bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predict-2nd: a tool for generalized protein local structure prediction
Authors: Katzman Sol , Barrett Christian , Thiltgen Grant , Karchin Rachel , Karplus Kevin 
Published: August 2008

Abstract
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

Abstract
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.
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

AbstractTo 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

AbstractApical 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

PurposeThe 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/approachA 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.FindingsThat 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/implicationsFurther 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 implicationsThe straightforward presentation of the themes in this paper should enhance practitioner understanding of the complex topic under consideration.Originality/valueThis 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

PurposeWith 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/approachThis paper is based on analysis of relevant literature and experience of the authors in designing several courses at Makerere University.FindingsThe 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/valueSome 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

PurposeThe 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/approachThis 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.FindingsThe 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 implicationsFindings and discovery of the study are significant in providing a general framework to establish an NDCHR in MalaysiaOriginality/valueThe 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

PurposeThe 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/approachThe 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).FindingsIt 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/valueThe 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

PurposeThe 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/approachCold 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.FindingsThe 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/implicationsSurface roughness and deformation values can be increased in further studies.Originality/valueThe 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

PurposeSafety 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/approachObserving 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.FindingsCombining 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/implicationsAccuracy in positioning is not taken into account.Originality/valueThis 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

PurposeThe article aims to offer an introduction to the special issue on changing education governance in Asia.Design/methodology/approachA brief overview of the issue is provided.FindingsThe 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/valueThe 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

PurposeThis 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/approachIt 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.FindingsThe 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 ImplicationsThe 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/valueThe paper explains how China's desire to achieve world class status within the area of higher education is being achieved.
Managing race equality in Scottish local councils in the aftermath of the Race Relations (Amendment) Act 2000
Authors: Hussain Asifa , Ishaq Mohammed 
Published: August 2008

PurposeMore than six years have elapsed since the much‐heralded Race Relations (Amendment) Act 2000 (hereafter also referred to as the “Act”) came into force. The Act had been prompted by concern at the lack of progress made in the sphere of racial equality despite the existence of the 1976 Race Relations Act. There were accusations that the 1976 Act was outdated and lacked the political teeth to be effective. The new Act imposed for the first time specific requirements on public sector institutions to be more proactive in promoting race equality. The duties would apply to public bodies that were previously exempt such as the Police and the National Health Service. This paper aims to focus on Scottish local councils and to examine the progress made by these public sector organisations in the field of race equality since the new Act came into force.Design/methodology/approachThe researchers carried out a postal survey of Scotland's 32 local authorities in order to assess the progress made in the area of race equality. Questions focused on examining the scale of progress in relation to both employment and service delivery.FindingsThe results revealed a mixed picture. On the positive side, most councils had initiated race awareness training programmes. The majority had also incorporated aspects of race equality into their equal opportunities policies and most had instituted measures to engage with ethnic minority communities. However, there are still areas where performance is unsatisfactory, including inadequacies in the ethnic monitoring of staff, failure to reflect the size of the ethnic minority community in the workforce, and the absence of a clear and distinctive policy on racial harassment in the workplace.Originality/valueThis research will be of great value to anyone who is interested in assessing whether the legislative duties imposed by the Act have been satisfied by Scotland's local authorities. It is the first study of its kind in Scotland and is likely to appeal to both practitioners in the public sector and to academics.