bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating risk of malignancy in adnexal masses: external validation of the ADNEX model and comparison with other frequently used ultrasound methods
Authors: Meys E. M. J. , Jeelof L. S. , Achten N. M. J. , Slangen B. F. M. , Lambrechts S. , Kruitwagen R. F. P. M. , Van Gorp T. 
Published: August 2016

ABSTRACTObjectivesTo validate externally the performance of the Assessment of Different NEoplasias in the adneXa (ADNEX) model and compare this model with other frequently used models in the differentiation between benign and malignant adnexal masses.MethodsIn this retrospective diagnostic accuracy study, we assessed data collected prospectively from patients with adnexal pathology who underwent real‐time transvaginal or transrectal ultrasound by a single expert ultrasonographer in a tertiary care hospital between July 2011 and July 2015. The presence of a malignancy was determined by subjective assessment and use of four prediction models: the ADNEX model, simple ultrasound‐based rules (simple rules), Logistic Regression model 2 (LR2) and the Risk of Malignancy Index (RMI), of which three different variants were assessed. Pathology was the clinical reference standard.ResultsIn total, 851 consecutive patients underwent ultrasound examination for an adnexal mass. For 326 patients (128 premenopausal and 198 postmenopausal), pathology results were available (211 (64.7%) benign; 115 (35.3%) malignant) and these were included in the analysis. The area under the receiver–operating characteristics curve (AUC) of the ADNEX model for the discrimination between benign and malignant tumors was 0.93 (95% CI, 0.89–0.95). AUCs for the subtypes of malignancy (i.e. borderline, Stage I–IV and metastatic adnexal tumors) ranged between 0.60 and 0.90. Only subjective assessment (AUC, 0.96 (95% CI, 0.93–0.98)) was superior to the ADNEX model (P = 0.01) in differentiating malignant from benign tumors. AUCs for the other models were 0.92 (95% CI, 0.89–0.95) for LR2, 0.85 (95% CI, 0.81–0.89) for RMI‐I, 0.82 (95% CI, 0.77–0.86) for RMI‐II and 0.84 (95% CI, 0.80–0.88) for RMI‐III. At the proposed cut‐off of ≥ 10%, the ADNEX model had the highest sensitivity (0.98 (95% CI, 0.93–1.00)) but the lowest specificity (0.62 (95% CI, 0.55–0.68)) compared with the other models. Both subjective assessment (sensitivity, 0.90 (95% CI, 0.83–0.95); specificity 0.91 (95% CI, 0.86–0.94)) and the simple rules model with inconclusive cases classified by subjective assessment (sensitivity, 0.89 (95% CI, 0.81–0.94); specificity, 0.90 (95% CI, 0.85–0.94)) had lower sensitivity, but their sensitivity and specificity were better balanced.ConclusionsAlthough the test performance of subjective assessment by an expert remains superior, the ADNEX model can help in the differentiation between benign and malignant ovarian tumors. The advantage of the ADNEX model as a polytomous model remains to be shown. © 2016 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
Formalising concurrent UML state machines using coloured Petri nets
Authors: André Étienne , Benmoussa Mohamed Mahdi , Choppy Christine 
Published: August 2016

Abstract
With the increasing complexity of dynamic concurrent systems, a phase of formal specification and formal verification is needed. UML state machines are widely used to specify dynamic systems behaviours. However, the official semantics of UML is described in a semi-formal manner, which renders the formal verification of complex systems delicate. In this paper, we propose a formalisation of UML state machines using coloured Petri nets. We consider in particular concurrent aspects (orthogonal regions, forks, joins, variables), the hierarchy induced by composite states and their associated activities, external, local or inter-level transitions, entry/exit/do behaviours, transition priorities, and shallow history pseudostates. We use a CD player as a motivating example, and run various verifications using CPN Tools.
Predation of wood mice (Apodemus sylvaticus) on hibernating bats
Authors: Haarsma Anne‐Jifke , Kaal Rutger 
Published: August 2016

AbstractBat hibernacula with high numbers of bats can become high‐risk areas, as they attract flying and non‐flying predators. In order to protect hibernating bats effectively, more knowledge about mortality factors is needed. During the winters of 2003–2015, we found 214 dead bats in 12 hibernacula in The Netherlands province of Zuid‐Holland. Most bat remains were found in December and January, with a second peak in April. Their remains showed a typical pattern of lesions consistent with those caused by predation by the wood mouse (Apodemus sylvaticus). Trail camera surveys showed that wood mice actively searched for bats. Predation pressure seemed to vary between winters, with a peak in the winters of 2004, 2011 and 2015. The annual mortality (relative to the maximum winter population size) caused by wood mouse predation varied between 0.1 and 8.8 %, with a maximum local effect of 83.6 %. The years with high wood mouse predation pressure were characterized by a long frost period and a low mast production of common oak in the preceding autumn. The size of a hibernaculum and the population density of its bats had an effect on predation‐dependent mortality. The highest predation risk occurred near the entrance of bunkers. From these results we tentatively conclude that predation is not incidental and that wood mice actively search for and kill hibernating bats or scavenge for weakened individuals.
Increased acid resistance of the archaeon,Metallosphaera sedulaby adaptive laboratory evolution
Authors: Ai Chenbing , McCarthy Samuel , Eckrich Valerie , Rudrappa Deepak , Qiu Guanzhou , Blum Paul 
Published: August 2016

AbstractExtremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78 % more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions. These unique genomic and transcriptomic features support a model for increased acid resistance arising from enhanced control over cytoplasmic pH.
Bioprocess development for extracellular production of recombinant human interleukin-3 (hIL-3) inPichia pastoris
Authors: Dagar Vikas Kumar , Adivitiya  , Devi Nirmala , Khasa Yogender Pal 
Published: August 2016

AbstractHuman interleukin-3 (hIL-3) is a therapeutically important cytokine involved in the maturation and differentiation of various cells of the immune system. The codon-optimized hIL-3 gene was cloned in fusion with the N-terminus α-mating factor signal peptide of Saccharomyces cerevisiae under an inducible alcohol oxidase 1 (AOX1) and constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter. A Zeocin concentration up to 2000 mg/L was used to select hyper-producers. The shake flask cultivation studies in the Pichia pastoris GS115 host resulted a maximum recombinant hIL-3 expression level of 145 mg/L in the extracellular medium under the control of AOX1 promoter. The batch fermentation strategy allowed us to attain a fairly pure glycosylated hIL-3 protein in the culture supernatant at a final concentration of 475 mg/L with a high volumetric productivity of 4.39 mg/L/h. The volumetric product concentration achieved at bioreactor level was 3.28 folds greater than the shake flask results. The 6x His-tagged protein was purified using Ni–NTA affinity chromatography and confirmed further by western blot analysis using anti-6x His tag antibody. The glycosylation of recombinant hIL-3 protein was confirmed in a PNGase F deglycosylation reaction where it showed a molecular weight band pattern similar to E. coli produced non-glycosylated hIL-3 protein. The structural properties of recombinant hIL-3 protein were confirmed by CD and fluorescence spectroscopy where protein showed 40 % α-helix, 12 % β-sheets with an emission maxima at 343 nm. MALDI-TOF-TOF analysis was used to establish the protein identity. The biological activity of purified protein was confirmed by the human erythroleukemia TF-1 cell proliferation assay.
Genomic Analysis of Genes Involved in the Biosynthesis of Very Long Chain Polyunsaturated Fatty Acids in Thraustochytrium sp. 26185
Authors: Zhao Xianming , Dauenpen Meesapyodsuk , Qu Cunmin , Qiu Xiao 
Published: August 2016

AbstractThraustochytrium sp. 26185 is a marine protist that can produce a large amount of docosahexaenoic acid (DHA, 22:6n‐3), an ω3 very long chain polyunsaturated fatty acid (VLCPUFA) of nutritional importance. However, the mechanism of how this fatty acid is synthesized and assembled into the storage lipid triacylglycerol is unclear. Here we report sequencing of the whole genome and genomic analysis of genes involved in the biosynthesis and assembly of the fatty acids in this species. Genome sequencing produced a total of 2,418,734,139 bp clean sequences with about 62 fold genome coverage. Annotation of the genome sequences revealed 10,797 coding genes. Among them, 10,216 genes could be assigned into 25 KOG classes where 451 genes were specifically assigned to the group of lipid transport and metabolism. Detailed analysis of these genes revealed co‐existence of both aerobic pathway and anaerobic pathways for the biosynthesis of DHA in this species. However, in the aerobic pathway, a key gene encoding stearate Δ9 desaturase introducing the first double bond to long chain saturated fatty acid 18:0 was missing from the genome. Genomic survey of genes involved in the acyl trafficking among glycerolipids showed that, unlike plants, this protist did not possess phosphatidylcholine:diacylglycerol cholinephosphotransferase, an important enzyme in bridging two types of glycerolipids, diacylglycerols (DAG) and phosphatidylcholines (PtdCho). These results shed new insight on the biosynthesis and assembly of VLCPUFA in the Thraustochytrium.
Olive Oil‐Based Lipid Emulsions Do Not Influence Platelet Receptor Expression in Comparison to Medium and Long Chain Triglycerides In vitro
Authors: Stoetzer Carsten , Nickel Katja , Weißig Annette , Großheim Marieke , Scheinichen Dirk , Doll Thorben , Jüttner Björn 
Published: August 2016

AbstractLipid emulsions influence platelet aggregation and receptor expression. However, the effect on platelet function is not fully explained. Therefore, the aim of this study was to examine the influence of the lipids Lipofundin®, Lipidem® and ClinOleic® on surface expressions of P‐selectin, GPIb and GPIIb/IIIa on platelets in vitro. Whole blood was incubated in two different concentrations (0.06 and 0.6 mg/ml) of LCT/MCT, n‐3/LCT/MCT and LCT‐MUFA for 30 min, followed by activation with TRAP‐6 or ADP for flow‐cytometric assay. Rates of P‐selectin, GPIb and GPIIb/IIIa expression were analyzed. There was a significant increase in GPIIb/IIIa‐ and P‐selectin‐expression after incubation with LCT/MCT and n‐3/LCT/MCT at the concentration of 0.6 mg/ml, without and after stimulation with TRAP‐6 and ADP. GPIb was significantly decreased. Accordingly, LCT‐MUFA had no effect on receptor expression of platelets in vitro. We demonstrated that LCT‐MUFA did not activate receptor expression of platelets whereas LCT/MCT significantly increased platelet aggregation in vitro. This finding should be noted for parenteral nutrition of intensive care patients and, in the future, might provide further insight into the pathogenic pathways of acute thromboembolic events. However, prospectively designed clinical studies are needed to support our results.
Measurement of specific storage of rock for supercritical carbon dioxide using constant flow pump and constant head permeability techniques
Authors: Arsyad Ardy , Mitani Yasuhiro , Ikemi Hiro 
Published: August 2016

Abstract
Advanced laboratory system of rock permeability test associated with constant flow pump, and constant head permeability techniques were developed to measure permeability and specific storage of rock for supercritical CO2. The laboratory system was designed to be capable in reproducing similar physical condition of deep aquifer within high pressure and high temperature where CO2 tends to be in supercritical state. To analyze the result of permeability tests, mathematical models of constant flow pump and constant head permeability techniques were modified to deal with two-phase flow drainage displacement of CO2-water in rock. For the examination of its applicability, experimental tests and numerical analysis were undertaken. The accuracy of the obtained specific storage was validated by employing a ratio of the specific storage of the rock specimen to the storage capacity of the pump used in the permeability test. It was found that the specific storage of low permeability sandstone for storing supercritical CO2 is 1.63 × 10−4 1/Pa, while large permeability sandstone has the specific storage for supercritical CO2 at 1.12 × 10−7 1/Pa. This finding suggested that advanced experimental system of constant flow pump and constant head permeability technique can be used as repeatable, accurate and standardized laboratory test in measuring specific storage of sedimentary rock for CO2 in supercritical state.
Major determinants for the selecting antithrombotic therapies in patients with nonvalvular atrial fibrillation in Japan (JAPAF study)
Authors: Kusakawa Koichi , Harada Kouji H. , Kagimura Tatsuo , Koizumi Akio 
Published: August 2016

AbstractBackgroundOral anticoagulants (OACs) can help prevent stroke in patients with nonvalvular atrial fibrillation (NVAF). The aim of this study was to characterize the use of OACs other than direct thrombin inhibitors (DTIs) for NVAF.MethodsPatients with NVAF taking antithrombotics other than DTIs were enrolled in this cross‐sectional study. Patient demographics and medication history were collected, and the patients were classified as taking antiplatelet monotherapy (AP), anticoagulant monotherapy (AC), or combination therapy (AP+AC). OAC users were also stratified as naïve (N; initiated within 6 months), switcher (S; switched within 6 months), or prevalent user (P; continued for >6 months).ResultsA total of 3053 patients (AP, 216; AC, 2381; AP+AC, 456) from 268 sites were enrolled from 2012 to 2013. Significant differences were observed in CHADS2 scores (AP/AC/AP+AC: 2.0/2.1/2.7, P<0.0001), angina complications (20.1/8.6/32.1, P<0.0001), myocardial infarction (5.1/2.8/18.1, P<0.0001), prothrombin time–international normalized ratio (PT–INR) (−/2.00/1.94, P=0.0350), and others. There were 2831 OAC users (N, 328; S, 213; P, 2290). Significant differences were observed in history of bleeding (N/S/P: 2.4/9.4/4.5, P<0.001), PT–INR (1.83/2.01/2.00, P<0.0001), and others.ConclusionsPatients taking AP+AC had higher CHADS2 scores than those taking an AP or AC alone. Additionally, the combination therapy (AP+AC) was preferred in patients with cardiovascular comorbidity. Changes in AC regimens were not influenced by CHADS2 scores or complications but influenced by history of bleeding. These characteristics were thus identified as major factors affecting the selection of antithrombotic regimens other than DTIs in patients with NVAF.
Trabajo en equipo y rendimiento académico en un curso de kinesiología empleando aprendizaje basado en equipos
Authors: Delgado Rivera Macarena , Fasce Henry Eduardo , Pérez Villalobos Cristhian , Rivera Fuentes Nancy , Salazar Saéz Pablo , Riquelme Vallejos Cacia , Campos Cerda Ivone 
Published: August 2016

Introducción: El aprendizaje basado en equipos (ABE) es una estrategia de aprendizaje activa, que fomenta competencias transversales, como el trabajo en equipo (TE). Considerando que el ABE implica definir metas de aprendizaje, planificar estrategias para alcanzarlas, cumpliendo tareas definidas y roles concretos, es esperable que promueva el desarrollo del TE.
Objetivo: Evaluar la relación entre las habilidades de TE y el rendimiento académico de los estudiantes de Kinesiología de una universidad privada chilena posterior a su participación en ABE.
Método: Diseño preexperimental. Se aplicó el ABE en 5 sesiones. Cincuenta y un estudiantes (43.14% mujeres, edad promedio: 23.61 años) trabajaron en 9 grupos. Al finalizar la asignatura se aplicó una escala tipo Likert para evaluar TE. Se evalúo el rendimiento mediante test individuales, test grupales y actividades de aplicación. La participación fue voluntaria, previo consentimiento informado.
Resultados: En cuanto a sus habilidades de TE, los estudiantes reportaron alta capacidad de planificación en equipo (80.9%), comunicación (68.8%) y baja capacidad de resolución de problemas colaborativos (25.5%). Las habilidades de TE no mostraron correlaciones significativas con los test individuales, pero sí una correlación directa con algunos test grupales y aplicaciones.
Conclusiones: Al finalizar el ABE, los estudiantes de Kinesiología presentan altos puntajes en la escala de TE en general. Resultados esperables pues la metodología permite desarrollar habilidades de TE, con el estímulo de alcanzar metas comunes al finalizar cada sesión y la asignatura en sí misma. En cuanto a la relación del TE y el rendimiento académico, esto se observó en algunos casos, que mostraría que temáticas familiares y situaciones desafiantes facilitan el TE. El TE es una competencia genérica relevante en la formación de profesionales. El ABE podría favorecerlo, aunque se requieren otros diseños experimentales para comprobarlo.
Rasch analysis resulted in an improved Norwegian version of the Pain Attitudes and Beliefs Scale(PABS)
Authors: Eland Nicolaas D. , Kvåle Alice , Ostelo Raymond W.J.G. , Strand Liv Inger 
Published: August 2016

Abstract

Background and aim
There is evidence that clinicians’ pain attitudes and beliefs are associated with the pain beliefs and illness perceptions of their patients and furthermore influence their recommendations for activity and work to patients with back pain. The Pain Attitudes and Beliefs Scale (PABS) is a questionnaire designed to differentiate between biomedical and biopsychosocial pain attitudes among health care providers regarding common low back pain. The original version had 36 items, and several shorter versions have been developed. Concern has been raised over the PABS’ internal construct validity because of low internal consistency and low explained variance. The aim of this study was to examine and improve the scale’s measurement properties and item performance.

Methods
A convenience sample of 667 Norwegian physiotherapists provided data for Rasch analysis. The biomedical and biopsychosocial subscales of the PABS were examined for unidimensionality, local response independency, invariance, response category function and targeting of persons and items. Reliability was measured with the person separation index (PSI). Items originally excluded by the developers of the scale because of skewness were re-introduced in a second analysis.

Results
Our analysis suggested that both subscales required removal of several psychometrically redundant and misfitting items to satisfy the requirements of the Rasch measurement model. Most biopsychosocial items needed revision of their scoring structure. Furthermore, we identified two items originally excluded because of skewness that improved the reliability of the subscales after reintroduction. The ultimate result was two strictly unidimensional subscales, each consisting of seven items, with invariant item ordering and free from any form of misfit. The unidimensionality implies that summation of items to valid total scores is justified. Transformation tables are provided to convert raw ordinal scores to unbiased interval-level scores. Both subscales were adequately targeted at the ability level of our physiotherapist population. Reliability of the biomedical subscale as measured with the PSI was 0.69. A low PSI of 0.64 for the biopsychosocial subscale indicated limitations with regard to its discriminative ability.

Conclusions
Rasch analysis produced an improved Norwegian version of the PABS which represents true (fundamental) measurement of clinicians’ biomedical and biopsychosocial treatment orientation. However, researchers should be aware of the low discriminative ability of the biopsychosocial subscale when analyzing differences and effect changes.

Implications
The study presents a revised PABS that provides interval-level measurement of clinicians’ pain beliefs. The revision allows for confident use of parametric statistical analysis. Further examination of discriminative validity is required.
Healthcare-Associated Infections in Pediatric and Neonatal Intensive Care Units: Impact of Underlying Risk Factors and Antimicrobial Resistance on 30-Day Case-Fatality in Italy and Brazil
Authors: Folgori Laura , Bernaschi Paola , Piga Simone , Carletti Michaela , Cunha Filippe Pirrone , Lara Paulo Henrique Rodriguez , de Castro Peixoto Nicholas Cafieiro , Alves Guimarães Bárbara Gomes , Sharland Mike , Araujo da Silva André Ricardo , Ciofi degli Atti Marta 
Published: August 2016

OBJECTIVESTo describe trends in the epidemiology of healthcare-associated Infections (HAIs) in pediatric/neonatal intensive care units (ICUs) and to evaluate risk factors and impact of multidrug resistance in children admitted to ICUs.DESIGNMulticenter, retrospective, cohort study with a nested case-control study conducted from January 1, 2010, through December 31, 2014.SETTINGThree tertiary care pediatric hospitals in Italy and Brazil with a total of 103 ICU beds.PATIENTSInclusion criteria were admission to ICU during the study period, age at onset less than 18 years, and microbiologically confirmed HAI.RESULTSA total of 538 HAIs in 454 children were included; 93.3% of patients had comorbidities. Bloodstream infections were the leading pattern (45.4%). The cumulative incidence of HAI was 3.6/100 ICU admissions and the crude 30-day fatality rate was 5.7/1,000 admissions. The most frequently isolated pathogens were Enterobacteriaceae, followed by Pseudomonas aeruginosa and Staphylococcus aureus. Forty-four percent of isolates were multidrug-resistant (MDR). Two multivariate logistic regressions were performed. Factors independently associated with an MDR-HAI were country, previous antibiotics, transplantation, major surgery, and colonization by an MDR strain. Factors independently associated with 30-day case fatality were country, previous transplantation, fungal infection, bloodstream infection, lower respiratory tract infection, and infection caused by MDR strains.CONCLUSIONSInfection control and prevention can limit the spread of MDR strains and improve outcomes. Targeted surveillance programs collecting neonatal and pediatric HAI/bloodstream infection data and outcomes would allow global benchmarking. The next step is to identify methods to monitor key HAIs and integrate these into affordable intervention programs.Infect Control Hosp Epidemiol 2016;1–8
NOTES ON THE GREEK ANTHOLOGY, BOOKS 1–5
Authors: Tueller Michael A. 
Published: August 2016

The following textual and interpretative notes were informed by the preparation of the first volume of the revised Greek Anthology for the Loeb Classical Library.Anth. Pal. 1.20 (Claudian)ἀρτιφανές, πολιοῦχε, παλαιγενές, υἱὲ νεογνέ,αἰὲν ἐὼν προεών τε, ὑπέρτατε, ὕστατε, Χριστέ,ἀθανάτοιο πατρός τε ὁμόχρονε, πάμπαν ὁμοῖε …2 ἐὼν ex αἰὼν P