bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photosystem II: the engine of life
Authors: Barber James 
Published: February 2003

1. Introduction 712. Electron transfer in PS II 723. (Mn)4cluster and mechanism of water oxidation 734. Organization and structure of the protein subunits 755. Organization of chlorophylls and redox active cofactors 816. Implications arising from the structural models 827. Perspectives 848. Acknowledgements 869. Addendum 8610. References 87Photosystem II (PS II) is a multisubunit membrane protein complex, which uses light energy to oxidize water and reduce plastoquinone. High-resolution electron cryomicroscopy and X-ray crystallography are revealing the structure of this important molecular machine. Both approaches have contributed to our understanding of the organization of the transmembrane helices of higher plant and cyanobacterial PS II and both indicate that PS II normally functions as a dimer. However the high-resolution electron density maps derived from X-ray crystallography currently at 3·7/3·8 Å, have allowed assignments to be made to the redox active cofactors involved in the light-driven water–plastoquinone oxidoreductase activity and to the chlorophyll molecules that absorb and transfer energy to the reaction centre. In particular the X-ray work has identified density that can accommodate the four manganese atoms which catalyse the water-oxidation process. The Mn cluster is located at the lumenal surface of the D1 protein and approximately 7 Å from the redox active tyrosine residue (YZ) which acts an electron/proton transfer link to the primary oxidant P680.+. The lower resolution electron microscopy studies, however, are providing structural models of larger PS II supercomplexes that are ideal frameworks in which to incorporate the X-ray derived structures.
Robotic stroke therapy assistant
Authors: Mahoney Richard M. , Van der Loos H. F. Machiel , Lum Peter S. , Burgar Chuck 
Published: February 2003

The Rehabilitation Technologies Division of Applied Resources Corp. (RTD-ARC) has engaged in a Phase I effort to commercialize a robotic bi-manual therapy machine for use in stroke rehabilitation, in cooperation with the VA Rehabilitation R&D Center in Palo Alto. The robotic therapy device, called ARCMIME here in order to differentiate
it from its clinical predecessor, has the potential to improve rehabilitation outcomes significantly for individuals who have upper limb impairments due to stroke and other brain injuries.This paper describes design considerations and clinical outcomes with regards to the Phase I system. It was found that the kinematically simpler system adequately replicated the data outcomes of the more sophisticated PUMA-based experimental test rig.
3 Expressions
Authors: PEYTON JONES SIMON 
Published: February 2003

3.1 Errors 193.2 Variables, Constructors, Operators, and Literals 203.3 Curried Applications and Lambda Abstractions 213.4 Operator Applications 213.5 Sections 223.6 Conditionals 233.7 Lists 233.8 Tuples 243.9 Unit Expressions and Parenthesized Expessions 253.10 Arithmetic Sequences 253.11 List Comprehensions 253.12 Let Expressions 273.13 Case Expressions 273.14 Do Expressions 293.15 Datatypes with Field Labels 293.16 Expression Type Signatures 323.17 Pattern Matching 32
17 List Utilities
Authors: PEYTON JONES SIMON 
Published: February 2003

17.1 Indexing Lists 18117.2 “Set” Operations 18117.3 List Transformations 18217.4 unfoldr 18217.5 Predicates 18317.6 The “By” Operations 18317.7 The “generic” Operations 18417.8 Further “zip” Operations 18417.9 Library List 184
21 Input/Output
Authors: PEYTON JONES SIMON 
Published: February 2003

21.1 I/O Errors 20721.2 Files and Handles 20821.3 Opening and Closing Files 21021.4 Determining the Size of a File 21121.5 Detecting the End of Input 21121.6 Buffering Operations 21121.7 Repositioning Handles 21321.8 Handle Properties 21321.9 Text Input and Output 21421.10 Examples 21521.11 Library IO 216
A proof-irrelevant model of Martin-Löf's logical framework
Authors: FRIDLENDER DANIEL 
Published: February 2003

We extend the proof-irrelevant model defined in Smith (1988) to the whole of Martin-Löf's
logical framework. The main difference here is the existence of a type whose objects
themselves represent types rather than proof-objects. This means that the model must now
be able to distinguish between objects with different degree of relevance: those that denote
proofs are irrelevant whereas those that denote types are not. In fact a whole hierarchy of
relevance exists.Another difference is the higher level of detail in the formulation of the formal theory, such
as the explicit manipulation of contexts and substitutions. This demands an equally detailed
definition of the model, including interpreting contexts and substitutions.We are thus led to a whole reformulation of the proof-irrelevant model. We present a model
that is built up from an arbitrary model of the untyped lambda calculus. We also show how
to extend it when the logical framework itself is enlarged with inductive definitions. In doing
so, a variant of Church numerals is introduced.As in Smith (1988), the model can only be defined in the absence of universes, and it is
useful to obtain an elementary proof of consistency and to prove the independence of
Peano's fourth axiom.
Recurrent miscarriage – a critical appraisal
Authors: Rai R 
Published: February 2003

Only 50% of all conceptions result in a live birth (Figure 1). Human
reproduction can therefore be viewed as being remarkably inefficient. However, the diametrically
opposite opinion that it is in fact a very efficient and selective process, designed to optimize
the outcome of pregnancy, deserves to be stated.Between 65% and 90% of clinically recognized
miscarriages are due to chromosome abnormalities, the occurrence of which is more closely related
to basal follicle-stimulating hormone (FSH) levels rather than to maternal age alone. In contrast
to women suffering a sporadic miscarriage, women who recurrently miscarry often, but not exclusively,
lose pregnancies with a normal chromosome content. Using a combination of conventional Geimsa
banding and the recently introduced technique of comparative genomic hybridization it has
been reported that 54% of pregnancy losses amongst women with recurrent miscarriage are euploid.
The challenge we face is to identify the causes of pregnancy loss amongst those couples who
recurrently lose such euploid conceptions.Whilst many conventionally held beliefs as to the aetiology and treatment of
women with recurrent miscarriage have not withstood critical scrutiny, significant
progress has been made. This progress is the subject of this review, which will also
highlight potential areas of future research.
Editorial
Authors: Myatt Tony 
Published: February 2003

This issue of Organised Sound focuses on mapping in computer music. Unlike many issues of the journal, all articles in this edition are related to the theme. The call for contributions resulted in a significant collection of work which covered a broad range of activity in the field. This number of articles would normally fill more than one issue of the journal but we decided to keep the collection together as a representative body of work.We were delighted to welcome Marcelo Wanderley as Guest Editor for this issue. I would like to thank him for his hard and diligent work throughout the preparation of this issue.
Sensing and mapping for interactive performance
Authors: Ng Kia 
Published: February 2003

This paper describes a trans-domain mapping (TDM) framework for translating meaningful activities from one creative domain onto another. The multi-disciplinary framework is designed to facilitate an intuitive and non-intrusive interactive multimedia performance interface that offers the users or performers real-time control of multimedia events using their physical movements. It is intended to be a highly dynamic real-time performance tool, sensing and tracking activities and changes, in order to provide interactive multimedia performances.From a straightforward definition of the TDM framework, this paper reports several implementations and multi-disciplinary collaborative projects using the proposed framework, including a motion and colour-sensitive system, a sensor-based system for triggering musical events, and a distributed multimedia server for audio mapping of a real-time face tracker, and discusses different aspects of mapping strategies in their context.Plausible future directions, developments and exploration with the proposed framework, including stage augmenta
tion, virtual and augmented reality, which involve sensing and mapping of physical and non-physical changes onto multimedia control events, are discussed.
Improvement of Monoclonal Antibody Production in Hybridoma Cells by Dimethyl Sulfoxide
Authors: Ling Wai Lam W. , Deng Liang , Lepore Joseph , Cutler Collette , Cannon‐Carlson Susan , Wang Yan , Voloch Marcio 
Published: February 2003

AbstractHybridoma cultures are routinely used as a source for monoclonal antibody (mAb) production necessary for preclinical evaluation. However, these cultures typically have low volumetric and specific productivities. In this article, we examined the use and the timing of addition of dimethyl sulfoxide (DMSO) as a medium additive to improve mAb production in our hybridoma clone 19 (c19) cultures. From shake flask studies, we defined the optimal DMSO concentration and time of addition for improved productivity. This timing coordinated with high cell viability and density. Hybridoma cultures treated with DMSO up to 0.3% (v/v) possessed cell densities and viabilities comparable to untreated control. We demonstrated that 0.2% (v/v) DMSO added to shake flask cultures at their maximal viable cell densities resulted in a 2‐fold increase in specific mAb production. This procedure was scaleable up to 20 L Cellbags (Wave Bioreactors) with similar titer improvement. Moreover, DMSO treatment did not affect the bioactivity or glycosylation profiles of the mAb.
Development of a Chinese Hamster Ovary Cell Line for Recombinant Adenovirus‐Mediated Gene Expression
Authors: Condon Russell G. G. , Schaefer Eugene J. , Santoro Marc , Longley Robert , Tsao Yung‐Shyeng , Zurawski Sandra M. , Liu Zhong 
Published: February 2003

AbstractRecombinant human adenovirus (rhAd) has been used extensively for functional protein expression in mammalian cells including those of human and nonhuman origin. High‐level protein production by rhAd vectors is expected in their permissive host cells, such as the human embryonic kidney 293 (HEK293) cell line. This is attributed primarily to the permissiveness of HEK293 to rhAd infection and their ability to support viral DNA replication by providing the missing El proteins. However, the HEK293 cells tend to suffer from cytopathic effect (CPE) as a result of virus replication. Under these circumstances, the host cell function is compromised and the culture viability will be reduced. Consequently, newly synthesized polypeptides may not be processed properly at posttranslational levels. Therefore, the usefulness of HEK293 cells for the expression of complex targets such as secreted proteins could be limited. In the search for a more robust cell line as a production host for rhAd expression vectors, a series of screening experiments was performed to isolate clones from Chinese hamster ovary‐K1 (CHO‐K1) cells. First, multiple rounds of infection of CHO‐K1 cells were performed utilizing an rhAd expressing GFP. After each cycle of infection, a small population of CHO cells with high GFP levels was enriched by FACS. Second, individual clones more permissive to human adenovirus infection were isolated from the highly enriched subpopulation by serial dilution. A single clone, designated CHO‐K1‐C5, was found to be particularly permissive to rhAd infection than the parental pool and has served as a production host in the successful expression of several secreted proteins.
Enhancement of Monoclonal Antibody Production by Lysine‐Containing Peptides
Authors: Franěk František , Eckschlager Tomáš , Katinger Hermann 
Published: February 2003

AbstractIn the search for peptides that could effectively enhance the monoclonal antibody production of a model hybridoma, the performance of five lysine‐containing peptides was compared. The capacity of the peptides to enhance the monoclonal antibody yield correlated with their growth‐suppressing activity. No correlation of the production‐enhancing activity with the character of the distribution of cell‐cycle phases could be found. All of the tested peptides, including the negative control peptide Gly‐Phe‐Gly, altered the cell‐cycle phases distribution in favor of the proportion of the S phase.The peptides added to the hybridoma culture were found to be gradually decomposed into dipeptides and free amino acids. Among the set of tested lysine‐containing di‐ to pentapeptides, the best results were obtained with the tripeptide Gly‐Lys‐Gly. The growth‐suppressing and production‐enhancing capacity of this peptide supplement was obviously associated with the temporary presence of the intact peptide molecule in the culture media, because the addition of a mixture of free amino acids constituting this peptide, i.e., glycine and lysine, displayed a different effect‐a slight promotion of cell growth.
Epstein‐Barr Virus Vectors Provide Prolonged Robust Factor IX Expression in Mice
Authors: Sclimenti Christopher R. , Neviaser Andrew S. , Baba Edward J. , Meuse Leonard , Kay Mark A. , Calos Michele P. 
Published: February 2003

AbstractWe demonstrate that vectors incorporating components from Epstein‐Barr virus (EBV) for retention and from human genomic DNA for replication greatly enhance the level and duration of marker gene expression in dividing cultured cells. The same types of vectors were tested in vivo by high‐pressure tail vein injection of naked DNA in mice, resulting in liver delivery and expression. The therapeutic gene was a human factor IX (hFIX) minigene comprising genomically derived 5′, 3′, and intronic sequences that provided relatively good gene expression in vivo. We demonstrated that addition of the EBV EBNA1 gene and its family of repeats binding sites provided a 10‐ to 100‐fold increase in prolonged hFIX expression in mouse liver. A single 25‐μg dose of vector DNA generated normal (>5 μg/mL) levels of hFIX throughout the 8 month duration of the experiment. Vector DNA with or without the EBV sequences was retained in liver cells, and vector replication was not a factor in these nondividing liver cells. Instead, it appears that enhancement of stable hFIX expression by the EBV components was responsible for the increased level and duration of therapeutic gene expression. The EBV sequences also significantly enhanced stable expression of a vector carrying the full genomic hFIX gene delivered to mouse liver. These results underline the crucial importance of appropriate gene expression signals on gene therapy vectors and the utility of EBV sequences in particular for increasing stable gene expression.
Sustained High‐Yield Production of Recombinant Proteins in Transiently Transfected COS‐7 Cells Grown on Trimethylamine‐Coated (Hillex) Microcarrier Beads
Authors: Knibbs Randall N. , Dame Michael , Allen Melissa R. , Ding Yunhong , Hillegas William J. , Varani James , Stoolman Lloyd M. 
Published: February 2003

AbstractThe present study shows that COS‐7 cells transiently transfected and maintained on positively charged (trimethylamine‐coated) microcarrier beads synthesize recombinant protein at higher levels and for longer periods of time than cells transfected and maintained on polystyrene flasks in monolayer culture. Sustained, high‐level synthesis was observed with secreted chimeric proteins (murine E‐selectin– and P‐selectin‐human IgM chimeras) and a secreted hematopoietic growth factor (granulocyte‐macrophage colony‐stimulating factor). Studies with green fluorescent protein indicated that the transfected cells attached more firmly to the trimethylamine‐coated microcarriers than to polystyrene flasks. After 10–14 days in culture, most of the transfected cells detached from the surface of the polystyrene flasks, whereas most transfected cells remained attached to the microcarriers. The transiently transfected microcarrier cultures produced higher levels of protein per transfected cell due to this prolonged attachment. The prolonged attachment and higher output of transfected cells on microcarriers resulted in a 5‐fold increase in protein production from a single transfection over two weeks. Thus, microcarrier‐based transient transfection yields quantities of recombinant proteins with a significant savings of time and reagents over monolayer culture.
Comparison of Batch and Perfusion Culture in Combination with Pilot‐Scale Expanded Bed Purification for the Production of Soluble Recombinant β‐Secretase
Authors: Lüllau E. , Kanttinen A. , Hassel J. , Berg M. , Haag‐Alvarsson A. , Cederbrant K. , Greenberg B. , Fenge C. , Schweikart F. 
Published: February 2003

Abstractβ‐Secretase is one of the prime targets for therapeutic intervention of Alzheimerapos;s disease. For the development of a secretase inhibitor a steady supply of large quantities of a homogeneous and active recombinant β‐secretase is a prerequisite. Therefore various culture modes were investigated using HEK‐293 cells stably transfected with soluble recombinant β‐secretase. The coupling of the Fc part of human IgG1 to the ectodomain of β‐secretase (residues 1–460) allowed a fast purification of the protein with rProtA expanded bed chromatography. Batch cultures of 5 to 50 L working volume run for 7 days showed reproducible cell growth and product yields of 3 mg/L purified protein. A 20 L perfusion culture was operated for 21 days, reaching a cell density of 30 × 106 cells/mL at a dilution rate of 2/d. The total product yield of the perfusion culture was 1.4 g of purified protein. The effect of different perfusion rates on cell growth, protein yield, and quality was investigated and compared to the results obtained in batch cultures. Protein quality was consistent as analyzed on 1D SDS‐PAGE, and the final product contained both the mature and the pro form of β‐secretase. Although the cell specific protein expression was slightly reduced in perfusion culture, a substantial increase in specific activity of over 75% was achieved. Some of the increase in activity can be explained by an increase in the percentage of the mature form of the recombinant protein.
Engineering mRNA Translation Initiation to Enhance Transient Gene Expression in Chinese Hamster Ovary Cells
Authors: Underhill Michèle F. , Coley Clare , Birch John R. , Findlay Alison , Kallmeier Robert , Proud Christopher G. , James David C. 
Published: February 2003

AbstractTo increase transient expression of recombinant proteins in Chinese hamster ovary cells, we have engineered their protein synthetic capacity by directed manipulation of mRNA translation initiation. To control this process we constructed a nonphosphorylatable Ser51Ala site‐directed mutant of eIF2α, a subunit of the trimeric eIF2 complex that is implicated in regulation of the global rate of mRNA translation initiation in eukaryotic cells. Phosphorylation of eIF2α by protein kinases inhibits eIF2 activity and is known to increase as cells perceive a range of stress conditions. Using single‐and dual‐gene plasmids introduced into CHO cells by electroporation, we found that transient expression of the eIF2α Ser51Ala mutant with firefly luciferase resulted in a 3‐fold increase in reporter activity, relative to cells transfected with reporter only. This effect was maintained in transfected cells for at least 48 h after transfection. Expression of the wild‐type eIF2α protein had no such effect. Elevated luciferase activity was associated with a reduction in the level of eIF2α phosphorylation in cells transfected with the mutant eIF2α construct. Transfection of CHO cells with the luciferase‐only construct resulted in a marked decrease in the global rate of protein synthesis in the whole cell population 6 h post‐transfection. However, expression of the mutant Ser51Ala or wild‐type eIF2α proteins restored the rate of protein synthesis in transfected cells to a level equivalent to or exceeding that of control cells. Associated with this, entry of plasmid DNA into cells during electroporation was visualized by confocal microscopy using a rhodamine‐labeled plasmid construct expressing green fluorescent protein. Six hours after transfection, plasmid DNA was present in all cells, albeit to a variable extent. These data suggest that entry of naked DNA into the cell itself functions to inhibit protein synthesis by signaling mechanisms affecting control of mRNA translation by eIF2. This work therefore forms the basis of a rational strategy to generically up‐regulate transient expression of recombinant proteins by simultaneous host cell engineering.
Quantitative Monitoring for Secreted Production of Human Interleukin‐2 in Stable Insect Drosophila S2 Cells Using a Green Fluorescent Protein Fusion Partner
Authors: Shin Hwa Sung , Lim Hye Jung , Cha Hyung Joon 
Published: February 2003

AbstractHuman interleukin‐2 (hIL‐2) production in Escherichia coliand insect cell/baculovirus expression systems can be inefficient. Here we investigated secreted production of hIL‐2 fused with green fluorescent protein (GFP) as a versatile fusion partner in optimized stably transfected insect Drosophila melanogasterS2 cells. This nonlytic S2 insect cell expression system employs a plasmid vector and allows for secretion of functional human proteins. We report that, following stable transfection and induction, S2 cells secreted hIL‐2 as a fusion protein (∼2.3 μg/mL yield), with a secretion efficiency of approximately 90%. Regression analysis indicated a single linear relationship existed between GFP fluorescence and hIL‐2 mass in both whole cell and secreted medium samples, indicating that in vivo monitoring and quantification of target foreign protein expression and even secretion is possible using this system. The simple comparative measurement of GFP fluorescence also allowed monitoring of secretion efficiency during periods of high GFP/hIL‐2 expression.
Stability of Recombinant Protein Production in the GS‐NS0 Expression System Is Unaffected by Cryopreservation
Authors: Barnes Louise M. , Bentley Catherine M. , Dickson Alan J. 
Published: February 2003

AbstractMammalian cells form a very important part of the repertoire of production systems available to scientists involved in the production of recombinant proteins. During the production of therapeutic proteins it is vital for regulatory approval of products that no phenotypic or genetic changes are observed in the cell line or product. As part of the generation and development of therapeutic protein production, cell lines have to be frozen at various stages to create cell banks. If cryopreservation and revival of frozen stocks were to give rise to any phenotypic changes in the cells, this would again be detrimental to the further development of that particular cell line. This study uses one of the most industrially important expression systems, the GS‐NS0 expression system, to examine the effect of cryopreservation on the growth and productivity profile of cell lines that exhibit differential degrees of stability during prolonged (production) culture periods. Results show that cryopreservation and revival procedures do not alter the stability characteristics of cell lines. This type of information is of great value in definition of protocols for cell line development.