bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards the creation of a flexible classification scheme for voluntarily reported transfusion and laboratory safety events
Authors: Whitehurst Julie M , Schroder John , Leonard Dave , Horvath Monica M , Cozart Heidi , Ferranti Jeffrey 
Published: May 2012

Abstract

Background
Transfusion and clinical laboratory services are high-volume activities involving complicated workflows across both ambulatory and inpatient environments. As a result, there are many opportunities for safety lapses, leading to patient harm and increased costs. Organizational techniques such as voluntary safety event reporting are commonly used to identify and prioritize risk areas across care settings. Creation of functional, standardized safety data structures that facilitate effective exploratory examination is therefore essential to drive quality improvement interventions. Unfortunately, voluntarily reported adverse event data can often be unstructured or ambiguously defined.

Results
To address this problem, we sought to create a “best-of-breed” patient safety classification for data contained in the Duke University Health System Safety Reporting System (SRS). Our approach was to implement the internationally recognized World Health Organization International Classification for Patient Safety Framework, supplemented with additional data points relevant to our organization. Data selection and integration into the hierarchical framework is discussed, as well as placement of the classification into the SRS. We evaluated the impact of the new SRS classification on system usage through comparisons of monthly average report rates and completion times before and after implementation. Monthly average inpatient transfusion reports decreased from 102.1 ± 14.3 to 91.6 ± 11.2, with the proportion of transfusion reports in our system remaining consistent before and after implementation. Monthly average transfusion report rates in the outpatient and homecare environments were not significantly different. Significant increases in clinical lab report rates were present across inpatient and outpatient environments, with the proportion of lab reports increasing after implementation. Report completion times increased modestly but not significantly from a practical standpoint.

Conclusions
A common safety vocabulary can facilitate integration of information from disparate systems and processes to permit meaningful measurement and interpretation of data to improve safety within and across organizations. Formation of a “best-of-breed” classification for voluntary reporting necessitates an internal examination of localized data needs and workflow in order to design a product that enables comprehensive data capture. A team of clinical, safety, and information technology experts is necessary to integrate the data structures into the reporting system. We have found that a “best-of-breed” patient safety classification provides a solid, extensible model for adverse event analysis, healthcare leader communication, and intervention identification.
Mangrove plant, Rhizophora mucronata (Lamk, 1804) mediated one pot green synthesis of silver nanoparticles and its antibacterial activity against aquatic pathogens
Authors: Umashankari Jaganathan , Inbakandan Dhinakarasamy , Ajithkumar Thipramalai T , Balasubramanian Thangavel 
Published: May 2012

Abstract

Background
Biosynthesis of nanoparticles has received increasing attention due to the growing need to develop safe, time-effective and environmentally friendly technologies for nano-materials synthesis. This paper reports the one pot green synthesis of silver nanoparticles (AgNPs) using the leaf bud extract of a mangrove plant, Rhizophora mucronata and their antimicrobial effects against aquatic pathogens. Highly stable AgNPs were synthesized by treating the mangrove leaf bud extract with aqueous silver nitrate solution at 15 psi pressure and 121°C for 5 minutes.

Results
The biosynthesized AgNPs were characterized by UV-visible spectrum, at 426 nm. The X-Ray Diffraction (XRD) pattern revealed the face-centered cubic geometry of AgNPs. Fourier Transform Infra Red (FTIR) spectroscopic analysis was carried out to identify the possible biomolecules responsible for biosynthesis of AgNPs from the leaf bud extract. The size and shape of the well-dispersed AgNPs were documented with the help of High Resolution Transmission Electron Microscopy (HRTEM) with a diameter ranged from 4 to 26 nm. However a maximum number of particles were observed at 4 nm in size. The antibacterial effects of AgNPs were studied against aquatic pathogens Proteus spp., Pseudomonas fluorescens and Flavobacterium spp., isolated from infected marine ornamental fish, Dascyllus trimaculatus.

Conclusion
This study reveals that the biosynthesized AgNPs using the leaf bud extract of a mangrove plant (R. mucronata) were found equally potent to synthetic antibiotics. The size of the inhibition zone increases when the concentration of the AgNPs increased and varies according to species.
Ten-year decrease of acquired methicillin-resistant Staphylococcus aureus (MRSA) bacteremia at a single institution: the result of a multifaceted program combining cross-transmission prevention and antimicrobial stewardship
Authors: Chalfine Annie , Kitzis Marie-Dominique , Bezie Yvonnick , Benali Adel , Perniceni Laurence , Nguyen Jean-Claude , Dumay Marie Françoise , Gonot Jacqueline , Rejasse Gilles , Goldstein Fred , Carlet Jean , Misset Benoît 
Published: May 2012

Abstract

Background
In France, the proportion of MRSA has been over 25% since 2000. Prevention of hospital-acquired (HA) MRSA spread is based on isolation precautions and antibiotic stewardship. At our institution, before 2000, the Infection Disease and the Infection Control teams had failed to reduce HA-MRSA rates.

Objectives and methods
We implemented a multifaceted hospital-wide prevention program and measured the effects on HA-MRSA colonization and bacteremia rates between 2000 and 2009. From 2000 to 2003, active screening and decontamination of ICU patients, hospital wide alcohol based hand rubs (ABHR) use, control of specific classes of antibiotics, compliance audits, and feed-backs to the care providers were successively implemented. The efficacy of the program was assessed by HA-MRSA colonized and bacteremic patient rates per 1000 patient-days in patients hospitalized for more than twenty-four hours.

Results
Compliance with the isolation practices increased between 2000 and 2009. Consumption of ABHR increased from 6.8 L to 27.5 L per 1000 patient-days. The use of antibiotic Defined Daily Doses (DDD) per 1000 patient-days decreased by 31%. HA-MRSA colonization decreased by 84% from 1.09 to 0.17 per 1000 patient-days and HA-MRSA bacteremia by 93%, from 0.15 to 0.01 per 1000 patient-days (p < 10−7 for each rate).

Conclusions
In an area highly endemic for MRSA, a multifaceted prevention program allows for sustainable reduction in HA-MRSA bacteremia rates.
Preclinical and clinical studies of estrogen deprivation support the PDGF/Abl pathway as a novel therapeutic target for overcoming endocrine resistance in breast cancer
Authors: Weigel Marion T , Ghazoui Zara , Dunbier Anita , Pancholi Sunil , Dowsett Mitch , Martin Lesley-Ann 
Published: May 2012

Abstract
Introduction
The majority of breast tumors at primary diagnosis are estrogen receptor positive (ER+). Estrogen (E) mediates its effects by binding to the ER. Therapies targeting the estrogenic stimulation of tumor growth reduce mortality from ER+ breast cancer. However, resistance remains a major clinical problem.

Methods
To identify molecular mechanisms associated with resistance to E-deprivation, we assessed the temporal changes in global gene expression during adaptation to long-term culture of MCF7 human breast cancer cells in the absence of estradiol (E2), long term estrogen deprived (LTED), that leads to recovery of proliferative status and models resistance to an aromatase inhibitor (AI). The expression levels of proteins were determined by western blotting. Proliferation assays were carried out using the dual platelet derived growth factor receptor (PDGFR)/Abelson tyrosine kinase (Abl) inhibitor nilotinib. Luciferase reporter assays were used to determine effects on ER-mediated transactivation. Changes in recruitment of cofactors to the gene regulated by estrogen in breast cancer 1 (GREB1) promoter were determined by chromatin immunoprecipitation (ChIP). Gene expression data were derived from 81 postmenopausal women with ER+ BC pre-treatment and at two-weeks post-treatment with single agent anastrozole in a neoadjuvant trial.

Results
The PDGF/Abl canonical pathway was significantly elevated as early as one week post E-deprivation (P = 1.94 E-04) and this became the top adaptive pathway at the point of proliferative recovery (P = 1.15 E-07). Both PDGFRβ and Abl protein levels were elevated in the LTED cells compared to wild type (wt)-MCF7 cells. The PDGF/Abl tyrosine kinase inhibitor nilotinib, suppressed proliferation in LTED cells in the presence or absence of E. Nilotinib also suppressed ER-mediated transcription by destabilizing the ER and reducing recruitment of amplified in breast cancer-1 (AIB1) and the CREB binding protein (CBP) to the promoter of the E-responsive gene GREB1. High PDGFRβ in primary ER+ breast cancer of 81 patients prior to neoadjuvant treatment with an AI was associated with poorer antiproliferative response. Additionally PDGFRβ expression increased after two weeks of AI therapy (1.25 fold, P = 0.003).

Conclusions
These preclinical and clinical data indicate that the PDGF/Abl signaling pathway merits clinical evaluation as a therapeutic target with endocrine therapy in ER+ breast cancer.
Combining intermediate levels of the Endotoxin Activity Assay (EAA) with other biomarkers in the assessment of patients with sepsis: results of an observational study
Authors: Yaguchi Arino , Yuzawa Junji , Klein David J , Takeda Munekasu , Harada Tomoyuki 
Published: May 2012

Abstract
Introduction
The Endotoxin Activity Assay (EAA) is a useful test to risk stratify patients with severe sepsis and assess for Gram negative infection. However, the significance of intermediate levels of EAA (0.4-0.59) at the bedside has not been well elucidated. The purpose of this study was to interpret intermediate EAA levels in clinical practice.

Methods
This retrospective observational study included all adult patients with suspected sepsis admitted to our medico-surgical intensive care unit (ICU) in whom EAA was measured from July 2008 to September 2011. Data collected included EAA, white blood cell (WBC) count and differential, C-reactive protein (CRP), procalcitonin (PCT) and bacterial cultures. Data were analyzed by comparative statistics.

Results
Two hundred and ten patients were studied. Ninety two (43%) patients had culture documented gram negative infection. Patients with Gram-negative organisms in cultures had significantly higher EAA levels (0.47, IQR 0.27) than those without any Gram-negative organisms in cultures (0.34, IQR 0.22) (p < 0.0001). For patients with intermediate EAA levels (0.40 to 0.59), PCT levels and presence of left shift of WBC significantly differed between patients with Gram negative organisms in their blood or other cultures and those who had no organisms in any of the cultures (4.9 versus 1.7 ng/mL, p < 0.05; 57.9 versus 18.9%, p < 0.0004, respectively).

Conclusions
We confirm that high levels of EAA in our cohort of patients with suspected sepsis are strongly associated with gram negative infection. In those patients with intermediate elevation in EAA levels, use of PCT and WBC differential can provide additional diagnostic value to clinicians at the bedside.
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
Authors: Varadarajan Avinash , Bradley Robert K , Holmes Ian H 
Published: May 2012

AbstractControlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools.
Selective maintenance of Drosophilatandemly arranged duplicated genes during evolution
Authors: Quijano Carlos , Tomancak Pavel , Lopez-Marti Jesus , Suyama Mikita , Bork Peer , Milan Marco , Torrents David , Manzanares Miguel 
Published: May 2012

Abstract
Background
The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the genome by random shuffling of DNA segments. Higher order structuring of the genome occurs in eukaryotes, where groups of physically linked genes are co-expressed. However, the contribution of gene duplication to gene order has not been analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression.

Results
We have catalogued ordered duplicated genes in Drosophila melanogaster, and found that one in five of all genes is organized as tandem arrays. Furthermore, among arrays that have been spatially conserved over longer periods than would be expected on the basis of random shuffling, a disproportionate number contain genes encoding developmental regulators. Using in situ gene expression data for more than half of the Drosophila genome, we find that genes in these conserved clusters are co-expressed to a much higher extent than other duplicated genes.

Conclusions
These results reveal the existence of functional constraints in insects that retain copies of genes encoding developmental and regulatory proteins as neighbors, allowing their co-expression. This co-expression may be the result of shared cis-regulatory elements or a shared need for a specific chromatin structure. Our results highlight the association between genome architecture and the gene regulatory networks involved in the construction of the body plan.
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication
Authors: Cardone Maria Francesca , Jiang Zhaoshi , D'Addabbo Pietro , Archidiacono Nicoletta , Rocchi Mariano , Eichler Evan E , Ventura Mario 
Published: May 2012

Abstract
Background
Chromosomal rearrangements, such as translocations and inversions, are recurrent phenomena during evolution, and both of them are involved in reproductive isolation and speciation. To better understand the molecular basis of chromosome rearrangements and their part in karyotype evolution, we have investigated the history of human chromosome 17 by comparative fluorescence in situ hybridization (FISH) and sequence analysis.

Results
Human bacterial artificial chromosome/p1 artificial chromosome probes spanning the length of chromosome 17 were used in FISH experiments on great apes, Old World monkeys and New World monkeys to study the evolutionary history of this chromosome. We observed that the macaque marker order represents the ancestral organization. Human, chimpanzee and gorilla homologous chromosomes differ by a paracentric inversion that occurred specifically in the Homo sapiens/Pan troglodytes/Gorilla gorilla ancestor. Detailed analyses of the paracentric inversion revealed that the breakpoints mapped to two regions syntenic to human 17q12/21 and 17q23, both rich in segmental duplications.

Conclusion
Sequence analyses of the human and macaque organization suggest that the duplication events occurred in the catarrhine ancestor with the duplication blocks continuing to duplicate or undergo gene conversion during evolution of the hominoid lineage. We propose that the presence of these duplicons has mediated the inversion in the H. sapiens/P. troglodytes/G. gorilla ancestor. Recently, the same duplication blocks have been shown to be polymorphic in the human population and to be involved in triggering microdeletion and duplication in human. These results further support a model where genomic architecture has a direct role in both rearrangement involved in karyotype evolution and genomic instability in human.
Staphylococcus aureus directly activates eosinophils via platelet-activating factor receptor
Authors: Hosoki Koa , Nakamura Akiko , Nagao Mizuho , Hiraguchi Yukiko , Tanida Hisashi , Tokuda Reiko , Wada Hideo , Nobori Tsutomu , Suga Shigeru , Fujisawa Takao 
Published: May 2012

Abstract
Staphylococcus aureus (SA) directly activates eosinophils via PAF receptor to induce degranulation, superoxide, and cytokine production, suggesting that SA colonization has pathological significance in atopic dermatitis.
Colonization by SA is associated with exacerbation of AD. Eosinophilic inflammation is a cardinal pathological feature of AD, but little is known about possible direct interaction between SA and eosinophils. PAFR appears to be involved in phagocytosis of Gram-positive bacteria by leukocytes. The objective of this study was to investigate whether SA directly induces eosinophil effector functions via PAFR in the context of AD pathogenesis. Peripheral blood eosinophils were cultured with heat-killed SA, and EDN release, superoxide generation, and adhesion to fibronectin-coated plates were measured. Cytokines, released in the supernatants, were quantified by multiplex bead immunoassays. FISH-labeled SA was incubated with eosinophils and visualized by confocal laser-scanning microscopy. PAFR-blocking peptide and PAFR antagonists were tested for inhibitory effects on SA-induced reactions. SA induced EDN release and superoxide generation by eosinophils in a dose-dependent manner. IL-5 significantly enhanced SA-induced EDN release. IL-5 and IL-17A significantly enhanced SA-induced superoxide generation. SA enhanced eosinophil adhesion to fibronectin, which was blocked by anti-CD49d, and induced eosinophil secretion of various cytokines/chemokines (IL-2R, IL-9, TNFR, IL-1β, IL-17A, IP-10, TNF-α, PDGF-bb, VEGF, and FGF-basic). After incubation of eosinophils with SA, FISH-labeled SA was visualized in the eosinophilsˈ cytoplasm, indicating phagocytosis. A PAFR-blocking peptide and two PAFR antagonists completely inhibited those reactions. In conclusion, SA directly induced eosinophil activation via PAFR. Blockade of PAFR may be a novel, therapeutic approach for AD colonized by SA.
A novel internalization motif regulates human IFN-γR1 endocytosis
Authors: Yancoski Judith , Sadat Mohammed A , Aksentijevich Nadia , Bernasconi Andrea , Holland Steven M , Rosenzweig Sergio D 
Published: May 2012

Abstract
A new type of internalization domain highly conserved in IFNγ receptors across species, regulates human IFNγR1 endocytosis.
This study tested the hypothesis that the IFN-γR1 287-YVSLI-91 intracellular motif regulates its endocytosis. IFN-γ exerts its biological activities by interacting with a specific cell-surface RC composed of two IFN-γR1 and two IFN-γR2 chains. Following IFN-γ binding and along with the initiation of signal transduction, the ligand and IFN-γR1 are internalized. Two major types of consensus-sorting signals are described in receptors, which are rapidly internalized from the plasma membrane to intracellular compartments: tyrosine-based and dileucine-based internalization motifs. Transfection of HEK 293 cells and IFN-γR1-deficient fibroblasts with WT and site-directed, mutagenesis-generated mutant IFN-γR1 expression vectors helped us to identify region IFN-γR1 287-YVSLI-291 as the critical domain required for IFN-γ-induced IFN-γR1 internalization and Y287 and LI290–291 as part of a common structure essential for receptor endocytosis and function. This new endocytosis motif, YxxLI, shares characteristics of tyrosine-based and dileucine-based internalization motifs and is highly conserved in IFN-γRs across species. The IFN-γR1 270-LI-271 dileucine motif, previously thought to be involved in this receptor endocytosis, showed to be unnecessary for receptor endocytosis.
Regulation of multiple target genes by miR-1 and miR-206 is pivotal for C2C12 myoblast differentiation
Authors: Goljanek-Whysall Katarzyna , Pais Helio , Rathjen Tina , Sweetman Dylan , Dalmay Tamas , Münsterberg Andrea 
Published: May 2012

SummaryMicroRNAs are short non-coding RNAs involved in post-transcriptional regulation of multiple messenger RNA targets. The miR-1/miR-206 family is expressed during skeletal muscle differentiation and is an integral component of myogenesis. To better understand miR-1/miR-206 function during myoblast differentiation we identified novel target mRNAs by microarray and characterized their function in C2C12 myoblasts. Candidate targets from the screen were experimentally validated together with target genes that were predicted by three different algorithms. Some targets characterised have a known function in skeletal muscle development and/or differentiation and include Meox2, RARB, Fzd7, MAP4K3, CLCN3 and NFAT5, others are potentially novel regulators of myogenesis, such as the chromatin remodelling factors Smarcd2 and Smarcb1 or the anti-apoptotic protein SH3BGRL3. The expression profiles of confirmed target genes were examined during C2C12 cell myogenesis. We found that inhibition of endogenous miR-1 and miR-206 by antimiRs blocked the downregulation of most targets in differentiating cells, thus indicating that microRNA activity and target interaction is required for muscle differentiation. Finally, we show that sustained expression of validated miR-1 and/or miR-206 targets resulted in increased proliferation and inhibition of C2C12 cell myogenesis. In many cases the expression of genes related to non-muscle cell fates, such as chondrogenesis, was activated. This indicates that the concerted downregulation of multiple microRNA targets is not only crucial to the skeletal muscle differentiation program but also serves to prevent alternative cell fate choices.
Association of bromodomain BET proteins with chromatin requires dimerization through the conserved motif B
Authors: Garcia-Gutierrez Pablo , Mundi Maria , Garcia-Dominguez Mario 
Published: May 2012

Summary
BET (bromodomain and extra terminal domain) family proteins are unique among bromodomain-containing proteins in that they not only associate with acetylated chromatin in interphase, but also remain attached to chromosomes during mitosis. Although the two tandem bromodomains are essential to display this behaviour, they do not suffice. In this work we report that a small conserved domain, motif B, is also required. A deletion mutant of this domain dissociates from mitotic chromosomes. However, inhibition of histone deacetylases alleviates dissociation. We also show that motif-B-dependent association with chromosomes is not restricted to mitosis. Interestingly, our results indicate that motif B constitutes a surface for homo- and hetero-dimerization between BET proteins. Finally, linked to the prominent role BET proteins play in cell proliferation, we report that ectopic expression of the family member Brd2 interferes with neuronal differentiation in P19 cells and in the vertebrate neural tube, probably because of preservation of adequate levels of cyclin A2 and cyclin D1. By contrast, a deletion mutant of motif B fails to perform in this way, highlighting the relevance of this domain for Brd2 function.