bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased risk for metachronous gastric adenocarcinoma following gastric MALT lymphoma—A US population‐based study
Authors: Palmela Carolina , Fonseca Cristina , Faria Rita , Baptista Rute Baeta , Ribeiro Sofia , Ferreira Alexandre Oliveira 
Published: September 2016

BackgroundGastric mucosa‐associated lymphoid tissue lymphoma (gMALT) and gastric adenocarcinoma (GC) are long‐term complications of chronic Helicobacter pylori (HP) gastritis. Treatment of HP infection induces remission in most patients with gMALT. Endoscopic follow‐up is not currently endorsed after complete remission. However, the risk of GC in these patients is unclear.ObjectiveThe objective of this study is to estimate GC risk in gMALT patients.MethodsThe National Cancer Institute Surveillance, Epidemiology and End Results 13 (SEER) database‐Nov 2014 Sub (1992–2012) was used to identify adult patients diagnosed with gMALT between 1992 and 2012. The standardized incidence ratio of second primary GC after a latency period of 12 months was calculated and compared to a reference SEER cohort of identical age, sex and time period. The risk of GC in these patients was also stratified by latency period (five years) and age.ResultsWe identified 2195 cases of gMALT lymphoma, and 20 (0.91%) of them subsequently developed GC with a relative risk (RR) of 4.32 (95% CI 2.64–6.67) compared to the American population. The median latency time was five years and the risk was maintained afterward (RR 4.92, 95% CI 2.45–8.79). When stratified by age group the risk was highest for the 45–64 group (RR 14.04, 95% CI 5.64–28.93).ConclusiongMALT lymphoma is associated with an increased risk of metachronous gastric adenocarcinoma. The risk is still present after more than five years of follow‐up. Further studies may clarify the most adequate follow‐up strategy.
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Authors: Khomtchouk Bohdan B. , Hennessy James R. , Wahlestedt Claes 
Published: September 2016

AbstractBackgroundHeatmaps are an indispensible visualization tool for examining large-scale snapshots of genomic activity across various types of next-generation sequencing datasets. However, traditional heatmap software do not typically offer multi-scale insight across multiple layers of genomic analysis (e.g., differential expression analysis, principal component analysis, gene ontology analysis, and network analysis) or multiple types of next-generation sequencing datasets (e.g., ChIP-seq and RNA-seq). As such, it is natural to want to interact with a heatmap’s contents using an extensive set of integrated analysis tools applicable to a broad array of genomic data types.ResultsWe propose a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis.ConclusionsMicroScope is hosted online as an R Shiny web application based on the D3 JavaScript library:http://microscopebioinformatics.org/. The methods are implemented in R, and are available as part of the MicroScope project at:https://github.com/Bohdan-Khomtchouk/Microscope.
Quality Oncology Practice Initiative Can Guide and Improve Oncology Providers’ Training in Brazil
Authors: Bergerot Cristiane Decat , Philip Errol J. , Bergerot Paulo Gustavo , Elias Simone , Guimarães Daiane Pereira , Forones Nora Manoukian , Baiocchi Otavio Cesar Carvalho Guimarães , Batista Nildo Alves , De Domenico Edvane Birelo Lopes 
Published: September 2016

Purpose It has become crucial to translate scientific findings and to find ways by which to mobilize local resources to improve the quality and accessibility of cancer care in developing countries. This study seeks to provide insight into challenge through examining differences in clinician documentation of patients with cancer treated at a Brazilian Public University Hospital. Methods ASCO Quality Oncology Practice Initiative (QOPI) measures were used to examine the care provided in the departments of breast, colorectal, lymphoma, gynecology, and lung cancers. For this study, data from a representative sample of patients receiving chemotherapy in the previous month were extracted and quality of cancer care indicators examined. Results Certain elements of medical care were consistently and appropriately documented, including cancer diagnosis and stage, chemotherapy planning, administration, and summary. In general, considering the specific cancer management measures, patients received recommended care in accordance with recognized guidelines. Despite this, a number of important gaps in care were identified, including the assessment and treatment of pain, documentation of chemotherapy intention, symptom and toxicity management, patients’ psychosocial status, and provision of a treatment summary at care completion. Conclusion These findings are encouraging in terms of adherence to core treatment guidelines in cancer care in Brazil. However, results suggest important opportunities for improving care across a number of domains, many of which represent a challenge throughout both developing and developed countries. This study may also provide preliminary guidance for enhancing educational and training programs for professionals and students alike, to implement high-quality, comprehensive cancer care.
Group B Streptococcus vaccine development: present status and future considerations, with emphasis on perspectives for low and middle income countries
Authors: Kobayashi Miwako , Vekemans Johan , Baker Carol J. , Ratner Adam J. , Le Doare Kirsty , Schrag Stephanie J. 
Published: September 2016

Globally, group BStreptococcus(GBS) remains the leading cause of sepsis and meningitis in young infants, with its greatest burden in the first 90 days of life. Intrapartum antibiotic prophylaxis (IAP) for women at risk of transmitting GBS to their newborns has been effective in reducing, but not eliminating, the young infant GBS disease burden in many high income countries. However, identification of women at risk and administration of IAP is very difficult in many low and middle income country (LMIC) settings, and is not possible for home deliveries. Immunization of pregnant women with a GBS vaccine represents an alternate pathway to protecting newborns from GBS disease, through the transplacental antibody transfer to the fetus in utero. This approach to prevent GBS disease in young infants is currently under development, and is approaching late stage clinical evaluation.This manuscript includes a review of the natural history of the disease, global disease burden estimates, diagnosis and existing control options in different settings, the biological rationale for a vaccine including previous supportive studies, analysis of current candidates in development, possible correlates of protection and current status of immunogenicity assays. Future potential vaccine development pathways to licensure and use in LMICs, trial design and implementation options are discussed, with the objective to provide a basis for reflection, rather than recommendations.
Quality of services of emergency medical care in terms of health care reform
Authors: Белобородов Алексей , Beloborodov Aleksey , Данилина Елена , Danilina Elena , Яковлева Екатерина , Yakovleva Ekaterina , Бутова Татьяна , Butova Tatyana , Белобородова Юлия , Beloborodova Yuliya 
Published: September 2016

The article deals with the question of quality assurance of emergency medical care. It is of vital importance in terms of reforming the system of healthcare in the Russian Federation, as the quality and availability of various types of medical services are priority indicators of reform. Quality ensuring of emergency medical care is the most important socially significant task of health care, which lies in maintaining the health of people in extreme conditions and in meeting the challenges of mortality reduction. This is resulted in increased attention to research in this area. Quality ensuring of emergency medical services actualizes the task of improving of its assessment methodology.
The methodological problems of services quality assessment in the system of emergency medical care limiting applied research are the subject of the study. The structure of emergency medical care is specified, the separation of concepts of &#34;medical service&#34; and &#34;medical care&#34; of services of emergency medical care is accomplished, and the concept of &#34;medical care&#34; is defined in the article. Based on the results of market research of patients’ satisfaction with quality of medical care in emergency hospital of Krasnoyarsk a structural model of services of emergency medical care has been created. This model reflects the patients’ understanding that the quality of service of emergency medical care is an integrated category, combining the quality of the result of medical services and quality of care.
Content analysis of the definition of basic concepts in the field of quality of health care has allowed to formulate the concept of &#34;service quality of emergency medical care”. Its difference is that the definition includes goal-setting of quality of emergency medical care as ensuring the effective medical care, as well as performance indicators of emergency medical care are formulated. The proposed concept and performance indicators of emergency medical care stimulate new directions for research in this area.
Comparison of magnetic resonance arthrography with arthroscopy for imaging of shoulder injuries: retrospective study
Authors: Saqib R , Harris J , Funk L 
Published: September 2016

BACKGROUND Arthroscopy is the established ‘gold standard’ diagnostic investigation for detection of shoulder disorders. We aimed to compare the diagnostic accuracy of arthroscopy with magnetic resonance arthrography (MRA) for detection of shoulder disorders. METHODS Patients who underwent arthroscopy by a single surgeon and preoperative MRA between February 2011 and March 2012 for shoulder instability were identified. MRAs were reported by experienced musculoskeletal radiologists. Labral tears, anterior labral tears, superior labral anterior posterior (SLAP) lesions, posterior labral tears, rotator-cuff tears (RCTs), osteoarthritis, loose bodies and Hill–Sachs lesions were identified. Sensitivity, specificity, positive predictive value and negative predictive value, positive likelihood ratio and negative likelihood ratio were calculated. RESULTS A total of 194 patients were identified. The sensitivity and specificity for anterior labral tears was 0.60 and 0.92, SLAP lesions was 0.75 and 0.81, posterior labral tears was 0.57 and 0.96, any labral tear was 0.87 and 0.76, Hill–Sachs lesions was 0.91 and 0.91, RCTs was 0.71 and 0.86, osteoarthritis was 0.72 and 0.95, and loose bodies was 0.22 and 0.96, respectively. The positive predictive value and negative predictive value for anterior labral tears were 0.88 and 0.71, SLAP lesions was 0.64 and 0.88, posterior labral tears was 0.74 and 0.45, any labral tear was 0.89 and 0.71, Hill–Sachs lesions was 0.66 and 0.98, RCTs was 0.47 and 0.95, osteoarthritis was 0.70 and 0.95, and loose bodies was 0.27 and 0.95, respectively. CONCLUSIONS MRA has high diagnostic accuracy for labral tears and Hill–Sachs lesions, but whether MRA should be the first-line imaging modality is controversial.
Choosing between the modified Ravitch and Nuss procedures for pectus excavatum: Considering the patients’s perspective
Authors: Elsayed HH , Hassaballa AS , Abdel Hady SM , Elbastawisy SE , Ahmed TA 
Published: September 2016

INTRODUCTION Pectus excavatum (PE) is the most common paediatric chest wall deformity. The majority of patients are treated for cosmetic purposes, with the modified Ravitch and Nuss procedures the most commonly performed. We tested the preferences of healthy individuals over their choice of procedure. METHODS The study was conducted from February to August 2014. A five-item illustrated questionnaire was administered to teenagers and young adults aged 14–26 years over their willingness to seek medical advice if they had PE, provided its cosmetic appearance was the only complaint. They were asked about their preference over the modified Ravitch and Nuss procedures, with the surgical details for both procedures explained by medical professionals, alongside illustrated outcomes. RESULTS Two hundred and two healthy individuals were interviewed. The median age was 19.5 years (14–26 years) and 141 (69.8%) were male. Sixty seven (33.2%) participants refused any intervention, while 11 (5.4%) initially wanted an intervention but refused after understanding the surgical procedures available. Of the 135 respondents who chose surgical correction, 84 (62.2%) preferred the modified Ravitch operation, while 51 (37.8%) preferred the Nuss procedure. The main reason for choosing the modified Ravitch technique was not having something metal in the chest, while most participants who chose the Nuss procedure felt that it was “cosmetically better”. CONCLUSIONS Patients have preferences over the choice of procedure for PE repair that can affect the treatment decision. Paediatric and thoracic surgeons should therefore be experienced in performing both procedures.
BitBox!: A case study interface for teaching real-time adaptive music composition for video games
Authors: McAlpine Kenneth 
Published: September 2016

Abstract
Real-time adaptive music is now well-established as a popular medium, largely through its use in video game soundtracks. Commercial packages, such as fmod, make freely available the underlying technical methods for use in educational contexts, making adaptive music technologies accessible to students. Writing adaptive music, however, presents a significant learning challenge, not least because it requires a different mode of thought, and tutor and learner may have few mutual points of connection in discovering and understanding the musical drivers, relationships and structures in these works. This article discusses the creation of ‘BitBox!’, a gestural music interface designed to deconstruct and explain the component elements of adaptive composition through interactive play. The interface was displayed at the Dare Protoplay games exposition in Dundee in August 2014. The initial proof-of-concept study proved successful, suggesting possible refinements in design and a broader range of applications.
Understanding sheet music as a medium to expand pedagogic practice
Authors: Thibeault Matthew D. 
Published: September 2016

Abstract
In the field of sound studies, a medium is the contingent network of recurring relations between people, practices, institutions and technologies. This article explores sheet music as a medium that can serve to expand the pedagogic practices typically pursued in music education. Understanding the medium of sheet music as a network also can encourage music educators to understand and critique how all practices are enmeshed in media. The theoretical perspective of expanded practices is then connected to two examples of classes exploring Beck’s sheet music project Song Reader: one, a class at Chicago’s Old Town School of Folk Music (OTSFM); and, two, a project the author undertook with a graduate music education course. Eight specific practices are presented through these two examples: one, to incorporate sheet music into new media practices; two, to connect a local community of musicians to an online community; three, to move sheet music beyond face to face concerts; four, to note how audiences now routinely produce content consumed by artists; five, to connect sheet music to amateur music-making; six, to reclaim popular music for participatory music-making; seven, to invite music educators to participate in the larger renaissance of amateurism; and, eight, for educators to join in the joy exemplified by Song Reader.
On the Hausdorff Dimension of CAT(κ)
Surfaces
Authors: Constantine David , Lafont Jean-François 
Published: September 2016

Abstract
We prove that a closed surface with a CAT(κ) metric has Hausdorff dimension = 2, and that there
are uniform upper and lower bounds on the two-dimensional Hausdorff measure of small metric balls. We
also discuss a connection between this uniformity condition and some results on the dynamics of the geodesic
flow for such surfaces. Finally,we give a short proof of topological entropy rigidity for geodesic flow on certain
CAT(−1) manifolds.
Hybrid textile heart valve prosthesis: preliminary in vitro evaluation
Authors: Vaesken Antoine , Pidancier Christian , Chakfe Nabil , Heim Frederic 
Published: September 2016

Abstract
Transcatheter aortic valve implantation (TAVI) is nowadays a popular alternative technique to surgical valve replacement for critical patients. Biological valve tissue has been used in these devices for over a decade now with over 100,000 implantations. However, material degradations due to crimping for catheter insertion purpose have been reported, and with only 6-year follow-up, no information is available about the long-term durability of biological tissue. Moreover, expensive biological tissue harvesting and chemical treatment procedures tend to promote the development of synthetic valve leaflet materials. Textile polyester (PET) material is characterized by outstanding folding and strength properties combined with proven biocompatibility and could therefore be considered as a candidate to replace biological valve leaflets in TAVI devices. Nevertheless, the material should be preferentially partly elastic in order to limit water hammer effects at valve closing time and prevent exaggerated stress from occurring into the stent and the valve. The purpose of the present work is to study in vitro the mechanical as well as the hydrodynamic behavior of a hybrid elastic textile valve device combining non-deformable PET yarn and elastic polyurethane (PU) yarn. The hybrid valve properties are compared with those of a non-elastic textile valve. Testing results show improved hydrodynamic properties with the elastic construction. However, under fatigue conditions, the interaction between PU and PET yarns tends to limit the valve durability.
Fatty acid production of tropical thraustochytrids from Malaysian mangroves
Authors: Ou Mei-Cing , Yeong Hui-Yin , Pang Ka-Lai , Phang Siew-Moi 
Published: September 2016

Abstract
A total of 33 tropical thraustochytrid isolates were isolated from fallen leaves of Malaysian mangroves. Phylogenetic analysis based on the 18S rRNA gene revealed that the majority of the 33 isolates belonged to the genus Aurantiochytrium, and only one isolate belonged to Parietichytrium. The specific growth rate and biomass productivity of the strains ranged from 0.17 to 0.93 day−1 and 0.03 to 0.62 g l−1 day−1, respectively. Lipid productivity ranged from 1.27 to 70.86 mg l−1 day−1. Fifteen fatty acids, dominated by C16:0 [19.5%–71.6% total fatty acid (TFA)], C15:0 (3.3%–43.1% TFA), C22:6n3 (1.5%–38.4% TFA) and C18:0 (2.9%–28.6% TFA), were identified. The total carotenoid content was shown to be a better chemotaxonomic character than fatty acid composition for the isolates. Aurantiochytrium sp. UMACC-T024 had the highest lipid productivity (70.86 mg l−1 day−1), and this was selected for an optimisation study. The optimal conditions for lipid production of Aurantiochytrium sp. UMACC-T024 were salinity 32, pH 7.5, 1% w/v glucose and 0.5 g l−1 yeast extract, which resulted in an enhanced lipid productivity of 263.37 mg l−1 day−1 at day 5.
A real-world evidence-based approach to laboratory reorganization using e-Valuate benchmarking data
Authors: Bonini Fabio , Barletta Giovanni , Plebani Mario 
Published: September 2016

AbstractBackground:Pressure to cut health-care costs has involved clinical laboratories underpinning the need to reduce cost per test through programs designed to consolidate activities and increase volumes. Currently, however, there is little evidence of the effectiveness of these measures. The aim of the present study was to verify whether a rational, evidence-based decision-making process might be achieved based on an activity-based cost analysis performed by collecting the data of all variables affecting cost per test.Methods:An activity-based costing analysis was performed using a program that provides collected data on performance indicators, benchmark between different laboratories based on performance indicators, and information on reorganization initiatives.Results:The data provided were used in two different settings to (1) verify the results of the internal re-organization of specific protein assay and (2) simulate some scenarios for the reorganization of autoimmune testing in the network of clinical laboratories in a large territory.Conclusions:The data produced by the e-Valuate project enabled the quantification of variation in costs, the utilization of human and technological resources and efficiency, both as final result of a reorganization project (proteins) and as a simulation of a possible future organization (autoimmune tests).
Retrospective validation of a β-trace protein interpretation algorithm for the diagnosis of cerebrospinal fluid leakage
Authors: Bernasconi Luca , Pötzl Theresa , Steuer Christian , Dellweg Alexander , Metternich Frank , Huber Andreas R. 
Published: September 2016

Abstract

Background:
Cerebrospinal fluid (CSF) leakage is a rare condition that can potentially lead to the development of serious complications. In the last decade, β-trace protein (β-TP) has been shown to be a valuable immunological biomarker that allows prompt and non-invasive identification of CSF leakage. At our institution, the measurement of β-TP has been included in the diagnostic work-up of CSF leakage for more than 10 years. According to our diagnostic algorithm, the presence of CSF in secretion is excluded when β-TP values are <0.7 mg/L, whereas β-TP values ≥1.3 mg/L indicate the presence of CSF in secretion. β-TP values between 0.7 and 1.29 mg/L indicate the presence of CSF if the β-TP ratio (β-TP secretion/β-TP serum) is ≥2. This study aimed to validate this diagnostic algorithm using clinically defined nasal/ear secretions.

Methods:
We performed a retrospective statistical analysis of three β-TP interpretation strategies using data of 236 samples originating from 121 patients with suspect CSF leakage received at our laboratory between 2004 and 2012.

Results:
The highest odds ratio was obtained when the proposed algorithm has been used for the interpretation of β-TP results, showing a sensitivity of 98.3% and a specificity of 96%. Positive and negative predictive values were 89.2% and 99.4%, respectively.

Conclusions:
Our data suggest that the proposed β-TP interpretation algorithm is a valuable tool for the diagnosis of CSF leakage in the clinical practice.
Geometric nonlinear free vibration of axially functionally graded non-uniform beams supported on elastic foundation
Authors: Lohar Hareram , Mitra Anirban , Sahoo Sarmila 
Published: September 2016

AbstractIn the present study non-linear free vibration analysis is performed on a tapered Axially Functionally Graded (AFG) beam resting on an elastic foundation with different boundary conditions. Firstly the static problem is carried out through an iterative scheme using a relaxation parameter and later on the subsequent dynamic problem is solved as a standard eigen value problem. Minimum potential energy principle is used for the formulation of the static problem whereas for the dynamic problem Hamilton’s principle is utilized. The free vibrational frequencies are tabulated for different taper profile, taper parameter and foundation stiffness. The dynamic behaviour of the system is presented in the form of backbone curves in dimensionless frequency-amplitude plane.