bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community history affects the predictability of microbial ecosystem development
Authors: Pagaling Eulyn , Strathdee Fiona , Spears Bryan M , Cates Michael E , Allen Rosalind J , Free Andrew 
Published: August 2013

Abstract
Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community’s previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.
Manipulating Acoustic Wavefront by Inhomogeneous Impedance and Steerable Extraordinary Reflection
Authors: Zhao Jiajun , Li Baowen , Chen Zhining , Qiu Cheng-Wei 
Published: August 2013

AbstractWe unveil the connection between the acoustic impedance along a flat surface and the reflected acoustic wavefront, in order to empower a wide wariety of novel applications in acoustic community. Our designed flat surface can generate double reflections: the ordinary reflection and the extraordinary one whose wavefront is manipulated by the proposed impedance-governed generalized Snell's law of reflection (IGSL). IGSL is based on Green's function and integral equation, instead of Fermat's principle for optical wavefront manipulation. Remarkably, via the adjustment of the designed specific acoustic impedance, extraordinary reflection can be steered for unprecedented acoustic wavefront while that ordinary reflection can be surprisingly switched on or off. The realization of the complex discontinuity of the impedance surface has been proposed using Helmholtz resonators.
A longitudinal study on α-synuclein in blood plasma as a biomarker for Parkinson's disease
Authors: Foulds Penelope G. , Diggle Peter , Mitchell J. Douglas , Parker Angela , Hasegawa Masato , Masuda-Suzukake Masami , Mann David M. A. , Allsop David 
Published: August 2013

AbstractThere have been no longitudinal studies on α-synuclein as a potential biomarker for the progression of Parkinson's disease (PD). Here, blood plasma ‘total α-synuclein’ and ‘Ser-129 phosphorylated α-synuclein’ were assayed at 4–6 monthly intervals from a cohort of 189 newly-diagnosed patients with PD. For log-transformed data, plasma total α-synuclein levels increased with time for up to 20 yrs after the appearance of initial symptoms (p = 0.012), whereas phosphorylated α-synuclein remained constant over this same period. The mean level of phosphorylated α-synuclein, but not of total α-synuclein, was higher in the PD plasma samples taken at first visit than in single samples taken from a group of 91 healthy controls (p = 0.012). Overall, we conclude that the plasma level of phosphorylated α-synuclein has potential value as a diagnostic tool, whereas the level of total α-synuclein could act as a surrogate marker for the progression of PD.
Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees
Authors: Sansom Robert S. , Wills Matthew A. 
Published: August 2013

AbstractFossils are vital for calibrating rates of molecular and morphological change through geological time and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences.
Glycosylation and functionality of recombinant β-glucocerebrosidase from various production systems
Authors: Tekoah Yoram , Tzaban Salit , Kizhner Tali , Hainrichson Mariana , Gantman Anna , Golembo Myriam , Aviezer David , Shaaltiel Yoseph 
Published: August 2013

The glycosylation of recombinant β-glucocerebrosidase, and in particular the exposure of mannose residues, has been shown to be a key factor in the success of ERT (enzyme replacement therapy) for the treatment of GD (Gaucher disease). Macrophages, the target cells in GD, internalize β-glucocerebrosidase through MRs (mannose receptors). Three enzymes are commercially available for the treatment of GD by ERT. Taliglucerase alfa, imiglucerase and velaglucerase alfa are each produced in different cell systems and undergo various post-translational or post-production glycosylation modifications to expose their mannose residues. This is the first study in which the glycosylation profiles of the three enzymes are compared, using the same methodology and the effect on functionality and cellular uptake is evaluated. While the major differences in glycosylation profiles reside in the variation of terminal residues and mannose chain length, the enzymatic activity and stability are not affected by these differences. Furthermore, the cellular uptake and in-cell stability in rat and human macrophages are similar. Finally, in vivo studies to evaluate the uptake into target organs also show similar results for all three enzymes. These results indicate that the variations of glycosylation between the three regulatory-approved β-glucocerebrosidase enzymes have no effect on their function or distribution.
Fluoroscopically Guided Extraforaminal Cervical Nerve Root Blocks: Analysis of Epidural Flow of the Injectate with Respect to Needle Tip Position
Authors: Shipley Kyle , Riew K. Daniel , Gilula Louis A. 
Published: August 2013

Study Design Retrospective evaluation of consecutively performed fluoroscopically guided cervical nerve root blocks. Objective To describe the incidence of injectate central epidural flow with respect to needle tip position during fluoroscopically guided extraforaminal cervical nerve root blocks (ECNRBs). Methods Between February 19, 2003 and June 11, 2003, 132 consecutive fluoroscopically guided ECNRBs performed with contrast media in the final injected material (injectate) were reviewed on 95 patients with average of 1.3 injections per patient. Fluoroscopic spot images documenting the procedure were obtained as part of standard quality assurance. An independent observer not directly involved in the procedures retrospectively reviewed the images, and the data were placed into a database. Image review was performed to determine optimal needle tip positioning for injectate epidural flow. Results Central epidural injectate flow was obtained in only 28.9% of injections with the needle tip lateral to midline of the lateral mass (zone 2). 83.8% of injectate went into epidural space when the needle tip was medial to midline of the lateral mass (zone 3). 100% of injectate flowed epidurally when the needle tip was medial to or at the medial cortex of the lateral mass (zone 4). There was no statistically significant difference with regards to central epidural flow and the needle tip position on lateral view. Conclusion To ensure central epidural flow with ECNRBs one must be prepared to pass the needle tip medial to midplane of the lateral mass or to medial cortex of the lateral mass. Approximately 16% of ECNRBs with needle tip medial to midline of the lateral mass did not flow into epidural space. One cannot claim a nerve block is an epidural block unless epidural flow of injectate is observed.
Activation of the canonical IKK complex by K63/M1-linked hybrid ubiquitin chains
Authors: Emmerich Christoph H. , Ordureau Alban , Strickson Sam , Arthur J. Simon C. , Pedrioli Patrick G. A. , Komander David , Cohen Philip 
Published: August 2013

Significance
Two types of ubiquitin chain are required to switch on one of the major signaling networks of the innate immune system that triggers the production of inflammatory mediators to combat infection by pathogens. This paper reports the unexpected discovery that both types of ubiquitin chain are attached covalently to one another and that the formation of one type of ubiquitin chain is dependent on the prior formation of the other. One function of these hybrid ubiquitin chains is to permit the colocalization of two different kinase complexes, thereby facilitating the activation of one kinase complex by the other to increase the speed of the response to infection.
Intégralement dans le champ des adverbes de complétude (totalement, entièrement, complètement, …)
Authors: Lenepveu Véronique 
Published: August 2013

In this paper, we study the french adverbs of completion totalement, complètement, entièrement and intégralement in the verbal domain, from a semantic point of view. Following Tenny (2000), we argue that completion adverbs with a quantitative value can only modify telic predicates (*regarder totalement le tableau / détruire totalement une ville). We also identify a qualitative use which doesn’t impose such a constraint (avoir totalement raison). Then, through the analysis of real exemples and of their typical context, we discuss the semantic properties of these different adverbs that are related in various ways to the expression of completion.
Downstream Impact of Urine Cultures Ordered without Indication at Two Acute Care Teaching Hospitals
Authors: Leis Jerome A. , Gold Wayne L. , Daneman Nick , Shojania Kaveh , McGeer Allison 
Published: August 2013

Antimicrobial therapy for asymptomatic bacteriuria (ASB) is recommended for pregnant patients and those undergoing genitourinary procedures. In other populations, treatment has not been demonstrated to confer benefit and is associated with adverse drug reactions, selection for infection with increasingly drug-resistant bacteria, and Clostridium difficile infection. We undertook a prospective audit of urine culture ordering practices among medical and surgical inpatients at 2 acute care teaching hospitals to identify the proportion of urine cultures ordered without clinical indication that lead to antimicrobial therapy for ASB.During August and September 2012, consecutive urine cultures from nonpregnant ward patients were identified within 24 hours of culture ordering. Each patient was interviewed by the study team to determine the presence of urinary tract infection (UTI) using standard surveillance criteria. Non-catheterized patients met clinical indications for UTI if they had fever (temperature >38°C) without another explanation or at least 1 urinary symptom (dysuria, urgency, frequency, costovertebral angle tenderness, or suprapubic pain or tenderness). Catheterized patients met clinical indications for UTI if they had fever, suprapubic pain, or costovertebral angle tenderness. Other reasons for ordering cultures were documented on the basis of care provider interviews before culture results were known. Culture results and antimicrobial prescriptions were documented 72 hours later. The study was approved by the research ethics boards of Mount Sinai Hospital (472 beds) and University Health Network (408 beds; Toronto General Hospital site).
Patients under Contact Precautions Have an Increased Risk of Injuries and Medication Errors A Retrospective Cohort Study
Authors: Karki Surendra , Leder Karin , Cheng Allen C. 
Published: August 2013

Contact precautions (CPs) may lead to adverse psychological effects, delays in access to services, and compromises in the quality of care and patient safety. These need to be balanced with the benefits in preventing transmission of resistant microorganisms. In this study, we aimed to quantify the effect of CPs on reported patient safety incidents.The Alfred hospital is a tertiary referral hospital in Melbourne, Australia. Previous studies have shown that colonization with vancomycin-resistant enterococcus (VRE) is endemic in our hospital. Patients found to be colonized with VRE are placed in CPs immediately and during each subsequent admission. At our facility, modified CPs practiced during the study period include isolation in single rooms with a dedicated toilet, use of gloves when entering the room, and gloves and gown if contact with body fluids is anticipated. The hospital has a computerized risk management system where relevant patient safety incidents are reported to facilitate institutional review and response. We conducted a retrospective cohort study using these routinely collected data, comparing the incidence rate of documented adverse events in patients prior and subsequent to initiation of CPs among patients colonized or infected with VRE. Patients with incident VRE detection between January 2009 and October 2010 were included.
Time-Saving Impact of an Algorithm to Identify Potential Surgical Site Infections
Authors: Knepper B. C. , Young H. , Jenkins T. C. , Price C. S. 
Published: August 2013

Objective.To develop and validate a partially automated algorithm to identify surgical site infections (SSIs) using commonly available electronic data to reduce manual chart review.Design.Retrospective cohort study of patients undergoing specific surgical procedures over a 4-year period from 2007 through 2010 (algorithm development cohort) or over a 3-month period from January 2011 through March 2011 (algorithm validation cohort).Setting.A single academic safety-net hospital in a major metropolitan area.Patients.Patients undergoing at least 1 included surgical procedure during the study period.Methods.Procedures were identified in the National Healthcare Safety Network; SSIs were identified by manual chart review. Commonly available electronic data, including microbiologic, laboratory, and administrative data, were identified via a clinical data warehouse. Algorithms using combinations of these electronic variables were constructed and assessed for their ability to identify SSIs and reduce chart review.Results.The most efficient algorithm identified in the development cohort combined microbiologic data with postoperative procedure and diagnosis codes. This algorithm resulted in 100% sensitivity and 85% specificity. Time savings from the algorithm was almost 600 person-hours of chart review. The algorithm demonstrated similar sensitivity on application to the validation cohort.Conclusions.A partially automated algorithm to identify potential SSIs was highly sensitive and dramatically reduced the amount of manual chart review required of infection control personnel during SSI surveillance.
Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools
Authors: Artigaud Sébastien , Gauthier Olivier , Pichereau Vianney 
Published: August 2013

AbstractBackground: Two-dimensional electrophoresis is a crucial method in proteomics that allows the characterization of proteins’ function and expression. This usually implies the identification of proteins that are differentially expressed between two contrasting conditions, for example, healthy versus diseased in human proteomics biomarker discovery and stressful conditions versus control in animal experimentation. The statistical procedures that lead to such identifications are critical steps in the 2-DE analysis workflow. They include a normalization step and a test and probability correction for multiple testing. Statistical issues caused by the high dimensionality of the data and large-scale multiple testing have been a more active topic in transcriptomics than proteomics, especially in microarray analysis. We thus propose to adapt innovative statistical tools developed for microarray analysis and incorporate them in the 2-DE analysis pipeline.Results: In this article, we evaluate the performance of different normalization procedures, different statistical tests and false discovery rate calculation methods with both real and simulated datasets. We demonstrate that the use of statistical procedures adapted from microarrays lead to notable increase in power as well as a minimization of false-positive discovery rate. More specifically, we obtained the best results in terms of reliability and sensibility when using the ‘moderate t-test’ from Smyth in association with classic false discovery rate from Benjamini and Hochberg.Availability: The methods discussed are freely available in the ‘prot2D’ open source R-package from Bioconductor (http://www.bioconductor.org//) under the terms of the GNU General Public License (version 2 or later).Contact: sebastien.artigaud@univ-brest.fr or sebastien.artigaud@gmx.com
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
Authors: Paull Evan O. , Carlin Daniel E. , Niepel Mario , Sorger Peter K. , Haussler David , Stuart Joshua M. 
Published: August 2013

Abstract
Motivation: Identifying the cellular wiring that connects genomic perturbations to transcriptional changes in cancer is essential to gain a mechanistic understanding of disease initiation, progression and ultimately to predict drug response. We have developed a method called Tied Diffusion Through Interacting Events (TieDIE) that uses a network diffusion approach to connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The method computes a subnetwork of protein–protein interactions, predicted transcription factor-to-target connections and curated interactions from literature that connects genomic and transcriptomic perturbations.
Results: Application of TieDIE to The Cancer Genome Atlas and a breast cancer cell line dataset identified key signaling pathways, with examples impinging on MYC activity. Interlinking genes are predicted to correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor character and suggest subtype-specific drug targets.
Availability: Software is available from the Stuart lab’s wiki: https://sysbiowiki.soe.ucsc.edu/tiedie.
Contact: jstuart@ucsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The code structure of the p53 DNA-binding domain and the prognosis of breast cancer patients
Authors: Sato Keiko , Hara Toshihide , Ohya Masanori 
Published: August 2013

Abstract
Motivation: The tumor-suppressor gene TP53 mutations are diverse in the central region encoding the DNA-binding domain. It has not been clear whether the prognostic significance for survival in breast cancer patients is the same for all types of mutations. Are there specific types of mutations carrying a worse prognosis? To understand the correlation between the mutations in the gene encoding the DNA-binding domain and the prognosis of breast cancer, we studied the code structure of the DNA-binding domain of breast cancer patients by using various artificial codes in information transmission.
Results: We indicated that the prognostic significance of all types of mutations in the DNA-binding domain is not the same, and that the DNA-binding domain having a certain code structure is important for estimating the prognosis of breast cancer patients.
Contact: keiko@is.noda.tus.ac.jp or hara@is.noda.tus.ac.jp
Strong variable linear polarization in the cool active star II Peg
Authors: Rosén L. , Kochukhov O. , Wade G. A. 
Published: August 2013

Abstract
Magnetic fields of cool active stars are currently studied polarimetrically using only circular polarization observations. Including linear polarization in the reconstruction of stellar magnetic fields allows more information about the magnetic field to be extracted and significantly improves the reliability of stellar magnetic field maps. The goal of this study is to initiate systematic observations of active stars in all four Stokes parameters and to identify cool stars for which linear polarization can be detected at a level sufficient for Zeeman–Doppler Imaging (ZDI). Four active RS CVn binaries, II Peg, HR 1099, IM Peg and σ Gem, were observed with the ESPaDOnS spectropolarimeter at the Canada–France–Hawaii Telescope during a time period from 2012 February to 2013 January. The least-squares deconvolution procedure was applied to derive mean polarization profiles of all four Stokes parameters. Linear polarization was detected in all four stars in at least one observation. At the same time, II Peg showed an exceptionally strong and highly variable linear polarization signature throughout all observations. This establishes II Peg as the first promising target for ZDI in all four Stokes parameters and suggests the feasibility of such an analysis with existing equipment for at least a few of the most active cool stars.
The investigation of relationship between lubricating oil and refrigerant in refrigerator compressors
Authors: Karaosmanoğlu Filiz , Yüzer Serkan , Kerpiççi Hüsnü , Durak Ertuğrul 
Published: August 2013

Purpose
– Refrigerant fraction and mixture viscosity values were determined for various operating conditions of compressors. The paper aims to discuss these issues.

Design/methodology/approach
– In this study, an experimental setup that can be used to obtain refrigerant mass fraction and mixture viscosity data is designed and constructed. With the experimental setup, R600a mineral and R134a polyolester compressor lubricant mixtures were examined.

Findings
– This study presents an experimental procedure for obtaining practical results related to refrigerants used in the refrigeration system. Some properties of refrigerant-lubricant mixtures are very important for the design of compressors and performance of the refrigeration cycle.

Originality/value
– The paper is of value in presenting an experimental procedure for obtaining practical results pertaining to the tribological and other properties performance of the refrigerants.