bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the usefulness of Lexis diagrams for quality improvement
Authors: Dahlin Sara 
Published: January 2020

AbstractBackgroundVisualization is important to aid practitioners in understanding local care processes and drive quality improvement (QI). Important aspects include timely feedback and ability to plot data over time. Moreover, the complexity of care also needs to be understood, as it affects the variation of care processes. However, there is a lack of QI methods visualizing multiple, related factors such as diagnosis date, death date, and cause of death to unravel their complexity, which is necessary to understand processes related to survival data. Lexis diagrams visualize individual patient processes as lines and mark additional factors such as key events. This study explores the potential of Lexis diagrams to support QI through survival data analysis, focusing on feedback, timeliness, and complexity, in a gynecological cancer setting in Sweden.MethodsLexis diagrams were produced based on data from a gynecological cancer quality registry (4481 patients). The usefulness of Lexis diagrams was explored through iterative data identification and analysis through semi-structured dialogues between the researcher and domain experts (clinically active care process owners) during five meetings. Visualizations were produced and adapted by the researcher between meetings, based on the dialogues, to ensure clinical relevance, resulting in three relevant types of visualizations.ResultsDomain experts identified different uses depending on diagnosis group and data visualization. Key results include timely feedback through close-to-real-time visualizations, supporting discussion and understanding of trends and hypothesis-building. Visualization of care process complexity facilitated evaluation of given care. Combined visualization of individual and population levels increased patient focus and may possibly also function to motivate practitioners and management.ConclusionLexis diagrams can aid understanding of survival data, triggering important dialogues between care givers and supporting care quality improvement and new perspectives, and can therefore complement survival curves in quality improvement.
Translation control of Enterovirus A71 gene expression
Authors: Lai Ming-Chih , Chen Han-Hsiang , Xu Peng , Wang Robert Y. L. 
Published: January 2020

AbstractUpon EV-A71 infection of a host cell, EV-A71 RNA is translated into a viral polyprotein. Although EV-A71 can use the cellular translation machinery to produce viral proteins, unlike cellular translation, which is cap-dependent, the viral RNA genome of EV-A71 does not contain a 5′ cap and the translation of EV-A71 protein is cap-independent, which is mediated by the internal ribosomal entry site (IRES) located in the 5′ UTR of EV-A71 mRNA. Like many other eukaryotic viruses, EV-A71 manipulates the host cell translation devices, using an elegant RNA-centric strategy in infected cells. During viral translation, viral RNA plays an important role in controlling the stage of protein synthesis. In addition, due to the cellular defense mechanism, viral replication is limited by down-regulating translation. EV-A71 also utilizes protein factors in the host to overcome antiviral responses or even use them to promote viral translation rather than host cell translation. In this review, we provide an introduction to the known strategies for EV-A71 to exploit cellular translation mechanisms.
Characteristic chest CT findings for progressive cavities in Mycobacterium avium complex pulmonary disease: a retrospective cohort study
Authors: Oshitani Yohei , Kitada Seigo , Edahiro Ryuya , Tsujino Kazuyuki , Kagawa Hiroyuki , Yoshimura Kenji , Miki Keisuke , Miki Mari , Kida Hiroshi 
Published: January 2020

Abstract
Background
Although cavities are an important finding in Mycobacterium avium complex pulmonary disease (MAC-PD), there is little information regarding the types of cavities that indicate disease progression. This study was performed to identify cavity characteristics that were associated with disease progression in patients with MAC-PD.

Methods
This retrospective cohort study included 97 patients presenting with MAC-PD with cavities between December 2006 and June 2016. We compared initial and final computed tomography (CT) findings, classified 52 and 45 patients in the progressive and non-progressive cavity groups, respectively, and examined the progression-related imaging features in initial CT images. A progressive cavity was defined by more than two-fold increase in internal diameter or emergence of a new cavity around the initial cavity.

Results
Patients in the progressive group were older (p < 0.001), had a lower body mass index (p = 0.043), and showed higher diabetes complication rates (p = 0.005). The initial CT in the progressive group showed a longer maximum internal diameter of the cavity (p < 0.001) and higher rates of cavities close to the chest wall (p < 0.001), multiple cavities (p = 0.023), consolidation around the cavity (p < 0.001), atelectasis (p = 0.011), and pleural thickening (p < 0.001). Multivariable logistic regression analysis revealed that the maximum internal diameter of the cavity (odds ratio [OR]: 1.11, 95% confidence interval [CI]: 1.02–1.21; p=0.012) and consolidation around the cavity (OR: 16.15, 95% CI: 4.05–64.46; p < 0.001) were significantly associated with progressive cavities. In cavities with a maximum internal diameter of ≥10 mm and simultaneous consolidation, the probability of progression was as high as 96.2%. The 10-year mortality rates in the progressive and non-progressive cavity groups were 46.7 and 9.8% (p < 0.001), respectively, while the 10-year respiratory failure rates were 28.1 and 0%, respectively (p < 0.001).

Conclusions
Large cavity size and consolidation on CT showed strong relationships with disease progression, which led to respiratory failure and high mortality rate.
Do cognitive aids reduce error rates in resuscitation team performance? Trial of emergency medicine protocols in simulation training (TEMPIST) in Australia
Authors: Hall Charlotte , Robertson Dean , Rolfe Margaret , Pascoe Sharene , Passey Megan E. , Pit Sabrina Winona 
Published: January 2020

Abstract
Background
Resuscitation of patients with time-critical and life-threatening illness represents a cognitive challenge for emergency room (ER) clinicians. We designed a cognitive aid, the Emergency Protocols Handbook, to simplify clinical management and team processes. Resuscitation guidelines were reformatted into simple, single step-by-step pathways. This Australian randomised controlled trial tested the effectiveness of this cognitive aid in a simulated ER environment by observing team error rates when current resuscitation guidelines were followed, with and without the handbook.

Methods
Resuscitation teams were randomised to manage two scenarios with the handbook and two without in a high-fidelity simulation centre. Each scenario was video-recorded. The primary outcome measure was error rates (the number of errors made out of 15 key tasks per scenario). Key tasks varied by scenario. Each team completed four scenarios and was measured on 60 key tasks. Participants were surveyed regarding their perception of the usefulness of the handbook.

Results
Twenty-one groups performed 84 ER crisis simulations. The unadjusted error rate in the handbook group was 18.8% (121/645) versus 38.9% (239/615) in the non-handbook group. There was a statistically significant reduction of 54.0% (95% CI 49.9–57.9) in the estimated percentage error rate when the handbook was available across all scenarios 17.9% (95% CI 14.4–22.0%) versus 38.9% (95% CI 34.2–43.9%). Almost all (97%) participants said they would want to use this cognitive aid during a real medical crisis situation.

Conclusion
This trial showed that by following the step-by-step, linear pathways in the handbook, clinicians more than halved their teams’ rate of error, across four simulated medical crises. The handbook improves team performance and enables healthcare teams to reduce clinical error rates and thus reduce harm for patients.

Trial registration
ACTRN12616001456448 registered: www.anzctr.org.au. Trial site: http://emergencyprotocols.org.au/
HTLV-1 bZIP factor: the key viral gene for pathogenesis
Authors: Matsuoka Masao , Mesnard Jean-Michel 
Published: January 2020

AbstractHuman T cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia-lymphoma (ATL) and inflammatory diseases. The HTLV-1 bZIP factor (HBZ) gene is constantly expressed in HTLV-1 infected cells and ATL cells. HBZ protein suppresses transcription of the tax gene through blocking the LTR recruitment of not only ATF/CREB factors but also CBP/p300. HBZ promotes transcription of Foxp3, CCR4, and T-cell immunoreceptor with Ig and ITIM domains (TIGIT). Thus, HBZ is critical for the immunophenotype of infected cells and ATL cells. HBZ also functions in its RNA form. HBZ RNA suppresses apoptosis and promotes proliferation of T cells. Since HBZ RNA is not recognized by cytotoxic T cells, HTLV-1 has a clever strategy for avoiding immune detection. HBZ plays central roles in maintaining infected T cells in vivo and determining their immunophenotype.
Perioperative routines and surgical techniques for saphenous vein harvesting in CABG surgery: a national cross-sectional study in Sweden
Authors: Larsson Hanna , Hälleberg-Nyman Maria , Friberg Örjan , Falk-Brynhildsen Karin 
Published: January 2020

Abstract
Background
The saphenous vein is the most commonly used conduit for coronary artery bypass grafting (CABG). Wound healing complications related to saphenous vein harvesting are common, with reported surgical site infection rates ranging from 2 to 20%. Patients’ risk factors, perioperative hygiene routines, and surgical technique play important roles in wound complications. Here we describe the perioperative routines and surgical methods of Swedish operating theatre (OT) nurses and cardiac surgeons.

Methods
A national cross-sectional survey with descriptive design was conducted to evaluate perioperative hygiene routines and surgical methods associated with saphenous vein harvesting in CABG. A web-based questionnaire was sent to OT nurses and cardiac surgeons at all eight hospitals performing CABG surgery in Sweden.

Results
Responses were received from all hospitals. The total response rate was 62/119 (52%) among OT nurses and 56/111 (50%) among surgeons.
Chlorhexidine 5 mg/mL in 70% ethanol was used at all eight hospitals. The OT nurses almost always (96.8%) performed the preoperative skin disinfection, usually for three to 5 minutes. Chlorhexidine was also commonly used before dressing the wound.
Conventional technique was used by 78.6% of the surgeons, “no-touch” by 30.4%, and both techniques by 9%. None of the surgeons used endoscopic vein harvesting. Type of suture and technique used for closing the wound differed markedly between the centres.

Conclusions
In this article we present insights into the hygiene routines and surgical methods currently used by OT nurses and cardiac surgeons in Sweden. The results indicate both similarities and differences between the centres. Local traditions might be the most important factors in determining which procedures are employed in the OT. There is a lack of evidence-based hygiene routines and surgical methods.
A pre-existing population of ZEB2+ quiescent cells with stemness and mesenchymal features dictate chemoresistance in colorectal cancer
Authors: Francescangeli Federica , Contavalli Paola , De Angelis Maria Laura , Careccia Silvia , Signore Michele , Haas Tobias Longin , Salaris Federico , Baiocchi Marta , Boe Alessandra , Giuliani Alessandro , Tcheremenskaia Olga , Pagliuca Alfredo , Guardiola Ombretta , Minchiotti Gabriella , Colace Lidia , Ciardi Antonio , D’Andrea Vito , La Torre Filippo , Medema JanPaul , De Maria Ruggero , Zeuner Ann 
Published: January 2020

Abstract
Background
Quiescent/slow cycling cells have been identified in several tumors and correlated with therapy resistance. However, the features of chemoresistant populations and the molecular factors linking quiescence to chemoresistance are largely unknown.

Methods
A population of chemoresistant quiescent/slow cycling cells was isolated through PKH26 staining (which allows to separate cells on the basis of their proliferation rate) from colorectal cancer (CRC) xenografts and subjected to global gene expression and pathway activation analyses. Factors expressed by the quiescent/slow cycling population were analyzed through lentiviral overexpression approaches for their ability to induce a dormant chemoresistant state both in vitro and in mouse xenografts. The correlation between quiescence-associated factors, CRC consensus molecular subtype and cancer prognosis was analyzed in large patient datasets.

Results
Untreated colorectal tumors contain a population of quiescent/slow cycling cells with stem cell features (quiescent cancer stem cells, QCSCs) characterized by a predetermined mesenchymal-like chemoresistant phenotype. QCSCs expressed increased levels of ZEB2, a transcription factor involved in stem cell plasticity and epithelial-mesenchymal transition (EMT), and of antiapototic factors pCRAF and pASK1. ZEB2 overexpression upregulated pCRAF/pASK1 levels resulting in increased chemoresistance, enrichment of cells with stemness/EMT traits and proliferative slowdown of tumor xenografts. In parallel, chemotherapy treatment of tumor xenografts induced the prevalence of QCSCs with a stemness/EMT phenotype and activation of the ZEB2/pCRAF/pASK1 axis, resulting in a chemotherapy-unresponsive state. In CRC patients, increased ZEB2 levels correlated with worse relapse-free survival and were strongly associated to the consensus molecular subtype 4 (CMS4) characterized by dismal prognosis, decreased proliferative rates and upregulation of EMT genes.

Conclusions
These results show that chemotherapy-naive tumors contain a cell population characterized by a coordinated program of chemoresistance, quiescence, stemness and EMT. Such population becomes prevalent upon drug treatment and is responsible for chemotherapy resistance, thus representing a key target for more effective therapeutic approaches.
Personalising psychotherapies for depression using a novel mixed methods approach: an example from Morita therapy
Authors: Sugg Holly Victoria Rose , Frost Julia , Richards David A. 
Published: January 2020

Abstract
Background
Current quantitative methods for personalising psychotherapies for depression are unlikely to be able to inform clinical decision-making for hundreds of years. Novel alternative methods to generate hypotheses for prospective testing are therefore required, and we showcase mixed methods as one such approach. By exploring patients’ perspectives in depth, and integrating qualitative and quantitative data at the level of the individual, we may identify new potential psychosocial predictors of psychotherapy outcomes, potentially informing the personalisation of depression treatment in a shorter timeframe. Using Morita therapy (a Japanese psychotherapy) as an exemplar, we thus explored how Morita therapy recipients’ views on treatment acceptability explain their adherence and response to treatment.

Methods
The Morita trial incorporated a pilot randomised controlled trial of Morita therapy versus treatment as usual for depression, and post-treatment qualitative interviews. We recruited trial participants from general practice record searches in Devon, UK, and purposively sampled data from 16 participants for our mixed methods analysis. We developed typologies of participants’ views from our qualitative themes, and integrated these with quantitative data on number of sessions attended and whether participants responded to treatment in a joint typologies and statistics display. We enriched our analysis using participant vignettes to demonstrate each typology.

Results
We demonstrated that (1) participants who could identify with the principles of Morita therapy typically responded to treatment, regardless of how many sessions they attended, whilst those whose orientation towards treatment was incompatible with Morita therapy did not respond to treatment, again regardless of treatment adherence and (2) participants whose personal circumstances impeded their opportunity to engage in Morita therapy attended the fewest sessions, though still benefitted from treatment if the principles resonated with them.

Conclusions
We identified new potential relationships between “orientation” and outcomes, and “opportunity” and adherence, which could not have been identified using existing non-integrative methods. This mixed methods approach warrants replication in future trials and with other psychotherapies to generate hypotheses, based on typologies (or profiles) of patients for whom a treatment is more or less likely to be suitable, to be tested in prospective trials.

Trial registration
Current Controlled Trials, ISRCTN17544090. Registered on 23 July 2015.
Early intervention for children at risk of visual processing dysfunctions from 1 year of age: a randomized controlled trial protocol
Authors: Kooiker Marlou J. G. , van der Linden Yoni , van Dijk Jenneke , van der Zee Ymie J. , Swarte Renate M. C. , Smit Liesbeth S. , van der Steen-Kant Sanny , Loudon Sjoukje E. , Reiss Irwin K. M. , Kuyper Kees , Pel Johan J. M. , van der Steen Johannes 
Published: January 2020

Abstract
Background
An increasing number of children are suffering from brain damage-related visual processing dysfunctions (VPD). There is currently a lack of evidence-based intervention methods that can be used early in development. We developed a visual intervention protocol suitable from 1 year of age. The protocol is structured, comprehensive and individually adaptive, and is paired with quantitative outcome assessments. Our aim is to investigate the effectiveness of this first visual intervention program for young children with (a risk of) VPD.

Methods
This is a single-blind, placebo-controlled trial that is embedded within standard clinical care. The study population consists of 100 children born very or extremely preterm (< 30 weeks) at 1 year of corrected age (CA), of whom 50% are expected to have VPD. First, children undergo a visual screening at 1 year CA. If they are classified as being at risk of VPD, they are referred to standard care, which involves an ophthalmic and visual function assessment and a (newly developed) visual intervention program. This program consists of a general protocol (standardized and similar for all children) and a supplement protocol (adapted to the specific needs of the child). Children are randomly allocated to an intervention group (starting upon inclusion at 1 year CA) or a control group (postponed: starting at 2 years CA). The control group will receive a placebo treatment. The effectiveness of early visual intervention will be examined with follow-up visual and neurocognitive assessments after 1 year (upon completion of the direct intervention) and after 2 years (upon completion of the postponed intervention).

Discussion
Through this randomized controlled trial we will establish the effectiveness of a new and early visual intervention program. Combining a general and supplement protocol enables both structured comparisons between participants and groups, and custom habilitation that is tailored to a child’s specific needs. The design ensures that all included children will benefit from participation by advancing the age at which they start receiving an intervention. We expect results to be applicable to the overall population of children with (a risk of) VPD early in life.

Trial registration
Netherlands Trial Register: NTR6952. Registered 19 January 2018.
Species-specific differences in Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti seroprevalence in Namibian wildlife
Authors: Seltmann Anne , Schares Gereon , Aschenborn Ortwin H. K. , Heinrich Sonja K. , Thalwitzer Susanne , Wachter Bettina , Czirják Gábor Á. 
Published: January 2020

Abstract
Background
Knowledge about parasitic infections is crucial information for animal health, particularly of free-ranging species that might come into contact with livestock and humans.

Methods
We investigated the seroprevalence of three tissue-cyst-forming apicomplexan parasites (Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti) in 506 individuals of 12 wildlife species in Namibia using in-house enzyme linked immunosorbent assays (indirect ELISAs applying purified antigens) for screening and immunoblots as confirmatory tests. We included six species of the suborder Feliformia, four species of the suborder Caniformia and two species of the suborder Ruminantia. For the two species for which we had most samples and life-history information, i.e. cheetahs (Acinonyx jubatus, n = 250) and leopards (Panthera pardus, n = 58), we investigated T. gondii seroprevalence in relation to age class, sex, sociality (solitary, mother-offspring group, independent sibling group, coalition group) and site (natural habitat vs farmland).

Results
All but one carnivore species (bat-eared fox Otocyon megalotis, n = 4) were seropositive to T. gondii, with a seroprevalence ranging from 52.4% (131/250) in cheetahs to 93.2% (55/59) in African lions (Panthera leo). We also detected antibodies to T. gondii in 10.0% (2/20) of blue wildebeest (Connochaetes taurinus). Adult cheetahs and leopards were more likely to be seropositive to T. gondii than subadult conspecifics, whereas seroprevalence did not vary with sex, sociality and site. Furthermore, we measured antibodies to N. caninum in 15.4% (2/13) of brown hyenas (Hyaena brunnea) and 2.6% (1/39) of black-backed jackals (Canis mesomelas). Antibodies to B. besnoiti were detected in 3.4% (2/59) of African lions and 20.0% (4/20) of blue wildebeest.

Conclusions
Our results demonstrate that Namibian wildlife species were exposed to apicomplexan parasites at different prevalences, depending on parasite and host species. In addition to serological work, molecular work is also needed to better understand the sylvatic cycle and the clear role of wildlife in the epidemiology of these parasites in southern Africa.