bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison of transmission characteristics of Salmonella enterica serovar Enteritidis between pair-housed and group-housed laying hens
Authors: Thomas Ekelijn , Bouma Annemarie , Klinkenberg Don 
Published: February 2011

Abstract
Human cases of bacterial gastro-enteritis are often caused by the consumption of eggs contaminated with Salmonella species, mainly Salmonella enterica serovar Enteriditis (Salmonella Enteritidis). To reduce human exposure, in several countries worldwide surveillance programmes are implemented to detect colonized layer flocks. The sampling schemes are based on the within-flock prevalence, and, as this changes over time, knowledge of the within-flock dynamics of Salmonella Enteritidis is required. Transmission of Salmonella Enteritidis has been quantified in pairs of layers, but the question is whether the dynamics in pairs is comparable to transmission in large groups, which are more representative for commercial layer flocks. The aim of this study was to compare results of transmission experiments between pairs and groups of laying hens. Experimental groups of either 2 or 200 hens were housed at similar densities, and 1 or 4 hens were inoculated with Salmonella Enteritidis, respectively. Excretion was monitored by regularly testing of fecal samples for the presence of Salmonella Enteritidis. Using mathematical modeling, the group experiments were simulated with transmission parameter estimates from the pairwise experiments. Transmission of the bacteria did not differ significantly between pairs or groups. This finding suggests that the transmission parameter estimates from small-scale experiments might be extrapolated to the field situation.
Taxon ordering in phylogenetic trees: a workbench test
Authors: Cerutti Francesco , Bertolotti Luigi , Goldberg Tony L , Giacobini Mario 
Published: February 2011

Abstract

Background
Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + μ)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus.

Results
Best results were obtained when taxa were reordered using geographic information. Information supporting phylogeographic analysis was recovered in the optimized tree, as evidenced by clustering of geographically close samples. Improving the trees using a separate genetic distance matrix altered the ordering of taxa, but not topology, moving the longest branches to the extremities, as would be expected since they are the most divergent lineages. Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used.

Conclusions
Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.
In vivo role of different domains and of phosphorylation in the transcription factor Nkx2-1
Authors: Silberschmidt Daniel , Rodriguez-Mallon Alina , Mithboakar Prathiba , Calì Gaetano , Amendola Elena , Sanges Remo , Zannini Mariastella , Scarfò Marzia , De Luca Pasquale , Nitsch Lucio , Di Lauro Roberto , De Felice Mario 
Published: February 2011

Abstract

Background
The transcription factor Nkx2-1 (also known as TTF-1, Titf1 or T/EBP) contains two apparently redundant activation domains and is post-translationally modified by phosphorylation. We have generated mouse mutant strains to assess the roles of the two activation domains and of phosphorylation in mouse development and differentiation.

Results
Mouse strains expressing variants of the transcription factor Nkx2-1 deleted of either activation domain have been constructed. Phenotypic analysis shows for each mutant a distinct set of defects demonstrating that distinct portions of the protein endow diverse developmental functions of Nkx2-1. Furthermore, a mouse strain expressing a Nkx2-1 protein mutated in the phosphorylation sites shows a thyroid gland with deranged follicular organization and gene expression profile demonstrating the functional role of phosphorylation in Nkx2-1.

Conclusions
The pleiotropic functions of Nkx2-1 are not all due to the protein as a whole since some of them can be assigned to separate domains of the protein or to specific post-translational modifications. These results have implication for the evolutionary role of mutations in transcription factors.
An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research
Authors: Legeai Fabrice , Malpel Sébastien , Montagné Nicolas , Monsempes Christelle , Cousserans François , Merlin Christine , François Marie-Christine , Maïbèche-Coisné Martine , Gavory Frédérick , Poulain Julie , Jacquin-Joly Emmanuelle 
Published: February 2011

Abstract

Background
Nocturnal insects such as moths are ideal models to study the molecular bases of olfaction that they use, among examples, for the detection of mating partners and host plants. Knowing how an odour generates a neuronal signal in insect antennae is crucial for understanding the physiological bases of olfaction, and also could lead to the identification of original targets for the development of olfactory-based control strategies against herbivorous moth pests. Here, we describe an Expressed Sequence Tag (EST) project to characterize the antennal transcriptome of the noctuid pest model, Spodoptera littoralis, and to identify candidate genes involved in odour/pheromone detection.

Results
By targeting cDNAs from male antennae, we biased gene discovery towards genes potentially involved in male olfaction, including pheromone reception. A total of 20760 ESTs were obtained from a normalized library and were assembled in 9033 unigenes. 6530 were annotated based on BLAST analyses and gene prediction software identified 6738 ORFs. The unigenes were compared to the Bombyx mori proteome and to ESTs derived from Lepidoptera transcriptome projects. We identified a large number of candidate genes involved in odour and pheromone detection and turnover, including 31 candidate chemosensory receptor genes, but also genes potentially involved in olfactory modulation.

Conclusions
Our project has generated a large collection of antennal transcripts from a Lepidoptera. The normalization process, allowing enrichment in low abundant genes, proved to be particularly relevant to identify chemosensory receptors in a species for which no genomic data are available. Our results also suggest that olfactory modulation can take place at the level of the antennae itself. These EST resources will be invaluable for exploring the mechanisms of olfaction and pheromone detection in S. littoralis, and for ultimately identifying original targets to fight against moth herbivorous pests.
pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes
Authors: Martínez-García Esteban , Calles Belén , Arévalo-Rodríguez Miguel , de Lorenzo Víctor 
Published: February 2011

AbstractBackgroundSince publication in 1977 of plasmid pBR322, many breakthroughs in Biology have depended on increasingly sophisticated vector platforms for analysis and engineering of given bacterial strains. Although restriction sites impose a certain format in the procedures for assembling cloned genes, every attempt thus far to standardize vector architecture and nomenclature has ended up in failure. While this state of affairs may still be tolerable for traditional one-at-a-time studies of single genes, the onset of systems and synthetic biology calls for a simplification -along with an optimization- of the currently unwieldy pool of genetic tools.ResultsThe functional DNA sequences present in the natural bacterial transposon Tn5have been methodically edited and refactored for the production of a multi-purpose genetic tool named pBAM1, which allows a range of manipulations in the genome of Gram-negative bacteria. This all-synthetic construct enhances the power of mini-transposon vectors for either de-construction or re-construction of phenotypesá la carteby incorporating features inspired in systems engineering: modularity, re-usability, minimization, and compatibility with other genetic tools. pBAM1 bears an streamlined, restriction site-freed and narrow-host range replication frame bearing the sequences of R6KoriV,oriTand an ampicillin resistance marker. These go along with a business module that contains a host-independent and hyperactive transposition platform forin vivoorin vitroinsertion of desired DNA into the genome of the target bacterium. All functional sequences were standardized for a straightforward replacement by equivalent counterparts, if required. pBAM1 can be delivered into recipient cells by either mating or electroporation, producing transposon insertion frequencies of 1.8 × 10-3and 1.02 × 10-7, respectively in the soil bacteriumPseudomonas putida. Analyses of the resulting clones revealed a 100% of unique transposition events and virtually no-cointegration of the donor plasmid within the target genome.ConclusionsThis work reports the design and performance of an all-synthetic mini-transposon vector. The power of the new system for both identification of new functions or for the construction of desired phenotypes is shown in a genetic survey of hyper-expressed proteins and regulatory elements that influence the expression of the σ54-dependentPupromoter ofP. putida.
The pharmacokinetics of cefazolin in patients undergoing elective & semi-elective abdominal aortic aneurysm open repair surgery
Authors: Douglas Alexandra , Altukroni Mahdi , Udy Andrew A , Roberts Michael S , Taraporewalla Kersi , Jenkins Jason , Lipman Jeffrey , Roberts Jason A 
Published: February 2011

Abstract

Background
Surgical site infections are common, so effective antibiotic concentrations at the sites of infection are required. Surgery can lead to physiological changes influencing the pharmacokinetics of antibiotics. The aim of the study is to evaluate contemporary peri-operative prophylactic dosing of cefazolin by determining plasma and subcutaneous interstitial fluid concentrations in patients undergoing elective of semi-elective abdominal aortic aneurysm (AAA) open repair surgery.

Methods/Design
This is an observational pharmacokinetic study of patients undergoing AAA open repair surgery at the Royal Brisbane and Women's Hospital. All patients will be administered 2-g cefazolin by intravenous injection within 30-minutes of the procedure. Participants will have samples from blood and urine, collected at different intervals. Patients will also have a microdialysis catheter inserted into subcutaneous tissue to measure interstitial fluid penetration by cefazolin. Participants will be administered indocyanine green and sodium bromide as well as have cardiac output monitoring performed and tetrapolar bioimpedance to determine physiological changes occurring during surgery. Analysis of samples will be performed using validated liquid chromatography tandem mass-spectrometry. Pharmacokinetic analysis will be performed using non-linear mixed effects modeling to determine individual and population pharmacokinetic parameters and the effect of peri-operative physiological changes on cefazolin disposition.

Discussion
The study will describe cefazolin levels in plasma and the interstitial fluid of tissues during AAA open repair surgery. The effect of physiological changes to the patient mediated by surgery will also be determined. The results of this study will guide clinicians and pharmacists to effectively dose cefazolin in order to maximize the concentration of antibiotics in the tissues which are the most common site of surgical site infections.
A multidisciplinary systematic review of the use of diagrams as a means of collecting data from research subjects: application, benefits and recommendations
Authors: Umoquit Muriah J , Tso Peggy , Burchett Helen ED , Dobrow Mark J 
Published: February 2011

Abstract

Background
In research, diagrams are most commonly used in the analysis of data and visual presentation of results. However there has been a substantial growth in the use of diagrams in earlier stages of the research process to collect data. Despite this growth, guidance on this technique is often isolated within disciplines.

Methods
A multidisciplinary systematic review was performed, which included 13 traditional healthcare and non-health-focused indexes, non-indexed searches and contacting experts in the field. English-language articles that used diagrams as a data collection tool and reflected on the process were included in the review, with no restriction on publication date.

Results
The search identified 2690 documents, of which 80 were included in the final analysis. The choice to use diagrams for data collection is often determined by requirements of the research topic, such as the need to understand research subjects' knowledge or cognitive structure, to overcome cultural and linguistic differences, or to understand highly complex subject matter. How diagrams were used for data collection varied by the degrees of instruction for, and freedom in, diagram creation, the number of diagrams created or edited and the use of diagrams in conjunction with other data collection methods. Depending on how data collection is structured, a variety of options for qualitative and quantitative analysis are available to the researcher. The review identified a number of benefits to using diagrams in data collection, including the ease with which the method can be adapted to complement other data collection methods and its ability to focus discussion. However it is clear that the benefits and challenges of diagramming depend on the nature of its application and the type of diagrams used.

Discussion/Conclusion
The results of this multidisciplinary systematic review examine the application of diagrams in data collection and the methods for analyzing the unique datasets elicited. Three recommendations are presented. Firstly, the diagrammatic approach should be chosen based on the type of data needed. Secondly, appropriate instructions will depend on the approach chosen. And thirdly, the final results should present examples of original or recreated diagrams. This review also highlighted the need for a standardized terminology of the method and a supporting theoretical framework.
Phylogenetic and recombination analysis of human bocavirus 2
Authors: Cheng Weixia , Chen Jinan , Xu Ziqian , Yu Jiemei , Huang Canping , Jin Miao , Li Huiying , Zhang Ming , Jin Yu , Duan Zhao-jun 
Published: February 2011

Abstract

Background
Human bocavirus 2(HBoV2) and other human bocavirus species (HBoV, HBoV3, and HBoV4) have been discovered recently. But the precise phylogenetic relationships among these viruses are not clear yet.

Methods
We collected 632 diarrhea and 162 healthy children in Lanzhou, China. Using PCR, Human bocavirus (HBoV), HBoV2, HBoV3 and HBoV4 were screened. The partial genes of NS, NP1 and VP, and two nearly complete sequences of HBoV2 were obtained.

Result
Phylogenetic analysis showed the different genes of HBoV2 strain were homogenous with different reference strains. HBoV3 may be a recombinant derived from HBoV and HBoV4. We also observed that the VP1 and VP2 region of HBoV3 is as similar to HBoV2 as to HBoV4.

Conclusions
A single genetic lineage of HBoV2 is circulating in children with and without gastroenteritis in Lanzhou, China. Current evidence in this study was not enough to support recombination between HBoV2 strains, and HBoV3 may be a recombinant between HBoV and the common ancestor of HBoV2 and HBoV4.
Administration of a novel penicillamine-bound membrane: a preventive and therapeutic treatment for abdominal adhesions
Authors: Zhang Qiang-Ye , Ma Sheng , Xi Dong , Zhang Wen-Tong , Li Ai-Wu 
Published: February 2011

Abstract

Background
Adhesions formation is a significant postsurgical complication. At present, there is no effective method for preventing adhesions formation [1], although barrier products such as Dextran (Dex) [2] and sodium hyaluronate (SH) [3] have proved the most clinically successful [4–6], This study is designed to investigate the preventive and therapeutic potential of a novel penicillamine-bound membrane for abdominal adhesions formation.

Methods
150 rats were involved in the present study. All animals were randomly divided into 6 groups (1 vehicle group and 5 test groups respectively treated with dextran, sodium hyaluronate, penicillamine, penicillamine-bound membrane or non-penicillamine-bound membrane). The occurrence, grade and score of abdominal adhesions were compared between the different groups. The breaking strength of incision was compared between the vehicle group and the penicillamine, membrane with/without penicillamine - treated groups. Expression of collagen type I was compared between the vehicle and penicillamine-treated group. The occurrence of adhesions was compared between the Dextran (Dex), sodium hyaluronate (SH), penicillamine-treated group and membrane with or without penicillamine- treated groups.

Results
Penicillamine and penicillamine-bound membrane had significant preventive effects on abdominal adhesions formation, better than dextran, sodium hyaluronate and non-penicillamine-bound membrane. However, neither of them influenced incision healing, although they insignificantly decreased the breaking strength of the incision. Penicillamine-bound membrane, which can be loaded locally and more efficaciously, shows greater advantages than penicillamine.

Conclusions
Penicillamine-bound membrane can be applied as an effective therapeutic intervention for abdominal adhesions with inconsequential side effects.
Development and applicability of Hospital Survey on Patient Safety Culture (HSOPS) in Japan
Authors: Ito Shinya , Seto Kanako , Kigawa Mika , Fujita Shigeru , Hasegawa Toshihiko , Hasegawa Tomonori 
Published: February 2011

Abstract

Background
Patient safety culture at healthcare organizations plays an important role in guaranteeing, improving and promoting overall patient safety. Although several conceptual frameworks have been proposed in the past, no standard measurement tool has yet been developed for Japan.

Methods
In order to examine possibilities to introduce the Hospital Survey on Patient Safety Culture (HSOPS) in Japan, the authors of this study translated the HSOPS into Japanese, and evaluated its factor structure, internal consistency, and construct validity. Healthcare workers (n = 6,395) from 13 acute care general hospitals in Japan participated in this survey.

Results
Confirmatory factor analysis indicated that the Japanese HSOPS' 12-factor model was selected as the most pertinent, and showed a sufficiently high standard partial regression coefficient. The internal reliability of the subscale scores was 0.46-0.88. The construct validity of each safety culture sub-dimension was confirmed by polychoric correlation, and by an ordered probit analysis.

Conclusions
The results of the present study indicate that the factor structures of the Japanese and the American HSOPS are almost identical, and that the Japanese HSOPS has acceptable levels of internal reliability and construct validity. This shows that the HSOPS can be introduced in Japan.
Atomic force microscopy investigation of the kinetic growth mechanisms of sputtered nanostructured Au film on mica: towards a nanoscale morphology control
Authors: Ruffino Francesco , Torrisi Vanna , Marletta Giovanni , Grimaldi Maria Grazia 
Published: February 2011

AbstractThe study of surface morphology of Au deposited on mica is crucial for the fabrication of flat Au films for applications in biological, electronic, and optical devices. The understanding of the growth mechanisms of Au on mica allows to tune the process parameters to obtain ultra-flat film as suitable platform for anchoring self-assembling monolayers, molecules, nanotubes, and nanoparticles. Furthermore, atomically flat Au substrates are ideal for imaging adsorbate layers using scanning probe microscopy techniques. The control of these mechanisms is a prerequisite for control of the film nano- and micro-structure to obtain materials with desired morphological properties. We report on an atomic force microscopy (AFM) study of the morphology evolution of Au film deposited on mica by room-temperature sputtering as a function of subsequent annealing processes. Starting from an Au continuous film on the mica substrate, the AFM technique allowed us to observe nucleation and growth of Au clusters when annealing process is performed in the 573-773 K temperature range and 900-3600 s time range. The evolution of the clusters size was quantified allowing us to evaluate the growth exponent 〈z〉 = 1.88 ± 0.06. Furthermore, we observed that the late stage of cluster growth is accompanied by the formation of circular depletion zones around the largest clusters. From the quantification of the evolution of the size of these zones, the Au surface diffusion coefficient was evaluated inD(T)=[(7.42×10−13)±(5.94×10−14)m2/s]exp(−(0.33±0.04)eVkT). These quantitative data and their correlation with existing theoretical models elucidate the kinetic growth mechanisms of the sputtered Au on mica. As a consequence we acquired a methodology to control the morphological characteristics of the Au film simply controlling the annealing temperature and time.
MUC4gene polymorphisms associate with endometriosis development and endometriosis-related infertility
Authors: Chang Cherry Yin-Yi , Chang Hui-Wen , Chen Chih-Mei , Lin Chia-Ying , Chen Chih-Ping , Lai Chih-Ho , Lin Wei-Yong , Liu Hsing-Ping , Sheu Jim Jinn-Chyuan , Tsai Fuu-Jen 
Published: February 2011

Abstract

Background
Mucin 4 (MUC4) plays an important role in protecting and lubricating the epithelial surface of reproductive tracts, but its role in the pathogenesis of endometriosis is largely unknown.

Methods
To correlate MUC4 polymorphism with the risk of endometriosis and endometriosis-related infertility, we performed a case-control study of 140 patients and 150 healthy women. Six unique single-nucleotide polymorphisms (SNPs) (rs882605, rs1104760, rs2688513, rs2246901, rs2258447 and rs2291652) were selected for this study. DNA fragments containing the target SNP sites were amplified by polymerase chain reaction using the TaqMan SNP Genotyping Assay System to evaluate allele frequency and distribution of genotype in MUC4 polymorphisms.

Results
Both the T/G genotype of rs882605 and the frequency of haplotype T-T (rs882605 and rs1104760) were higher in patients than in controls and were statistically significant. The frequency of the C allele at rs1104760, the C allele at rs2688513, the G allele at rs2246901 and the A allele at rs2258447 were associated with advanced stage of endometriosis. Moreover, the G allele at rs882605 was verified as a key genetic factor for infertility in patients. Protein sequence analysis indicated that amino acid substitutions by genetic variations at rs882605, rs2688513 and rs2246901 occur in the putative functional loops and the type D von Willebrand factor (VWFD) domain in the MUC4 sequence.

Conclusions

MUC4 polymorphisms are associated with endometriosis development and endometriosis-related infertility in the Taiwanese population.