bluuebunny/crossref_metadata_2025 huggingface dataset:
Zilienkrankheiten unter besonderer Berücksichtigung der primären ziliären Dyskinesie
Authors: Omran H. , Olbrich H.
Published: August 2010

Die primäre ziliäre Dyskinesie („primary ciliary dyskinesia“, PCD) ist eine klinisch und genetisch heterogene Gruppe von Erkrankungen. Der Phänotyp der Erkrankung erklärt sich durch angeborene Defekte motiler respiratorischer Flimmerhärchen (Zilien), die zu einer verminderten mukoziliären Reinigung der Atemwege führt. Bei den meisten PCD-Varianten kommt es zu einer Randomisierung der Links-rechts-Körperasymmetrie, da nodale Zilien während der frühen embryonalen Entwicklung ebenfalls eine Dysmotilität aufweisen. Etwa die Hälfte der PCD-Patienten weisen daher einen Situs inversus (Kartagener-Syndrom) oder eine Heterotaxie auf. Mittlerweile konnten Mutationen in 9 Genen, die für axonemale Motorproteine oder zytoplasmatische Assemblierungsfaktoren kodieren, nachgewiesen werden. Für 2 X-chromosomale syndromale PCD-Varianten, die entweder mit Retinitis pigmentosa oder mentaler Retardierung einhergehen, wurden die Gendefekte aufgeklärt. Bei klinischem Verdacht sollte die Diagnose mittels Hochfrequenzvideomikroskopie (Zilienschlaganalyse) gesichert werden. Nicht alle PCD-Varianten weisen elektronenmikroskopische oder immunfluoreszenzmikroskopische Defekte auf. Die detaillierte Diagnostik erlaubt dann eine gezielte genetische Diagnostik.
Nephronophthise
Authors: König J. , Konrad M.
Published: August 2010

Die Nephronophthise (NPH) ist eine autosomal-rezessive Nierenerkrankung, die sich zumeist im Kindes- und Jugendalter manifestiert. Im Verlauf der Erkrankung kommt es zu einer progredienten Niereninsuffizienz und häufig auch zu einer Zystenbildung der Nieren. Aufgrund der hohen phänotypischen Variabilität mit und ohne extrarenale Beteiligung ist eine klare klinische Diagnose nicht immer möglich. Die hohe klinische Variabilität spiegelt sich auch in einer erheblichen genetischen Heterogenität wider, bislang konnten Mutationen in 11 verschiedenen Genen (NPHP1–9, NPHP11 und NPHP1L) identifiziert werden. Die Charakterisierung dieser Gene hat entscheidend zum besseren Verständnis der Pathophysiologie der NPH beigetragen. So basiert das Konzept der gestörten Zilienfunktion als gemeinsamer Pathomechanismus der zystischen Nierenerkrankungen insgesamt nicht zuletzt auf der Entdeckung der NPHP-Gene. Eine frühzeitige korrekte Diagnose zur Vermeidung von Sekundärschäden im Rahmen der Niereninsuffizienz ist für die Patienten sehr wichtig. Wir möchten in dieser Übersicht die klinischen Verlaufsformen der NPH darstellen und bekannte Genotyp-Phänotyp-Korrelationen beschreiben.
Assessing the Impact of Suicide Exclusion Periods on Life Insurance
Authors: Yip Paul , Pitt David , Wang Yan , Wu Xueyuan , Watson Ray , Huggins Richard , Xu Ying
Published: August 2010

Background: We study the impact of suicide-exclusion periods, common in life insurance policies in Australia, on suicide and accidental death rates for life-insured individuals. If a life-insured individual dies by suicide during the period of suicide exclusion, commonly 13 months, the sum insured is not paid. Aims: We examine whether a suicide-exclusion period affects the timing of suicides. We also analyze whether accidental deaths are more prevalent during the suicide-exclusion period as life-insured individuals disguise their death by suicide. We assess the relationship between the insured sum and suicidal death rates. Methods: Crude and age-standardized rates of suicide, accidental death, and overall death, split by duration since the insured first bought their insurance policy, were computed. Results: There were significantly fewer suicides and no significant spike in the number of accidental deaths in the exclusion period for Australian life insurance data. More suicides, however, were detected for the first 2 years after the exclusion period. Higher insured sums are associated with higher rates of suicide. Conclusions: Adverse selection in Australian life insurance is exacerbated by including a suicide-exclusion period. Extension of the suicide-exclusion period to 3 years may prevent some “insurance-induced” suicides – a rationale for this conclusion is given.
The Impact of Patient Suicide on the Professional Reactions and Practices of Mental Health Caregivers and Social Workers
Authors: Gulfi Alida , Castelli Dransart Dolores Angela , Heeb Jean-Luc , Gutjahr Elisabeth
Published: August 2010

Background: Mental health and social professionals are at high risk of experiencing at least one patient suicide during their career. Aims: This paper investigates the impact of patient suicide on the reactions and working practices of mental health and social professionals. It also examines how such an impact may vary depending on the professionals’ characteristics, their relationship with the patient, as well as the institutional setting in which they work. Methods: 275 professionals working in sociomedical institutions in French-speaking Switzerland completed a questionnaire. Results: Patient suicide can cause a wide range of long-lasting reactions and changes in the working practices of mental health and social professionals. Professional’s gender, place of suicide, as well as responsibility for and emotional attachment to the patient significantly influence the impact that a patient suicide has on such professionals. Professional’s age, the type of profession, the number of suicides experienced, and previous suicide attempts by the deceased patient were also found to play a significant role with regard to changes in working practices. Conclusions: Beyond the emotional and professional impact, patient suicide may have also a formative influence, encouraging professionals to review and improve their working practices. Recommendations to help mental health and social professionals who have experienced a patient suicide are discussed.
Repetition of Suicide Attempts
Authors: Bertolote José M. , Fleischmann Alexandra , De Leo Diego , Phillips Michael R. , Botega Neury J. , Vijayakumar Lakshmi , De Silva Damani , Schlebusch Lourens , Nguyen Van Tuong , Sisask Merike , Bolhari Jafar , Wasserman Danuta
Published: August 2010

Background: Attempted suicide is a strong risk factor for subsequent suicidal behaviors. Innovative strategies to deal with people who have attempted suicide are needed, particularly in resource-poor settings. Aims: To evaluate a brief educational intervention and periodic follow-up contacts (BIC) for suicide attempters in five culturally different sites (Campinas, Brazil; Chennai, India; Colombo, Sri Lanka; Karaj, Islamic Republic of Iran; and Yuncheng, People’s Republic of China) as part of the WHO Multisite Intervention Study on Suicidal Behaviors (SUPRE-MISS). Methods: Among the 1,867 suicide attempters enrolled in the emergency departments of the participating sites, 922 (49.4%) were randomly assigned to a brief intervention and contact (BIC) group and 945 (50.6%) to a treatment as usual (TAU) group. Repeated suicide attempts over the 18 months following the index attempt – the secondary outcome measure presented in this paper – were identified by follow-up calls or visits. Subsequent completed suicide – the primary outcome measure – has been reported in a previous paper. Results: Overall, the proportion of subjects with repeated suicide attempts was similar in the BIC and TAU groups (7.6% vs. 7.5%, χ² = 0.013; p = .909), but there were differences in rates across the five sites. Conclusions: This study from five low- and middle-income countries does not confirm the effectiveness of brief educational intervention and follow-up contacts for suicide attempters in reducing subsequent repetition of suicide attempts up to 18 months after discharge from emergency departments.
DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data
Authors: Liu Bao-Hong , Yu Hui , Tu Kang , Li Chun , Li Yi-Xue , Li Yuan-Yuan
Published: August 2010

Summary: Gene coexpression analysis was developed to explore gene interconnection at the expression level from a systems perspective, and differential coexpression analysis (DCEA), which examines the change in gene expression correlation between two conditions, was accordingly designed as a complementary technique to traditional differential expression analysis (DEA). Since there is a shortage of DCEA tools, we implemented in an R package ‘DCGL’ five DCEA methods for identification of differentially coexpressed genes and differentially coexpressed links, including three currently popular methods and two novel algorithms described in a companion paper. DCGL can serve as an easy-to-use tool to facilitate differential coexpression analyses.

Contact:  yyli@scbit.org and yxli@scbit.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ontology- and graph-based similarity assessment in biological networks
Authors: Wang Haiying , Zheng Huiru , Azuaje Francisco
Published: August 2010

Summary: A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different ‘guilt-by-association’ analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a ‘semantic similarity’ space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks.

Availability:  http://rosalind.infj.ulst.ac.uk/SimTrek.html

Contact:  francisco.azuaje@crp-sante.lu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A study of the efficiency of pooling in haplotype estimation
Authors: Kuk Anthony Y. C. , Xu Jinfeng , Yang Yaning
Published: August 2010

Motivation: It has been claimed in the literature that pooling DNA samples is efficient in estimating haplotype frequencies. There is, however, no theoretical justification based on calculation of statistical efficiency. In fact, the limited evidence given so far is based on simulation studies with small numbers of loci. With rapid advance in technology, it is of interest to see if pooling is still efficient when the number of loci increases.

Methods: Instead of resorting to simulation studies, we make use of asymptotic statistical theory to perform exact calculation of the efficiency of pooling relative to no pooling in the estimation of haplotype frequencies. As an intermediate step, we use the log-linear formulation of the haplotype probabilities and derive the asymptotic variance–covariance matrix of the maximum likelihood estimators of the canonical parameters of the log-linear model.

Results: Based on our calculations under linkage equilibrium, pooling can suffer huge loss in efficiency relative to no pooling when there are more than three independent loci and the alleles are not rare. Pooling works better for rare alleles. In particular, if all the minor allele frequencies are 0.05, pooling maintains an advantage over no pooling until the number of independent loci reaches 6. High linkage disequilibrium effectively reduces the number of independent loci by ruling out certain haplotypes from occurring. Similar calculations of efficiency for the case of no pooling justify the common belief that it is not worthwhile to use molecular methods to resolve the phase ambiguity of individual genotype data.

Availability: The R codes for the calculation are available at http://www.stat.nus.edu.sg/∼staxj/pooling

Contact:  stakuka@nus.edu.sg
Clinical Use of Immunosuppressants in Duchenne Muscular Dystrophy
Authors: Iannitti Tommaso , Capone Stefania , Feder David , Palmieri Beniamino
Published: August 2010

Duchenne muscular dystrophy (DMD) is a degenerative disease primarily affecting voluntary muscles with secondary consequences on heart and breathing muscles. DMD is an X-linked recessive disease that results in the loss of dystrophin, a key muscle protein. Inflammation can play different roles in DMD; it can be a secondary response to muscle degeneration, a primary cause of degeneration, or can contribute to the disease progression. Several immunosuppressants have been used with the aim to reduce the inflammation associated with DMD. Most recently, myoblast transplantation has shown the possibility to restore the dystrophin lack in the DMD patient's muscle fibers and this evidence has emphasized the importance of the use of immunosuppressants and the necessity of studying them and their secondary effects. The aim of this review is to analyze the main immunosuppressants drugs starting from the mdx mice experiments and concluding with the most recent human clinical studies.
Isolated Neck Extensor Myopathy: Is it Responsive to Immunotherapy?
Authors: Muppidi Srikanth , Saperstein David S , Shaibani Aziz , Nations Sharon P , Vernino Steven , Wolfe Gil I
Published: August 2010

Objective:

To determine if isolated neck extensor myopathy (INEM) is responsive to immunosuppressive treatment.

Methods:

We retrospectively reviewed charts of patients with INEM from 2002 to 2008 to identify patients and determine the response to immunomodulatory therapy. Clinical, electrodiagnostic, histologic, and radiographic data were reviewed.

Results:

Four patients were identified during the study period. Three were women. The age of onset of neck extensor weakness ranged from 58 to 78 years. Serum creatine kinase levels were within normal limits in all patients. None had clinical, laboratory, or electrophysiological findings to suggest a generalized neuromuscular disorder. On electrodiagnostic studies, all patients had myopathic changes with or without irritative features in cervical paraspinal muscles. No inflammation was present on muscle biopsy from three of the patients. All patients received one or more immunosuppressive agents. Neck strength improved by 1 point or greater on the Medical Research Council scale in all subjects with a peak response observed between 3 and 6 months after treatment initiation.

Conclusions:

A trial of immunosuppressive agents should be offered to patients with INEM because a subset will improve. Rigorously defined, INEM is a noninflammatory myopathy. However, a focal myositis could be missed on muscle biopsy and may explain the favorable response to treatment.
Chronic Inflammatory Demyelinating Polyneuropathy and Respiratory Failure Due to Phrenic Nerve Involvement
Authors: Tataroglu Cengiz , Ozkul Ayca , Sair Ahmet
Published: August 2010

In this article, 2 patients with chronic inflammatory demyelinating polyneuropathy (CIDP) are presented. These patients developed respiratory failure which could not be explained by any cardiac or pulmonary pathology. The first case had pure motor involvement and probable CIDP, and the second case had severe sensorial dysfunction and an ataxic picture in addition to motor symptoms. His clinical picture was compatible with distal acquired demyelinating sensory neuropathy without M protein. Electrophysiologic investigations of both patients disclosed impaired phrenic nerve conduction and neurogenic motor unit changes in the diaphragm. Both patients showed a moderate response to immunotherapy. Distal acquired demyelinating sensory and pure motor variant of CIDP can be a cause of respiratory dysfunction. Different clinical patterns of CIDP should be evaluated for phrenic nerve involvement.
Jeotgalicoccus halophilus sp. nov., isolated from salt lakes
Authors: Liu Wen-Yan , Jiang Lin-Lin , Guo Chun-Jing , Yang Su Sheng
Published: August 2010

Two slightly halophilic bacterial strains, C1-52T and YD-9, were isolated from Daban and Aiding salt lakes in Xinjiang, China, respectively. The isolates were Gram-positive, non-endospore-forming, non-motile, facultatively anaerobic cocci. Colonies were pale yellow, and a light pink, diffusible pigment was produced after a few additional days of incubation. The isolates grew optimally with 2–3 % (w/v) NaCl, at pH 7.5 and at 30–35 °C. The peptidoglycan type was l-Lys–Gly3–4–l-Ala(Gly). The menaquinones were MK-7 (83.2 %) and MK-6 (16.8 %). The major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content of strains C1-52T and YD-9 was 41.2 and 41.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains C1-52T and YD-9 were closely related to Jeotgalicoccus psychrophilus YKJ-115T (98.0 and 97.1 % 16S rRNA gene sequence similarity, respectively), followed by Jeotgalicoccus halotolerans YKJ-101T (97.1 and 96.8 %). Strains C1-52T and YD-9 shared, respectively, 20 and 11 % DNA–DNA relatedness with J. halotolerans JCM 11198T and 8 and 13 % with J. psychrophilus JCM 11199T. DNA–DNA relatedness between the isolates was 91 %. On the basis of phenotypic and phylogenetic distinctiveness, strains C1-52T and YD-9 belonged to the same species, which should be placed in the genus Jeotgalicoccus as a novel species. The name Jeotgalicoccus halophilus sp. nov. is proposed, with the type strain C1-52T ( = CGMCC 1.8911T  = NBRC 105788T).
Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter
Authors: Xiao Jing , Luo Yingxue , Xu Jing , Xie Shujie , Xu Jun
Published: August 2010

The taxonomic status of an actinobacterium that changed colour during growth, strain 42H12-1T, isolated from deep-sea sediment collected from the Atlantic Ocean, was established using a combination of genotypic and phenotypic data. Strain 42H12-1T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Modestobacter. The highest sequence similarity by blast analysis was to Modestobacter versicolor CP153-2T (98.5 %) and the second-highest sequence similarity was to Modestobacter multiseptatus AA-826T (97.5 %). DNA–DNA relatedness of only 12 % (sd 1.82 %) between strain 42H12-1T and M. versicolor DSM 16678T differentiated them as members of separate genomic species. Colonies of strain 42H12-1T were black on oligotrophic medium, but orange to red, turning black, on copiotrophic medium. The peptidoglycan contained meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and an unknown aminophospholipid. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and C17 : 1ω8c. The DNA G+C content was 72.3±1 mol%. Strain 42H12-1T ( = DSM 45201T  = CGMCC 4.5581T) is assigned as the type strain of a novel species of the genus Modestobacter, for which the name Modestobacter marinus sp. nov. is proposed.
Agromyces flavus sp. nov., an actinomycete isolated from soil
Authors: Chen Jie , Chen Hua-Mei , Zhang Yu-Qin , Wei Yu-Zhen , Li Qiu-Ping , Liu Hong-Yu , Su Jing , Zhang Yue-Qin , Yu Li-Yan
Published: August 2010

A Gram-positive, non-motile strain, designated CPCC 202695T, was isolated from a soil sample collected from the Qinghai–Tibet plateau, north-west China. Strain CPCC 202695T contained rhamnose, glucose and galactose in the cell wall as diagnostic sugars and 2,4-diaminobutyric acid, alanine, glutamic acid and glycine in the peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. MK-12 was the predominant menaquinone and anteiso-C15 : 0 (34.2 %), iso-C15 : 0 (19.8 %), iso-C16 : 0 (12.7 %) and anteiso-C17 : 0 (11.1 %) were the major fatty acids. 16S rRNA gene sequence similarities (94.2–97.1 %) between the isolate and the type strains of recognized species of the genus Agromyces indicated that strain CPCC 202695T was a member of the genus Agromyces. DNA–DNA relatedness clearly separated strain CPCC 202695T from its closest relatives. The phenotypic and genotypic data demonstrated that strain CPCC 202695T represents a novel species of the genus Agromyces, for which the name Agromyces flavus sp. nov. is proposed. The type strain is CPCC 202695T ( = KCTC 19578T  = CCM 7623T).
Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility
Authors: Wang Bao-Zhan , Guo Peng , Zheng Jin-Wei , Hang Bao-Jian , Li Lian , He Jian , Li Shun-Peng
Published: August 2010

A synthetic pyrethroid (SP)-degrading bacterial strain, designated JZ-1T, was isolated from activated sludge of a SP-manufacturing wastewater treatment facility and studied using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JZ-1Tbelonged to the genusSphingobium, showing highest sequence similarities toSphingobium faniaeDSM 21829T(98.6 %),Sphingobium cloacaeJCM 10874T(98.5 %),Sphingobium vermicompostiDSM 21299T(97.4 %) andSphingobium ummarienseCCM 7431T(96.9 %). The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of the cellular fatty acids C18 : 1ω7c, C19 : 0cyclo ω8c, 11 methyl C18 : 1ω7c, C16 : 0and C14 : 02-OH, and the G+C content of the genomic DNA also supported the affiliation of the strain with the genusSphingobium. Strain JZ-1Tshowed low DNA–DNA relatedness values withS. faniaeDSM 21829T(30.2 %),S. cloacaeJCM 10874T(23.3 %),S. vermicompostiDSM 21299T(10.9 %) andS. ummarienseCCM 7431T(7.9 %). Based on its phylogenetic position and its phenotypic and genotypic properties, strain JZ-1Trepresents a novel species of the genusSphingobium, for which the nameSphingobium wenxiniaesp. nov. is proposed. The type strain is JZ-1T( = CGMCC 1.7748T = DSM 21828T).
Rhizomicrobium electricum sp. nov., a facultatively anaerobic, fermentative, prosthecate bacterium isolated from a cellulose-fed microbial fuel cell
Authors: Kodama Yumiko , Watanabe Kazuya
Published: August 2010

A facultatively anaerobic, prosthecate bacterium, strain Mfc52T, was isolated from a microbial fuel cell inoculated with soil and fed with cellulose as the sole fuel. Cells were Gram-negative, non-spore-forming, straight or slightly curved rods, and some of them had one or two polar prosthecae (stalks). Cells reproduced by binary fission or by budding from mother cells having prosthecae. Strain Mfc52T fermented various sugars and produced lactate, acetate and fumarate. Ferric iron, nitrate, oxygen and fumarate served as electron acceptors, while sulfate and malate did not. Nitrate was reduced to nitrite. The DNA G+C content was 64.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Mfc52T was affiliated with the genus Rhizomicrobium in the class Alphaproteobacteria and most closely related to Rhizomicrobium palustre with a sequence similarity of 97 %. Based on these physiological and phylogenetic characteristics, the name Rhizomicrobium electricum sp. nov. is proposed; the type strain is Mfc52T ( = JCM 15089T  = KCTC 5806T).
Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil
Authors: Cai Man , Wang Lu , Cai Hua , Li Yan , Wang Ya-Nan , Tang Yue-Qin , Wu Xiao-Lei
Published: August 2010

Four bacterial strains, SL014B-41A4T, SL014B-20A1T, SL014B-76A1 and SL014B-79A, isolated from a crude oil-contaminated saline soil of Shengli Oilfield, China, were investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL014B-41A4T belonged to the genus Salinarimonas in the order Rhizobiales, with the highest sequence similarity with Salinarimonas rosea YIM YD3T (98.3 %). The DNA–DNA relatedness of strain SL014B-41A4T to S. rosea YIM YD3T was 27.03±3.0 %. Strain SL014B-41A4T was Gram-negative staining, facultatively anaerobic and produced deep red pigment in artificial seawater medium. Cells of strain SL014B-41A4T were rod-shaped (0.6–4.0×1.25–25 µm), motile with a single polar flagellum and often formed branches. The strain contained Q-10 as the predominant respiratory ubiquinone and C18 : 1ω7c (57.5 %), C16 : 0 (16.4 %) and 10-methyl C19 : 0 (9.1 %) as the major fatty acids. Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were actinobacteria and belonged to the genus Tessaracoccus in the family Propionibacteriaceae of the order Actinomycetales with the highest 16S rRNA gene sequence similarities with Tessaracoccus flavescens SST-39T (96.4 %), Tessaracoccus lubricantis KISS-17SeT (96.2 %) and Tessaracoccus bendigoensis Ben 106T (94.7 %). Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were Gram-positive staining, facultatively anaerobic, non-endospore-forming, non-motile, acid-fast and oval to rod-shaped (0.48×0.5–1.0 µm). These three novel strains had ll-diaminopimelic acid (DAP) as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-9(H4) as the only menaquinone and anteiso-C15 : 0 (67.11–76.14 %) as the major cellular fatty acid. The G+C contents of the genomic DNA of strain SL014B-41A4T and strains SL014B-20A1T, SL014B-76A1 and SL014B-79A were 67.68 mol% and 65.65–67.17 mol%, respectively. Based on phenotypic and genotypic characteristics, strain SL014B-41A4T represents a novel species of the genus Salinarimonas, for which the name Salinarimonas ramus is proposed, with strain SL014B-41A4T ( = DSM 22962T = CGMCC 1.9161T) as the type strain. Strains SL014B-20A1T, SL014B-76A1 and SL014B-79A represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus oleiagri is proposed, with strain SL014B-20A1T ( = DSM 22955T = CGMCC 1.9159T) as the type strain.
Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted
Authors: Chi Fru E.
Published: August 2010

Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.
The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery
Authors: Parry Trevor J. , Theisen Joshua W.M. , Hsu Jer-Yuan , Wang Yuan-Liang , Corcoran David L. , Eustice Moriah , Ohler Uwe , Kadonaga James T.
Published: August 2010

The TCT motif (polypyrimidine initiator) encompasses the transcription start site of nearly all ribosomal protein genes in Drosophila and mammals. The TCT motif is required for transcription of ribosomal protein gene promoters. The TCT element resembles the Inr (initiator), but is not recognized by TFIID and cannot function in lieu of an Inr. However, a single T-to-A substitution converts the TCT element into a functionally active Inr. Thus, the TCT motif is a novel transcriptional element that is distinct from the Inr. These findings reveal a specialized TCT-based transcription system that is directed toward the synthesis of ribosomal proteins.
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
Authors: Chavez Lukas , Jozefczuk Justyna , Grimm Christina , Dietrich Jörn , Timmermann Bernd , Lehrach Hans , Herwig Ralf , Adjaye James
Published: August 2010

The generation of genome-wide data derived from methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) has become a major tool for epigenetic studies in health and disease. The computational analysis of such data, however, still falls short on accuracy, sensitivity, and speed. We propose a time-efficient statistical method that is able to cope with the inherent complexity of MeDIP-seq data with similar performance compared with existing methods. In order to demonstrate the computational approach, we have analyzed alterations in DNA methylation during the differentiation of human embryonic stem cells (hESCs) to definitive endoderm. We show improved correlation of normalized MeDIP-seq data in comparison to available whole-genome bisulfite sequencing data, and investigated the effect of differential methylation on gene expression. Furthermore, we analyzed the interplay between DNA methylation, histone modifications, and transcription factor binding and show that in contrast to de novo methylation, demethylation is mainly associated with regions of low CpG densities.
The basolateral amygdala and nucleus accumbens core mediate dissociable aspects of drug memory reconsolidation
Authors: Théberge Florence R.M. , Milton Amy L. , Belin David , Lee Jonathan L.C. , Everitt Barry J.
Published: August 2010

A distributed limbic-corticostriatal circuitry is implicated in cue-induced drug craving and relapse. Exposure to drug-paired cues not only precipitates relapse, but also triggers the reactivation and reconsolidation of the cue-drug memory. However, the limbic cortical-striatal circuitry underlying drug memory reconsolidation is unclear. The aim of this study was to investigate the involvement of the nucleus accumbens core and the basolateral amygdala in the reconsolidation of a cocaine-conditioned stimulus-evoked memory. Antisense oligodeoxynucleotides (ASO) were infused into each structure to knock down the expression of the immediate-early genezif268, which is known to be required for memory reconsolidation. Control infusions used missense oligodeoxynucleotides (MSO). The effects of zif268 knockdown were measured in two complementary paradigms widely used to assess the impact of drug-paired CSs upon drug seeking: the acquisition of a new instrumental response with conditioned reinforcement and conditioned place preference. The results show that both intranucleus accumbens core and intrabasolateral amygdala zif268 ASO infusions at memory reactivation impaired the reconsolidation of the memory underlying a cocaine-conditioned place preference. However, knockdown of zif268 in the nucleus accumbens at memory reactivation had no effect on the memory underlying the conditioned reinforcing properties of the cocaine-paired CS measured subsequently, and this is in contrast to the marked impairment observed previously following intrabasolateral amygdala zif268 ASO infusions. These results suggest that both the basolateral amygdala and nucleus accumbens core are key structures within limbic cortical-striatal circuitry where reconsolidation of a cue-drug memory occurs. However reconsolidation of memory representations formed during Pavlovian conditioning are differentially localized in each site.
A new paradigm of leadership development
Authors: Casserley Tim , Critchley Bill
Published: August 2010

Purpose

This paper aims to present a paradigm shift in the way leaders are developed, more suited to the new order that is emerging as the recession recedes.

Design/methodology/approach

The prevailing notion that leadership is synonymous with being in control of an organization is challenged, together with the belief that leadership development is primarily concerned with modifying behavior in line with a set of success criteria. The paper explores how these twin assumptions contributed to the financial crisis, and presents an alternative approach based on research with high achievers experiencing severe stress.

Findings

Practices that leaders use to retain a sense of balance and resourcefulness are defined, along with those associated with pursuing work irresponsibly. These form the basis of an alternative approach to the development of leaders – “sustainable leadership” – predicated on the integration of three core individual processes and their engagement with the culture of the organization. Practical examples of applying this approach in the current business environment are described.

Research limitations/implications

Future research might consider the effect of developing sustainable leadership on the long‐term performance of the organization and its responsibilities in the broader environment.

Practical implications

in order to foster leadership that acts in service to the long‐term health and performance of the organization and its broader environment, it is necessary to adopt an approach to leadership development that recognizes that the leader's physical and psychological health determines effective performance, and that business and markets do not operate in isolation from society but are inextricably linked.

Originality/value

The paper addresses how to sustain the leader's psychological and physiological health and their performance, and the link between this and creating sustainable organizations.
Learning and performance journeys
Authors: Pritchard Neville
Published: August 2010

Purpose

This paper aims to demonstrate the significance and potential of learning as a performance lever.

Design/methodology/approach

Through experience of working within a number of organizations across varied industries the author has formulated a clear link between learning and performance. This paper intends to demonstrate an approach that ensures a collaborative responsibility between learning functions and organization management in the deployment of learning opportunities in a performance journey from current to expected levels.

Findings

The paper considers that learning and performance journeys can be combined and managed to greater effect if training is not treated as a one‐off event and that change is more likely if the responsibility for learning and performance is held by individuals and the coordination of learning opportunity support is led by specialists yet implemented in an integrated way by all.

Practical implications

There are a number of implications: the concept of learning and performance journeys being coordinated to ensure transfer of learning to the workplace rather than a focus on single training events or interventions; the use of multi‐media approaches to the provision of learning opportunity to enable improved performance over time; the focus of measurement, reporting and subsequent adjustments to the provision of learning on performance outputs rather than measurement of training inputs.

Originality/value

The paper demonstrates learning and performance journeys as a concept. It is of significant value to heads of learning and development and organization management involved in change and the achievement of strategy and vision.
Leadership in unprecedented times
Authors: Dickson Andy
Published: August 2010

Purpose

This paper aims to raise awareness that successful businesses of the future will need to pay attention to more than just the traditional economic model. Social and environmental issues need to be considered when setting strategy.

Design/methodology/approach

The paper uses examples from successful organizations and the benefits they have experienced.

Findings

There are sources of competitive advantage in social and environmental issues.

Research limitations/implications

Success for a business is not guaranteed. It depends on the market and the innovation and the courage, capability and capacity to implement.

Practical implications

Any business can do this if it is motivated to do so.

Originality/value

By looking at wider social and environmental issues businesses can move beyond compliance to exciting opportunities that can differentiate them in the marketplace. This is not about responsibility but opportunity.
How training in project management can help businesses to get back on track
Authors: Edmonds John
Published: August 2010

Purpose

In the 1990s project management was a growing area, now it is almost impossible to go to any organization where there is not a project. This growth has been so fast that many people find themselves in charge of projects, with none of the special skills required. This paper aims to focus on the issues.

Design/methodology/approach

The solution is to provide training as it is through the discipline of project management that all the enablers for change required to survive in the business world today canbe delivered. There is a de facto process based method for effective project management, widely used by the UK government and the private sector both in the UK and internationally, known as PRINCE2®.

Findings

Effective project management training emphasizes structure, creativity and flexibility. The right type of training can offer multiple benefits to an organization to provide a tighter control over resources and an improved level of project risk. It can also raise the management skills of individuals, providing them with greater work satisfaction and long‐term career prospects.

Originality/value

Great project management training should be delivered by subject matter experts who can deliver training experiences that are inspirational and rewarding. Organizations from all business sectors need to invest in good project management training experts who are prepared to engage with their organization's strategic aims and objectives in a partnership rather than supplier role. Those looking to develop their way out of the credit crunch and to secure the future of their staff, customers and business should be taking a serious look at making that investment.
E‐resource helpdesk into virtual reference: identifying core competencies
Authors: Resnick Taryn , Ugaz Ana , Burford Nancy
Published: August 2010

Purpose

The purpose of this paper is to determine core competencies, for use as a foundation for staffing and training, and necessary to provide effective electronic resource (ER) access support.

Design/methodology/approach

The authors analyzed 580 ER access problem reports in a large academic library system to measure the specific skill(s) required for effective problem resolution. Problem reports were drawn equally from two different reporting systems: one using web forms and e‐mail and the other featuring real‐time user interaction.

Findings

Abilities fostered in reference work related to communication with users, staff, and vendors were by far the most crucial and highly used in successful problem solving, followed by the knowledge to make appropriate referrals within the organization.

Research limitations/implications

Results reported are from one institution, albeit one which serves a very large user population with diverse information needs which provided a broad range of users and problem types.

Practical implications

Staffing for an access support service should draw upon employees whose skill set includes assisting users with more traditional information access, such as reference, as well as employees with expertise in areas such as licensing.

Originality/value

Resolving user‐reported online access issues is a mission‐critical library service function. The paper offers an objective demonstration that the skills leading to success in access support are the same communication skills valued in reference services and that the mechanism used for providing a virtual reference service can also be used for handling user‐access problems. Identifying and ranking these skills provides structure and best practice standards for continuous training and staff assessment.
Research behavior patterns of business students
Authors: Dubicki Eleonora
Published: August 2010

Purpose

The purpose of this paper is to look at the research needs of undergraduate and graduate business students at Monmouth University.

Design/methodology/approach

Students were surveyed regarding the types of business course assignments that require research and the number of sources which must be cited for these research projects. The information‐seeking behaviors of business students used in gathering these sources were examined, looking at where these students began their research, which tools they used, and the challenges they faced in conducting research. The paper also investigated the students' preferred methods of seeking assistance in completing their research, as well as how they evaluated the credibility of sources they uncovered.

Findings

Student research requirements for homework assignments were fairly evenly distributed between very often/often and sometimes/never. Overall, students noted that presentations required research very often or often. Only 2.35 percent reported no research for short papers, with graduate students representing the largest group who indicated no research required for short papers. By contrast, 81 percent of seniors responded that they conducted research for short papers either very often or often. When preparing long papers (over six pages), students most frequently reported that research requirements were required sometimes. During the qualitative phase of the project, students revealed their frustration with doing research on very specific topics assigned by professors.

Originality/value

The results of this research can assist librarians in two important areas: collection management and instruction.
Systematic review of research methods: the case of business instruction
Authors: Manning Fiegen Ann
Published: August 2010

Purpose

The purpose of this paper is to assess the body of business instruction literature by academic librarians against evolving models for evidence‐based research.

Design/methodology/approach

The paper used systematic review and inter‐rater reliability of the literature of business information research instruction to test two attributes of research quality: the evidence‐based levels of evidence and the EBLIP critical analysis checklist.

Findings

Intervention questions and case studies are the most popular research methods on the EBL levels of evidence scale. The majority of articles score below 75 on the EBLIP critical appraisal checklist. Prediction questions are represented by higher levels of evidence and study quality. Intervention questions paired with the cohort design and exploratory questions paired with survey design indicate strong areas of research quality. The case study method, while most popular, showes lower scores across all question types yet revealed some high‐quality benchmark examples.

Research limitations/implications

Error is possible when distinguishing between cohort and case study – some articles may fall into one or the other study design. Rater training was conducted only once, and best practices for inter‐rater reliability recommend multiple rounds to achieve higher rater agreement.

Practical implications

Recommendations are presented for ways to improve the evidence base of research articles and suggest areas for professional development opportunities for librarian researchers wishing to increase the quality of research publications.

Originality/value

The paper goes beyond the narrative review of the literature of business instruction to measure the research methods employed in those publications against two evidence‐based standards. The results will show where the literature stands as a maturing discipline and provide recommendations for increasing the levels of evidence for future research.
Redirecting library instruction based on socioeconomic data
Authors: Adebonojo Leslie , Ellis Mark , Campbell Kathy , Hawkins Michael
Published: August 2010

Purpose

This paper aims to utilize data collected at the national, state, and local level to analyze our library instruction (LI) program with the goal of designing a program to best suit student needs.

Design/methodology/approach

The collection and analysis of national, state, and local economic and computer access and usage statistics was carried out.

Findings

Although most incoming freshmen at East Tennessee State University have access to computers and can perform basic computer functions, they do not have the skill set necessary to do college‐level research.

Practical implications

Sherrod Library needs to continue providing traditional LI classes. Furthermore, new ways to train incoming freshmen in research methods need to be developed.

Originality/value

The use of national, state, and local economic and computer access and usage statistics to create a profile of our students in order to assess LI and outreach programs.
The effectiveness of a university's single‐session information literacy instruction
Authors: Lei Hsieh Ma , Holden Hugh A.
Published: August 2010

Purpose

The purpose of this paper it to determine the effectiveness of “single‐session” information literacy instruction as it was integrated into the curriculum of a general education course at Monmouth University, New Jersey.

Design/methodology/approach

Two types of assessment instrument were used: a pre‐ and post‐test to measure any changes in learning outcomes of information literacy (IL) concepts after an IL instruction (ILI) session, and a student survey conducted after the post‐test. Installed on the course management system, these assessments were administered by teaching faculty over three semesters.

Findings

Single‐session ILI had a positive if not dramatic impact on learning outcomes. The pre‐ and post‐test instrument was able to show specific strengths and weaknesses in the students' comprehension of IL concepts. And the survey revealed that most students believed that their ILI was valuable.

Research limitations/implications

The paper did not employ a control group – a common practice in similar studies – although doing so could result in richer data and would conform the paper to general practices.

Originality/value

The results of this assessment study concur with other research that supports the position that single‐session ILI has a measurably significant positive effect on student learning outcomes.