bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hospital Discharge Bags and Breastfeeding at 6 Months
Authors: Sadacharan Radha , Grossman Xena , Matlak Stephanie , Merewood Anne 
Published: December 2013

Background: Distribution of industry-sponsored formula sample packs to new mothers undermines breastfeeding. Objective: Using data from the Infant Feeding Practices Study II (IFPS II), we aimed to determine whether receipt of 4 different types of bags was associated with exclusive breastfeeding during the first 6 months of life. Methods: We extracted data from IFPS II questionnaires. Type of discharge bag received was categorized as “formula bag,” “coupon bag,” “breastfeeding supplies bag,” or “no bag”. We examined exclusive breastfeeding status at 10 weeks (post hoc) and at 6 months using univariate descriptive analyses and multivariate logistic regression models, controlling for sociodemographic and attitudinal variables. Results: Overall, 1868 (81.4%) of women received formula bags, 96 (4.2%) received coupon bags, 46 (2.0%) received breastfeeding supplies bags, and 284 (12.4%) received no bag. By 10 weeks, recipients of breastfeeding supplies bags or no bag were significantly more likely to be exclusively breastfeeding than formula bag recipients. In the adjusted model, compared to formula bag/coupon bag recipients, recipients of breastfeeding supplies bag/no bag were significantly more likely to breastfeed exclusively for 6 months (odds ratio = 1.58; 95% confidence interval, 1.06-2.36). Conclusion: The vast majority of new mothers received formula sample packs at discharge, and this was associated with reduced exclusive breastfeeding at 10 weeks and 6 months. Bags containing breastfeeding supplies or no bag at all were positively associated with exclusive breastfeeding at 10 weeks and 6 months.
Changing trends in antibiotic resistance for urinary E. coli infections over five years in a university hospital
Authors: Teoh Penelope , Basarab Adriana , Pickering Ruth , Ali Ahmed , Hayes Matthew , Somani Bhaskar K 
Published: December 2013

Objective We wanted to look at the antibiotic resistance patterns in our university teaching hospital for E. coli cultured from urine to assess the resistance profiles to common antibiotics used in the hospital. Patients and methods Results were obtained of all positive urine cultures between January 2007 and December 2011 both from the hospital and urology department. Trends in susceptibility and resistance data for E. coli to trimethoprim, amoxicillin, ciprofloxacin, gentamicin and nitrofurantoin were examined. Results A total of 40,722 hospital urine specimens were culture positive in the five-year period, of which 15,311 (37.6%) grew E. coli. Across the hospital there was no evidence of change in resistance to trimethoprim over the five-year period (38.1% in 2007 compared to 36.6% in 2011; p = 0.313). The percentage resistance to amoxicillin rose slightly (52.6% to 54.4%), and this was statistically significant (p = 0.011). Overall there was a statistically significant fall in resistance to ciprofloxacin but resistance has remained stable for the last three years (15.5% to 13.5%, p = 0.013). A trend of increasing resistance to gentamicin (p = 0.002) resulted from the 2007 baseline of 3.4% to 4.9% in 2008, but resistance remained stably low thereafter. Resistance to nitrofurantoin fell significantly (from 10.4% to 1.6%; p ≤ 0.0005). Conclusions The number of E. coli-positive urine cultures from hospital in-patients remained broadly stable over this five-year period. Resistance to trimethoprim and amoxicillin remains high. Gentamicin resistance remains low, but the statistically significant rise over the five-year period suggests resistance rates should continue to be carefully monitored. Nitrofurantoin resistance is very low and has significantly decreased. This narrow-spectrum antibiotic should be considered the mainstay for treating uncomplicated urinary tract infections in females.
The Immediate Effect of Lateral Wedge Insoles, With and Without a Subtalar Strap, on the Lateral Trunk Lean Motion in Patients With Knee Osteoarthritis
Authors: Esfandiari Elham , Kamyab Mojtaba , Yazdi Hamid Reza , Foroughi Nasim , Sanjari Mohammad Ali 
Published: December 2013

Background: Orthotic interventions for knee osteoarthritis (OA) aim to reduce mechanical loading on the medial compartment of the knee and may lessen the lateral trunk lean as the most important compensatory gait strategy. The lateral wedge insole is a known orthotic intervention for knee OA. However, the question whether the addition of a subtalar strap to the wedge improves its effect has not been addressed in the literature. Objective: To compare the effects of lateral wedge insoles, with and without a subtalar strap, on the lateral trunk lean in patients with knee OA. Methods: Twenty-three patients aged over 40 years, with grade I or II OA of the medial compartment of one knee, based on the American College of Rheumatology criteria, were included in this study. The patients were diagnosed with OA based on a clinical examination, and the diagnosis was confirmed with radiographs. A 3-dimensional motion measurement system was used to collect the gait data for 3 different conditions: (1) with no insole, (2) with a lateral wedge insole, and (3) with a lateral wedge insole and a subtalar strap. The immediate effect of the 3 test conditions on the lateral trunk lean was compared during a gait cycle a stance phase and at the point of midstance. Results: Based on the laboratory coordinate system, the 3 conditions had no significant effect on the lateral trunk lean during a gait cycle and a stance phase and at the point of midstance in patients with knee OA. Conclusion: The results of this study demonstrated that the lateral wedge insoles, with and without a subtalar strap, had no immediate effect on the lateral trunk lean in patients with knee OA. However, the long-term effect of lateral wedge insoles on the lateral trunk lean in these patients requires further investigation.
Early response with dasatinib or imatinib in chronic myeloid leukemia: 3-year follow-up from a randomized phase 3 trial (DASISION)
Authors: Jabbour Elias , Kantarjian Hagop M. , Saglio Giuseppe , Steegmann Juan Luis , Shah Neil P. , Boqué Concepción , Chuah Charles , Pavlovsky Carolina , Mayer Jiří , Cortes Jorge , Baccarani Michele , Kim Dong-Wook , Bradley-Garelik M. Brigid , Mohamed Hesham , Wildgust Mark , Hochhaus Andreas 
Published: December 2013

Key Points
In a 3-year follow-up of the DASatinib versus Imatinib Study In treatment-Naive CML patients trial, first-line dasatinib resulted in faster and deeper responses compared with imatinib. Deeper responses at 3, 6, and 12 months were associated with better 3-year progression-free survival and overall survival.
Pyroptosis and adaptive immunity mechanisms are promptly engendered in mesenteric lymph-nodes during pig infections with Salmonella enterica serovar Typhimurium
Authors: Martins Rodrigo Prado , Aguilar Carmen , Graham James E , Carvajal Ana , Bautista Rocío , Claros M Gonzalo , Garrido Juan J 
Published: December 2013

Abstract
In this study, we explored the transcriptional response and the morphological changes occurring in porcine mesenteric lymph-nodes (MLN) along a time course of 1, 2 and 6 days post infection (dpi) with Salmonella Typhimurium. Additionally, we analysed the expression of some Salmonella effectors in tissue to complete our view of the processes triggered in these organs upon infection. The results indicate that besides dampening apoptosis, swine take advantage of the flagellin and prgJ expression by Salmonella Typhimuriun to induce pyroptosis in MLN, preventing bacterial dissemination. Furthermore, cross-presentation of Salmonella antigens was inferred as a mechanism that results in a rapid clearance of pathogen by cytotoxic T cells. In summary, although the Salmonella Typhimurium strain employed in this study was able to express some of its major virulence effectors in porcine MLN, a combination of early innate and adaptive immunity mechanisms might overcome virulence strategies employed by the pathogen, enabling the host to protect itself against bacterial spread beyond gut-associated lymph-nodes. Interestingly, we deduced that clathrin-mediated endocytosis could contribute to mechanisms of pathogen virulence and/or host defence in MLN of Salmonella infected swine. Taken together, our results are useful for a better understanding of the critical protective mechanisms against Salmonella that occur in porcine MLN to prevent the spread of infection beyond the intestine.
Soybean peroxidase-mediated degradation of an azo dye– a detailed mechanistic study
Authors: Ali Liaquat , Algaithi Rowdha , Habib Hosam M , Souka Usama , Rauf Muhammad A , Ashraf S Salman 
Published: December 2013

Abstract

Background
Peroxidases are emerging as an important class of enzymes that can be used for the efficient degradation of organic pollutants. However, detailed studies identifying the various intermediates produced and the mechanisms involved in the enzyme-mediated pollutant degradation are not widely published.

Results
In the present study, the enzymatic degradation of an azo dye (Crystal Ponceau 6R, CP6R) was studied using commercially available soybean peroxidase (SBP) enzyme. Several operational parameters affecting the enzymatic degradation of dye were evaluated and optimized, such as initial dye concentration, H2O2 dosage, mediator amount and pH of the solution. Under optimized conditions, 40 ppm dye solution could be completely degraded in under one minute by SBP in the presence of H2O2 and a redox mediator. Dye degradation was also confirmed using HPLC and TOC analyses, which showed that most of the dye was being mineralized to CO2 in the process.

Conclusions
Detailed analysis of metabolites, based on LC/MS results, showed that the enzyme-based degradation of the CP6R dye proceeded in two different reaction pathways- via symmetric azo bond cleavage as well as asymmetric azo bond breakage in the dye molecule. In addition, various critical transformative and oxidative steps such as deamination, desulfonation, keto-oxidation are explained on an electronic level. Furthermore, LC/MS/MS analyses confirmed that the end products in both pathways were small chain aliphatic carboxylic acids.
Differential marker expression by cultures rich in mesenchymal stem cells
Authors: Wetzig Andrew , Alaiya Ayodele , Al-Alwan Monther , Pradez Christian Benedict , Pulicat Manogaran S , Al-Mazrou Amer , Shinwari Zakia , Sleiman Ghida Majed , Ghebeh Hazem , Al-Humaidan Hind , Gaafar Ameera , Kanaan Imaduddin , Adra Chaker 
Published: December 2013

AbstractBackgroundMesenchymal stem cells have properties that make them amenable to therapeutic use. However, the acceptance of mesenchymal stem cells in clinical practice requires standardized techniques for their specific isolation. To date, there are no conclusive marker (s) for the exclusive isolation of mesenchymal stem cells. Our aim was to identify markers differentially expressed between mesenchymal stem cell and non-stem cell mesenchymal cell cultures. We compared and contrasted the phenotype of tissue cultures in which mesenchymal stem cells are rich and rare. By initially assessing mesenchymal stem cell differentiation, we established that bone marrow and breast adipose cultures are rich in mesenchymal stem cells while, in our hands, foreskin fibroblast and olfactory tissue cultures contain rare mesenchymal stem cells. In particular, olfactory tissue cells represent non-stem cell mesenchymal cells. Subsequently, the phenotype of the tissue cultures were thoroughly assessed using immuno-fluorescence, flow-cytometry, proteomics, antibody arrays and qPCR.ResultsOur analysis revealed that all tissue cultures, regardless of differentiation potential, demonstrated remarkably similar phenotypes. Importantly, it was also observed that common mesenchymal stem cell markers, and fibroblast-associated markers, do not discriminate between mesenchymal stem cell and non-stem cell mesenchymal cell cultures. Examination and comparison of the phenotypes of mesenchymal stem cell and non-stem cell mesenchymal cell cultures revealed three differentially expressed markers – CD24, CD108 and CD40.ConclusionWe indicate the importance of establishing differential marker expression between mesenchymal stem cells and non-stem cell mesenchymal cells in order to determine stem cell specific markers.
The precise timeline of transcriptional regulation reveals causation in mouse somitogenesis network
Authors: Fongang Bernard , Kudlicki Andrzej 
Published: December 2013

AbstractBackgroundIn vertebrate development, the segmental pattern of the body axis is established as somites, masses of mesoderm distributed along the two sides of the neural tube, are formed sequentially in the anterior-posterior axis. This mechanism depends on waves of gene expression associated with the Notch, Fgf and Wnt pathways. The underlying transcriptional regulation has been studied by whole-transcriptome mRNA profiling; however, interpretation of the results is limited by poor resolution, noisy data, small sample size and by the absence of a wall clock to assign exact time for recorded points.ResultsWe present a method of Maximum Entropy deconvolution in both space and time and apply it to extract, from microarray timecourse data, the full spatiotemporal expression profiles of genes involved in mouse somitogenesis. For regulated genes, we have reconstructed the temporal profiles and determined the timing of expression peaks along the somite cycle to a single-minute resolution. Our results also indicate the presence of a new class of genes (including Raf1 and Hes7) with two peaks of activity in two distinct phases of the somite cycle. We demonstrate that the timeline of gene expression precisely reflects their functions in the biochemical pathways and the direction of causation in the regulatory networks.ConclusionsBy applying a novel framework for data analysis, we have shown a striking correspondence between gene expression times and their interactions and regulations during somitogenesis. These results prove the key role of finely tuned transcriptional regulation in the process. The presented method can be readily applied to studying somite formation in other datasets and species, and to other spatiotemporal processes.
Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes
Authors: Colasuonno Pasqualina , Maria Mastrangelo Anna , Blanco Antonio , Gadaleta Agata 
Published: December 2013

AbstractBackgroundThe importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome.ResultsHere we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such asBrachypodiumand rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice andBrachypodiumspecies, respectively.ConclusionsIn the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing.
Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle
Authors: Scully Erin D , Hoover Kelli , Carlson John E , Tien Ming , Geib Scott M 
Published: December 2013

AbstractBackgroundWood-feeding insects often work in collaboration with microbial symbionts to degrade lignin biopolymers and release glucose and other fermentable sugars from recalcitrant plant cell wall carbohydrates, including cellulose and hemicellulose. Here, we present the midgut transcriptome of larvalAnoplophora glabripennis, a wood-boring beetle with documented lignin-, cellulose-, and hemicellulose- degrading capabilities, which provides valuable insights into how this insect overcomes challenges associated with feeding in woody tissue.ResultsTranscripts from putative protein coding regions of over 9,000 insect-derived genes were identified in theA. glabripennismidgut transcriptome using a combination of 454 shotgun and Illumina paired-end reads. The most highly-expressed genes predicted to encode digestive-related enzymes were trypsins, carboxylesterases, β-glucosidases, and cytochrome P450s. Furthermore, 180 unigenes predicted to encode glycoside hydrolases (GHs) were identified and included several GH 5, 45, and 48 cellulases, GH 1 xylanases, and GH 1 β-glucosidases. In addition, transcripts predicted to encode enzymes involved in detoxification were detected, including a substantial number of unigenes classified as cytochrome P450s (CYP6B) and carboxylesterases, which are hypothesized to play pivotal roles in detoxifying host tree defensive chemicals and could make important contributions toA. glabripennis’expansive host range. While a large diversity of insect-derived transcripts predicted to encode digestive and detoxification enzymes were detected, few transcripts predicted to encode enzymes required for lignin degradation or synthesis of essential nutrients were identified, suggesting that collaboration with microbial enzymes may be required for survival in woody tissue.ConclusionsA. glabripennisproduces a number of enzymes with putative roles in cell wall digestion, detoxification, and nutrient extraction, which likely contribute to its ability to thrive in a broad range of host trees. This system is quite different from the previously characterized termite fermentation system and provides new opportunities to discover enzymes that could be exploited for cellulosic ethanol biofuel production or the development of novel methods to control wood-boring pests.
Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense
Authors: Li Chunqiang , Shao Jiaofang , Wang Yejun , Li Wenbin , Guo Dianjing , Yan Bin , Xia Yiji , Peng Ming 
Published: December 2013

AbstractBackgroundCavendish, the most widely grown banana cultivar, is relatively resistant to Race 1 ofFusarium oxysporumf. sp.cubense(Foc1) which caused widespread Panama disease during the first half of the 20thcentury but is susceptible to Tropical Race 4 of Foc (Foc TR4) which is threatening world banana production. The genome of the diploid speciesMusa acuminatawhich is the ancestor of a majority of triploid banana cultivars has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and for biological research. The knowledge of global gene expression patterns influenced by infection of different Foc races will help to understand the host responses to the infection.ResultsRNA samples from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina technology. Analysis of the banana transcriptome led to identification of over 842 genes that were not annotated by theMusagenome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc TR4 were used to monitor the infection process. Both Foc1 and Foc TR4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. Digital gene expression (DGE) profiling analysis reveal that the infection by Foc1 and Foc TR4 caused very similar changes in the global gene expression profiles in the banana roots during the first two days of infection. The Foc infection led to induction of many well-known defense-related genes. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors (ERF) were among the strongly induced genes by both Foc1 and Foc TR4.ConclusionsBoth Foc1 and Foc TR4 are able to spread into the vascular system of banana roots during the early infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection.
Reprogramming of lysosomal gene expression by interleukin-4 and Stat6
Authors: Brignull Louise M , Czimmerer Zsolt , Saidi Hafida , Daniel Bence , Villela Izabel , Bartlett Nathan W , Johnston Sebastian L , Meira Lisiane B , Nagy Laszlo , Nohturfft Axel 
Published: December 2013

AbstractBackgroundLysosomes play important roles in multiple aspects of physiology, but the problem of how the transcription of lysosomal genes is coordinated remains incompletely understood. The goal of this study was to illuminate the physiological contexts in which lysosomal genes are coordinately regulated and to identify transcription factors involved in this control.ResultsAs transcription factors and their target genes are often co-regulated, we performed meta-analyses of array-based expression data to identify regulators whose mRNA profiles are highly correlated with those of a core set of lysosomal genes. Among the ~50 transcription factors that rank highest by this measure, 65% are involved in differentiation or development, and 22% have been implicated in interferon signaling. The most strongly correlated candidate was Stat6, a factor commonly activated by interleukin-4 (IL-4) or IL-13. Publicly available chromatin immunoprecipitation (ChIP) data from alternatively activated mouse macrophages show that lysosomal genes are overrepresented among Stat6-bound targets. Quantification of RNA from wild-type and Stat6-deficient cells indicates that Stat6 promotes the expression of over 100 lysosomal genes, including hydrolases, subunits of the vacuolar H+ATPase and trafficking factors. While IL-4 inhibits and activates different sets of lysosomal genes, Stat6 mediates only the activating effects of IL-4, by promoting increased expression and by neutralizing undefined inhibitory signals induced by IL-4.ConclusionsThe current data establish Stat6 as a broadly acting regulator of lysosomal gene expression in mouse macrophages. Other regulators whose expression correlates with lysosomal genes suggest that lysosome function is frequently re-programmed during differentiation, development and interferon signaling.