bluuebunny/crossref_metadata_2025 huggingface dataset:
Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein
Authors: Wu Ying , Kondrashkina Elena , Kayatekin Can , Matthews C. Robert , Bilsel Osman
Published: August 2008

The earliest kinetic folding events for (βα)
8
barrels reflect the appearance of off-pathway intermediates. Continuous-flow microchannel mixing methods interfaced to small-angle x-ray scattering (SAXS), circular dichroism (CD), time-resolved Förster resonant energy transfer (trFRET), and time-resolved fluorescence anisotropy (trFLAN) have been used to directly monitor global and specific dimensional properties of the partially folded state in the microsecond time range for a representative (βα)
8
barrel protein. Within 150 μs, the α-subunit of Trp synthase (αTS) experiences a global collapse and the partial formation of secondary structure. The time resolution of the folding reaction was enhanced with trFRET and trFLAN to show that, within 30 μs, a distinct and autonomous partially collapsed structure has already formed in the N-terminal and central regions but not in the C-terminal region. A distance distribution analysis of the trFRET data confirmed the presence of a heterogeneous ensemble that persists for several hundreds of microseconds. Ready access to locally folded, stable substructures may be a hallmark of repeat-module proteins and the source of early kinetic traps in these very common motifs. Their folding free-energy landscapes should be elaborated to capture this source of frustration.
Transcriptome-based systematic identification of extracellular matrix proteins
Authors: Manabe Ri-ichiroh , Tsutsui Ko , Yamada Tomiko , Kimura Mina , Nakano Itsuko , Shimono Chisei , Sanzen Noriko , Furutani Yutaka , Fukuda Tomohiko , Oguri Yasuko , Shimamoto Keiko , Kiyozumi Daiji , Sato Yuya , Sado Yoshikazu , Senoo Haruki , Yamashina Shohei , Fukuda Shiro , Kawai Jun , Sugiura Nobuo , Kimata Koji , Hayashizaki Yoshihide , Sekiguchi Kiyotoshi
Published: August 2008

Extracellular matrix (ECM), which provides critical scaffolds for all adhesive cells, regulates proliferation, differentiation, and apoptosis. Different cell types employ customized ECMs, which are thought to play important roles in the generation of so-called niches that contribute to cell-specific functions. The molecular entities of these customized ECMs, however, have not been elucidated. Here, we describe a strategy for transcriptome-wide identification of ECM proteins based on computational screening of >60,000 full-length mouse cDNAs for secreted proteins, followed by
in vitro
functional assays. These assays screened the candidate proteins for ECM-assembling activities, interactions with other ECM molecules, modifications with glycosaminoglycans, and cell-adhesive activities, and were then complemented with immunohistochemical analysis. We identified 16 ECM proteins, of which seven were localized in basement membrane (BM) zones. The identification of these previously unknown BM proteins allowed us to construct a body map of BM proteins, which represents the comprehensive immunohistochemistry-based expression profiles of the tissue-specific customization of BMs.
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome
Authors: Jones Brian V. , Begley Máire , Hill Colin , Gahan Cormac G. M. , Marchesi Julian R.
Published: August 2008

Bile salt hydrolases (BSHs) catalyze the “gateway” reaction in a wider pathway of bile acid modification by the gut microbiota. Because bile acids function as signaling molecules regulating their own biosynthesis, lipid absorption, cholesterol homeostasis, and local mucosal defenses in the intestine, microbial BSH activity has the potential to greatly influence host physiology. However, the function, distribution, and abundance of BSH enzymes in the gut community are unknown. Here, we show that BSH activity is a conserved microbial adaptation to the human gut environment with a high level of redundancy in this ecosystem. Through metagenomic analyses we identified functional BSH in all major bacterial divisions and archaeal species in the gut and demonstrate that BSH is enriched in the human gut microbiome. Phylogenetic analysis illustrates that selective pressure in the form of conjugated bile acid has driven the evolution of members of the Ntn_CGH-like family of proteins toward BSH activity in gut-associated species. Furthermore, we demonstrate that BSH mediates bile tolerance
in vitro
and enhances survival in the murine gut
in vivo
. Overall, we demonstrate the use of function-driven metagenomics to identify functional anchors in complex microbial communities, and dissect the gut microbiome according to activities relevant to survival in the mammalian gastrointestinal tract.
Heat shock factor 1 regulates lifespan as distinct from disease onset in prion disease
Authors: Steele Andrew D. , Hutter Gregor , Jackson Walker S. , Heppner Frank L. , Borkowski Andrew W. , King Oliver D. , Raymond Gregory J. , Aguzzi Adriano , Lindquist Susan
Published: August 2008

Prion diseases are fatal, transmissible, neurodegenerative diseases caused by the misfolding of the prion protein (PrP). At present, the molecular pathways underlying prion-mediated neurotoxicity are largely unknown. We hypothesized that the transcriptional regulator of the stress response, heat shock factor 1 (HSF1), would play an important role in prion disease. Uninoculated HSF1 knockout (KO) mice used in our study do not show signs of neurodegeneration as assessed by survival, motor performance, or histopathology. When inoculated with Rocky Mountain Laboratory (RML) prions HSF1 KO mice had a dramatically shortened lifespan, succumbing to disease ≈20% faster than controls. Surprisingly, both the onset of home-cage behavioral symptoms and pathological alterations occurred at a similar time in HSF1 KO and control mice. The accumulation of proteinase K (PK)-resistant PrP also occurred with similar kinetics and prion infectivity accrued at an equal or slower rate. Thus, HSF1 provides an important protective function that is specifically manifest after the onset of behavioral symptoms of prion disease.
Further insights into the mechanism of the reaction of activated bleomycin with DNA
Authors: Chow Marina S. , Liu Lei V. , Solomon Edward I.
Published: August 2008

Bleomycin (BLM) is a glycopeptide anticancer drug that effectively carries out single- and double-stranded DNA cleavage. Activated BLM (ABLM), a low-spin ferric-hydroperoxide, BLM–Fe
III
–OOH, is the last intermediate detected before DNA cleavage. We have previously shown through experiments and DFT calculations that both ABLM decay and reaction with H atom donors proceed via direct H atom abstraction. However, the rate of ABLM decay had been previously found, based on indirect methods, to be independent of the presence of DNA. In this study, we use a circular dichroism (CD) feature unique to ABLM to directly monitor the kinetics of ABLM reaction with a DNA oligonucleotide. Our results show that the ABLM + DNA reaction is appreciably faster, has a different kinetic isotope effect, and has a lower Arrhenius activation energy than does ABLM decay. In the ABLM reaction with DNA, the small normal
k
H
/
k
D
ratio is attributed to a secondary solvent effect through DFT vibrational analysis of reactant and transition state (TS) frequencies, and the lower
E
a
is attributed to the weaker bond involved in the abstraction reaction (C–H for DNA and N–H for the decay in the absence of DNA). The DNA dependence of the ABLM reaction indicates that DNA is involved in the TS for ABLM decay and thus reacts directly with BLM–Fe
III
–OOH instead of its decay product.
Functional stoichiometry of the unitary calcium-release-activated calcium channel
Authors: Ji Wei , Xu Pingyong , Li Zhengzheng , Lu Jingze , Liu Lin , Zhan Yi , Chen Yu , Hille Bertil , Xu Tao , Chen Liangyi
Published: August 2008

Two proteins, STIM1 in the endoplasmic reticulum and Orai1 in the plasma membrane, are required for the activation of Ca
2+
release-activated Ca
2+
(CRAC) channels at the cell surface. How these proteins interact to assemble functional CRAC channels has remained uncertain. Here, we determine how many Orai1 and STIM1 molecules are required to form a functional CRAC channel. We engineered several genetically expressed fluorescent Orai1 tandem multimers and a fluorescent, constitutively active STIM1 mutant. The tandem multimers assembled into CRAC channels, as seen by rectifying inward currents and by cytoplasmic calcium elevations. CRAC channels were visualized as fluorescent puncta in total internal reflection microscopy. With single-molecule imaging techniques, it was possible to observe photo-bleaching of individual fluorophores and to count the steps of bleaching as a measure of the stoichiometry of each CRAC channel complex. We conclude that the subunit stoichiometry in an active CRAC channel is four Orai1 molecules and two STIM1 molecules. Fluorescence resonance energy transfer experiments also showed that four Orai1 subunits form the assembled channel. From the fluorescence intensity of single fluorophores, we could estimate that our transfected HEK293 cells had almost 400,000 CRAC channels and that, when intracellular Ca
2+
stores were depleted, the channels clustered in aggregates containing ≈1,300 channels, amplifying the local Ca
2+
entry.
La penetración del modelo gramatical ‘general’ de tipo escolar en España
Authors: Lépinette Brigitte
Published: August 2008

En este artículo estudiamos la penetración, en el ámbito escolar español, de la gramática ‘general’ entre el final del siglo XVIII y el XIX (hasta 1845). Nuestro objetivo consistirá en mostrar que la difusión de este tipo de gramática en España, al igual que en Francia, está ligada no sólo a evolucionesinternas, de tipo teórico, i.e. en relación con concepciones puramente lingüísticas, sino que se halla también determinada – y ello, de forma decisiva, aunque no sorprendente para los historiógrafos de la lingüística – por acontecimientos externos a la propia lingüística, como son los cambios en el marco escolar o en la legislación educativa. Mostraremos también que el inicio (en las últimas décadas del siglo XVIII) y el punto de llegada (a mediados del siglo XIX) de dicha penetración son, grosso modo, sincrónicos en los dos países, aunque no coinciden ni en el tiempo intermedio ni en el modo según el cual ésta ocurrió.
The Birth of Applied Linguistics
Authors: Linn Andrew R.
Published: August 2008

The major claim of this article is that there is an independent and clearly defined chapter in the development of linguistics, beginning in the 1880s, which represents the birth of modern applied linguistics, and which has been overlooked in linguistic historiography because of the comparative marginalisation of applied linguistics in the literature. This is the Anglo-Scandinavian School, a phrase its members used to describe themselves. Pioneers within phonetics, these linguists applied their phonetic knowledge to a range of ‘real world’ language issues, notably language-teaching reform, orthographic reform, language planning, and the study of the spoken language. As well as presenting the ideas of the Anglo-Scandinavian School and how they were developed, this article interrogates the notion of a school in intellectual history and proposes that it may in fact be more fruitful to view intellectual history in terms of discourse communities.
The “Scientific Linguist” Goes to War
Authors: Velleman Barry L.
Published: August 2008

During World War II there arose in the United States an urgent need for intensive foreign language instruction that emphasized the spoken language. Beginning in April, 1943, the U. S. Army Specialized Training Program (ASTP) established approximately 500 intensive speaking courses in over 30 languages in fifty-five United States universities. After a single year, the program was suddenly abandoned, owing to combat personnel needs. The present study proposes to describe the sources, implementation, content, materials development, and methods of the ASTP in foreign languages. The study analyzes the ASTP Spanish language materials, explores the attempts at assessing the speaking proficiency of trainees of the program, and evaluates the program’s contributions to subsequent pedagogical approaches and assessment in the United States.
Two lives, two times
Authors: Cohler Bertram J.
Published: August 2008

Life stories such as memoirs reflect the interplay of autobiographical reasoning, and collective remembrance at a time and in a place where memoirs are written. Using this perspective for understanding life-writing, I discuss memoirs written by two women who were formerly internees in the Nazi extermination camp of Auschwitz-Birkenau. Olga Lengyel (1909–2001) lost her entire family in the camp and wrote her memoir in Paris just after the war. Her account describes the atrocities that she observed with few reflections on her own experiences. Mira Ryczke Kimmelman, (1923–) wrote her memoir more than half a century later as an emigre to the United States after the war where she and her husband raised their children and where she is presently an active participant in the survivor community. Her memoir is written as what Tomkins and McAdams have portrayed as a characteristic American redemptive account of successfully overcoming adversity. Following a happy childhood and suffering through the Shoah, Mira Kimmelman is a generative mentor who lectures on her experiences and leads tours for young people back to her homeland. She is concerned that the next generation be spared the suffering of the Shoah.
From one woman to everyman
Authors: Halverson Erica Rosenfeld
Published: August 2008

In this article, I extend Labov’s narrative analysis of personal experience (Labov, 1972, 1997; Labov & Waletzky, 1967/1997) to demonstrate how personal narratives that are taken up and transformed into pieces for public performance work within a reportability continuum that balances the individual storyteller’s perspective while incorporating the voices of the community to which these individuals belong. I use the case of the About Face Youth Theatre, a Chicago-based theatre company that engages lesbian, gay, bisexual, transgendered, and questioning youth in the dramaturgical process, to demonstrate how narratives are transformed from highly reportable, personal narratives, to highly credible, generic adaptations, to performances that result in the construction of positive, public identities that expose normalness without sacrificing particularity. This process can provide adolescents who experience stigma in public contexts with the opportunity to understand how they see themselves, how others see them, and how they fit into their communities and to fit these perspectives together into a more coherent sense of self.
Negotiating the reception of stories in conversation
Authors: Norrick Neal R.
Published: August 2008

In this article, I explore strategies storytellers use to increase listener response to their performances, such as (1) repeating a salient phrase, particularly a piece of dialogue; (2) adding an explanation of the point of a story; (3) drawing out some consequence of the story; and particularly (4) the unobtrusive strategy of producing a minimal response to draw out a more extensive reaction from listeners. This last strategy came to light in a large-scale corpus-based search. Instead of working from a set of narratives, I begin by looking at a linguistic element, namely items from the class of discourse markers like so and y’know in all kinds of contexts in a very large corpus, and slowly narrowed my focus to narrative passages within the whole array of examples. In the process, I discovered distributions and functions for items, which have not been described in previous research on conversational narrative.
A two-time-scale dynamic-model approach for magnetic and kinetic profile control in advanced tokamak scenarios on JET
Authors: Moreau D. , Mazon D. , Ariola M. , De Tommasi G. , Laborde L. , Piccolo F. , Sartori F. , Tala T. , Zabeo L. , Boboc A. , Bouvier E. , Brix M. , Brzozowski J. , Challis C.D. , Cocilovo V. , Cordoliani V. , Crisanti F. , De La Luna E. , Felton R. , Hawkes N. , King R. , Litaudon X. , Loarer T. , Mailloux J. , Mayoral M. , Nunes I. , Surrey E. , Zimmerman O.
Published: August 2008

Real-time simultaneous control of several radially distributed magnetic and kinetic plasma parameters is being investigated on JET, in view of developing integrated control of advanced tokamak scenarios. This paper describes the new model-based profile controller which has been implemented during the 2006–2007 experimental campaigns. The controller aims to use the combination of heating and current drive (H&CD) systems—and optionally the poloidal field (PF) system—in an optimal way to regulate the evolution of plasma parameter profiles such as the safety factor, q(x), and gyro-normalized temperature gradient,
. In the first part of the paper, a technique for the experimental identification of a minimal dynamic plasma model is described, taking into account the physical structure and couplings of the transport equations, but making no quantitative assumptions on the transport coefficients or on their dependences. To cope with the high dimensionality of the state space and the large ratio between the time scales involved, the model identification procedure and the controller design both make use of the theory of singularly perturbed systems by means of a two-time-scale approximation. The second part of the paper provides the theoretical basis for the controller design. The profile controller is articulated around two composite feedback loops operating on the magnetic and kinetic time scales, respectively, and supplemented by a feedforward compensation of density variations. For any chosen set of target profiles, the closest self-consistent state achievable with the available actuators is uniquely defined. It is reached, with no steady state offset, through a near-optimal proportional-integral control algorithm. Conventional optimal control is recovered in the limiting case where the ratio of the plasma confinement time to the resistive diffusion time tends to zero. Closed-loop simulations of the controller response have been performed in preparation for experiments, and typical results are shown. Finally, in the last section of the paper, the first experimental results using this dynamic-model approach to control the plasma current and the safety factor profile on JET, either with the three H&CD systems or also with the PF system as an additional actuator, are presented and discussed.
SNAP predicts effect of mutations on protein function
Authors: Bromberg Yana , Yachdav Guy , Rost Burkhard
Published: August 2008

Summary: Many non-synonymous single nucleotide polymor-phisms (nsSNPs) in humans are suspected to impact protein function. Here, we present a publicly available server implementation of the method SNAP (screening for non-acceptable polymorphisms) that predicts the functional effects of single amino acid substitutions. SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.

Availability: Web-server: http://www.rostlab.org/services/SNAP; downloadable program available upon request.

Contact:  bromberg@rostlab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Predict-2nd: a tool for generalized protein local structure prediction
Authors: Katzman Sol , Barrett Christian , Thiltgen Grant , Karchin Rachel , Karplus Kevin
Published: August 2008

Motivation: Predictions of protein local structure, derived from sequence alignment information alone, provide visualization tools for biologists to evaluate the importance of amino acid residue positions of interest in the absence of X-ray crystal/NMR structures or homology models. They are also useful as inputs to sequence analysis and modeling tools, such as hidden Markov models (HMMs), which can be used to search for homology in databases of known protein structure. In addition, local structure predictions can be used as a component of cost functions in genetic algorithms that predict protein tertiary structure. We have developed a program (predict-2nd) that trains multilayer neural networks and have applied it to numerous local structure alphabets, tuning network parameters such as the number of layers, the number of units in each layer and the window sizes of each layer. We have had the most success with four-layer networks, with gradually increasing window sizes at each layer.

Results: Because the four-layer neural nets occasionally get trapped in poor local optima, our training protocol now uses many different random starts, with short training runs, followed by more training on the best performing networks from the short runs. One recent addition to the program is the option to add a guide sequence to the profile inputs, increasing the number of inputs per position by 20. We find that use of a guide sequence provides a small but consistent improvement in the predictions for several different local-structure alphabets.

Availability: Local structure prediction with the methods described here is available for use online at http://www.soe.ucsc.edu/compbio/SAM_T08/T08-query.html. The source code and example networks for PREDICT-2ND are available at http://www.soe.ucsc.edu/~karplus/predict-2nd/ A required C++ library is available at http://www.soe.ucsc.edu/~karplus/ultimate/

Contact:  karplus@soe.ucsc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
SynBioSS: the synthetic biology modeling suite
Authors: Hill Anthony D. , Tomshine Jonathan R. , Weeding Emma M. B. , Sotiropoulos Vassilios , Kaznessis Yiannis N.
Published: August 2008

Summary: SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorithms.

Availability: SynBioSS is available under the GNU General Public License at http://synbioss.sourceforge.net.

Contact:  yiannis@cems.umn.edu

Supplementary information: Tutorials and documentation are available at the SynBioSS web site: http://synbioss.sourceforge.net.
Crammer's Corner
Authors: Taylor Clare , Riley Ben
Published: August 2008

As the training year draws to an end for many GP Specialty Registrars, this issue of Crammer's Corner looks beyond the nMRCGP assessments and gives a GP Specialty Registrar's summary of the current changes affecting doctors entering the wider world of general practice.
The Combined Contraceptive
Authors: Simon Chantal
Published: August 2008

Eighty percent of women receive contraceptive advice and treatment through their GP. A sexually active woman has an 85% chance of becoming pregnant within a year without contraception and roughly one in three pregnancies are unplanned. Inadequate advice and choice results in women being dissatisfied with their method of contraception and not using methods correctly. Combined contraceptives are preferred by many women because they are reliable, yet easily and rapidly reversible, and are generally well tolerated. This article aims to give an overview guiding GPs in training on choice of the combined contraceptive as a method of contraception and prescription and monitoring of combined contraceptives in primary care.
Urticaria and Angio-Oedema
Authors: Simon Chantal
Published: August 2008

The term urticaria (also known as ‘hives’ or ‘nettle rash’) is widely used to describe a superficial swelling of the epidermis and mucous membranes that results in a red, raised, itchy rash that can be localized or generalized. This rash is described as weals. The rash may be localized or generalized and acute or chronic. Most patients with urticaria do not have systemic reactions, but allergic urticaria and some physical urticarias may occasionally progress to anaphylaxis. However, urticaria is often a feature of anaphylactic reactions. Angio-oedema is a deeper form of urticaria with swelling in the dermis and submucosal or subcutaneous tissues. It may occur alone, or concurrently with urticaria, affecting up to 50% of patients with chronic urticaria.
Psoriasis
Authors: Chiu Keith , Devlukia Sneha , Issa Saleh , Charlton Rodger C.
Published: August 2008

Psoriasis (derived from the Greek word psora meaning to itch) is a common immune-mediated papulosquamous skin disease. First recognized as an independent condition by English dermatologist Robert Willan in 1798, the term is now used to include a variety of clinical appearances with different morphology, distribution, severity and course. Although common, the pathogenesis of psoriasis is not well understood and involves a multitude of genetic and environmental factors. Management of psoriasis includes controlling the extent and severity of disease and its complications, improving the patient's quality of life while minimizing potentially toxic side effects of treatments. This review aims to provide an overview of this complex condition, from its presentation, diagnosis, management in primary care and the referral criteria to secondary care.
Sea-going hardware for the cloud albedo method of reversing global warming
Authors: Salter Stephen , Sortino Graham , Latham John
Published: August 2008

Following the review by Latham
et al
. (Latham
et al
. 2008
Phil. Trans. R. Soc. A
366
) of a strategy to reduce insolation by exploiting the Twomey effect, the present paper describes in outline the rationale and underlying engineering hardware that may bring the strategy from concept to operation. Wind-driven spray vessels will sail back and forth perpendicular to the local prevailing wind and release micron-sized drops of seawater into the turbulent boundary layer beneath marine stratocumulus clouds. The combination of wind and vessel movements will treat a large area of sky. When residues left after drop evaporation reach cloud level they will provide many new cloud condensation nuclei giving more but smaller drops and so will increase the cloud albedo to reflect solar energy back out to space. If the possible power increase of 3.7 W m
−2
from double pre-industrial CO
2
is divided by the 24-hour solar input of 340 W m
−2
, a global albedo increase of only 1.1 per cent will produce a sufficient offset. The method is
not
intended to make new clouds. It will just make existing clouds whiter. This paper describes the design of 300 tonne ships powered by Flettner rotors rather than conventional sails. The vessels will drag turbines resembling oversized propellers through the water to provide the means for generating electrical energy. Some will be used for rotor spin, but most will be used to create spray by pumping 30 kg s
−1
of carefully filtered water through banks of filters and then to micro-nozzles with piezoelectric excitation to vary drop diameter. The rotors offer a convenient housing for spray nozzles with fan assistance to help initial dispersion. The ratio of solar energy reflected by a drop at the top of a cloud to the energy needed to make the surface area of the nucleus on which it has grown is many orders of magnitude and so the spray quantities needed to achieve sufficient global cooling are technically feasible.
Reframing the climate change challenge in light of post-2000 emission trends
Authors: Anderson Kevin , Bows Alice
Published: August 2008

The 2007 Bali conference heard repeated calls for reductions in global greenhouse gas emissions of 50 per cent by 2050 to avoid exceeding the 2°C threshold. While such endpoint targets dominate the policy agenda, they do not, in isolation, have a scientific basis and are likely to lead to dangerously misguided policies. To be scientifically credible, policy must be informed by an understanding of cumulative emissions and associated emission pathways. This analysis considers the implications of the 2°C threshold and a range of post-peak emission reduction rates for global emission pathways and cumulative emission budgets. The paper examines whether empirical estimates of greenhouse gas emissions between 2000 and 2008, a period typically modelled within scenario studies, combined with short-term extrapolations of current emissions trends, significantly constrains the 2000–2100 emission pathways. The paper concludes that it is increasingly unlikely any global agreement will deliver the radical reversal in emission trends required for stabilization at 450 ppmv carbon dioxide equivalent (CO2e). Similarly, the current framing of climate change cannot be reconciled with the rates of mitigation necessary to stabilize at 550 ppmv CO2e and even an optimistic interpretation suggests stabilization much below 650 ppmv CO2e is improbable.
Enthusiasm-Based or Evidence-Based Charities: Personal Reflections Based on the Project P.A.T.H.S. in Hong Kong
Authors: Shek Daniel T. L.
Published: August 2008

In charitable foundations throughout the world, different approaches are used to allocate funding. As many projects with good will (i.e., enthusiasm-based charity) actually fail to help those who really need it, it is argued that the evidence-based approach (i.e., charity guided by scientific evidence) represents the best strategy to support projects that can really help the needy. Using this approach, scientific research findings are systematically used to (1) understand the nature of the problem and/or social needs, (2) design appropriate intervention programs based on the best available evidence, and (3) systematically evaluate the outcomes of the developed program. Using the Project P.A.T.H.S. funded by the Hong Kong Jockey Club Charities Trust as an example, the characteristics underlying this approach are outlined. The systematic use of scientific evidence in the Project P.A.T.H.S. is exemplary in different Chinese societies. This project provides much insight for charitable foundations and funding bodies locally and globally.
Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene–Metabolite Correlations inArabidopsis
Authors: Yonekura-Sakakibara Keiko , Tohge Takayuki , Matsuda Fumio , Nakabayashi Ryo , Takayama Hiromitsu , Niida Rie , Watanabe-Takahashi Akiko , Inoue Eri , Saito Kazuki
Published: August 2008

To complete the metabolic map for an entire class of compounds, it is essential to identify gene–metabolite correlations of a metabolic pathway. We used liquid chromatography–mass spectrometry (LC-MS) to identify the flavonoids produced by Arabidopsis thaliana wild-type and flavonoid biosynthetic mutant lines. The structures of 15 newly identified and eight known flavonols were deduced by LC-MS profiling of these mutants. Candidate genes presumably involved in the flavonoid pathway were delimited by transcriptome coexpression network analysis using public databases, leading to the detailed analysis of two flavonoid pathway genes, UGT78D3 (At5g17030) and RHM1 (At1g78570). The levels of flavonol 3-O-arabinosides were reduced in ugt78d3 knockdown mutants, suggesting that UGT78D3 is a flavonol arabinosyltransferase. Recombinant UGT78D3 protein could convert quercetin to quercetin 3-O-arabinoside. The strict substrate specificity of UGT78D3 for flavonol aglycones and UDP-arabinose indicate that UGT78D3 is a flavonol arabinosyltransferase. A comparison of flavonol profile in RHM knockout mutants indicated that RHM1 plays a major role in supplying UDP-rhamnose for flavonol modification. The rate of flavonol 3-O-glycosylation is more affected than those of 7-O-glycosylation by the supply of UDP-rhamnose. The precise identification of flavonoids in conjunction with transcriptomics thus led to the identification of a gene function and a more complete understanding of a plant metabolic network.
ARABIDOPSIS THALIANA HOMEOBOX GENE1Establishes the Basal Boundaries of Shoot Organs and Controls Stem Growth
Authors: Gómez-Mena Concepción , Sablowski Robert
Published: August 2008

Apical meristems play a central role in plant development. Self-renewing cells in the central region of the shoot meristem replenish the cell population in the peripheral region, where organ primordia emerge in a predictable pattern, and in the underlying rib meristem, where new stem tissue is formed. While much is known about how organ primordia are initiated and their lateral boundaries established, development at the interface between the stem and the meristem or the lateral organs is poorly understood. Here, we show that the BELL-type ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) is required for proper development of the boundary between the stem and both vegetative and reproductive organs and that this role partially overlaps with that of CUP-SHAPED COTYLEDON genes. During the vegetative phase, ATH1 also functions redundantly with light-activated genes to inhibit growth of the region below the shoot meristem. Consistent with a role in inhibiting stem growth, ATH1 is downregulated at the start of inflorescence development and ectopic ATH1 expression prevents growth of the inflorescence stem by reducing cell proliferation. Thus, ATH1 modulates growth at the interface between the stem, meristem, and organ primordia and contributes to the compressed vegetative habit of Arabidopsis thaliana.
Addled by authentication: recent changes to password systems in British academic libraries
Authors: Joint Nicholas
Published: August 2008

Purpose

The purpose of this paper is to outline the general principles behind changes in digital library authentication policy and practice in the UK from 2006 to date.

Design/methodology/approach

A brief review of the main features in the recent history of digital library authentication in the UK, emphasising the paradoxes underlying authentication and data protection and describing the problems faced by individual stakeholders in addressing the issues of federated access management.

Findings

That the adoption of new models of authentication involves supporting all parties involved in the national authentication project as they work through the difficult process of change management in this area, and that credible leadership of the change process is vital. Ultimately, broader issues concerning information literacy and the pervasive grasp of data protection principles in our contemporary information society are raised by the examination of this topic.

Research limitations/implications

Further in depth examination of the practical benefits of data protection and information management legislation is desirable, especially in light of the pervasively low levels of information literate understanding of these topics, of which federated access management is merely one example.

Practical implications

The straightforward presentation of the themes in this paper should enhance practitioner understanding of the complex topic under consideration.

Originality/value

This investigation reviews some technical areas of recent authentication developments in order to highlight the broader administrative meaning and impact of these innovations.
Financial management and budgeting strategies for LIS programmes
Authors: Okello‐Obura Constant , Kigongon‐Bukenya I.M.N.
Published: August 2008

Purpose

With the dwindling state funding to support higher education, Universities have been forced to initiate many private programmes to not only generate income for the Universities but also to respond to the high demand for higher qualifications and skills demanded for globally. This in turn has put on pressure on University departments to initiate new programmes, budget for them and manage the resources accruing from these programmes. The central question is how these academic programmes are budgeted for and the budgeting strategy adopted by Library and Information Science (LIS) schools. The purpose of this article is to examine the budgeting strategies applicable in LIS and recommends appropriate strategies to be adopted for budgeting for LIS programmes. It also recommends financial management issues that LIS school educators/managers should consider.

Design/methodology/approach

This paper is based on analysis of relevant literature and experience of the authors in designing several courses at Makerere University.

Findings

The paper makes a review of budgeting strategies applicable to LIS institutions and makes recommendations for the key areas that should be considered by LIS schools in budgeting for new academic programmes. It concludes by making emphasis on financial management and proper budgeting as an important tool in surviving the closure in the global re‐organisation in higher education.

Originality/value

Some LIS schools have closed especially in South Africa. The issue is financial sustainability. This article addresses this central issue that need to be carefully considered by LIS schools to ensure that LIS programmes are budgeted for properly.
Establishing the national digital cultural heritage repository in Malaysia
Authors: Abd Manaf Zuraidah
Published: August 2008

Purpose

The purpose of this study is to uncover the perceptions of information professionals with regards to the establishment of a National Digital Cultural Heritage Repository Center (NDCHR) in Malaysia.

Design/methodology/approach

This study adopts a modified Delphi study to identify the factors that contribute towards the establishment of an NDCHR in Malaysia. A three‐round modified Delphi study was used in this study to obtain consensus among the experts with regards to the factors that contribute towards the establishment of the central repository.

Findings

The establishment of an NDCHR requires collaboration efforts among the different types of cultural institution in Malaysia. The aspiration of the establishment to improve accessibility, resource discovery, preservation and promotion of the nation's cultural heritage information would contribute toward restructuring some common grounds and thinking among the different types of cultural institutions with respect to effective approaches to managing and organising the nation's digital cultural heritage information.

Practical implications

Findings and discovery of the study are significant in providing a general framework to establish an NDCHR in Malaysia

Originality/value

The outcome of the study will contribute toward the establishment of a central repository for digital cultural heritage information in Malaysia.
Tribological behavior of the synthetic chlorine‐ and fluorine‐containing silicon oil as aerospace lubricant
Authors: Weng Lijun , Wang Haizhong , Feng Dapeng , Liu Weimin , Xue Qunji
Published: August 2008

Purpose

The purpose of this paper is to examine the tribological behavior of the synthetic chlorine‐ and fluorine‐containing silicon oil as an aerospace lubricant.

Design/methodology/approach

The chlorinated‐phenyl and methyl terminated silicone oil (CPSO), chlorinated‐phenyl and trifluorinated‐propyl with methyl terminated silicone oil (FCPSO) were prepared. Their physical properties such as saturated vapor pressure and the evaporation weight loss were evaluated. The tribological properties of the silicon oils under moderate load were investigated with an Optimol SRV oscillating friction and wear tester, as well as Four‐ball friction and wear tester according to the standard method of ASTM D 4172 under higher load. The elemental composition generated on steel ball surface were analyzed on a scanning electron microscope with a Kevex energy dispersive X‐ray analyzer attachment (SEM/EDS), and the chemical nature of elements on worn surface lubricated with FCPSO were studied by X‐ray photoelectron spectrometer (XPS).

Findings

It is found that the CPSO and FCPSO show good tribological behavior for steel/CuSn alloy tribological pairs and are superior to hosphazene (X‐1P) and perfluoropolyether in terms of friction‐reduction ability and anti‐wear performance. The anti‐wear performance of FCPSO as lubricants for steel‐steel contacts is superior to CPSO. The EDS results showed existence of F and Si on the worn surface with lubrication of FCPSO, while XPS results indicated the occurrence of tribochemical reaction of FCPSO with friction pair during sliding process with the formation of FeCl2, FeF2 and the absorption silicon oil films on the lubricated metal surface.

Originality/value

The results substantiate that chemical reactive elemental such as chlorine or fluorine, which is substituted into silicon oil, helps to improve the anti‐wear and load‐carrying capacity of the liquid lubricant. So the excellent thermal stability, low‐temperature fluidity, very low‐saturated vapor pressure and excellent lubricity for steel/CuSn alloy of the silicon oil of FCPSO and CPSO make it an attractive alternative to conventional liquid lubricant for space mechanism.
Effect of surface roughness on weldability in aluminium sheets joined by cold pressure welding
Authors: Sahin Mumin
Published: August 2008

Purpose

The purpose of this paper is to examine the effects of the welding deformation and surface roughness in cold pressure welding on the tensile strength and the fatigue strength of joined sheets. Additionally, the paper seeks to analyse the hardness variations and microstructures at the welding interface.

Design/methodology/approach

Cold pressure welding is a method of joining similar or dissimilar ductile metals. It can be applied by bringing into close contact the surfaces of virgin metal specimens that appear due to the breakdown of the surface layers caused by bulk plastic deformation. Cold pressure welding is applied to test parts without too long a delay after the preparation of surfaces. The application of welding in 10 min affects importantly the weld strength. As this time is increased, the weld strength of the joints is decreased. The determination of deformation amount is found by determination of the reduction (R) at the total thickness of the two parts after the welding process.

Findings

The weld strength increases as the surface roughness and weld deformation of the joined sheets increase. The length of bond zones increases with increasing deformation. Therefore, the weld strength of parts depends on the length of bond zones. Then, there is an effect of surface roughness on the welding strength. Joined sheets show resistance to little fluctuating tensile stress. It is observed that the parts rupture from the welding‐interface hardness values are about the same at interfaces of sheets having different surface roughness and equal deformation (60 per cent). But, if it is considered that hardness of aluminium material purchased is about 53 HV, it can be said that the hardness increases in joined parts because of local hardening during deformation in cold pressure welding method as lap welding. Bond formation at interfaces of joined sheets having Ra=5 μm surface roughness and deformation ratio 60 per cent is shown to be successful in the microstructure photo.

Research limitations/implications

Surface roughness and deformation values can be increased in further studies.

Originality/value

The paper offers insight into the effects of surface roughness on weldability.
Maximum allowable manipulator mass based on cycle time, impact safety and pinching safety
Authors: Vermeulen M.M.A. , Wisse M.
Published: August 2008

Purpose

Safety is an important issue when manipulators operate in an environment where humans are present, such as the agriculture industry. An intrinsically safe mechanical system guarantees human safety when electronics or controls fail. However, industry also demands a certain operating velocity. A low inertia is the most important aspect to combine safety with a useful operating velocity, because this will limit the amount of kinetic or potential energy in the system and the required actuation forces. Low‐actuation forces limit the amount of static contact pressure between manipulator and human, a requirement for intrinsic safety. Low energy means that less contact force is required to put the manipulator to a stop in collision, an additional requirement. The goal of this paper is to find the maximum industrially applicable, manipulator mass for which intrinsic mechanical safety is guaranteed.

Design/methodology/approach

Observing existing and proposed manipulators in agriculture results in a required cycle time of 0.9 s, trajectory of 0.8 m and payload of 2 kg. Three important trade‐offs applying to the manipulator are identified. The first is between maximum velocity and acceleration, using cycle time and trajectory. The second is between maximum acceleration and mass, based on a measure for pain in contact pressure. The third is between maximum velocity and mass, using a collision model and the contact pressure during collision.

Findings

Combining all three trade‐offs results in an allowable arm effective inertia of 5.1 kg. Taking payload into account and converting to a realistic mass distribution results in a total mass of 9.3 kg. Compared to existing manipulators, both mass and payload are ambitious but realistic for the future development of an intrinsically safe manipulator.

Research limitations/implications

Accuracy in positioning is not taken into account.

Originality/value

This paper combines safety criteria on maximum energy and maximum static pressure, while also taking industrial applicable operating velocity into account.
Changing education governance and management in Asia
Authors: Ho Mok Ka
Published: August 2008

Purpose

The article aims to offer an introduction to the special issue on changing education governance in Asia.

Design/methodology/approach

A brief overview of the issue is provided.

Findings

The article notes that one of the prominent issues running through the issue is the dilemma between the assertion of academic freedom and the deepening governance/management reforms in schools and universities.

Originality/value

The article highlights that the issue offers a distinct comparative perspective in analyzing recent changes in education governance and management in selected Asian societies.
Massification, bureaucratization and questing for “world‐class” status
Authors: Ngok Kinglun
Published: August 2008

Purpose

This article aims to review the latest developments of the higher education sector in China since the mid‐1990s by focusing on the expansion of university education.

Design/methodology/approach

It is argued that while massification of higher education is an important indication of the progress in China's higher education system, the quest for world‐class universities indicates China's ambition to earn international reputation in higher education sector compatible with its increasing economic power.

Findings

The driving force of these two developments is from the state, which demonstrates the dominant role of the Chinese government in higher education policy and administration. However, the ambitious state constitutes both a driving force and a constraint for China's higher education. The strengthening administrative control accompanied by the financial benefits from the government has led to bureaucratization of China's universities. China's world‐class pursuit necessitates a fundamental change of the existing pattern of relationship between the state and university and university governance model.

Practical Implications

The strategic plan to build up world‐class universities shows that China is not satisfied with the quantitative growth of its higher education, but is seeking to achieve a breakthrough in quality higher education.

Originality/value

The paper explains how China's desire to achieve world class status within the area of higher education is being achieved.