bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practice Effects and Test–Retest Reliability of the Continuous Performance Test, Identical Pairs Version in Patients with Schizophrenia over Four Serial Assessments
Authors: Chen Kuan-Wei , Lin Gong-Hong , Chen Nan-Cheng , Wang Ji-Kuan , Hsieh Ching-Lin 
Published: January 2020

AbstractObjectiveThe purposes of this study were to examine the practice effects and test–retest reliability of the Continuous Performance Test, Identical Pairs version (CPT-IP) over four serial assessments in patients with schizophrenia.MethodFifty-six patients with schizophrenia were assessed with the CPT-IP four times, once per week. The CPT-IP contains four indices: “2-digit score,” “3-digit score,” “4-digit score,” and “total score.”ResultsThe four indices showed trivial-to-small practice effects (Cohen’s d = −0.13–0.24), good-to-excellent test–retest reliability (ICC = 0.62–0.88), and unacceptable random measurement error (MDC% = 33.8%–110.8%).ConclusionsThe total score had the best reliability among the four indices. Although practice effects of the four indices all appeared cumulative, all four CPT-IP indices reached a plateau after the second assessment. These results indicate that clinicians should interpret the change scores of the CPT-IP conservatively and use the total-score index in their routine repeated assessments.
AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics
Authors: Madrid-Gambin Francisco , Oller-Moreno Sergio , Fernandez Luis , Bartova Simona , Giner Maria Pilar , Joyce Christopher , Ferraro Francesco , Montoliu Ivan , Moco Sofia , Marco Santiago 
Published: January 2020

Abstract

Summary
Nuclear magnetic resonance (NMR)-based metabolomics is widely used to obtain metabolic fingerprints of biological systems. While targeted workflows require previous knowledge of metabolites, prior to statistical analysis, untargeted approaches remain a challenge. Computational tools dealing with fully untargeted NMR-based metabolomics are still scarce or not user-friendly. Therefore, we developed AlpsNMR (Automated spectraL Processing System for NMR), an R package that provides automated and efficient signal processing for untargeted NMR metabolomics. AlpsNMR includes spectra loading, metadata handling, automated outlier detection, spectra alignment and peak-picking, integration and normalization. The resulting output can be used for further statistical analysis. AlpsNMR proved effective in detecting metabolite changes in a test case. The tool allows less experienced users to easily implement this workflow from spectra to a ready-to-use dataset in their routines.

Availability and implementation
The AlpsNMR R package and tutorial is freely available to download from http://github.com/sipss/AlpsNMR under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Frailty to predict unplanned hospitalization, stroke, bleeding, and death in atrial fibrillation
Authors: Gugganig Rebecca , Aeschbacher Stefanie , Leong Darryl P , Meyre Pascal , Blum Steffen , Coslovsky Michael , Beer Jürg H , Moschovitis Giorgio , Müller Dominic , Anker Daniela , Rodondi Nicolas , Stempfel Samuel , Mueller Christian , Meyer-Zürn Christine , Kühne Michael , Conen David , Osswald Stefan ,   for the Swiss-AF Investigators
Published: January 2020

Abstract

Aims
Atrial fibrillation (AF) and frailty are common, and the prevalence is expected to rise further. We aimed to investigate the prevalence of frailty and the ability of a frailty index (FI) to predict unplanned hospitalizations, stroke, bleeding, and death in patients with AF.

Methods and results
Patients with known AF were enrolled in a prospective cohort study in Switzerland. Information on medical history, lifestyle factors, and clinical measurements were obtained. The primary outcome was unplanned hospitalization; secondary outcomes were all-cause mortality, bleeding, and stroke. The FI was measured using a cumulative deficit approach, constructed according to previously published criteria and divided into three groups (non-frail, pre-frail, and frail). The association between frailty and outcomes was assessed using multivariable-adjusted Cox regression models. Of the 2369 included patients, prevalence of pre-frailty and frailty was 60.7% and 10.6%, respectively. Pre-frailty and frailty were associated with a higher risk of unplanned hospitalizations [adjusted hazard ratio (aHR) 1.82, 95% confidence interval (CI) 1.49–2.22; P &lt; 0.001; and aHR 3.59, 95% CI 2.78–4.63, P &lt; 0.001], all-cause mortality (aHR 5.07, 95% CI 2.43–10.59; P &lt; 0.001; and aHR 16.72, 95% CI 7.75–36.05; P &lt; 0.001), and bleeding (aHR 1.53, 95% CI 1.11–2.13; P = 0.01; and aHR 2.46, 95% CI 1.61–3.77; P &lt; 0.001). Frailty, but not pre-frailty, was associated with a higher risk of stroke (aHR 3.29, 95% CI 1.2–8.39; P = 0.01).

Conclusion
Over two-thirds of patients with AF are pre-frail or frail. These patients have a high risk for unplanned hospitalizations and other adverse events. These findings emphasize the need to carefully evaluate these patients. However, whether screening for pre-frailty and frailty and targeted prevention strategies improve outcomes needs to be shown in future studies.

Clinical trial registration
Clinicaltrials.gov identifier number: NCT02105844.
Training curriculum for European thoracic surgeons: a joint initiative of the European Society of Thoracic Surgeons and the European Respiratory Society
Authors: Massard Gilbert , Tabin Nathalie , Konge Lars , Frick Anna Elisabeth , Batirel Hasan , Brunelli Alessandro , Elia Stefano , Huertgen Martin , Molins Laureano , Papagiannopoulos Kostas , Subotic Dragan , van Schil Paul , Varela Gonzalo , van Raemdonck Dirk 
Published: January 2020

Abstract
Because of the differing definitions of the margins of thoracic surgery as a specialty and the variability in the training curricula among European countries, the European Society of Thoracic Surgeons formed a task force to elaborate a consensual proposal. The first step comprised creating a harmonized syllabus that was completed and published in 2018. This publication presents a proposal for a curriculum upon which the task force and the external expert reviewers have agreed. The curriculum was developed by the task force: each module and item describe the expected level of knowledge, skills and attitudes to be attained by the participants; learning opportunities, assessment tools and minimal clinical exposures have been defined as well. Competence in terms of non-technical skills has been defined for each module according to the CanMEDS (http://www.royalcollege.ca/rcsite/canmeds/canmeds-framework-e) glossary. The different modules were subsequently submitted to an internal and an external review process and re-edited accordingly before final validation. The authors hope that this document will serve as a roadmap for both thoracic surgical trainees and mentors. It should further guide continuous professional development. However, evolving scientific and technological advances are expected to modify the diagnosis and treatment of diseases and disorders in the future and hence will mandate periodical revisions of the document.
Toll-like receptor 3 mediates ischaemia/reperfusion injury after cardiac transplantation
Authors: Gollmann-Tepeköylü Can , Graber Michael , Pölzl Leo , Nägele Felix , Moling Rafael , Esser Hannah , Summerer Bianca , Mellitzer Vanessa , Ebner Susanne , Hirsch Jakob , Schäfer Georg , Hackl Hubert , Cardini Benno , Oberhuber Rupert , Primavesi Florian , Öfner Dietmar , Bonaros Nikolaos , Troppmair Jakob , Grimm Michael , Schneeberger Stefan , Holfeld Johannes , Resch Thomas 
Published: January 2020

Abstract

OBJECTIVES
Ischaemia and subsequent reperfusion during heart transplantation inevitably result in donor organ injury. Toll-like receptor (TLR)-3 is a pattern recognition receptor activated by viral and endogenous RNA released by injured cells. We hypothesized that ischaemia/reperfusion injury (IRI) leads to RNA release with subsequent TLR3 activation in transplanted hearts.

METHODS
Human endothelial cells were subjected to IRI and treated with TLR3 agonist polyinosinic–polycytidylic acid or a TLR3/double-stranded RNA complex inhibitor. TLR3 activation was analysed using reporter cells. Gene expression profiles were evaluated via next-generation sequencing. Neutrophil adhesion was assessed in vitro. Syngeneic heart transplantation of wild-type or Tlr3−/− mice was performed following 9 h of cold ischaemia. Hearts were analysed for inflammatory gene expression, cardiac damage, apoptosis and infiltrating leucocytes.

RESULTS
IRI resulted in RNA release with subsequent activation of TLR3. Treatment with a TLR3 inhibitor abrogated the inflammatory response upon IRI. In parallel, TLR3 stimulation caused activation of the inflammasome. Endothelial IRI resulted in TLR3-dependent adhesion of neutrophils. Tlr3−/− animals showed reduced intragraft and splenic messenger ribonucleic acid (mRNA) expression of proinflammatory cytokines, resulting in decreased myocardial damage, apoptosis and infiltrating cells. Tlr3 deficiency protected from cardiac damage, apoptosis and leucocyte infiltration after cardiac transplantation.

CONCLUSIONS
We uncover the release of RNA by injured cells with subsequent activation of TLR3 as a crucial pathomechanism of IRI. Our data indicate that TLR3 represents a novel target in the prevention of IRI in solid organ transplantation.
Body site-specific microbiota reflect sex and age-class among wild spotted hyenas
Authors: Rojas Connie A , Holekamp Kay E , Winters Andrew D , Theis Kevin R 
Published: January 2020

ABSTRACTHost-associated microbial communities, henceforth ‘microbiota’, can affect the physiology and behavior of their hosts. In mammals, host ecological, social and environmental variables are associated with variation in microbial communities. Within individuals in a given mammalian species, the microbiota also partitions by body site. Here, we build on this work and sequence the bacterial 16S rRNA gene to profile the microbiota at six distinct body sites (ear, nasal and oral cavities, prepuce, rectum and anal scent gland) in a population of wild spotted hyenas (Crocuta crocuta), which are highly social, large African carnivores. We inquired whether microbiota at these body sites vary with host sex or social rank among juvenile hyenas, and whether they differ between juvenile females and adult females. We found that the scent gland microbiota differed between juvenile males and juvenile females, whereas the prepuce and rectal microbiota differed between adult females and juvenile females. Social rank, however, was not a significant predictor of microbiota profiles. Additionally, the microbiota varied considerably among the six sampled body sites and exhibited strong specificity among individual hyenas. Thus, our findings suggest that site-specific niche selection is a primary driver of microbiota structure in mammals, but endogenous host factors may also be influential.
Prevalence and antimicrobial resistance of Listeria species and molecular characterization of Listeria monocytogenes isolated from retail ready-to-eat foods
Authors: Arslan Seza , Özdemir Fatma 
Published: January 2020

ABSTRACT
A wide variety of foods can be contaminated with Listeria species, especially L. monocytogenes. Ready-to-eat (RTE) foods are predominantly associated with human listeriosis caused by L. monocytogenes. Therefore, this study aimed to assess the presence of Listeria species in RTE foods and to characterize L. monocytogenes isolates by means of detection of virulence markers, serotypes and genetic relatedness. Of the 300 RTE food samples, 59 (19.7%) were positive for Listeria species: L. innocua (13.3%), L. monocytogenes (5%), L. welshimerii (2.3%), L. grayi subsp. murrayi (1.3%), L. grayi (1%), L. ivanovii (1%) and L. ivanovi subsp. londoniensis (0.3%). All L. monocytogenes isolates identified were positive for the actA, iap, inlA, inlB, inlC, inlJ, plcA and prfA virulence genes and biofilm. The isolates were serotyped as 1/2c (33.3%), 4b (26.7%), 1/2a (26.7%), 1/2b (6.7%) and 3c (6.7%) by the multiplex-PCR and agglutination methods. PCR-restriction fragment length polymorphism with AluI and MluCI resulted in three and two profiles, respectively. Pulsed-field gel electrophoresis differentiated the L. monocytogenes isolates into 15 ApaI and 12 AscI patterns. Antimicrobial resistance of all Listeria isolates was determined by the disk diffusion method. Most L. monocytogenes isolates were sensitive to antimicrobials used in the treatment of listeriosis. This study shows the presence of potential pathogenic and antimicrobial-resistant L. monocytogenes in RTE foods that may lead to consumer health risks.
Enzyme replacement therapy in mice lacking arylsulfatase B targets bone-remodeling cells, but not chondrocytes
Authors: Hendrickx Gretl , Danyukova Tatyana , Baranowsky Anke , Rolvien Tim , Angermann Alexandra , Schweizer Michaela , Keller Johannes , Schröder Jörg , Meyer-Schwesinger Catherine , Muschol Nicole , Paganini Chiara , Rossi Antonio , Amling Michael , Pohl Sandra , Schinke Thorsten 
Published: January 2020

AbstractMucopolysaccharidosis type VI (MPS-VI), caused by mutational inactivation of the glycosaminoglycan-degrading enzyme arylsulfatase B (Arsb), is a lysosomal storage disorder primarily affecting the skeleton. We have previously reported that Arsb-deficient mice display high trabecular bone mass and impaired skeletal growth. In the present study, we treated them by weekly injection of recombinant human ARSB (rhARSB) to analyze the impact of enzyme replacement therapy (ERT) on skeletal growth and bone remodeling. We found that all bone-remodeling abnormalities of Arsb-deficient mice were prevented by ERT, whereas chondrocyte defects were not. Likewise, histologic analysis of the surgically removed femoral head from an ERT-treated MPS-VI patient revealed that only chondrocytes were pathologically affected. Remarkably, a side-by-side comparison with other cell types demonstrated that chondrocytes have substantially reduced capacity to endocytose rhARSB, together with low expression of the mannose receptor. We finally took advantage of Arsb-deficient mice to establish quantification of chondroitin sulfation for treatment monitoring. Our data demonstrate that bone-remodeling cell types are accessible to systemically delivered rhARSB, whereas the uptake into chondrocytes is inefficient.
Development of automated annotation software for human embryo morphokinetics
Authors: Feyeux M , Reignier A , Mocaer M , Lammers J , Meistermann D , Barrière P , Paul-Gilloteaux P , David L , Fréour T 
Published: January 2020

Abstract

STUDY QUESTION
Is it possible to develop an automated annotation tool for human embryo development in time-lapse devices based on image analysis?

SUMMARY ANSWER
We developed and validated an automated software for the annotation of human embryo morphokinetic parameters, having a good concordance with expert manual annotation on 701 time-lapse videos.

WHAT IS KNOWN ALREADY
Morphokinetic parameters obtained with time-lapse devices are increasingly used for the assessment of human embryo quality. However, their annotation is time-consuming and can be slightly operator-dependent, highlighting the need to develop fully automated approaches.

STUDY DESIGN, SIZE, DURATION
This monocentric study was conducted on 701 videos originating from 584 couples undergoing IVF with embryo culture in a time-lapse device. The only selection criterion was that the duration of the video must be over 60 h.

PARTICIPANTS/MATERIALS, SETTING, METHODS
An automated morphokinetic annotation tool was developed based on gray level coefficient of variation and detection of the thickness of the zona pellucida. The detection of cellular events obtained with the automated tool was compared with those obtained manually by trained experts in clinical settings.

MAIN RESULTS AND THE ROLE OF CHANCE
Although some differences were found when embryos were considered individually, we found an overall concordance between automated and manual annotation of human embryo morphokinetics from fertilization to expanded blastocyst stage (r2 = 0.92).

LIMITATIONS, REASONS FOR CAUTION
These results should undergo multicentric external evaluation in order to test the overall performance of the annotation tool. Getting access to the export of 3D videos would enhance the quality of the correlation with the same algorithm and its extension to the 3D regions of interest. A technical limitation of our work lies within the duration of the video. The more embryo stages the video contains, the more information the script has to identify them correctly.

WIDER IMPLICATIONS OF THE FINDINGS
Our system paves the way for high-throughput analysis of multicentric morphokinetic databases, providing new insights into the clinical value of morphokinetics as a predictor of embryo quality and implantation.

STUDY FUNDING/COMPETING INTEREST(S)
This study was partly funded by Finox-Gedeon Richter Forward Grant 2016 and NeXT (ANR-16-IDEX-0007). We have no conflict of interests to declare.

TRIAL REGISTRATION NUMBER
N/A
Long-term follow-up of Bentall procedure using the Perimount bioprosthesis and the Valsalva graft
Authors: Chirichilli Ilaria , Irace Francesco Giosuè , D’Aleo Salvatore , Folino Giulio , Weltert Luca Paolo , Scaffa Raffaele , Nardella Saverio , De Paulis Ruggero 
Published: January 2020

Abstract

OBJECTIVES
Bentall procedure is the gold standard for aortic root pathologies when valve repair is not feasible. The development of durable bioprosthetic valves and improved vascular conduits allowed the implementation of bioprosthetic composite grafts; hereby, we performed a retrospective analysis of long-term follow-up of Bentall procedure using the Valsalva graft and the Perimount Magna Ease prosthesis.

METHODS
From June 2000 to March 2019, 309 patients received an aortic root and valve replacement with a bioprosthetic composite graft. The mean age was 69 ± 6.9 years, and the majority were men (88%); most of them were affected by aortic stenosis (86%) and the mean aortic root diameter was 48.6 ± 5.5 mm.

RESULTS
Freedom from cardiac death was 76.8% [confidence interval (CI) 32.5–94.0] at 16 years. Freedom from thromboembolism, haemorrhage, structural valve deterioration and infective endocarditis was 98.2% (CI 96.0–98.9), 95.2% (CI 87.1–98.2), 87.5% (CI 63.2–97.1) and 79.6% (CI 45.3–95.6) at 16 years, respectively. Freedom from reoperation was 74.7% (CI 41.9–90.6).

CONCLUSIONS
These data indicate that, in experienced centres, the Bentall procedure is a safe and effective intervention. This is the first long-term follow-up that analyses the results after implantation of a composite graft made with the Perimount Magna Ease aortic valve and the Valsalva graft.
Analysis on the monitoring system of energy conservation and comfort in office buildings based on internet of things
Authors: Li Dongmei 
Published: January 2020

Abstract
In order to reduce the cost of central air conditioning, we need to reduce its energy consumption. This paper briefly introduced Internet of Things and the energy-saving and comfort monitoring system of central air conditioning based on the Internet of Things. The system took comfort degree as constraint and energy efficiency as objective to control energy saving of central air conditioning. Company X in Guanghan, Sichuan, China, was taken as an example for analysis. The system was compared with the energy-saving control system which took temperature and power as constraints. Compared with before the energy-saving control, the proportion of air conditioning downtime in the working hours of employees increased after the implementation of the two kinds of energy-saving control systems, and the proportion of downtime under the energy-saving control system designed in this study was larger; in addition, after the control of the two kinds of energy-saving systems, the energy efficiency of the air conditioning significantly improved, and the air conditioning under the control of the energy-saving system proposed in this study had more improvement in energy efficiency and higher energy-saving efficiency. The energy-saving control method proposed in this study can effectively reduce the power consumption of the central air conditioning in the office.
Electrophysiological properties of neurons grown on soft polymer scaffolds reveal the potential to develop neuromimetic culture environments
Authors: Evans Michael G , Al-Shakli Arwa , Chari Divya M 
Published: January 2020

Abstract
Tissue engineering methodologies for various physiological systems are seeing a significant trend towards 3D cell culture in or on ‘soft’ polymeric hydrogel materials, widely considered to provide a more biomimetic environment for cell growth versus ‘hard’ materials such as glass or plastic. Progress has been slower with 3D neural cell culture with current studies overwhelmingly reliant on hard substrates. Accordingly, our knowledge of the alterations in electrochemical properties of neurons propagated in soft materials is relatively limited. In this study, primary cortical neurons and glial cells were seeded onto the surface of collagen hydrogels and grown in vitro for 7–8 days. At this time, neurons had formed a complex neurite web interspersed with astrocytes. Neuronal patch clamp recordings revealed voltage-gated Na+ and K+ currents in voltage clamp and action potentials in current clamp. When measured at voltages close to maximum activation, both currents were &gt;1 nA in mean amplitude. When compared to primary cortical neurons cultured on glass coverslips, but otherwise under similar conditions (Evans et al., 2017), the Na+ current from hydrogel neurons was found to be significantly larger although there were no differences in the K+ current amplitude, membrane potential, input resistance or cell capacitance. We speculate that the larger size of the neuronal voltage-dependent Na+ current in the hydrogels is related to the better biomimetic properties of the soft material, being close to values reported for neurons recorded in brain slices. The results highlight the potential benefits offered by neuronal culture on soft and biomimetic polymeric materials for neural tissue engineering studies.