bluuebunny/crossref_metadata_2025 huggingface dataset:
PERMORY-MPI: a program for high-speed parallel permutation testing in genome-wide association studies
Authors: Steiß Volker , Letschert Thomas , Schäfer Helmut , Pahl Roman
Published: February 2012

Summary: PERMORY is software for accelerated permutation testing of genome-wide association studies (GWAS). We have parallelized PERMORY using the Message-Passing Interface resulting in a nearly linear speedup. Furthermore, we added accelerated analysis of GWAS using quantitative phenotypes, and an accurate estimation of the effective number of independent tests.

Availability and implementation: Free download from http://permory.org

Contact:  rpahl@staff.uni-marburg.de; volker.steiss@mni.thm.de
GMD: measuring the distance between histograms with applications on high-throughput sequencing reads
Authors: Zhao Xiaobei , Sandelin Albin
Published: February 2012

Summary:  GMD (generalized minimum distance of distributions) is an R package to assess the similarity between spatial distributions of read-based sequencing data such as ChIP-seq and RNA-seq. GMD calculates the optimal distance between pairs of normalized signal distributions, optionally sliding one distribution over the other to ‘align’ the distributions. GMD also provides graphical and downstream clustering tools.

Availability: The R package GMD source code is available at http://cran.r-project.org/web/packages/GMD/ under GPL license

Contact:  xiaobei@binf.ku.dk; mailto:albin@binf.ku.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Care of the International Traveller
Authors: Shiner Alice
Published: February 2012

Managing the health of our globetrotting population is a challenging yet fascinating aspect of general practice. Overseas travellers may return from journeys with symptoms as exotic and unheard of as their far-flung destinations. Pre-travel health can also be a mystery as this tends to fall under the remit of practice nurses in most surgeries. Yet, GPs are expected to have at least some knowledge of travel health, particularly in our increasingly globalized world.
Evolutionary Meta-Analysis of Solanaceous Resistance Gene and Solanum Resistance Gene Analog Sequences and a Practical Framework for Cross-Species Comparisons
Authors: Quirin Edmund A. , Mann Harpartap , Meyer Rachel S. , Traini Alessandra , Chiusano Maria Luisa , Litt Amy , Bradeen James M.
Published: February 2012

Cross-species comparative genomics approaches have been employed to map and clone many important disease resistance (R) genes from Solanum species—especially wild relatives of potato and tomato. These efforts will increase with the recent release of potato genome sequence and the impending release of tomato genome sequence. Most R genes belong to the prominent nucleotide binding site-leucine rich repeat (NBS-LRR) class and conserved NBS-LRR protein motifs enable survey of the R gene space of a plant genome by generation of resistance gene analogs (RGA), polymerase chain reaction fragments derived from R genes. We generated a collection of 97 RGA from the disease-resistant wild potato S. bulbocastanum, complementing smaller collections from other Solanum species. To further comparative genomics approaches, we combined all known Solanum RGA and cloned solanaceous NBS-LRR gene sequences, nearly 800 sequences in total, into a single meta-analysis. We defined R gene diversity bins that reflect both evolutionary relationships and DNA cross-hybridization results. The resulting framework is amendable and expandable, providing the research community with a common vocabulary for present and future study of R gene lineages. Through a series of sequence and hybridization experiments, we demonstrate that all tested R gene lineages are of ancient origin, are shared between Solanum species, and can be successfully accessed via comparative genomics approaches.
Management of Almond Leaf Scorch Disease: Long-Term Data on Yield, Tree Vitality, and Disease Progress
Authors: Sisterson Mark S. , Ledbetter Craig A. , Chen Jianchi , Higbee Bradley S. , Groves Russell L. , Daane Kent M.
Published: February 2012

Almond leaf scorch disease (ALSD) has been a chronic problem for California almond growers. This disease is caused by the bacterial pathogen Xylella fastidiosa and is transmitted by xylem-feeding insects. Previous research suggested that retaining, rather than roguing, ALSD-affected trees may be more economically beneficial because ALSD-affected trees produced a reasonable yield and did not die over a 3-year period. Because almond orchards are kept in production for approximately 25 years, longer-term data are needed to fully evaluate the merits of retaining ALSD-affected trees. Extension of yield evaluations from 3 to 5 years demonstrated that yield loss due to ALSD was consistent over 5 years, with yields of ALSD-affected trees reduced by 20 and 40% compared with unaffected trees for ‘Nonpareil’ and ‘Sonora’, respectively. To assess risk of ALSD-affected trees serving as a source of inocula for secondary (tree-to-tree) spread and to evaluate vitality of ALSD-affected trees, previous surveys of two orchards were extended from 3 to 6 or 7 years. The relationship between disease incidence (percentage of trees infected) and survey year was linear for all cultivars examined at both orchards. Furthermore, at each orchard, the spatial location of infections detected after the first survey was random with respect to the spatial location of infections identified during the first survey, suggesting that ALSD-affected trees retained in orchards did not serve as a source for secondary spread. Over the 6- to 7-year study period, death of ALSD-affected trees was rare, with only 9% of ALSD-affected trees dying. Because orchards used in this study had relatively high disease incidence, 61 orchards containing Sonora were surveyed to determine typical levels of ALSD incidence. ALSD was widespread, with at least one infected tree in 56% of orchards surveyed, but incidence was typically low (mean incidence = 0.47%). Collectively, the results suggest that retaining ALSD-affected trees may be economically beneficial in older orchards.
First Report of Erwinia amylovora Causing Fire Blight on Plum (Prunus domestica) in Hungary
Authors: Végh A. , Némethy Zs. , Hajagos L. , Palkovics L.
Published: February 2012

During July 2011, a severe, unusual disease symptom was observed on young shoots on a 10-year old plum tree (Prunus domestica L. ‘d'Agen’) in the city of Budaörs, near Budapest. The naturally infected shoots showed typical symptoms of fire blight including terminal shoots with brown-to-black necrotic lesions and later, shepherd's crook deformation. Symptoms were the same as fire blight, symptoms reported from other hosts and locations. The first occurrence of fire blight on European plum was recorded in Germany in 2002 (4). Shoots containing regions of dead and healthy tissue were surface sterilized with ethanol (50-mg sample homogenized with 500 μl of sterile water and 50 μl of the homogenate streaked to King's B agar medium). After 48 h of incubation at 26°C, the medium contained pure cultures of a bacterium with white mucoid colonies, which is morphologically consistent with E. amylovora (1). Isolates were gram negative and induced a hypersensitive reaction in tobacco (Nicotiana tabacum L. ‘White Burley’) leaves (2). Biochemical tests were also used for identification, and the results of API 20E and API 50 CH kits (Biomérieux, Marcy l'Etoile, France), demonstrated that the bacterium belongs to Enterobacteriaceae. Pathogenicity was tested by injecting five healthy young plum shoots from the same tree with a 10-μl bacterial suspension of 107 CFU/ml. Controls were injected with sterile distilled water. Shoots were kept at 26°C and 80 to 100% relative humidity. Five days after inoculation, dark brown-to-black lesions and shepherd's crook symptoms were observed only on inoculated shoots. The bacterium was reisolated from lesions on inoculated shoots, fulfilling Koch's postulates. No lesions were observed on controls. For molecular identification of the pathogen, the 16S rDNA region was amplified from isolate EA-PlumBo1 with a general bacterial primer pair (63f forward and 1389r reverse) (3). The PCR products were cloned into a pGEM T-Easy plasmid vector (Promega, Madison, WI) and were transformed into Escherichia coli DH5α cells. A recombinant plasmid (2A2.5) was sequenced by M13 forward and reverse primers. The sequence was deposited in GenBank (Accession No. HE610678) and showed 99 to 100% sequence homology with a number of E. amylovora isolates, including type strain AJ233410 with 99% similarity and 100% homology with sequences FN434113 and FN666575, where the complete genomes are known. On the basis of the symptoms, colony morphology, biochemical tests, and 16S rDNA sequence homology, the pathogen was identified as E. amylovora. To our knowledge, this is the first report of a natural outbreak of fire blight on plum in Hungary and the presence of the pathogen may seriously influence local stone fruit production in the future.

References: (1) E. O. King et al. J. Lab. Clin. Med. 44:301, 1954. (2) Z. Klement. Nature 199:299, 1963. (3) A. M. Osborn et al. Environ. Microbiol. 2:39, 2000. (4) J. L. Vanneste et al. Acta Hortic. 590:89, 2002.
Use of Phosphonate to Manage Foliar Potato Late Blight in Developing Countries
Authors: Kromann Peter , Pérez Willmer G. , Taipe Arturo , Schulte-Geldermann Elmar , Sharma Buddhi Prakash , Andrade-Piedra Jorge L. , Forbes Gregory A.
Published: February 2012

Twenty phosphonate products found in the agrochemical market in Ecuador and Peru were evaluated in bioassays for the control of foliar potato late blight, caused by Phytophthora infestans. Eight phosphonate products were evaluated in 16 field experiments done in Peru, Ecuador, Kenya, and Nepal. A meta-analysis across locations involving 71 combinations of potato genotype by site and year demonstrated a significant relationship between phosphonate application rate and efficacy for controlling late blight on potato foliage. The meta-analysis revealed that phosphonate rates of approximately 2.5 g a.i./liter provided efficacy similar to that of the conventional contact fungicides mancozeb and chlorothalonil used at similar rates. At rates higher than 2.5 g a.i./liter, the efficacy of phosphonate was superior to the contact fungicides. Overall, late blight control by phosphonate appeared relatively stable in field experiments across locations. An analysis of field experiments and 64 combinations of potato genotype by site and year showed no correlation between the susceptibility level of potato genotypes and efficacy of phosphonates. The cost of both phosphonate compounds and contact fungicides varied greatly among the countries of the field study; however, in Kenya, control with phosphonate was clearly less expensive than with mancozeb.
Mechanisms Involved in Cardioprotective Effects of Pravastatin Administered during Reoxygenation in Human Myocardium In Vitro
Authors: Lemoine Sandrine , Allouche Stéphane , Coulbault Laurent , Cornet Valérie , Massetti Massimo , Galera Philippe , Gérard Jean-Louis , Hanouz Jean-Luc
Published: February 2012

Background

The authors investigated the effect of pravastatin during reoxygenation after myocardial hypoxia and examined the involvement of nitric oxide synthase, mitochondrial permeability transition pore, and expression of markers of apoptosis in human myocardium in vitro.

Methods

Human atrial trabeculae were exposed to hypoxia for 30 min and reoxygenation for 60 min (control group; n = 10). Pravastatin (5, 10, 50, 75 μM; n = 6 in each group) was administered throughout the reoxygenation. In separate groups (n = 6 in each group), pravastatin 50 μM was administered in the presence of 200 μM L-NG-nitroarginine methyl ester, a nitric oxide synthase inhibitor, and 50 μM atractyloside, the mitochondrial permeability transition pore opener. The primary endpoint was the developed force of contraction at the end of reoxygenation, expressed as a percentage of baseline (mean ± SD). Protein expression of BAD, phospho-BAD, caspase 3, Pim-1 kinase, and Bcl-2 were measured using Western immunoblotting.

Results

The administration of 10 (77 ± 5% of baseline), 50 (86 ± 6%), and 75 μM (88 ± 13%) pravastatin improved the force of contraction at the end of reoxygenation, compared with that of the control group (49 ± 11%; P < 0.001). These beneficial effects were prevented by L-NG-nitroarginine methyl ester and atractyloside. Compared with control group, the administration of 5 μM pravastatin did not modify the force of contraction. Pravastatin increased the phosphorylation of BAD, activated the expression of Pim-1 kinase and Bcl-2, and maintained the caspase 3 concentration relative to that of the respective untreated controls.

Conclusions

Pravastatin, administered at reoxygenation, protected the human myocardium by preventing the mitochondrial permeability transition pore opening, phosphorylating BAD, activating nitric oxide synthase, Pim-1 kinase, and Bcl-2, and preserving the myocardium against the caspase 3 activation.
Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil
Authors: Moß Karin S. , Hartmann Stefan C. , Müller Isabell , Fritz Christina , Krügener Sven , Zibek Susanne , Hirth Thomas , Rupp Steffen
Published: February 2012

A bacterial strain named IGB-41T was isolated from a soil sample from an ant hill near Stuttgart, Germany. The strain was Gram-negative, rod-shaped, motile and facultatively anaerobic. Phylogenetic analysis based on 16S rRNA grouped the strain IGB-41T within the class

Betaproteobacteria

into the family

Neisseriaceae

together with

Silvimonas amylolytica

NBRC 103189T,

Silvimonas iriomotensis

NBRC 103188T and

Silvimonas terrae

KM-45T as the closest relatives with sequence similarities of 96.7, 96.6 and 96.1 %, respectively. The G+C content of the genomic DNA was determined to be 61.5 mol% and quinone analysis revealed Q-8 as the only detectable quinone. Major cellular fatty acids were identified as C16 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and C18 : 1ω7c . Strain IGB-41T was unique in harbouring phosphoaminolipids, aminolipids and glycoaminolipids when compared with

Silvimonas amylolytica

NBRC 103189T in polar lipid analysis. On the basis of the physiological, phenotypic and genotypic characteristics of strain IGB-41T, we suggest that the novel strain should be assigned to a new genus Amantichitinum and novel species Amantichitinum ursilacus. The type species of the genus Amantichitinum is Amantichitinum ursilacus and the type strain is IGB-41T ( = DSM 23761T = CIP 110167T).
Rhodococcus canchipurensis sp. nov., an actinomycete isolated from a limestone deposit site
Authors: Nimaichand Salam , Sanasam Suchitra , Zheng Liu-Qiang , Zhu Wen-Yong , Yang Ling-Ling , Tang Shu-Kun , Ningthoujam Debananda S. , Li Wen-Jun
Published: February 2012

A novel actinobacterial strain, MBRL 353T, was isolated from a sample collected from a limestone quarry at Hundung, Manipur, India. Comparison of 16S rRNA gene sequences of strain MBRL 353Tand other members of the genusRhodococcusshowed sequence similarities ranging from 95.5 to 98.2 %, with strain MBRL 353Tshowing closest sequence similarity toRhodococcus triatomaeIMMIB RIV-085T(98.2 %) andRhodococcus equiDSM 20307T(97.2 %). DNA–DNA hybridization results, however, revealed that DNA–DNA relatedness values between strain MBRL 353TandR. triatomaeDSM 44892T(43.4 %) andR. equiDSM 20307T(33.4 %) were well below the 70 % limit for species identification. Strain MBRL 353Tcontainedmeso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose in the cell wall. Mycolic acids were present. The major fatty acids were C16 : 0(45.7 %), C18 : 1ω9c(18.2 %) and 10-methyl C18 : 0(11.3 %). The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 69.2 mol%. The phenotypic and genotypic data showed that strain MBRL 353Tmerits recognition as a representative of a novel species of the genusRhodococcusfor which the nameRhodococcus canchipurensissp. nov. is proposed; the type strain is MBRL 353T( = KCTC 19851T = JCM 17578T).
Natronococcus roseus sp. nov., a haloalkaliphilic archaeon from a hypersaline lake
Authors: Corral P. , Gutiérrez M. C. , Castillo A. M. , Domínguez M. , Lopalco P. , Corcelli A. , Ventosa A.
Published: February 2012

A novel halophilic archaeon, strain CG-1T, belonging to the genus

Natronococcus

was isolated from sediment of the soda lake Chagannor in Inner Mongolia, China. The colonies of this strain were pink pigmented, the intensity of the colour decreased when the cells grew at salt saturation levels. The cells were non-motile cocci and strictly aerobic. Hypotonic treatment did not cause cell lysis, even in distilled water. Strain CG-1T grew at 15–30.0 % (w/v) NaCl and at 30–50 °C and pH 8.0–11.0, with optimal growth occurring at 25–30 % (w/v) NaCl, 37–45 °C and pH 9–9.5. MgCl2 was not required for growth. Strain CG-1T was most closely related to the type strains of

Natronococcus amylolyticus

Ah-36T, Natronococcus jeotgali B1T and

Natronococcus occultus

SP4T, with which it shared 98.4 %, 96.2 and 95.7 % 16S rRNA gene sequence similarity, respectively. The polar lipids consisted of C20C20 and C20C25 derivatives of phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and minor phospholipid components. No glycolipids were detected. The DNA G+C content of strain CG-1T was 62.1 mol%. DNA–DNA hybridization with

N. amylolyticus

DSM 10524T, phylogenetically the most closely related species, was 39 %; this value showed that strain CG-1T constituted a different genospecies. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA–DNA hybridization studies revealed that strain CG-1T belongs to the genus

Natronococcus

and constitutes a novel species for which the name Natronococcus roseus sp. nov. is proposed. The type strain is CG-1T ( = CECT 7984T = IBRC-M 10656T = JCM 17958T).
Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs
Authors: Hannigan Geoffrey D. , Krivogorsky Bogdana , Fordice Daniel , Welch Jacqueline B. , Dahl John L.
Published: February 2012

Several intermediate-growing, photochromogenic bacteria were isolated from sphagnum peat bogs in northern Minnesota, USA. Acid-fast staining and 16S rRNA gene sequence analysis placed these environmental isolates in the genus

Mycobacterium

, and colony morphologies and PCR restriction analysis patterns of the isolates were similar. Partial sequences of hsp65 and dnaJ1 from these isolates showed that

Mycobacterium arupense

ATCC BAA-1242T was the closest mycobacterial relative, and common biochemical characteristics and antibiotic susceptibilities existed between the isolates and

M. arupense

ATCC BAA-1242T. However, compared to nonchromogenic

M. arupense

ATCC BAA-1242T, the environmental isolates were photochromogenic, had a different mycolic acid profile and had reduced cell-surface hydrophobicity in liquid culture. The data reported here support the conclusion that the isolates are representatives of a novel mycobacterial species, for which the name Mycobacterium minnesotense sp. nov. is proposed. The type strain is DL49T ( = DSM 45633T = JCM 17932T = NCCB 100399T).
Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment
Authors: Gao Zhao-Ming , Liu Xin , Zhang Xi-Ying , Ruan Ling-Wei
Published: February 2012

A moderately thermophilic and strictly anaerobic bacterium, designated HS1T, was isolated from offshore hot spring sediment in Xiamen, China. Cells were Gram-negative, catalase-positive, oxidase-negative, slender and flexible rods without flagella. The strain could grow at 35–55 °C (optimum at 50 °C) and in 1–8 % NaCl (w/v; optimum 2–4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HS1Twas affiliated with the familyMarinilabiliaceaeand shared a distant relationship with the previously described genera. The isolate was most closely related toAnaerophaga thermohalophilaFru22Twith 16S rRNA gene sequence similarity of 92.4 %, followed by the other members of the familyMarinilabiliaceaewith 88.7–91.1 % similarity. The dominant cellular fatty acids were iso-C15 : 0and anteiso-C15 : 0. The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE) and an unknown polar lipid. The genomic DNA G+C content was 38.7 mol%. Besides the phylogenetically distant relationship, strain HS1Twas obviously distinguished from the most closely related genera in several phenotypic properties including colony colour and pigment production, optimal temperature, optimal NaCl, relation to O2, bicarbonate/carbonate requirement, catalase activity, nitrate reduction, fermentation products and cellular fatty acid profile. Based on the phenotypic and phylogenetic data, strain HS1Trepresents a novel species of a new genus, for which the nameThermophagus xiamenensisgen. nov., sp. nov. is proposed. The type strain of the type species is HS1T( = DSM 19012T = CGMCCC 1.5071T).
Altererythrobacter troitsensis sp. nov., isolated from the sea urchin Strongylocentrotus intermedius
Authors: Nedashkovskaya Olga I. , Cho Sung-Heun , Joung Yochan , Joh Kiseong , Kim Mi Na , Shin Kee-Sun , Oh Hyun Woo , Bae Kyung Sook , Mikhailov Valery V. , Kim Seung Bum
Published: February 2012

An aerobic, halotolerant, Gram-negative bacterium was isolated from the sea urchin Strongylocentrotus intermedius and subjected to taxonomic characterization. The strain, designated KMM 6042T, was rod-shaped, motile and yellow-pigmented. Phylogenetic analysis indicated that the strain was most closely related to the type strain of

Altererythrobacter dongtanensis

, and the level of 16S rRNA gene sequence similarity between the two was 99.0 %. However, the DNA–DNA relatedness between the two strains was 34.4±7.6 %. Physiological and chemotaxonomic properties clearly distinguished the novel strain from other species of the genus

Altererythrobacter

. It is thus evident from the phylogenetic and phenotypic analyses that strain KMM 6042T merits recognition as a novel species of the genus

Altererythrobacter

, for which the name Altererythrobacter troitsensis sp. nov. (type strain, KMM 6042T = KCTC 12303T = JCM 17037T) is proposed.
Remaking memories: Reconsolidation updates positively motivated spatial memory in rats
Authors: Jones Bethany , Bukoski Elizabeth , Nadel Lynn , Fellous Jean-Marc
Published: February 2012

There is strong evidence that reactivation of a memory returns it to a labile state, initiating a restabilization process termed reconsolidation, which allows for updating of the memory. In this study we investigated reactivation-dependent updating using a new positively motivated spatial task in rodents that was designed specifically to model a human list-learning paradigm. On Day 1, rats were trained to run to three feeders (List 1) for rewards. On Day 2, rats were trained to run to three different feeders (List 2) in either the same (Reminder condition) or a different (No Reminder condition) experimental context than on Day 1. On Day 3, rats were cued to recall List 1. Rats in the Reminder condition made significantly more visits to List 2 feeders (intrusions) during List 1 recall than rats in the No Reminder condition, indicating that the reminder triggered reactivation and allowed integration of List 2 items into List 1. This reminder effect was selective for the reactivated List 1 memory, as no intrusions occurred when List 2 was recalled on Day 3. No intrusions occurred when retrieval took place in a different context from the one used at encoding, indicating that the expression of the updated memory is dependent upon the retrieval context. Finally, the level of intrusions was highest when retrieval took place immediately after List 2 learning, and generally declined when retrieval occurred 1–4 h later, indicating that the List 2 memory competed with short-term retrieval of List 1. These results demonstrate the dynamic nature of memory over time and the impact of environmental context at different stages of memory processing.
Amino Acid Residues Critical for the Specificity for Betaine Aldehyde of the Plant ALDH10 Isoenzyme Involved in the Synthesis of Glycine Betaine
Authors: Díaz-Sánchez Ángel G. , González-Segura Lilian , Mújica-Jiménez Carlos , Rudiño-Piñera Enrique , Montiel Carmina , Martínez-Castilla León P. , Muñoz-Clares Rosario A.
Published: February 2012

Plant Aldehyde Dehydrogenase10 (ALDH10) enzymes catalyze the oxidation of ω-primary or ω-quaternary aminoaldehydes, but, intriguingly, only some of them, such as the spinach (Spinacia oleracea) betaine aldehyde dehydrogenase (SoBADH), efficiently oxidize betaine aldehyde (BAL) forming the osmoprotectant glycine betaine (GB), which confers tolerance to osmotic stress. The crystal structure of SoBADH reported here shows tyrosine (Tyr)-160, tryptophan (Trp)-167, Trp-285, and Trp-456 in an arrangement suitable for cation-π interactions with the trimethylammonium group of BAL. Mutation of these residues to alanine (Ala) resulted in significant K  m(BAL) increases and V  max/K  m(BAL) decreases, particularly in the Y160A mutant. Tyr-160 and Trp-456, strictly conserved in plant ALDH10s, form a pocket where the bulky trimethylammonium group binds. This space is reduced in ALDH10s with low BADH activity, because an isoleucine (Ile) pushes the Trp against the Tyr. Those with high BADH activity instead have Ala (Ala-441 in SoBADH) or cysteine, which allow enough room for binding of BAL. Accordingly, the mutation A441I decreased the V  max/K  m(BAL) of SoBADH approximately 200 times, while the mutation A441C had no effect. The kinetics with other ω-aminoaldehydes were not affected in the A441I or A441C mutant, demonstrating that the existence of an Ile in the second sphere of interaction of the aldehyde is critical for discriminating against BAL in some plant ALDH10s. A survey of the known sequences indicates that plants have two ALDH10 isoenzymes: those known to be GB accumulators have a high-BAL-affinity isoenzyme with Ala or cysteine in this critical position, while non GB accumulators have low-BAL-affinity isoenzymes containing Ile. Therefore, BADH activity appears to restrict GB synthesis in non-GB-accumulator plants.
Myths and realities of digital reference services
Authors: Bakeri Abu Bakar Ahmad
Published: February 2012

Purpose

The purpose of this paper is to determine whether differences exist between public and private universities' web sites in terms of visibility and accessibility of the web sites.

Design/methodology/approach

The approach that was taken to study the issue of visibility and accessibility is using the software Alexa and EvalAccess respectively. Alexa is able to determine web site usage, which is an indicator of online quality by showing the number of in‐links and web traffic volume of the web sites. Using Alexa ten public universities' web sites and ten private universities' web sites were ranked. Similarly, EvalAccess is used to evaluate the accessibility problems of these web sites.

Findings

It is found, in the case of public universities' web sites, that the International Islamic University Malaysia has the highest in‐links while Universiti Teknologi Malaysia has the highest web traffic volume. In the case of private universities' web sites, the Multimedia University has the highest in‐links, while the Malaysia University of Science and Technology has the highest web traffic volume. In respect of accessibility problems, the private universities' web sites are having more problems compared to public universities' web sites.

Research limitations/implications

This research on the visibility and accessibility issues of universities' web sites is limited to the situation in Malaysia where public universities are more prominent and seldom face financial constraints if compared with private universities. This research shows that top ranked universities' web sites, whether they are from public or private universities, are highly visible and accessible.

Social implications

It is highly important for those universities' web sites that are not highly visible and accessible that the universities should initiate the necessary measures to improve the development of their web sites.

Originality/value

Not much research has been addressed to issues on visibility and accessibility of universities' web sites in developing countries and this research is conducted to fill that gap.
User satisfaction surveys as decision making resources at the University of Bologna
Authors: Citti Alessandra , Politi Angela , Sabattini Fulvia , Semenzato Chiara
Published: February 2012

Purpose

The academic libraries of the University of Bologna situated in Cesena, Forlì, Ravenna and Rimini carried out two surveys about users' satisfaction, in order to improve services. This paper aims to present the results of these surveys.

Design/methodology/approach

Two surveys were carried out: in 2007 and in 2010. The second one aimed to verify whether the actions adopted following the 2007 questionnaire had been appreciated. The 2007 survey adopted the interviewer‐assisted administration technique, the 2010 was online.

Findings

The 2010 questionnaire gave information about users' expectations and actions to be taken: the number of students unaware of advanced services is high. Librarians will work to broaden the use of them.

Research limitations/implications

The online questionnaire was adopted because in 2007 many professors could not come to the library during the two‐weeks survey. The result was that a higher number of professors answered the questionnaire, but fewer students. That was probably due to the fact that most students do not use the institutional e‐address. The authors aim to move to a double questionnaire giving in 2013: interviewer‐assisted administration and online.

Practical implications

The number of students unaware of advanced services is high; librarians need to work to broaden the use of them.

Social implications

The survey was an opportunity to focus on the importance of the collaboration between faculty and librarians. The best results are achieved by working together: they share the same mission. If they join their different competencies, they can be integrated.

Originality/value

The paper has a double approach: quantitative and qualitative. Moreover, during the same week of the survey a focus group is carried out, to focus on the critical areas of the questionnaire and offer support for actions.
Case study on digital library's user viscosity in Chongqing University Library
Authors: Yang Xinya , Yuan Hui , Cheng Huanwen , Liu Pak‐sing Andrew
Published: February 2012

Purpose

It is important for digital library to attract users to be reliant on the library. Besides providing research resources, the library still has many ways to achieve this goal. This article aims to experiment on the library merit system which provides different ways to enhance users' viscosity on using library.

Design/methodology/approach

For the experiment, a merit system was developed and implemented; users' feedback was collected by a questionnaire survey for analysis.

Findings

The results showed that the degree of users' viscosity on the digital library was increased and several areas for a successful digital library portal should be paid more attention to.

Originality/value

The merit system can successfully increase users' viscosity with digital library.
Smart materials use in active disassembly
Authors: Chiodo Joseph , Jones Nick
Published: February 2012

Purpose

Smart materials (SMs) have the potential for facilitating active disassembly (AD). Select SMs are used in the design of devices to aid product disassembly. The purpose of this paper is to compare different AD approaches and highlight future work and potential.

Design/methodology/approach

This work is a survey of the collated AD research employing only Smart and “made Smart” materials work from various published work in the field from companies and academia since its original invention. The introduction gives general discussion of AD with cost implications and how the technology could offer very lean dismantling. An overview of the history of the work is given with the context of the implications for the need for a technology like AD to retain critical materials.

Findings

Besides a survey to date, comparisons were made of each AD technology application highlighting advantages and challenges. Comparisons were also made prior to this in alternative disassembly strategies to give context to the potential usefulness of the technology.

Practical implications

Only AD with SMs or “made Smart” were highlighted with some considerations for potential candidates.

Originality/value

A survey of AD work only employing SMs and “made‐Smart” materials to date. Comparisons of each AD application were made highlighting advantages and challenges. Comparisons were made between AD and alternative disassembly strategies to give context to the potential usefulness of the technology. The conclusion included an overview of work with consideration for future work. A candidate technology with the most potential was discussed.
Modeling and analyzing of variation propagation in aeronautical thin‐walled structures automated riveting
Authors: Cheng Hui , Wang Run‐Xiao , Li Yuan , Zhang Kai‐Fu
Published: February 2012

Purpose

Assembly variations, which will propagate along the assembly process, are inevitable and difficult to analyze in Aeronautical Thin‐Walled Structures (ATWS) assembly. The purpose of this paper is to present a new method for analyzing the variation propagation of ATWS with automated riveting.

Design/methodology/approach

The paper addresses the variation propagation model and method by first, forming a novel Stage‐State model to represent the process of automated riveting. Second, the effect of positioning error on assembly variation is defined as propagation variation (PV), and propagation matrix of key characteristic points (KCP) is discussed. Third, the effect between the variations in each stage is defined as expansion variation (EV). According to the analysis of mismatch error and the reference transformation, the expansion matrix is formed.

Findings

The model can solve the variation propagation problem of ATWS with automated riveting efficiently, which is shown as an example of this paper.

Practical implications

The variation obtained by the model and method presented in this paper is in conformity with the variation measured in experiments.

Originality/value

The propagation variation and expansion variation is proposed for the first time, and variations are studied according to novel propagation matrix and expansion matrix.
Separation of concerns on the orchestration of operations in flexible manufacturing
Authors: Veiga Germano , Malaca Pedro , Norberto Pires J. , Nilsson Klas
Published: February 2012

Purpose

The growing complexity of industrial robot work‐cells calls for the use of advanced orchestration techniques to promote flexibility and reusability. This paper aims to present a solution based on service‐oriented platforms that endorses the separation of concerns, coordination and execution.

Design/methodology/approach

This paper starts with the evaluation of available tools for the orchestration and service generation. Endorsing the missing features depicted in that evaluation, the paper describes developments of concepts and software and the evaluation made.

Findings

From the early evaluations made in this paper, the SCXML‐based purposed language is more adapted to the industrial robotic cell scenario than existing alternatives. The generation of services allow the integration without knowledge from any programming language.

Practical implications

This approach's main drawback, as described by some users, was the lack of some programming features: simple math operations and conditional statements.

Originality/value

This paper fulfils two partially unsolved problems: adequate languages for orchestration of service oriented on the device level and purposes techniques for the specification of services using robot programming languages.
Integration of JIT flexible manufacturing, assembly and disassembly using a simulation approach
Authors: Pisuchpen Roongrat
Published: February 2012

Purpose

In the real world many companies combine the operations of manufacturing, assembly and disassembly. Thus, the integration of just‐in‐time FMS, FAS, and flexible disassembly system (DAS) models poses an interesting problem. The purpose of this paper is to provide major emphasis on a new simulation model for design and performance evaluation of a flexible assembly and disassembly system with dual Kanban under a stochastic system. This paper also primarily investigates the effect of varying the number of kanban cards, mean inter‐arrival time of demand and locations of the bottlenecks on the performance integration of JIT flexible manufacturing, assembly and disassembly systems.

Design/methodology/approach

Simulation is carried out in ARENA and data is analyzed using multivariate analysis of variance (MANOVA). This paper investigates the effect of varying number of kanban cards, mean inter‐arrival time of demand, and locations of the bottlenecks on the performance integration of JIT flexible manufacturing, assembly and disassembly systems. The performance measures that are simultaneously considered are the fill rate, work in process, and mean cycle time. This paper emphasizes that understanding the interactions between the variables and their effects on system performance is of utmost importance for managers in improving performance processes.

Findings

In manufacturing practice, there are many industrial units that represent the mixture of the referred three models. This paper presents a new simulation model for design and performance evaluation of a flexible assembly and disassembly system with dual kanban. The simulation results are statistically compared with MANOVA. MANOVA is used to perform the test with multiple objective functions, e.g. with the average production cycle time, percentage average fill rate, and work‐in‐process. The conclusion to be drawn is that minimized WIP can be obtained by higher percentage average fill rate, lower WIP, small average part cycles times, and increasing in kanban cards while simultaneously retaining full customer satisfaction.

Originality/value

The researcher presents the newly developed kanban system into the production system of JIT flexible manufacturing, assembly and disassembly system with simulation technique. Furthermore, by assigning time factors to the models, several performance measures can be easily computed. Then, the researcher tests the effect of the number of kanban card on integration of JIT flexible manufacturing, assembly and disassembly systems using a simulation approach, the simulation model is developed using the ARENA simulation package. The results are applied to a small case study. For a single product under the integration of JIT flexible manufacturing, assembly and disassembly systems, as the number of kanban cards increase, the fill rate along with work in process and the mean cycle time increases as well.
Sensor‐less insertion strategy for an eccentric peg in a hole of the crankshaft and bearing assembly
Authors: Su Jianhua , Qiao Hong , Ou Zhicai , Zhang Yuren
Published: February 2012

Purpose

The purpose of this paper is to give a novel sensor‐less manipulation strategy for the high‐precision assembly of an eccentric peg into a hole.

Design/methodology/approach

Based on the authors' previous work on the attractive region, this paper proposes the sensorless eccentric peg‐hole insertion strategy. The analysis is based on the visible strategic behaviors by decomposing the high‐dimensional configuration space of the eccentric peg‐hole into two low dimensional configuration subspaces. Then, the robotic manipulations can be designed in the configuration subspaces. Finally, a typical industry application, fitting an eccentric crankshaft into a bearing hole of the automotive air‐conditioners, is used to validate the presented strategy.

Findings

The attractive region constructed in the configuration space has been applied to guide the robotic manipulations, such as, the locating and the insertion.

Practical implications

The designed robotic assembly system without using force sensor or flexible wrist has an advantage in terms of expense and durability for the automotive air‐conditioners manufacturing industry.

Originality/value

Most previous work on sensorless manipulation strategy has concentrated on inserting a symmetric peg into a hole. However, for the assembly of an eccentric peg into a hole, the robotic manipulations should be explored in a high‐dimensional configuration space as the six‐DOFs of the eccentric peg. In this paper, the decomposition method of the high‐dimensional configuration space would make the system analysis visible; then, the assembly strategy can be easily designed in the two subspaces.
Resource sharing in a cloud computing age
Authors: Goldner Matt , Birch Katie
Published: February 2012

Purpose

The purpose of this paper is to provide an overview of the historical development of interlibrary loan, identify key milestones such as the codification of ILL practices and development of new technologies to facilitate those practices, and assess the impact that changes in technology and publishing are having upon resource sharing in the digital age.

Design/methodology/approach

The authors conduct an extensive historical review of global developments in resource sharing and then conduct a PEST analysis of societal factors affecting present day resource sharing.

Findings

Resource sharing continues to grow but there is a need to work together to find solutions to problems of distributed knowledge bases, incompatible systems, and electronic formats which often prohibit sharing of materials between libraries. Librarians must work with publishers, politicians, and systems developers to ensure that there is the same or equivalent rights to electronic materials as there is to print publications and that resource sharing systems can support new models of sharing and acquiring materials in multiple formats.

Originality/value

This paper provides a global perspective on the challenges of library resource sharing in the digital age.
RapidILL: an enhanced, low cost and low impact solution to interlending
Authors: Delaney Thomas G. , Richins Micheal
Published: February 2012

Purpose

The paper aims to provide an overview of the RapidILL requesting system and describes its operation and the benefits derived by its users, including significant cost savings through elimination of various fees, expedited processing, maximum use of a library's own print and electronic journal holdings, and dramatic reductions in the amount of staff time required for processing interlibrary loan requests.

Design/methodology/approach

This paper takes the form of a general review and is written by developers with first‐hand knowledge of how the system works.

Findings

Libraries participating in RapidILL experience significant savings in both cost and staff time as a result of functionality built into the system.

Practical implications

Over 200 libraries currently use the RapidILL system, both in the USA and beyond its borders.

Originality/value

This paper provides extensive information on the functionality of the RapidILL system but also will be of interest to libraries that use other interlibrary loan systems.
Light at the end of the tunnel: transitioning from one interlending system to another
Authors: Jilovsky Cathie , Howells Sharon
Published: February 2012

Purpose

This paper aims to outline the transition of two libraries from one automated interlending system (OCLC VDX) to another (Relais ILL).

Design/methodology/approach

The paper provides historical background and context for the change, the transition planning, processes undertaken to ensure success, and the challenges and lessons learned along the way.

Findings

The authors report that, although the transition process went fairly smoothly, libraries planning for a similar transition should build some flexibility into their overall planning process and be prepared to pay close attention to their communication processes.

Originality/value

Libraries planning a transition from one interlending system to another will find this paper quite useful. Any library using either the VDX or Relais interlibrary systems will find the appendix of comparable ISO ILL terminology helpful as well.
Add to cart? E‐commerce, self‐service and the growth of interlibrary loan
Authors: Mak Collette
Published: February 2012

Purpose

This paper seeks to examine the application of e‐commerce practices in libraries and the effect of those practices on interlibrary loan traffic among research libraries in the USA.

Design/methodology/approach

This paper identifies key e‐commerce features and where parallel features exist in the discovery and request processes. In an age of unprecedented information access, instant communication, and large‐scale commercial information sources, the growth of interlibrary loan among US research libraries cannot be attributed solely to cost. A major factor in the continued growth of interlibrary loan must be, in part, attributed to the adoption by libraries of standard e‐commerce practices.

Findings

The author's research indicates that adoption of standard e‐commerce practices by libraries has resulted in a dramatic increase of interlibrary loan traffic among research libraries in the USA.

Originality/value

The research conducted for this paper is original and the findings add a unique perspective to the value of e‐commerce practices in libraries by focusing on the impact those services have had on interlibrary loan operations.
Streamlining interlibrary loan and document delivery workflows: tools, techniques, and outcomes
Authors: Moreno Margarita
Published: February 2012

Purpose

This paper aims to describe a review of interlending and document delivery work processes at the National Library of Australia, the purpose of which was to develop a new integrated approach to interlending and document delivery services and to improve turnaround times for users by reducing administrative functions and improving request management processes.

Design/methodology/approach

This paper provides a brief overview of business process modeling notation (BPMN) and its use in the National Library to evaluate workflows, reports on implementation of the project's recommendations, and highlights lessons learned.

Findings

Good communication and teamwork were critical to the project's success. Use of the BPMN enabled stakeholders to retain objectivity when evaluating existing workflows. The new workflows and processes resulted in demonstrably greater customer satisfaction.

Originality/value

Discussions of Relais ILL customization to streamline workflows and facilitate e‐commerce are especially useful. The paper describes library application of both BPMN and Prince 2 project management methodology.
Global resource sharing from a Pacific Northwest perspective
Authors: Bean Margaret , Nance Heidi , Frederiksen Linda
Published: February 2012

Purpose

This paper aims to describe the international interlibrary loan (ILL) experience of three academic libraries in the Pacific Northwest and analyze factors impacting the success of international ILL. The authors seek to speculate on three possible scenarios going forward and conclude with a call to action.

Design/methodology/approach

The authors apply PEST and SWOT techniques, using their own institutions as case studies.

Findings

Some of the most critical factors affecting international ILL at their home institutions include the terms of electronic license agreements, open access, and physical delivery costs.

Originality/value

The internal and external factors affecting international ILL at these institutions are broadly applicable to all types of libraries throughout the world.