bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone
Authors: Mahony Andrew A. , Buultjens Andrew H. , Ballard Susan A. , Grabsch Elizabeth A. , Xie Shirley , Seemann Torsten , Stuart Rhonda L. , Kotsanas Despina , Cheng Allen , Heffernan Helen , Roberts Sally A. , Coombs Geoffrey W. , Bak Narin , Ferguson John K. , Carter Glen C. , Howden Benjamin P. , Stinear Timothy P. , Johnson Paul D. R. 
Published: April 2018

Abstract
Background
Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of vanB E. faecium - ST796 - very near its time of origin from hospitals in three Australian states and New Zealand.

Methods
Following near-simultaneous outbreaks of ST796 in multiple institutions, we gathered then tested colonization and bloodstream infection isolates’ antimicrobial resistance (AMR) phenotypes, and phylogenomic relationships using whole genome sequencing (WGS). Patient meta-data was explored to trace the spread of ST796.

Results
A novel clone of vanB E. faecium (ST796) was first detected at one Australian hospital in late 2011, then in two New Zealand hospitals linked by inter-hospital transfers from separate Melbourne hospitals. ST796 also appeared in hospitals in South Australia and New South Wales and was responsible for at least one major colonization outbreak in a Neonatal Intensive Care Unit without identifiable links between centers. No exceptional AMR was detected in the isolates. While WGS analysis showed very limited diversity at the core genome, consistent with recent emergence of the clone, clustering by institution was observed.

Conclusions
Evolution of new E. faecium clones, followed by recognized or unrecognized movement of colonized individuals then rapid intra-institutional cross-transmission best explain the multi-center, multistate and international outbreak we observed.
Strain, disinfectant, concentration, and contact time quantitatively impact disinfectant efficacy
Authors: West Alyssa M. , Teska Peter J. , Lineback Caitlinn B. , Oliver Haley F. 
Published: April 2018

Abstract
Background
Transmission of healthcare-associated infections caused by antibiotic- and multi-drug resistant (MDR) pathogens (e.g. Methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa) are a major concern in patient care facilities. Disinfectant usage is critical to control and prevent pathogen transmission, yet the relationships among strain, disinfectant type, contact time, and concentration are not well-characterized. We hypothesized that there would be significant differences in disinfectant efficacy among clinically relevant strains under off-label disinfectant conditions, but there would be less no differences among at registered label use concentrations and contact times. The purpose of this study was to quantify the effect of disinfectant concentration and contact time on the bactericidal efficacy of clinically relevant strains of S. aureus and P. aeruginosa.

Methods
Accelerated hydrogen peroxide (AHP), quaternary ammonium compounds (Quat), and sodium hypochlorite were tested at label and reduced contact times and concentrations against four MDR P. aeruginosa strains and four MRSA strains. Quantitative EPA method MB-25-02 was used to measure disinfectant efficacy reported as log10 reduction.

Results
Both off-label disinfectant concentrations and contact times significantly affected efficacy of all disinfectants tested. Bactericidal efficacy varied among MRSA and P. aeruginosa strains.

Conclusions
The quantitative disinfectant efficacy method used highlights the inter-strain variability that exists within a bacterial species. It also underscores the need for a disinfectant validation method that takes these variances into account.
Pet owner and vet interactions: exploring the drivers of AMR
Authors: Smith Matt , King Caroline , Davis Mark , Dickson Adele , Park Jeni , Smith Fraser , Currie Kay , Flowers Paul 
Published: April 2018

Abstract
Background
Antimicrobial resistance (AMR) is a growing public health problem across the world. As the negative consequences of AMR become apparent at local, national and international levels, more attention is being focussed on the variety of mechanisms by which AMR is potentiated. We explore how interactions between pet owners and veterinarians represent a key arena in which AMR-related behaviours can be shaped.

Methods
In depth semi-structured interviews were carried out with pet owners (n = 23) and vets (n = 16) across the UK in 2017. A thematic analysis approach was taken, with inductively gathered data analysed deductively using a behavioural framework to identified key behaviours emerging from participant accounts which were amenable to change.

Results
Interactions between vets and pet owners were characterised by misunderstandings and misconceptions around antibiotics by pet owners, and a lack of clarity about the positions and intentions of the other party. Vets and pet owners had differing perceptions of where pressure to prescribe antibiotics inappropriately originated. Vets perceived it was mostly pet owners who pushed for inappropriate antibiotics, whereas pet owners reported they felt it was vets that overprescribed. Low levels of understanding of AMR in general were apparent amongst pet owners and understandings with regard to AMR in pets specifically were almost non-existent in the sample.

Conclusions
Improved use of antibiotics could be assisted by educating the pet owning public and by guideline development for companion animal vets, concurrent development of mandatory legislation, increased consultation time to facilitate better communication, development of vet training on antimicrobial therapy and stewardship led interactions with pet owners, and increased levels of knowledge of pet-related AMR amongst pet owners.
Uncovering the Oppenheimer Siddur: using scientific analysis to reveal the production process of a medieval illuminated Hebrew manuscript
Authors: Wijsman Suzanne , Neate Sarah , Kogou Sotiria , Liang Haida 
Published: April 2018

Abstract
The aim of this research was to use non-invasive scientific analysis to uncover evidence of the planning process and relationship between pigments used in text copying and artwork production in the Oppenheimer Siddur (Oxford Bodleian Library MS Opp. 776), an illuminated 15th-century Hebrew prayer book. In many medieval Hebrew illuminated manuscripts, the authorship of the artwork is unknown. This manuscript’s colophon states that it was copied by its scribe-owner for personal family use but does not confirm who was responsible for the artwork. Prior deductive analysis suggested that the scribe-owner may also have been the manuscript’s artist, based on common motifs and an apparent shared colour palette appearing in both texts and artwork. Visual examination using high resolution digital images also identified points of contact between pigments used in the manuscript’s texts and artwork, raising questions about the pigment application sequence, and concurrent versus sequential text copying and artwork production. An in-house developed remote spectral imaging system (PRISMS) with 10 filters spanning the spectral range from 400 to 880 nm was modified for close-range application to image two of the folios to examine the sequence of production, identify the pigments and compare the materials used for the illumination and the text. Optical microscopy and Fourier Transform Infrared spectroscopy in the attenuated total reflection mode (FTIR-ATR) were used directly on the folios to complement the spectral imaging data in binding media and pigment identification. The results revealed close matches in reflectance spectra for the colorants and inks used in both text copying and illuminations, suggesting that the same mixture of colorants and inks have been used. The spectral imaging in the near infrared bands revealed a hidden underdrawing, indicating a design change during production of the manuscript, and the outlining of letters prior to coloured pigment being applied. The pigment use, the variation in the binder for different pigments and some elements of its production were found to be consistent with those described in historical sources. The evidence from this study supports the hypothesis that the scribe applied pigments for the manuscript’s artwork at the same time he did some of the scribal work which has implications for understandings of Jewish medieval visual cultures.
Reconstructing Van Gogh’s palette to determine the optical characteristics of his paints
Authors: Geldof Muriel , Proaño Gaibor Art Ness , Ligterink Frank , Hendriks Ella , Kirchner Eric 
Published: April 2018

Abstract
The colors of Field with Irises near Arles, painted by Van Gogh in Arles in 1888, have changed considerably. To get an idea of how this painting, as well as other works by Van Gogh, looked shortly after their production, the Revigo (Re-assessing Vincent van Gogh’s colors) research project was initiated. The aim of this project was to digitally visualize the original colors of paintings and drawings by Vincent van Gogh, using scientific methods backed by expert judgement where required. We adopted an experimental art technological approach and physically reconstructed Van Gogh’s full palette of oil paints, closely matching those he used to paint Field with Irises near Arles. Sixteen different paints were reconstructed, among which the most light-sensitive pigments and linseed oil, which is prone to yellowing, were produced according to 19th century practice. The resulting pigments and oils were chemically analyzed and compared to those used by Van Gogh. The ones that resembled his paints the most were used in the paint reconstructions. Other pigments were either obtained from the Cultural Heritage Agency’s collection of historical pigments, or purchased from Kremer Pigmente. The reconstructed paints were subsequently used to calculate the absorption K and scattering S parameters of the individual paints. Using Kubelka–Munk theory, these optical parameters could in turn be used to determine the color of paint mixtures. We applied this method successfully to digitally visualize the original colors of Field with Irises near Arles. Moreover, the set of optical parameters presented here can similarly be applied to calculate digital visualizations of other paintings by Van Gogh and his contemporaries.
A technical study of the materials and manufacturing process used in the Gallery wall paintings from the Jokhang temple, Tibet
Authors: Song Yan , Gao Feng , Nevin Austin , Guo Juwen , Zhou Xiao , Wei Shuya , Li Qianqian 
Published: April 2018

Abstract
Wall paintings from the Jokhang temple, Lhasa, Tibet, China cover over 4000 m2. In order to protect these valuable paintings and to provide more conclusive information regarding the date of the painting scheme from the outer north Gallery, painting materials and techniques have been studied using optical and scanning electron microscopy, X-ray diffraction and raman spectroscopy. Organic materials were analysed with pyrolysis-gas chromatography–mass spectrometry. The wall painting technique is typical of Tibetan paintings and includes multiple layers of locally sourced materials. Analytical results demonstrate the presence of natural and synthetic pigments, including cinnabar (HgS), malachite (CuCO3·Cu(OH)2), azurite (2CuCO3·Cu(OH)2), orpiment (As2S3), red lead (Pb3O4), synthetic ultramarine blue (Na3CaAl3Si3O12S) and emerald green (Cu(C2H3O2)2·3Cu(AsO2)2) which allow us to date the paintings from the mid to late nineteenth century. The binding media is a kind of animal glue which is likely to be bovine or yak glue, the traditional medium used in Tibet. Gilding was applied as gold powder or gold foil. In the past a sealing material or varnish containing drying oil (maybe tung oil) and pine resin was applied to the surface to protect the paintings.
Putting transitivity to the test: a review of the Sydney and Cardiff models
Authors: Bartley Leanne Victoria 
Published: April 2018

AbstractIn Systemic Functional Linguistics (SFL), the system of Transitivity is a common means by which to analyse both isolated clauses as well as clauses in context. To date, two Transitivity models have emerged. The first and more established of the two is the Sydney model, which was proposed by Halliday (Journal of Linguistics 3(1):37–81, 1967; An introduction to functional grammar, 1985; An introduction to functional grammar, 1994) and more latterly developed by himself and Christian Matthiessen (Halliday and Matthiessen, An introduction to functional grammar, 2004; Halliday’s introduction to functional grammar, 2014). The second is the Cardiff Grammar (CG) model put forward by Fawcett (Cognitive linguistics and social interaction: Towards an integrated model of a systemic functional grammar and the other components of a communicating mind, 1980; The semantics of clause and verb for relational processes in English, 1987) as an alternative to the former and, which has subsequently been elaborated by Neale (More delicate Transitivity: Extending the process type system networks for English to include full semantic classifications, 2002; Matching corpus data and system networks, 2006). Although both models have various strengths, neither model is void of limitations. Thus, the aim of this paper is to describe, compare and draw on the inadequacies associated with either one or both of the aforementioned systems, which have come to light following substantial research on Transitivity. All in all, several issues are raised here in order to highlight particular areas that need to be addressed if we are to ensure a systematic and delicate analysis of Transitivity patterns across texts.
Nasopharyngeal brushing: a convenient and feasible sampling method for nucleic acid‐based nasopharyngeal carcinoma research
Authors: Zhang Pei‐Fen , Zheng Xiao‐Hui , Li Xi‐Zhao , Tian Tian , Zhang Shao‐Dan , Hu Ye‐Zhu , Jia Wei‐Hua 
Published: April 2018

AbstractBackgroundTissue specimens for nasopharyngeal carcinoma (NPC) research are scarce because of sampling difficulties. Previous studies have suggested non‐invasive nasopharyngeal brushing as an effective sampling method for NPC diagnosis. The present study aimed to evaluate the feasibility of nasopharyngeal brushing in the acquisition of NPC nucleic acids for research.MethodsNasopharyngeal brushing samples were acquired from 24 healthy individuals and 48 NPC patients. Tissues from 48 NPC and 18 nasopharyngitis patients were collected by endoscopic biopsy. The expression levels of tumor suppressor genes (TSGs) and Epstein–Barr virus (EBV)‐encoded microRNAs as well as EBV DNA copy number were measured by quantitative polymerase chain reaction in both types of samples.ResultsAmong six TSGs examined, the expression levels of two genes were significantly decreased in nasopharyngeal brushing and tissue samples from NPC patients as compared with those from healthy/nasopharyngitis individuals. Four EBV‐encoded microRNAs, mir‐bart1‐5p, mir‐bart5, mir‐bart6‐5p, and mir‐bart17‐5p, were significantly up‐regulated in both NPC brushing and tissue samples compared with those from healthy/nasopharyngitis controls (P < 0.001). EBV DNA was significantly increased in both nasopharyngeal brushing samples (P < 0.001) and tissue samples (P < 0.001) from NPC patients in comparison with those from healthy controls.ConclusionsNasopharyngeal brushing can obtain sufficient tumoral materials for the analysis of viral nucleic acid, including EBV‐encoded microRNAs and EBV DNA. For the detection of TSG expression, nasopharyngeal brushings was feasible but inferior to tissue samples. This study confirms nasopharyngeal brushing as an applicable sampling method that can aid in nucleic acid‐based NPC research.
Performance of the Brazilian version of GloboDiet software for dietary intake assessment
Authors: Marchetti Beatriz Schirrmeister , Steluti Josiane , Fisberg Regina Mara , Marchioni Dirce Maria Lobo 
Published: April 2018

Abstract
Background
GloboDiet is a software that conducts the interview of the 24-h dietary recall (24HR) guided by a standardized routine. The successful experience of adapting this software in different cultural contexts in Europe led to the extension of the project to Latin American countries. Brazil was one of the selected countries to start the project in collaboration with IARC, and a Brazilian version of the GloboDiet software was developed. Therefore, this study aimed to estimate food intake using the Brazilian version of GloboDiet software and compare whether there is concordance of the estimated intake of energy, carbohydrates, protein, and lipids between the GloboDiet and Nutrition Data System for Research—NDSR software.

Methods
We considered a sub-sample of 100 adult individuals from ISA-Capital 2008 survey, a population-based study of resident in the urban area of São Paulo, Brazil. We obtained dietary intake data through the 24HR using the NDSR software. In this study, the 24HR of the same 100 individuals were entered in GloboDiet software—Brazilian version. Then, statistical analyses were performed considering Bland and Altman analysis and Kappa statistic to evaluate the agreement between the software. It also used the terciles of energy and macronutrients.

Results
The mean (SD) obtained for energy, protein, carbohydrate, and lipids in the NDSR was 2386.47 (444.25) kcal, 100.08 (35.33) g, 286.75 (84.02) g, and 87.34 (28.32) g, respectively. In comparison, the SD obtained in the GloboDiet for those same variables was 2279.67 (655.50) kcal, 92.94 (38.35) g, 277.62 (93.86) g, and 83.12 (33.69) g, respectively. The mean (95% CI of agreement limits) of the differences between two measurements for energy, protein, carbohydrate, and lipids is 106.8 (− 961.3; 1174.9) kcal, 7.142 (− 58.6; 72.9) g, 9.1 (− 128.958; 147.208), and 4.2 (− 64.039; 72.489) g, respectively. From the Kappa statistic, we verified a slight and significant agreement (p < 0.05) considering the tertiles of energy and macronutrient between the software.

Conclusions
The Brazilian version of GloboDiet software seems to have a good performance when compared to NDSR software. However, further researchers are needed to validate the dietary intake from GloboDiet.
Cumulative Burden of Morbidity Among Testicular Cancer Survivors After Standard Cisplatin-Based Chemotherapy: A Multi-Institutional Study
Authors: Kerns Sarah L. , Fung Chunkit , Monahan Patrick O. , Ardeshir-Rouhani-Fard Shirin , Abu Zaid Mohammad I. , Williams AnnaLynn M. , Stump Timothy E. , Sesso Howard D. , Feldman Darren R. , Hamilton Robert J. , Vaughn David J. , Beard Clair , Huddart Robert A. , Kim Jeri , Kollmannsberger Christian , Sahasrabudhe Deepak M. , Cook Ryan , Fossa Sophie D. , Einhorn Lawrence H. , Travis Lois B. ,   for the Platinum Study Group
Published: April 2018

PurposeIn this multicenter study, we evaluated the cumulative burden of morbidity (CBM) among > 1,200 testicular cancer survivors and applied factor analysis to determine the co-occurrence of adverse health outcomes (AHOs).Patients and MethodsParticipants were ≤ 55 years of age at diagnosis, finished first-line chemotherapy ≥ 1 year previously, completed a comprehensive questionnaire, and underwent physical examination. Treatment data were abstracted from medical records. A CBM score encompassed the number and severity of AHOs, with ordinal logistic regression used to assess associations with exposures. Nonlinear factor analysis and the nonparametric dimensionality evaluation to enumerate contributing traits procedure determined which AHOs co-occurred.ResultsAmong 1,214 participants, approximately 20% had a high (15%) or very high/severe (4.1%) CBM score, whereas approximately 80% scored medium (30%) or low/very low (47%). Increased risks of higher scores were associated with four cycles of either ifosfamide, etoposide, and cisplatin (odds ratio [OR], 1.96; 95% CI, 1.04 to 3.71) or bleomycin, etoposide, and cisplatin (OR, 1.44; 95% CI, 1.04 to 1.98), older attained age (OR, 1.18; 95% CI, 1.10 to 1.26), current disability leave (OR, 3.53; 95% CI, 1.57 to 7.95), less than a college education (OR, 1.44; 95% CI, 1.11 to 1.87), and current or former smoking (OR, 1.28; 95% CI, 1.02 to 1.63). CBM score did not differ after either chemotherapy regimen ( P = .36). Asian race (OR, 0.41; 95% CI, 0.23 to 0.72) and vigorous exercise (OR, 0.68; 95% CI, 0.52 to 0.89) were protective. Variable clustering analyses identified six significant AHO clusters (χ2P < .001): hearing loss/damage, tinnitus (OR, 16.3); hyperlipidemia, hypertension, diabetes (OR, 9.8); neuropathy, pain, Raynaud phenomenon (OR, 5.5); cardiovascular and related conditions (OR, 5.0); thyroid disease, erectile dysfunction (OR, 4.2); and depression/anxiety, hypogonadism (OR, 2.8).ConclusionFactors associated with higher CBM may identify testicular cancer survivors in need of closer monitoring. If confirmed, identified AHO clusters could guide the development of survivorship care strategies.
Immune-Mediated Myelopathies
Authors: Wingerchuk Dean M. 
Published: April 2018

ABSTRACT

PURPOSE OF REVIEW
This article reviews the clinical presentation, diagnostic evaluation, and management of immune-mediated myelopathies.

RECENT FINDINGS
The discovery of several neural autoantibodies and their antigenic targets has revolutionized the investigation and treatment of immune-mediated myelopathies. Detection of these serologic biomarkers can support or establish a diagnosis of an autoimmune myelopathy, and, in the case of paraneoplastic syndromes, indicate the likely presence of an underlying malignancy. Distinctive lesion patterns detected on spinal cord or brain MRI narrow the differential diagnosis in patients with acute or subacute inflammatory myelopathies, including those not associated with autoantibody markers.

SUMMARY
Immune-mediated myelopathies usually present acutely or subacutely and have a broad differential diagnosis. A systematic diagnostic approach using data from the clinical setting and presentation, MRI lesion patterns, CSF data, and autoantibody markers can differentiate these disorders from noninflammatory myelopathies, often with precise disease classification. This, in turn, provides prognostic information, especially whether the disorder is likely to relapse, and facilitates therapeutic decision making. Diagnostic accuracy informs selection of acute immunotherapy aimed at arresting and reversing recent neurologic injury and, when necessary, selection of long-term treatment for prevention of disease progression or relapse.
Liability for Referrals to Other Physicians
Authors: Kass Joseph S. 
Published: April 2018

ABSTRACT
This article presents four hypothetical cases that demonstrate ways in which neurologists may be vulnerable to liability for how they manage patients they refer to other physicians for consultations. This article also discusses the importance of protecting neurologists from claims of negligence through documentation, which includes the rationale for ordering a consultation, deferring a consultation, or disagreeing with a consultant’s recommendations. Lastly, the article discusses the importance of including patients in the decision-making process and detailing these conversations in the medical record.