bluuebunny/crossref_metadata_2025_split huggingface dataset:
So What Difference Does it Make? Mapping the Outcomes of Citizen Engagement
Authors: Gaventa John , Barrett Gregory 
Published: June 2011

SummaryOver the last two decades, the idea that citizen engagement and participation can contribute to improved governance and development outcomes has been mainstreamed in development policy and discourse. Yet despite the normative beliefs that underpin this approach, the impact of participation on improved democratic and developmental outcomes has proved difficult to assess. Where previous research studies have attempted to demonstrate impact, they tend to be limited to single interventions, a small number of country contexts or by various conceptual and methodological constraints.In this paper, we report on a meta‐case study analysis of a ten‐year research programme on citizenship, participation and accountability which analysed a non‐randomised sample of 100 research studies of four types of citizen engagement in 20 countries. By mapping the observable effects of citizen participation through a close reading of these studies, we created a typology of four democratic and developmental outcomes, including (a) the construction of citizenship, (b) the strengthening of practices of participation, (c) the strengthening of responsive and accountable states, and (d) the development of inclusive and cohesive societies.We find that citizen participation produces positive effects across these outcome types, though in each category there are also examples of negative outcomes of citizen participation. We also find that these outcomes vary according to the type of citizen engagement and to political context. These findings have important implications for the design of and support for participatory programmes meant to improve state responsiveness and effectiveness.
On thinning of chains in MCMC
Authors: Link William A. , Eaton Mitchell J. 
Published: June 2011

Summary1. Markov chain Monte Carlo (MCMC) is a simulation technique that has revolutionised the analysis of ecological data, allowing the fitting of complex models in a Bayesian framework. Since 2001, there have been nearly 200 papers using MCMC in publications of the Ecological Society of America and the British Ecological Society, including more than 75 in the journal Ecology and 35 in the Journal of Applied Ecology.2. We have noted that many authors routinely ‘thin’ their simulations, discarding all but every kth sampled value; of the studies we surveyed with details on MCMC implementation, 40% reported thinning.3. Thinning is often unnecessary and always inefficient, reducing the precision with which features of the Markov chain are summarised. The inefficiency of thinning MCMC output has been known since the early 1990’s, long before MCMC appeared in ecological publications.4. We discuss the background and prevalence of thinning, illustrate its consequences, discuss circumstances when it might be regarded as a reasonable option and recommend against routine thinning of chains unless necessitated by computer memory limitations.
β-Glucuronidase as a Sensitive and Versatile Reporter in Actinomycetes
Authors: Myronovskyi Maksym , Welle Elisabeth , Fedorenko Viktor , Luzhetskyy Andriy 
Published: June 2011

ABSTRACT

Here we describe a versatile and sensitive reporter system for actinomycetes that is based on
gusA
, which encodes the β-glucuronidase enzyme. A series of
gusA-
containing transcriptional and translational fusion vectors were constructed and utilized to study the regulatory cascade of the phenalinolactone biosynthetic gene cluster. Furthermore, these vectors were used to study the efficiency of translation initiation at the ATG, GTG, TTG, and CTG start codons. Surprisingly, constructs using a TTG start codon showed the best activity, whereas those using ATG or GTG were approximately one-half or one-third as active, respectively. The CTG fusion showed only 5% of the activity of the TTG fusion. A suicide vector, pKGLP2, carrying
gusA
in its backbone was used to visually detect merodiploid formation and resolution, making gene targeting in actinomycetes much faster and easier. Three regulatory genes,
plaR1
,
plaR2
, and
plaR3
, involved in phenalinolactone biosynthesis were efficiently replaced with an apramycin resistance marker using this system. Finally, we expanded the genetic code of actinomycetes by introducing the nonproteinogenic amino acid
N
-epsilon-cyclopentyloxycarbonyl-
l
-lysine with the GusA protein as a reporter.
Novel Family of Carbohydrate-Binding Modules Revealed by the Genome Sequence of Spirochaeta thermophila DSM 6192
Authors: Angelov Angel , Loderer Christoph , Pompei Susanne , Liebl Wolfgang 
Published: June 2011

ABSTRACT

Spirochaeta thermophila
is a thermophilic, free-living, and cellulolytic anaerobe. The genome sequence data for this organism have revealed a high density of genes encoding enzymes from more than 30 glycoside hydrolase (GH) families and a noncellulosomal enzyme system for (hemi)cellulose degradation. Functional screening of a fosmid library whose inserts were mapped on the
S. thermophila
genome sequence allowed the functional annotation of numerous GH open reading frames (ORFs). Seven different GH ORFs from the
S. thermophila
DSM 6192 genome, all putative β-glycanase ORFs according to sequence similarity analysis, contained a highly conserved novel GH-associated module of unknown function at their C terminus. Four of these GH enzymes were experimentally verified as xylanase, β-glucanase, β-glucanase/carboxymethylcellulase (CMCase), and CMCase. Binding experiments performed with the recombinantly expressed and purified GH-associated module showed that it represents a new carbohydrate-binding module (CBM) that binds to microcrystalline cellulose and is highly specific for this substrate. In the course of this work, the new CBM type was only detected in
Spirochaeta
, but recently we found sequences with detectable similarity to the module in the draft genomes of
Cytophaga fermentans
and
Mahella australiensis
, both of which are phylogenetically very distant from
S. thermophila
and noncellulolytic, yet inhabit similar environments. This suggests a possibly broad distribution of the module in nature.
Evidence of Burkholderia pseudomallei-Specific Immunity in Patient Sera Persistently Nonreactive by the Indirect Hemagglutination Assay
Authors: Harris Patrick N. A. , Williams Natasha L. , Morris Jodie L. , Ketheesan Natkunam , Norton Robert E. 
Published: June 2011

ABSTRACTThe indirect hemagglutination assay (IHA) is the most frequently used serological test to confirm exposure toBurkholderia pseudomallei. Patients with culture-confirmed disease often have a nonreactive IHA at presentation and occasionally fail to seroconvert on serial testing. We investigated whether using antigens derived from the cultured isolates of persistently IHA-nonreactive patient sera improved the sensitivity of the IHA. In addition, we assessed the antigen-specific lymphocyte response in this group of patients to a panel ofB. pseudomalleiantigens, including those derived from their own cultured isolates. Eleven patients with culture-proven melioidosis were identified as having persistently IHA-nonreactive sera. A modified IHA using erythrocytes sensitized with patient isolate-derived antigen tested against convalescent-phase serum was performed. The majority (82%) of sera showed a negative (≤1:5) result, one was borderline (1:20), and one was positive at the cutoff value (1:40). IHA-nonreactive sera were also tested by enzyme immunoassay (EIA), with 73% (8/11) demonstrating IgG positivity. In addition, lymphocytes isolated from persistently IHA-nonreactive patient sera demonstrated significantly increased proliferation in response toB. pseudomalleiantigens compared to controls. These studies demonstrate the presence ofB. pseudomallei-specific antibody by EIA andB. pseudomallei-specific lymphocytes in patient sera categorized as persistently nonreactive according to the IHA. New immunoassays are required and should incorporateB. pseudomalleiantigens that are immunoreactive for this subset of IHA-nonreactive patient sera.
Functional Dissection of a Candida albicans Zinc Cluster Transcription Factor, the Multidrug Resistance Regulator Mrr1
Authors: Schubert Sabrina , Popp Christina , Rogers P. David , Morschhäuser Joachim 
Published: June 2011

ABSTRACT

The overexpression of the
MDR1
gene, which encodes a multidrug efflux pump of the major facilitator superfamily, is a frequent cause of resistance to the widely used antimycotic agent fluconazole and other toxic compounds in the pathogenic yeast
Candida albicans
. The zinc cluster transcription factor Mrr1 controls
MDR1
expression in response to inducing chemicals, and gain-of-function mutations in
MRR1
are responsible for the constitutive
MDR1
upregulation in fluconazole-resistant
C. albicans
strains. To understand how Mrr1 activity is regulated, we identified functional domains of this transcription factor. A hybrid protein consisting of the N-terminal 106 amino acids of Mrr1 and the transcriptional activation domain of Gal4 from
Saccharomyces cerevisiae
constitutively induced
MDR1
expression, demonstrating that the DNA binding domain is sufficient to target Mrr1 to the
MDR1
promoter. Using a series of C-terminal truncations and systematic internal deletions, we could show that Mrr1 contains multiple activation and inhibitory domains. One activation domain (AD1) is located in the C terminus of Mrr1. When fused to the tetracycline repressor TetR, this distal activation domain induced gene expression from a TetR-dependent promoter. The deletion of an inhibitory region (ID1) located near the distal activation domain resulted in constitutive activity of Mrr1. The additional removal of AD1 abolished the constitutive activity, but the truncated Mrr1 still could activate the
MDR1
promoter in response to the inducer benomyl. These results demonstrate that the activity of Mrr1 is regulated in multiple ways and provide insights into the function of an important mediator of drug resistance in
C. albicans
.
Alterations in the β Flap and β′ Dock Domains of the RNA Polymerase Abolish NusA-Mediated Feedback Regulation of the
metY
-
nusA
-
infB
Operon
Authors: Bylund Göran O. , Nord Stefan , Lövgren J. Mattias , Wikström P. Mikael 
Published: June 2011

ABSTRACT

The RimM protein in
Escherichia coli
is important for the
in vivo
maturation of 30S ribosomal subunits and a Δ
rimM
mutant grows poorly due to assembly and translational defects. These deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, RbfA, encoded by the
metY-nusA-infB
operon. Among these suppressors are mutations in
nusA
that impair the NusA-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the
metY-nusA-infB
operon. We describe here the isolation of two new mutations, one in
rpoB
and one in
rpoC
(encoding the β and β′ subunits of the RNA polymerase, respectively), that increase the synthesis of RbfA by preventing NusA from stimulating termination at the internal intrinsic transcriptional terminators of the
metY-nusA-infB
operon. The
rpoB2063
mutation changed the isoleucine in position 905 of the β flap-tip helix to a serine, while the
rpoC2064
mutation duplicated positions 415 to 416 (valine-isoleucine) at the base of the β′ dock domain. These findings support previously published
in vitro
results, which have suggested that the β flap-tip helix and β′ dock domain at either side of the RNA exit tunnel mediate the binding to NusA during transcriptional pausing and termination.
Crystal Structure of Bacillus anthracis Phosphoglucosamine Mutase, an Enzyme in the Peptidoglycan Biosynthetic Pathway
Authors: Mehra-Chaudhary Ritcha , Mick Jacob , Beamer Lesa J. 
Published: June 2011

ABSTRACT

Phosphoglucosamine mutase (PNGM) is an evolutionarily conserved bacterial enzyme that participates in the cytoplasmic steps of peptidoglycan biosynthesis. As peptidoglycan is essential for bacterial survival and is absent in humans, enzymes in this pathway have been the focus of intensive inhibitor design efforts. Many aspects of the structural biology of the peptidoglycan pathway have been elucidated, with the exception of the PNGM structure. We present here the crystal structure of PNGM from the human pathogen and bioterrorism agent
Bacillus anthracis
. The structure reveals key residues in the large active site cleft of the enzyme which likely have roles in catalysis and specificity. A large conformational change of the C-terminal domain of PNGM is observed when comparing two independent molecules in the crystal, shedding light on both the apo- and ligand-bound conformers of the enzyme. Crystal packing analyses and dynamic light scattering studies suggest that the enzyme is a dimer in solution. Multiple sequence alignments show that residues in the dimer interface are conserved, suggesting that many PNGM enzymes adopt this oligomeric state. This work lays the foundation for the development of inhibitors for PNGM enzymes from human pathogens.
Draft Genome Sequence of the Thermoalkaliphilic Caldalkalibacillus thermarum Strain TA2.A1
Authors: Kalamorz Falk , Keis Stefanie , McMillan Duncan G. G. , Olsson Karen , Stanton Jo-Ann , Stockwell Peter , Black Mik A. , Klingeman Dawn M. , Land Miriam L. , Han Cliff S. , Martin Stanton L. , Becher S. Anette , Peddie Catherine J. , Morgan Hugh W. , Matthies Doreen , Preiß Laura , Meier Thomas , Brown Steven D. , Cook Gregory M. 
Published: June 2011

ABSTRACT

The genes and molecular machines that allow for a thermoalkaliphilic lifestyle have not been defined. To address this goal, we report on the improved high-quality draft genome sequence of
Caldalkalibacillus thermarum
strain TA2.A1, an obligately aerobic bacterium that grows optimally at pH 9.5 and 65 to 70°C on a wide variety of carbon and energy sources.
Genome Sequence of the Chlamydophila abortus Variant Strain LLG
Authors: Sait Michelle , Clark Ewan M. , Wheelhouse Nick , Livingstone Morag , Spalding Lucy , Siarkou Victoria I. , Vretou Evangelia , Smith David G. E. , Lainson F. Alex , Longbottom David 
Published: June 2011

ABSTRACT

Chlamydophila abortus
is a common cause of ruminant abortion. Here we report the genome sequence of strain LLG, which differs genotypically and phenotypically from the wild-type strain S26/3. Genome sequencing revealed differences between LLG and S26/3 to occur in pseudogene content, in transmembrane head/inc family proteins, and in biotin biosynthesis genes.
Genome Sequence of the Curdlan-Producing Agrobacterium sp. Strain ATCC 31749
Authors: Ruffing Anne M. , Castro-Melchor Marlene , Hu Wei-Shou , Chen Rachel R. 
Published: June 2011

ABSTRACT

Agrobacterium
sp. ATCC 31749 is an industrial strain for the commercial production of curdlan, an important exopolysaccharide with food and medical applications. Here we report the genome sequence of the curdlan-producing strain ATCC 31749. Genome sequencing is the first step toward the understanding of regulation of curdlan biosynthesis.
De Novo
Sequencing and Assembly of the Whole Genome of Novosphingobium sp. Strain PP1Y
Authors: D'Argenio V. , Petrillo M. , Cantiello P. , Naso B. , Cozzuto L. , Notomista E. , Paolella G. , Di Donato A. , Salvatore F. 
Published: June 2011

ABSTRACT

Novosphingobium
sp. strain PP1Y is a marine bacterium specifically adapted to use fuels as an energy source. We sequenced and assembled its entire genome using the Roche 454 genome sequencer system, which led to the identification of two plasmids and one megaplasmid, besides a 3.9-Mb circular chromosome.
Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20
Authors: Hauser Loren J. , Land Miriam L. , Brown Steven D. , Larimer Frank , Keller Kimberly L. , Rapp-Giles Barbara J. , Price Morgan N. , Lin Monica , Bruce David C. , Detter John C. , Tapia Roxanne , Han Cliff S. , Goodwin Lynne A. , Cheng Jan-Fang , Pitluck Samuel , Copeland Alex , Lucas Susan , Nolan Matt , Lapidus Alla L. , Palumbo Anthony V. , Wall Judy D. 
Published: June 2011

ABSTRACT

Desulfovibrio alaskensis
G20 (formerly
Desulfovibrio desulfuricans
G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7-Mb genome sequence to provide insights into its physiology.
Draft Genome Sequence of Methylophaga aminisulfidivorans MP
T
Authors: Han Gui Hwan , Kim Wonduck , Chun Jongsik , Kim Si Wouk 
Published: June 2011

ABSTRACT

Methylophaga aminisulfidivorans
MP
T
is a restricted facultatively marine methylotrophic bacterium that grows on methanol, methylated amines, dimethyl sulfide, and dimethyl sulfoxide. Here we present the high-quality draft genome sequence of
M. aminisulfidivorans
MP
T
(KCTC 12909
T
= JCM 14647
T
), consisting of a chromosome (3,092,085 bp) and a plasmid (16,875 bp).
Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India
Authors: Avasthi Tiruvayipati Suma , Kumar Narender , Baddam Ramani , Hussain Arif , Nandanwar Nishant , Jadhav Savita , Ahmed Niyaz 
Published: June 2011

ABSTRACT

Uropathogenic
Escherichia coli
(UPEC) causes serious infections in people at risk and has a significant environmental prevalence due to contamination by human and animal excreta. In developing countries, UPEC assumes importance in certain dwellings because of poor community/personal hygiene and exposure to contaminated water or soil. We report the complete genome sequence of
E. coli
strain NA114 from India, a UPEC strain with a multidrug resistance phenotype and the capacity to produce extended-spectrum beta-lactamase. The genome sequence and comparative genomics emanating from it will be significant in under-standing the genetic makeup of diverse UPEC strains and in boosting the development of new diagnostics/vaccines.
Evaluation of Oral Antiseptic Rinsing before Sputum Collection To Reduce Contamination of Mycobacterial Cultures
Authors: Peres Renata L. , Palaci Moisés , Loureiro Rafaela B. , Dietze Reynaldo , Johnson John L. , Golub Jonathan E. , Ruffino-Netto A. , Maciel Ethel L. 
Published: June 2011

ABSTRACTTo assess whether rinsing with oral antiseptics before sputum collection would reduce contamination of mycobacterial cultures, 120 patients with suspected tuberculosis were randomly assigned to rinse with chlorhexidine or cetylpyridinium mouthwash before collection. The culture contamination rate was significantly lower after rinsing with chlorhexidine before collection, especially for cultures grown in MGIT medium.
Emerging Severe and Fatal Infections Due to Klebsiella pneumoniae in Two University Hospitals in France
Authors: Decré Dominique , Verdet Charlotte , Emirian Aurélie , Le Gourrierec Thibault , Petit Jean-Claude , Offenstadt Georges , Maury Eric , Brisse Sylvain , Arlet Guillaume 
Published: June 2011

ABSTRACT

Severe infections caused by hypermucoviscous
Klebsiella
pneumoniae
have been reported in Southeast Asian countries over the past several decades. This report shows their emergence in France, with 12 cases observed during a 2-year period in two university hospitals. Two clones (sequence type 86 [ST86] and ST380) of serotype K2 caused five rapidly fatal bacteremia cases, three of which were associated with pneumonia, whereas seven liver abscess cases were caused by K1 strains of ST23.
Computed tomographic perfusion imaging of non-hemorrhagic cerebral hyperperfusion syndrome and reversal following medical treatment after carotid artery angioplasty and stenting
Authors: Vasquez Raul A , Waters Michael F , Skowlund Christopher J , Mocco J , Hoh Brian L 
Published: June 2011

Objective and importanceCerebral hyperperfusion syndrome (CHS) is an infrequent syndrome observed in carotid endarterectomy and carotid angioplasty and stenting (CAS). The case history is presented of a patient with CT perfusion imaging of non-hemorrhagic CHS and reversal following medical treatment after CAS.Clinical presentationA right-handed Caucasian man in his late 70s presented with sudden onset right upper extremity plegia and anesthesia and right facial parasthesias with complete resolution within 24 h. CT angiography (CTA) revealed 75% left cervical carotid artery stenosis. The patient underwent uneventful left CAS. Six hours after the procedure he developed verbal perseveration and right upper extremity paresis. CT perfusion imaging showed increased mean transient time in the left parieto-occipital lobe without changes in cerebral blood flow or cerebral blood volume. A clinical diagnosis of CHS was suspected. Several hours after lowering the blood pressure his symptoms improved. A follow-up CTA with CT perfusion was performed which showed complete resolution of the previously observed changes in mean transient time. The patient was discharged home without neurological sequelae.ConclusionThis is the first report to our knowledge of CT perfusion imaging for CHS with post-symptomatic imaging following clinical resolution. Prompt CHS evaluation may include CT perfusion imaging to assist diagnostic accuracy. Rigorous blood pressure control remains the mainstay of treatment.
Over-the-catheter retrieval of a retained microcatheter following Onyx embolization: a technical report
Authors: Newman C Benjamin , Park Min S , Kerber Charles W , Levy Michael L , Barr John D , Pakbaz R Sean 
Published: June 2011

BackgroundBrain arteriovenous malformations are vascular lesions that are increasingly being treated with endovascular embolization. A potential complication with endovascular embolization is microcatheter entrapment within the embolic material. In the present report, a novel technique for the retrieval of microcatheters retained during Onyx embolization of intracranial lesions is described.Clinical presentationTwo patients (one boy and one girl, aged 13 and 15 years, respectively) with arteriovenous malformations (one unruptured, one ruptured; Spetzler–Martin grades 4 and 3) presented for embolization.InterventionDuring Onyx 18 embolization of the arteriovenous malformations, Echelon-10 microcatheters became entrapped into the arterial feeders by casts of the Onyx. Initial attempts to remove the microcatheters by traction were unsuccessful. The hubs of the microcatheters were transected and Concentric Medical Outreach distal access catheters were then advanced over the microcatheters and positioned at the proximal aspects of the microcatheter-Onyx plugs. Using the Outreach catheters for countertraction, the Echelon-10 microcatheters were then successfully released from the Onyx plugs under fluoroscopic visualization without significant distortion of the arteries. There were no complications related to the microcatheter extractions.ConclusionsA novel technique, which may be useful in the removal of retained microcatheters during Onyx embolization of Brain arteriovenous malformations, is presented.