bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation and Characterization of Uniform Near IR Polystyrene Nanoparticles
Authors: Pellach Michal , Margel Shlomo 
Published: January 2014

AbstractBiomaterials for in vivo fluorescence imaging are required to be biocompatible, nontoxic, photostable and highly fluorescent. Fluorescence must be in the near infrared (NIR) region of the electromagnetic spectrum to avoid absorption and autofluorescence of endogenous tissues. NIR fluorescent polystyrene nanoparticles may be considered ideal biomaterials for in vivo imaging applications. These NIR nanoparticles were prepared by a swelling process of polystyrene template nanoparticles with a hydrophobic NIR dye dissolved in a water‐miscible swelling solvent, a method developed for preparation of nonbiodegradable nanoparticles, for NIR fluorescent bioimaging applications. This method overcomes common problems that occur with dye entrapment during nanoparticle formation such as loss of fluorescence and size polydispersity. Fluorescence intensity of the nanoparticles was found to be size dependent, and was optimized for differently sized nanoparticles. The resulting NIR nanoparticles were also found to be more fluorescent and highly photostable compared to the free dye in solution, showing their potential as biomaterials for in vivo fluorescence imaging.
Skatole Metabolism in the Pigs with Reduced Testicular Oestrogen Synthesis
Authors: Zamaratskaia G , Berger T 
Published: January 2014

ContentThe objectives of the study were to investigate the involvement of oestrogens in the regulation of skatole levels in pigs. In total, 44 intact male pigs, siblings from 10 litters, were included in the study. Pigs were orally treated weekly with either 0.1 mg letrozole/kg body weight to reduce endogenous oestrogens or the canola oil vehicle. Fat and liver samples were collected at slaughter at 16, 20 and 40 weeks of age. Skatole and androstenone levels in fat and activities of hepatic cytochrome P4501A1, CYP1A2, CYP2A19 and CYP2E1 were analysed. Letrozole treatment did not significantly change either the levels of skatole or activities of skatole‐metabolising enzymes, suggesting that oestrogens are not responsible for gender‐related differences in skatole concentrations in porcine tissues.
Creative Activism and Art Against Urban Renaissance and Social Exclusion – Space Sensitive Approaches to the Study of Collective Action and Belonging
Authors: Youkhana Eva 
Published: January 2014

AbstractCreative activism and urban art are increasingly being used as an instrument to collectively re‐appropriate the urban space and thus articulate urban belonging and citizenship from below. In cities worldwide, where different politics of place stimulate capitalist appropriation, individuals and groups use the public space as a laboratory for resistance, creative act, and as a medium for communication. As such, creative activism is a strategy for those who are widely excluded from social, political, cultural, and economic participation. Collectives are built through joint actions and experiences that are translated into the production situated forms of urban belonging. By drawing on space sensitive and situationist approaches and the power of creativity as an important moment in the analysis of action, the paper provides examples of how collective action and belonging is produced under conditions of contentious politics and exclusion that go beyond social norms, the social containment of institutions,and imposed collective identities.
Neighborhood Scale and Collective Efficacy: Does Size Matter?
Authors: Stein Rachel E. 
Published: January 2014

AbstractThe theory of collective efficacy emphasizes the role of the neighborhood as a unit of social control that can deter crime. The neighborhood unit is most often defined as a census tract or a similar administratively defined measure. These neighborhood definitions are not always sociologically meaningful. That is, administratively defined geographical areas do not necessarily align with residents' perceptions of their neighborhood's boundaries, which incorporate the familiarity with an area and interactions with other residents. Officially defined neighborhoods often present an inaccurate representation of collective efficacy, as these areas are not likely to function as a cohesive social unit. An alternative measure of “bespoke” neighborhoods is presented in geographical research. The bespoke neighborhood identifies a neighborhood area as the distance from a specific point or the number of people situated nearest to a specific location. This concept takes into consideration each resident's unique definition of the neighborhood. In addition, the bespoke neighborhood can be assessed on different scales to identify the most appropriate neighborhood size, where patterns of behavior are most meaningful. Bespoke neighborhoods can be used to identify sociologically meaningful neighborhoods that can inform the theory of collective efficacy.
Cardamine hirsuta: a versatile genetic system for comparative studies
Authors: Hay Angela S. , Pieper Bjorn , Cooke Elizabeth , Mandáková Terezie , Cartolano Maria , Tattersall Alexander D. , Ioio Raffaele D. , McGowan Simon J. , Barkoulas Michalis , Galinha Carla , Rast Madlen I. , Hofhuis Hugo , Then Christiane , Plieske Jörg , Ganal Martin , Mott Richard , Martinez‐Garcia Jaime F. , Carine Mark A. , Scotland Robert W. , Gan Xiangchao , Filatov Dmitry A. , Lysak Martin A. , Tsiantis Miltos 
Published: January 2014

SummaryA major goal in biology is to identify the genetic basis for phenotypic diversity. This goal underpins research in areas as diverse as evolutionary biology, plant breeding and human genetics. A limitation for this research is no longer the availability of sequence information but the development of functional genetic tools to understand the link between changes in sequence and phenotype. Here we describe Cardamine hirsuta, a close relative of the reference plant Arabidopsis thaliana, as an experimental system in which genetic and transgenic approaches can be deployed effectively for comparative studies. We present high‐resolution genetic and cytogenetic maps for C. hirsuta and show that the genome structure of C. hirsuta closely resembles the eight chromosomes of the ancestral crucifer karyotype and provides a good reference point for comparative genome studies across the Brassicaceae. We compared morphological and physiological traits between C. hirsuta and A. thaliana and analysed natural variation in stamen number in which lateral stamen loss is a species characteristic of C. hirsuta. We constructed a set of recombinant inbred lines and detected eight quantitative trait loci that can explain stamen number variation in this population. We found clear phylogeographic structure to the genetic variation in C. hirsuta, thus providing a context within which to address questions about evolutionary changes that link genotype with phenotype and the environment.
Refined NrfA Phylogeny Improves PCR-Based
nrfA
Gene Detection
Authors: Welsh Allana , Chee-Sanford Joanne C. , Connor Lynn M. , Löffler Frank E. , Sanford Robert A. 
Published: January 2014

ABSTRACT

Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new
nrfA
-containing isolates.
nrfA
amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.
Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia
Authors: Men Yujie , Seth Erica C. , Yi Shan , Allen Robert H. , Taga Michiko E. , Alvarez-Cohen Lisa 
Published: January 2014

ABSTRACTCorrinoids are essential cofactors of reductive dehalogenases inDehalococcoides mccartyi, an important bacterium in bioremediation, yet sequencedD. mccartyistrains do not possess the complete pathway forde novocorrinoid biosynthesis.Pelosinussp. andDesulfovibriosp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growingD. mccartyistrain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)- and lactate-amended medium in cocultures withDesulfovibrio vulgarisHildenborough (DvH) orPelosinus fermentansR7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.
Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains
Authors: Gonzalez-Escalona Narjol , Timme Ruth , Raphael Brian H. , Zink Donald , Sharma Shashi K. 
Published: January 2014

ABSTRACT

Clostridium botulinum
is a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA
+
OrfX
−
) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA
−
OrfX
+
) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producing
C. botulinum
strains: two strains with the HA
+
OrfX
−
cluster (69A and 32A) and one strain with the HA
−
OrfX
+
cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly available
C. botulinum
group I strains revealed five distinct lineages. Strains 69A and 32A clustered with the
C. botulinum
type A1 Hall group, and strain CDC297 clustered with the
C. botulinum
type Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination of
C. botulinum
group I strains and demonstrates the utility of this analysis in quickly differentiating
C. botulinum
strains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.
Persistence of Infectious Shiga Toxin-Encoding Bacteriophages after Disinfection Treatments
Authors: Allué-Guardia Anna , Martínez-Castillo Alexandre , Muniesa Maite 
Published: January 2014

ABSTRACTIn Shiga toxin-producingEscherichia coli(STEC), induction of Shiga toxin-encoding bacteriophages (Stx phages) causes the release of free phages that can later be found in the environment. The ability of Stx phages to survive different inactivation conditions determines their prevalence in the environment, the risk ofstxtransduction, and the generation of new STEC strains. We evaluated the infectivity and genomes of two Stx phages (Φ534 and Φ557) under different conditions. Infectious Stx phages were stable at 4, 22, and 37°C and at pH 7 and 9 after 1 month of storage but were completely inactivated at pH 3. Infective Stx phages decreased moderately when treated with UV (2.2-log10reduction for an estimated UV dose of 178.2 mJ/cm2) or after treatment at 60 and 68°C for 60 min (2.2- and 2.5-log10reductions, respectively) and were highly inactivated (3 log10) by 10 ppm of chlorine in 1 min. Assays in a mesocosm showed lower inactivation of all microorganisms in winter than in summer. The number of Stx phage genomes did not decrease significantly in most cases, and STEC inactivation was higher than phage inactivation under all conditions. Moreover, Stx phages retained the ability to lysogenizeE. coliafter some of the treatments.
Life History Analysis of Integrative and Conjugative Element Activation in Growing Microcolonies of Pseudomonas
Authors: Reinhard Friedrich , van der Meer Jan Roelof 
Published: January 2014

ABSTRACT

Integrative and conjugative elements (ICE) are in some ways parasitic mobile DNA that propagate vertically through replication with the bacterial host chromosome but at low frequencies can excise and invade new recipient cells through conjugation and reintegration (horizontal propagation). The factors that contribute to successful horizontal propagation are not very well understood. Here, we study the influence of host cell life history on the initiation of transfer of a model ICE named ICE
clc
in bacteria of the genus
Pseudomonas
. We use time-lapse microscopy of growing and stationary-phase microcolonies of ICE
clc
bearing cells in combination with physiological staining and gene reporter analysis in stationary-phase suspended cells. We provide evidence that cell age and cell lineage are unlikely to play a role in the decision to initiate the ICE
clc
transfer program. In contrast, cells activating ICE
clc
show more often increased levels of reactive oxygen species and membrane damage than nonactivating cells, suggesting that some form of biochemical damage may make cells more prone to ICE
clc
induction. Finally, we find that ICE
clc
active cells appear spatially at random in a microcolony, which may have been a selective advantage for maximizing ICE
clc
horizontal transmission to new recipient species.
Identification and Characterization of a Second Quorum-Sensing System in Agrobacterium tumefaciens A6
Authors: Wang Chao , Yan Chunlan , Fuqua Clay , Zhang Lian-Hui 
Published: January 2014

ABSTRACT

Quorum sensing (QS) is a widespread mechanism of bacterial communication in which individual cells produce and respond to small chemical signals. In
Agrobacterium tumefaciens
, an acylhomoserine lactone-dependent QS mechanism is known to regulate the replication and conjugation of the tumor-inducing (Ti) plasmid. Most of the QS regulatory proteins are encoded within the Ti plasmid. Among them, TraI is the LuxI-type enzyme synthesizing the QS signal
N
-3-oxooctanoyl-
l
-homoserine lactone (3OC8HSL), TraR is the LuxR-type transcriptional factor that recognizes 3OC8HSL, and TraM is an antiactivator that antagonizes TraR. Recently, we identified a TraM homolog encoded by the
traM2
gene in the chromosomal background of
A. tumefaciens
A6. In this study, we further identified additional homologs (TraI2 and TraR2) of TraI and TraR in this strain. We showed that similar to TraI, TraI2 could predominantly synthesize the QS signal 3OC8HSL. We also showed that TraR2 could recognize 3OC8HSL and activate the
tra
box-containing promoters as efficiently as TraR. Further analysis showed that
traM2
,
traI2
, and
traR2
are physically linked on a mobile genetic element that is not related to the Ti plasmid. These findings indicate that
A. tumefaciens
A6 carries a second QS system that may play a redundant role in the regulation of the replication and conjugation of the Ti plasmid.
Use of strategies to improve retention in primary care randomised trials: a qualitative study with in-depth interviews
Authors: Brueton V C , Stevenson F , Vale C L , Stenning S P , Tierney J F , Harding S , Nazareth I , Meredith S , Rait G 
Published: January 2014

ObjectiveTo explore the strategies used to improve retention in primary care randomised trials.DesignQualitative in-depth interviews and thematic analysis.Participants29 UK primary care chief and principal investigators, trial managers and research nurses.MethodsIn-depth face-to-face interviews.ResultsPrimary care researchers use incentive and communication strategies to improve retention in trials, but were unsure of their effect. Small monetary incentives were used to increase response to postal questionnaires. Non-monetary incentives were used although there was scepticism about the impact of these on retention. Nurses routinely used telephone communication to encourage participants to return for trial follow-up. Trial managers used first class post, shorter questionnaires and improved questionnaire designs with the aim of improving questionnaire response. Interviewees thought an open trial design could lead to biased results and were negative about using behavioural strategies to improve retention. There was consensus among the interviewees that effective communication and rapport with participants, participant altruism, respect for participant's time, flexibility of trial personnel and appointment schedules and trial information improve retention. Interviewees noted particular challenges with retention in mental health trials and those involving teenagers.ConclusionsThe findings of this qualitative study have allowed us to reflect on research practice around retention and highlight a gap between such practice and current evidence. Interviewees describe acting from experience without evidence from the literature, which supports the use of small monetary incentives to improve the questionnaire response. No such evidence exists for non-monetary incentives or first class post, use of which may need reconsideration. An exploration of barriers and facilitators to retention in other research contexts may be justified.
Distal aspiration with retrievable stent assisted thrombectomy for the treatment of acute ischemic stroke
Authors: Humphries William , Hoit Daniel , Doss Vinodh T , Elijovich Lucas , Frei Donald , Loy David , Dooley Gwen , Turk Aquilla S , Chaudry Imran , Turner Raymond , Mocco J , Morone Peter , Fiorella David , Siddiqui Adnan , Mokin Maxim , Arthur Adam S 
Published: January 2014

ObjectiveFlexible large lumen aspiration catheters and stent retrievers have recently become available in the USA for the revascularization of large vessel occlusions presenting within the context of acute ischemic stroke (AIS). We describe a multicenter experience using a combined aspiration and stent retrieval technique for thrombectomy.DesignA retrospective analysis to identify patients receiving combined manual aspiration and stent retrieval for treatment of AIS between August 2012 and April 2013 at six high volume stroke centers was conducted. Outcome variables, including recanalization rate, post-treatment National Institutes of Health Stroke Scale (NIHSS) score, symptomatic intracranial hemorrhage, discharge 90 day modified Rankin Scale (mRS) score, and mortality were evaluated.Results105 patients were found that met the inclusion criteria for this retrospective study. Successful recanalization (Thrombolysis in Cerebral Infarction score 2B) was achieved in 92 (88%) of these patients. 44% of patients had favorable (mRS score 0–2) outcomes at 90 days. There were five (4.8%) symptomatic intracerebral hemorrhages and three procedure related deaths (2.9%).ConclusionsMechanical thrombectomy utilizing combined manual aspiration with a stent retriever is an effective and safe strategy for endovascular recanalization of large vessel occlusions presenting within the context of AIS.
Outcome of surgical treatment for umbilical swellings in bovine youngstock
Authors: Williams H. J. , Gillespie A. V. , Oultram J. W. , Cripps P. J. , Holman A. N. 
Published: January 2014

Umbilical swellings are commonly identified in calves and can be caused by hernia formation, infection of the remnants of umbilical vessels or a combination of both. Ninety‐one cases with umbilical swellings were admitted to the Leahurst Farm Animal Practice (LFAP) between July 2004 and February 2012; 55 were simple hernias and 36 had associated infection. Eighty‐seven cases underwent surgery of which 86 survived until discharge. Postoperative complications occurred in 65/86 animals (73 per cent). In 51 cases (81 per cent) this was classified as minor requiring no additional treatment. Placement of a prosthetic mesh was associated with a higher OR for developing severe postoperative complication when compared with those not receiving a mesh (OR=19.3; 95% CI 4.5 to 83.5). Long‐term survival results were available for 49 animals, 22 of which were remaining in the herd with a median age of 1346 days (3.7 years). Of the 27 animals which had exited the herd, 16 were adult dairy cows, 7 were dairy heifers, 2 were beef animals and 2 exited at an unknown stage. Umbilical surgery in calves carries a good prognosis, although placement of a mesh increases the risk of complications occurring in the postoperative period.
Estimating farm‐level private expenditure on veterinary medical inputs in England
Authors: Gilbert W. , Rushton J. 
Published: January 2014

The current re‐evaluation of responsibility and cost sharing between the public and private sectors with reference to animal health and welfare (AHW) would be improved by a greater understanding of the contributions made at farm level. This knowledge would facilitate the design of a cost‐sharing system which best balances technical, economic and political objectives. This paper presents a framework by which the farm‐level investment in AHW can be assessed. An evaluation of data available for the framework was made and, as a benchmark, an estimate of total expenditure on veterinary medical inputs for commercial agricultural holdings in England calculated. In 2010/2011 it is calculated that farmers on commercial holdings in England spent £230 million on veterinary medicines and fees, with an additional £160 million being spent for horses kept on non‐commercial holdings. By contrast, for 2012/2013, Defra budgeted £277 million on AHW. The results presented emphasise the critical importance of generating sufficient evidence to support the development of an efficient, equitable and sustainable AHW strategy.