over a range of feed rates for which the cutting mechanisms vary from ploughing-dominated to shearing-dominated. The minimum chip thickness effect is found to cause feed rate dependent instability at low feed rates, and the range of unstable feed rates depends on the axial depth of cut. The effects of process faults on microend mill vibrations have also been studied and the influence of the unbalance from the faults is found to be significant as spindle speed is increased. The stability characteristics due to the regenerative effect have been studied. The results show that the stability lobes from the second mode of the microend mill, which are generally neglected in macroscale end milling, affect the microend mill stability significantly.
Simultaneous Modular Product Scheduling and Manufacturing Cell Reconfiguration Using a Genetic Algorithm
Authors: Ye Hegui , Liang Ming
Published: October 2006

Modular product design can facilitate the diversification of product variety at a low cost. Reconfigurable manufacturing, if planned properly, is able to deliver high productivity and quick responsiveness to market changes. Together, the two could provide an unprecedented competitive edge to a manufacturing company. The production of a family of modular products in a reconfigurable manufacturing system often requires reorganizing the manufacturing system in such a way that each configuration corresponds to one product variant in the same family. The successful implementation of this strategy lies in proper scheduling of the modular product operations and optimal selection of a configuration for producing each product variant. These two issues are closely related and have a strong impact on each other. Nevertheless, they have often been treated separately, rendering inefficient, infeasible, and conflicting decisions. As such, an integrated model is developed to address the two problems simultaneously. The objective is to minimize the sum of the manufacturing cost components that are affected by the two planning decisions. These include reconfiguration cost, machine idle cost, material handling cost, and work-in-process cost incurred in producing a batch of product variants. Due to the combinatorial nature of the problem, a genetic algorithm (GA) is proposed to provide quick and near-optimal solutions. A case study is conducted using a steering column to illustrate the application of the integrated approach. Our computational experience shows that the proposed GA substantially outperforms a popular optimization software package, LINGO, in terms of both solution quality and computing efficiency.
Investigation of magnetic damping on an air track
Authors: Xie Xiao , Wang Zhu-ying , Gu Pingping , Jian Zhi-jian , Chen Xiao-lin , Xie Zhong
Published: October 2006

A more effective experimental method is used to analyze the effect of magnetic damping on a nonferromagnetic air track. Due to the continuous interaction between the horizontal air track and the moving magnets fixed on the air-track glider, the experiment can be easily done with low-cost photoelectric detecting techniques. A simple model is proposed based on Faraday’s law, the Lorentz force law, and Ampere’s law. Analytic expressions for the position, the velocity, and the magnetic damping force of the moving magnets as a function of time are obtained. Systematic measurements were performed and the results are in good agreement with the model. The method provides a simple teaching platform for introductory physics demonstrations and undergraduate courses in experimental physics.
Playing Quantum Physics Jeopardy with zero-energy eigenstates
Authors: Gilbert L. P. , Belloni M. , Doncheski M. A. , Robinett R. W.
Published: October 2006

We describe an example of an exact, quantitative Jeopardy-type quantum mechanics problem. This problem type is based on the conditions in one-dimensional quantum systems that allow an energy eigenstate for the infinite square well to have zero curvature and zero energy when suitable Dirac delta functions are added. This condition and its solution are not often discussed in quantum mechanics texts and have interesting pedagogical consequences.
Revisiting the 1888 Hertz experiment
Authors: Faccio Daniele , Clerici Matteo , Tambuchi Davide
Published: October 2006

We revisit the original experiment performed by Hertz in 1888 and use a simple setup to produce electromagnetic waves with a frequency in the range of 3MHz. By doing a Fourier analysis of the signal captured by a resonant antenna, we can study the behavior of the RLC series circuit, frequency splitting of coupled resonances, and the characteristics of the near-field emitted by the loop antenna.
Graviton physics
Authors: Holstein Barry R.
Published: October 2006

The interactions of gravitons with matter are calculated in parallel with the familiar photon case. It is shown that graviton scattering amplitudes can be factorized into a product of familiar electromagnetic forms. The cross sections for various reactions are evaluated straightforwardly using helicity methods.
Genome Rearrangements, Deletions, and Amplifications in the Natural Population of
Bartonella henselae
Authors: Lindroos Hillevi , Vinnere Olga , Mira Alex , Repsilber Dirk , Näslund Kristina , Andersson Siv G. E.
Published: October 2006

Cats are the natural host for
Bartonella henselae
, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38
Bartonella henselae
strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoints in areas of the genomic islands. We observed no difference in gene content or structure between feline and human strains. Rather, the results suggest multiple sources of human infection from feline
B. henselae
strains of diverse genotypes. Additionally, the microarray hybridizations revealed DNA amplification in some strains in the so-called chromosome II-like region. The amplified segments were centered at a position corresponding to a putative phage replication initiation site and increased in size with the duration of cultivation. We hypothesize that the variable gene pool in the
B. henselae
population plays an important role in the establishment of long-term persistent infection in the natural host by promoting antigenic variation and escape from the host immune response.
Switched or Not?: the Structure of Unphosphorylated CheY Bound to the N Terminus of FliM
Authors: Dyer Collin M. , Dahlquist Frederick W.
Published: October 2006

Phosphorylation of
Escherichia coli
CheY increases its affinity for its target, FliM, 20-fold. The interaction between BeF
3
−
-CheY, a phosphorylated CheY (CheY∼P) analog, and the FliM sequence that it binds has been described previously in molecular detail. Although the conformation that unphosphorylated CheY adopts in complex with FliM was unknown, some evidence suggested that it is similar to that of CheY∼P. To resolve the issue, we have solved the crystallographic structure of unphosphorylated, magnesium(II)-bound CheY in complex with a synthetic peptide corresponding to the target region of FliM (the 16 N-terminal residues of FliM [FliM
16
]). While the peptide conformation and binding site are similar to those of the BeF
3
−
-CheY-FliM
16
complex, the inactive CheY conformation is largely retained in the unphosphorylated Mg
2+
-CheY-FliM
16
complex. Communication between the target binding site and the phosphorylation site, observed previously in biochemical experiments, is enabled by a network of conserved side chain interactions that partially mimic those observed in BeF
3
−
-activated CheY. This structure makes clear the active role that the β4-α4 loop plays in the Tyr
87
-Tyr
106
coupling mechanism that enables allosteric communication between the phosphorylation site and the target binding surface. Additionally, this structure provides a high-resolution view of an intermediate conformation of a response regulator protein, which had been generally assumed to be two state.
An RpoH-Like Heat Shock Sigma Factor Is Involved in Stress Response and Virulence inBrucella melitensis16M
Authors: Delory Marie , Hallez Régis , Letesson Jean-Jacques , De Bolle Xavier
Published: October 2006

B. melitensis16M genome analysis revealed the presence of six putative sigma factor-encoding genes:rpoD,rpoH1,rpoH2,rpoE1,rpoE2, andrpoN. We mutated all these genes exceptrpoD. Phenotypic analysis of the mutants reveals that a strain carrying anrpoH2null mutation (ΔrpoH2) is impaired for growth at 21 and 42°C and shows increased sensitivity to hydrogen peroxide. Compared to the wild-type strain, the ΔrpoH2mutant is attenuated in all virulence models tested. Three other null mutants (ΔrpoH1, ΔrpoE1, and ΔrpoE2mutants) are also defective for survival in mice at 4 weeks postinfection. We also demonstrated thatrpoH2deletion strongly reduces the expression of two major virulence factors inB. melitensis, the type IV secretion system and the flagellum.
O Acetylation of the Enterobacterial Common Antigen Polysaccharide Is Catalyzed by the Product of the
yiaH
Gene of
Escherichia coli
K-12
Authors: Kajimura Junko , Rahman Arifur , Hsu James , Evans Matthew R. , Gardner Kevin H. , Rick Paul D.
Published: October 2006

The carbohydrate component of the enterobacterial common antigen (ECA) of
Escherichia coli
K-12 occurs primarily as a water-soluble cyclic polysaccharide located in the periplasm (ECA
CYC
) and as a phosphoglyceride-linked linear polysaccharide located on the cell surface (ECA
PG
). The polysaccharides of both forms are comprised of the amino sugars
N
-acetyl-
d
-glucosamine (GlcNAc),
N
-acetyl-
d
-mannosaminuronic acid (ManNAcA), and 4-acetamido-4,6-dideoxy-
d
-galactose (Fuc4NAc). These amino sugars are linked to one another to form trisaccharide repeat units with the structure →3-α-
d
-Fuc4NAc-(1→4)-β-
d
-ManNAcA-(1→4)-α-
d
-GlcNAc-(1→. The hydroxyl group in the 6 position of the GlcNAc residues of both ECA
CYC
and ECA
PG
are nonstoichiometrically esterified with acetyl groups. Random transposon insertion mutagenesis of
E. coli
K-12 resulted in the generation of a mutant defective in the incorporation of
O
-acetyl groups into both ECA
CYC
and ECA
PG
. This defect was found to be due to an insertion of the transposon into the
yiaH
locus, a putative gene of unknown function located at 80.26 min on the
E. coli
chromosomal map. Bioinformatic analyses of the predicted
yiaH
gene product indicate that it is an integral inner membrane protein that is a member of an acyltransferase family of enzymes found in a wide variety of organisms. The results of biochemical and genetic experiments presented here strongly support the conclusion that
yiaH
encodes the
O
-acetyltransferase responsible for the incorporation of
O
-acetyl groups into both ECA
CYC
and ECA
PG
. Accordingly, we propose that this gene be designated
wecH
.
Evolution of Transmembrane Protein Kinases Implicated in Coordinating Remodeling of Gram-Positive Peptidoglycan: Inside versus Outside
Authors: Jones Greg , Dyson Paul
Published: October 2006

Members of a family of serine/threonine protein kinases (STPKs), unique to gram-positive bacteria, comprise an intracellular kinase domain and reiterated extracellular PASTA (for “penicillin-binding protein and serine/threonine kinase associated”) domains. PASTA domains exhibit low affinity for β-lactam antibiotics that are structurally similar to their likely normal ligands: stem peptides of unlinked peptidoglycan. The PASTA-domain STPKs are found in the actinobacteria and firmicutes and, as exemplified by PknB of
Mycobacterium tuberculosis
, they are functionally implicated in aspects of growth, cell division, and development. Whereas the kinase domains are well conserved, there is a wide divergence in the sequences of the multiple PASTA domains. Closer inspection reveals position-dependent evolution of individual PASTA domains: a domain at one position within a gene has a close phylogenetic relationship with a domain at a similar position in an orthologous gene, whereas neighboring domains have clearly diverged one from one another. A similar position-dependent relationship is demonstrated in the second family of proteins with multiple PASTA domains: the high-molecular-weight type II penicillin-binding protein (PBP2x) family. These transpeptidases are recruited to the division site by a localized pool of unlinked peptidoglycan. We infer that protein localization is guided by low-affinity interactions between structurally different unlinked peptidoglycan stem peptides and individual PASTA domains. The STPKs possess a greater multiplicity and diversity of PASTA domains, allowing interactions with a wider range of stem-peptide ligands. These interactions are believed to activate the intracellular kinase domain, allowing an STPK to coordinate peptidoglycan remodeling and reproduction of a complex cell wall structure.
Novel Conserved Assembly Factor of the Bacterial Flagellum
Authors: Titz Björn , Rajagopala Seesandra V. , Ester Claudia , Häuser Roman , Uetz Peter
Published: October 2006

TP0658 (FliW) and its orthologs, conserved proteins of unknown function in
Treponema pallidum
and other species, interact with a C-terminal region of flagellin (FlaB1-3 in
T. pallidum
; FliC in most other species). Mutants of orthologs in
Bacillus subtilis
and
Campylobacter jejuni
(
yviF
, CJ1075) showed strongly reduced motility. TP0658 stabilizes flagellin in a way similar to FliS, suggesting that TP0658 is a conserved assembly factor for the bacterial flagellum.
A New GntR Family Transcriptional Regulator inStreptomyces coelicolorIs Required for Morphogenesis and Antibiotic Production and Controls Transcription of an ABC Transporter in Response to Carbon Source
Authors: Hillerich Brandan , Westpheling Janet
Published: October 2006

We recently reported the isolation and initial characterization of a transposon-generated mutation that resulted in defects in both morphogenesis and antibiotic production inStreptomyces coelicolor. The insertion identified the SCO7168 open reading frame whose predicted product is a GntR family transcriptional regulator. Here, we show that this gene acts to repress transcription of itself as well as a series of genes immediately adjacent to it on theS. coelicolorchromosome that likely encode an ATP-binding cassette (ABC)-type transporter for carbohydrate uptake. Transcription of this transporter is strongly induced by growth on relatively poor carbon sources such as trehalose and melibiose and weakly induced by lactose and glycerol but not glucose, and induction is not repressed by the presence of glucose. Constructed deletions of the ABC transporter itself resulted in the suppression of the original transposon mutation, suggesting that inappropriate expression of the ABC transporter is responsible, at least in part, for the mutant phenotype. Because this transporter responds to the presence of α-glucosides and has similarity to two other carbohydrate transporters of this class, we have named the genes of the transporteragl3E,agl3F, andagl3Gand the GntR-like protein that regulates transcription of the transporteragl3Rin accordance with established nomenclature. We suggest thatagl3Ris one of a number of homologous proteins inStreptomyces(there are 57 putative GntR family regulators in theS. coelicolorgenome) that respond to nutritional and/or environmental signals to control genes that affect morphogenesis and antibiotic production.
Selective Promoter Recognition by Chlamydial σ28Holoenzyme
Authors: Shen Li , Feng Xiaogeng , Yuan Yuan , Luo Xudong , Hatch Thomas P. , Hughes Kelly T. , Liu Jun S. , Zhang You-xun
Published: October 2006

The σ transcription factor confers the promoter recognition specificity of RNA polymerase (RNAP) in eubacteria.Chlamydia trachomatishas three known sigma factors, σ66, σ54, and σ28. We developed two methods to facilitate the characterization of promoter sequences recognized byC. trachomatisσ28(σ28Ct). One involved the arabinose-induced expression of plasmid-encoded σ28Ctin a strain ofEscherichia colidefective in the σ28structural gene,fliA. The second was an analysis of transcription in vitro with a hybrid holoenzyme reconstituted withE. coliRNAP core and recombinant σ28Ct. These approaches were used to investigate the interactions of σ28Ctwith the σ28Ct-dependenthctBpromoter and selectedE. coliσ28(σ28Ec)-dependent promoters, in parallel, compared with the promoter recognition properties of σ28EC. Our results indicate that RNAP containing σ28Cthas at least three characteristics: (i) it is capable of recognizing some but not all σ28EC-dependent promoters; (ii) it can distinguish different promoter structures, preferentially activating promoters with upstream AT-rich sequences; and (iii) it possesses a greater flexibility than σ28ECin recognizing variants with different spacing lengths separating the −35 and −10 elements of the core promoter.
Identification and Characterization of BicistronicspeBandprsAGene Expression in the Group A Streptococcus
Authors: Ma Yongsheng , Bryant Amy E. , Salmi Dan B. , Hayes-Schroer Susan M. , McIndoo Eric , Aldape Michael J. , Stevens Dennis L.
Published: October 2006

Severe, invasive group A streptococcal infections have reemerged worldwide, and extracellular toxins, including streptococcal pyrogenic exotoxin B (SpeB), have been implicated in pathogenesis. The genetic regulation of SpeB is not fully understood, and the mechanisms involved in the processing of the protoxin to its enzymatically active form have not been definitively established. The present work demonstrated that the genes encoding SpeB (speB) and a peptidyl-prolyl isomerase (prsA) constitute an operon with transcription initiated from two promoters upstream ofspeB. Further, thespeB-prsAoperon was transcribed as a bicistronic mRNA. This finding is in contrast to the generally accepted notion thatspeBis transcribed only as a monocistronic gene. In addition,prsAhas its own promoter, and transcription from this promoter starts in early log phase, prior to the transcription ofspeB. Genomic disruption ofprsAdecreased the production of enzymatically active SpeB but not the level of the pro-SpeB zymogen. Taken together, these results demonstrate thatprsAis required for production of fully mature, enzymatically active SpeB.
Best practice in primary care pathology: review 7
Authors: Smellie W S A , Forth J , Smart S R S , Galloway M J , Irving W , Bareford D , Collinson P O , Kerr K G , Summerfield G , Carey P J , Minhas Rubin
Published: October 2006

This seventh best-practice review examines four series of common primary care questions in laboratory medicine: (1) blood count abnormalities 2; (2) cardiac troponins; (3) high-density lipoprotein cholesterol; and (4) viral diseases 2. The review is presented in a question–answer format, with authorship attributed for each question series. The recommendations are a précis of guidance found using a standardised literature search of national and international guidance notes, consensus statements, health policy documents and evidence-based medicine reviews, supplemented by Medline Embase searches to identify relevant primary research documents. The recommendations are not standards, but form a guide to be set in the clinical context. Most are consensus based rather than evidence based. They will be updated periodically to take account of new information.
The total mesorectal excision specimen for rectal cancer: a review of its pathological assessment
Authors: Parfitt Jeremy R , Driman David K
Published: October 2006

Total mesorectal excision (TME) refers to the surgical removal of the complete perirectal soft tissue envelope, using sharp instruments under direct vision, and has become the contemporary standard of care for patients with rectal cancer. Pathologists play a key role in the evaluation of these specimens, including the quality assurance of surgical performance, as well as evaluation of the circumferential radial margin (CRM). While the latter is the most significant predictor of local recurrence, the quality of the excised mesorectum is another important factor in assessing the risk of local recurrence in patients with a negative CRM. Since proper pathological assessment of the TME specimen provides important prognostic information, as well as critical feedback to surgeons regarding technical performance, it is important to have adequate guidelines for the macroscopic handling of these specimens. The CLASSICC study of the Medical Research Council in the United Kingdom, as well as the Dutch TME trial have introduced a new standard for the pathological assessment of TME specimens, including an approach that involves assessment in both the fresh and fixed states, at least 48 hours of fixation of an intact specimen, with observations made on both the external appearance and cross-sectional slices. This article reviews the pathological assessment of the TME specimen, including basic definitions, current international guidelines, an approach to evaluating the mesorectum and a discussion of special issues relating to margins, lymph node retrieval and effects of neoadjuvant therapy.