bluuebunny/crossref_metadata_2025_split huggingface dataset:
Device associated –health care associated infections monitoring, prevention and cost assessment at intensive care unit of University Hospital in Poland (2015–2017)
Authors: Duszynska Wieslawa , Rosenthal Victor Daniel , Szczesny Aleksander , Zajaczkowska Katarzyna , Fulek Michal , Tomaszewski Jacek 
Published: October 2020

Abstract
Background
Device-associated health care-associated infections (DA-HAIs) in intensive care unit (ICU) patients constitute a major therapeutic issue complicating the regular hospitalisation process and having influence on patients’ condition, length of hospitalisation, mortality and therapy cost.

Methods
The study involved all patients treated > 48 h at ICU of the Medical University Teaching Hospital (Poland) from 1.01.2015 to 31.12.2017. The study showed the surveillance and prevention of DA-HAIs on International Nosocomial Infection Control Consortium (INICC) Surveillance Online System (ISOS) 3 online platform according to methodology of the INICC multidimensional approach (IMA).

Results
During study period 252 HAIs were found in 1353 (549F/804M) patients and 14,700 patient-days of hospitalisation. The crude infections rate and incidence density of DA-HAIs was 18.69% and 17.49 ± 2.56 /1000 patient-days. Incidence density of ventilator-associated pneumonia (VAP), central line-associated bloodstream infection (CLA-BSI) and catheter-associated urinary tract infection (CA-UTI) per 1000 device-days were 12.63 ± 1.49, 1.83 ± 0.65 and 6.5 ± 1.2, respectively. VAP(137) constituted 54.4% of HAIs, whereas CA-UTI(91) 36%, CLA-BSI(24) 9.6%.The most common pathogens in VAP and CA-UTI was multidrug-resistant (MDR) Acinetobacter baumannii (57 and 31%), and methicillin-resistant Staphylococcus epidermidis (MRSE) in CLA-BSI (45%). MDR Gram negative bacteria (GNB) 159 were responsible for 63.09% of HAIs. The length of hospitalisation of patients with a single DA-HAI at ICU was 21(14–33) days, while without infections it was 6.0 (3–11) days; p = 0.0001. The mortality rates in the hospital-acquired infection group and no infection group were 26.1% vs 26.9%; p = 0.838; OR 0.9633;95% CI (0.6733–1.3782). Extra cost of therapy caused by one ICU acquired HAI was US$ 11,475/Euro 10,035. Hand hygiene standards compliance rate was 64.7%, while VAP, CLA-BSI bundles compliance ranges were 96.2–76.8 and 29–100, respectively.

Conclusions
DA-HAIs was diagnosed at nearly 1/5 of patients. They were more frequent than in European Centre Disease Control report (except for CLA-BSI), more frequent than the USA CDC report, yet less frequent than in limited-resource countries (except for CA-UTI). They prolonged the hospitalisation period at ICU and generated substantial additional costs of treatment with no influence on mortality. The Acinetobacter baumannii MDR infections were the most problematic therapeutic issue. DA-HAIs preventive methods compliance rate needs improvement.
Effect of DNMT3A polymorphisms on CpG island hypermethylation in gastric mucosa
Authors: Takano Hikaru , Shibata Tomoyuki , Nakamura Masakatsu , Sakurai Naoko , Hayashi Tasuku , Ota Masafumi , Nomura-Horita Tomoe , Hayashi Ranji , Shimasaki Takeo , Otsuka Toshimi , Tahara Tomomitsu , Arisawa Tomiyasu 
Published: October 2020

Abstract
Background
CpG methylation of tumor suppressor genes occurs in the early stage of carcinogenesis. Detecting risk factors for aberrant CpG methylation is clinically important for predicting cancer development. DNA methyltransferase (DNMT) 3a is considered to play critical roles in the DNA methylation process during pathogenesis. In this study, we evaluated the association between DNMT3A polymorphisms (rs6733868 and rs13428812) and CpG methylation status in non-cancerous gastric mucosa.

Methods
We determined the DNMT3A genotype and CpG methylation status of 4 genes (p14ARF, p16INK4a, DAPK, and CDH1) in 510 subjects without gastric cancer. Helicobacter pylori (HP) infection status was determined by the rapid urease test, urea breath test, speculum examination, or serum antibody test. We determined the DNMT3A genotype using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP). CpG methylation status was determined by methylation-specific polymerase chain reaction (MSP). When the methylated band was stronger than 10 ng/μL according to the DNA marker, we judged CpG island hypermethylation (CIHM) to be present. Associations between genotypes and susceptibilities were assessed by logistic regression analysis.

Results
The minor allele frequencies of both polymorphisms (rs6733868 and rs13428812) were lower in the CpG methylated groups of each of the 4 genes (p14ARF, p16INK4a, DAPK, and CDH1). Using a dominant genetic model, rs6733868 was significantly associated with the hypermethylation of each gene, whereas rs13428812 was associated with the methylation of 3 genes (all except p14ARF). When low-CIHM was defined as 1 or 2 CpG islands methylated and high-CIHM was defined as 3 or more CpG islands methylated, carrying the minor allele of rs6733868 was associated with both decreased low- and high-CIHM, and that of rs13428812 also was associated with a decrease. Comparing low-CIHM with high-CIHM, carrying the minor alleles of rs6733868 or rs13428812 was related to decreased susceptibility to high-CIHM. In HP-infected subjects, carrying the minor alleles of rs6733868 or rs13428812 had a significantly greater association with decreased susceptibility to high-CIHM.

Conclusions
Our study indicates that polymorphisms of DNMT3A are associated with the accumulation of gene methylation in gastric mucosa. Carrying the minor alleles of rs6733868 or rs13428812 inhibits aberrant gene methylations, which are typically enhanced by HP infection.
Risk factors and incidence of suction loss during small incision lenticule extraction (SMILE) in 8493 eyes
Authors: Huang Tian-Ze , Shen Ling , Yu Xiao-Ning , Jin Hong-Ying 
Published: October 2020

Abstract
Background
To report the incidence and risk factors of suction loss during small incision lenticule extraction (SMILE).

Methods
This retrospective comparative case control study included 8493 eyes of 4261 patients. Patients underwent SMILE surgery between January 2014 and September 2019 were included. Videos of suction loss were reviewed, and the direct causes of suction loss were noted. An independent samples t-test was used for comparisons between the suction loss group and the control group. A binary logistic regression model was used to determine the possible significant risk factors that might increase the likelihood of suction loss during SMILE surgery.

Results
Suction loss occurred in 31 (0.37%) eyes of 30 patients; 23 (74.2%) cases occurred in the right eye (the first operative eye) and 8 (25.8%) cases occurred in the left eye. Among the 30 patients, 23 (76.7%) were male and 7 (23.3%) were female. The incidence in the six consecutive years were 0, 2.13, 0.34, 0.24, 0.22, and 0.25%. Head and eye movements during surgery caused suction loss in 16 (51.6%) and 15 (48.4%) eyes, respectively. Comparison between the suction loss group and the control group showed that the first operative eye and male sex are at a significantly high risk for suction loss (p < 0.05).

Conclusions
The risk factors of suction loss were first operative eye and male sex. Head and eye movements due to patient anxiety are the most common direct causes of suction loss. Surgeon’s experience may help to reduce the incidence of suction loss. Preoperative education and better communication during surgery needs to be emphasized.

Trial registration
Retrospectively registered. ChiCTR-ORC-17011040. Registered 1 April 2017. Name of registry: The observation of clinical results after corneal refractive surgery. Data of enrolment of the first participant to the trial: 1 January 2014.
Collaborative model of care between Orthopaedics and allied healthcare professionals in knee osteoarthritis (CONNACT): study protocol for an effectiveness-implementation hybrid randomized control trial
Authors: Tan Bryan Yijia , Pereira Michelle Jessica , Yang Su-Yin , Hunter David J. , Skou Soren Thorgaard , Thumboo Julian , Car Josip 
Published: October 2020

AbstractBackgroundKnee Osteoarthritis (OA) is a leading cause of global disability. TheCollaborative Model of Care between Orthopaedics and Allied Healthcare Professionals (CONNACT)Model of Care (MoC) was developed by optimizing evidence-based non-surgical treatments to deliver value-based care for people with knee OA. The primary aim of this study is to determine the clinical effectiveness of the CONNACT MoC (3 months) compared to usual care. The secondary aims are: a) To determine the cost-effectiveness and b) To develop an evaluation and implementation framework to inform large scale implementation for this MoC.MethodologyType 1 Effectiveness-Implementation Hybrid Trial using an explanatory sequential mixed-method approach. The study consists of 3 components. The first component is the pragmatic, parallel-arm, single-blinded randomized control trial. Inclusion criteria are patients with knee OA based on the National Institute of Health and Care Excellence (NICE) criteria with radiographic severity of greater than Kellgren-Lawrence 1, and Knee Injury and OA Outcome Score (KOOS4) of equal or less than 75. Exclusion criteria include other forms of arthritis, history of previous knee arthroplasty or wheelchair-bound patient. KOOS4is the primary outcome measure at 3 months, 6 months and 1 year. Secondary outcomes include KOOS individual subscales, quality of life scoring, functional performance, global, diet and psychological related outcomes. The second component is an economic evaluation of the cost-effectiveness of the CONNACT MoC using a societal perspective. The third component is an implementation and evaluation framework using process evaluation under the RE-AIM framework using a mixed-method approach. Sample size of 100 patients has been calculated.DiscussionCONNACT MoC is a complex intervention. In line with the MRC guidance for developing and evaluating complex interventions, a pilot feasibility study was completed and a comprehensive approach including an RCT, economic evaluation and process evaluation is described in this study protocol. Results from this study will help clinicians, healthcare administrators and policymakers guide the sustainable and effective implementation of the CONNACT MoC for knee OA and serve as a basis for similar multidisciplinary MoC for chronic degenerative musculoskeletal conditions to be developed.Trial registrationClinicaltrials.govIdentifier:NCT03809975. Registered January 182,019.
Automatic analysis of summary statements in virtual patients - a pilot study evaluating a machine learning approach
Authors: Hege Inga , Kiesewetter Isabel , Adler Martin 
Published: October 2020

Abstract
Background
The ability to compose a concise summary statement about a patient is a good indicator for the clinical reasoning abilities of healthcare students. To assess such summary statements manually a rubric based on five categories - use of semantic qualifiers, narrowing, transformation, accuracy, and global rating has been published. Our aim was to explore whether computer-based methods can be applied to automatically assess summary statements composed by learners in virtual patient scenarios based on the available rubric in real-time to serve as a basis for immediate feedback to learners.

Methods
We randomly selected 125 summary statements in German and English composed by learners in five different virtual patient scenarios. Then we manually rated these statements based on the rubric plus an additional category for the use of the virtual patients’ name. We implemented a natural language processing approach in combination with our own algorithm to automatically assess 125 randomly selected summary statements and compared the results of the manual and automatic rating in each category.

Results
We found a moderate agreement of the manual and automatic rating in most of the categories. However, some further analysis and development is needed, especially for a more reliable assessment of the factual accuracy and the identification of patient names in the German statements.

Conclusions
Despite some areas of improvement we believe that our results justify a careful display of the computer-calculated assessment scores as feedback to the learners. It will be important to emphasize that the rating is an approximation and give learners the possibility to complain about supposedly incorrect assessments, which will also help us to further improve the rating algorithms.
The influence of empowered work environments on the psychological experiences of nursing assistants during COVID-19: a qualitative study
Authors: Travers Jasmine L. , Schroeder Krista , Norful Allison A. , Aliyu Sainfer 
Published: October 2020

AbstractBackgroundNursing Assistants (NA) who feel empowered tend to perform their duties better, have higher morale and job satisfaction, and are less likely to leave their jobs. Organizational empowerment practices in hospitals likely shape the psychological experiences of empowerment among these personnel; however, little is known about this relationship.ObjectiveWe used qualitative inquiry to explore the relationship between organizational empowerment structural components and feelings of psychological empowerment among hospital frontline workers during a public health emergency.MethodsKanter’s Theory of Structural Empowerment and Spreitzer’s Psychological Empowerment in the Workplace Framework were applied to identify the conceptual influences of organizational practices on psychological experiences of empowerment. In-depth interviews were conducted with a convenience sample of NAs, caring for hospitalized COVID-19 patients. Directed content analysis was performed to generate a data matrix consisting of the psychological experiences of meaning, competence, self-determination, and impact embedded under the organizational structural components of information, resources, support, and opportunity.ResultsThirteen NAs (mean age = 42 years, 92% female) completed interviews.Information, or lack thereof, provided to the NAs influenced feelings of fear, preparation, and autonomy.Resources(e.g., protocols, equipment, and person-power) made it easier to cope with overwhelming emotions, affected the NAs’ abilities to do their jobs, and when limited, drove NAs to take on new roles. NAs noted thatsupportwas mostly provided by nurses and made the NAs feel appreciated, desiring to contribute more. While NAs felt they could consult leadership when needed, several felt leadership showed little appreciation for their roles and contributions. Similar to support, theopportunityto take care of COVID-19 patients yielded a diverse array of emotions, exposed advances and gaps in NA preparation, and challenged NAs to autonomously develop new care practices and processes.ConclusionManagement and empowerment of healthcare workers are critical to hospital performance and success. We found many ways in which the NAs’ psychological experiences of empowerment were shaped by the healthcare system’s empowerment-related structural conditions during a public health emergency. To further develop an empowered and committed critical workforce, hospitals must acknowledge the organizational practice influence on the psychological experiences of empowerment among NAs.
A machine learning analysis of a “normal-like” IDH-WT diffuse glioma transcriptomic subgroup associated with prolonged survival reveals novel immune and neurotransmitter-related actionable targets
Authors: Nguyen H. D. , Allaire A. , Diamandis P. , Bisaillon M. , Scott M. S. , Richer M. 
Published: October 2020

AbstractBackgroundClassification of primary central nervous system tumors according to the World Health Organization guidelines follows the integration of histologic interpretation with molecular information and aims at providing the most precise prognosis and optimal patient management. According to the cIMPACT-NOW update 3, diffuse isocitrate dehydrogenase-wild type (IDH-WT) gliomas should be graded as grade IV glioblastomas (GBM) if they possess one or more of the following molecular markers that predict aggressive clinical course: EGFR amplification, TERT promoter mutation, and whole-chromosome 7 gain combined with chromosome 10 loss.MethodsThe Cancer Genome Atlas (TCGA) glioma expression datasets were reanalyzed in order to identify novel tumor subcategories which would be considered as GBM-equivalents with the current diagnostic algorithm. Unsupervised clustering allowed the identification of previously unrecognized transcriptomic subcategories. A supervised machine learning algorithm (k-nearest neighbor model) was also used to identify gene signatures specific to some of these subcategories.ResultsWe identified 14 IDH-WT infiltrating gliomas displaying a “normal-like” (NL) transcriptomic profile associated with a longer survival. Genes such as C5AR1 (complement receptor), SLC32A1 (vesicular gamma-aminobutyric acid transporter), MSR1 (or CD204, scavenger receptor A), and SYT5 (synaptotagmin 5) were differentially expressed and comprised in gene signatures specific to NL IDH-WT gliomas which were validated further using the Chinese Glioma Genome Atlas datasets. These gene signatures showed high discriminative power and correlation with survival.ConclusionNL IDH-WT gliomas represent an infiltrating glioma subcategory with a superior prognosis which can only be detected using genome-wide analysis. Differential expression of genes potentially involved in immune checkpoint and amino acid signaling pathways is providing insight into mechanisms of gliomagenesis and could pave the way to novel treatment targets for infiltrating gliomas.
Adapting hospital capacity to meet changing demands during the COVID-19 pandemic
Authors: McCabe Ruth , Schmit Nora , Christen Paula , D’Aeth Josh C. , Løchen Alessandra , Rizmie Dheeya , Nayagam Shevanthi , Miraldo Marisa , Aylin Paul , Bottle Alex , Perez-Guzman Pablo N. , Ghani Azra C. , Ferguson Neil M. , White Peter J. , Hauck Katharina 
Published: October 2020

Abstract
Background
To calculate hospital surge capacity, achieved via hospital provision interventions implemented for the emergency treatment of coronavirus disease 2019 (COVID-19) and other patients through March to May 2020; to evaluate the conditions for admitting patients for elective surgery under varying admission levels of COVID-19 patients.

Methods
We analysed National Health Service (NHS) datasets and literature reviews to estimate hospital care capacity before the pandemic (pre-pandemic baseline) and to quantify the impact of interventions (cancellation of elective surgery, field hospitals, use of private hospitals, deployment of former medical staff and deployment of newly qualified medical staff) for treatment of adult COVID-19 patients, focusing on general and acute (G&A) and critical care (CC) beds, staff and ventilators.

Results
NHS England would not have had sufficient capacity to treat all COVID-19 and other patients in March and April 2020 without the hospital provision interventions, which alleviated significant shortfalls in CC nurses, CC and G&A beds and CC junior doctors. All elective surgery can be conducted at normal pre-pandemic levels provided the other interventions are sustained, but only if the daily number of COVID-19 patients occupying CC beds is not greater than 1550 in the whole of England. If the other interventions are not maintained, then elective surgery can only be conducted if the number of COVID-19 patients occupying CC beds is not greater than 320. However, there is greater national capacity to treat G&A patients: without interventions, it takes almost 10,000 G&A COVID-19 patients before any G&A elective patients would be unable to be accommodated.

Conclusions
Unless COVID-19 hospitalisations drop to low levels, there is a continued need to enhance critical care capacity in England with field hospitals, use of private hospitals or deployment of former and newly qualified medical staff to allow some or all elective surgery to take place.
MR-proANP and incident cardiovascular disease in patients with type 2 diabetes with and without heart failure with preserved ejection fraction
Authors: Jensen Jesper , Schou Morten , Kistorp Caroline , Faber Jens , Hansen Tine W. , Jensen Magnus T. , Andersen Henrik U. , Rossing Peter , Vilsbøll Tina , Jørgensen Peter G. 
Published: October 2020

Abstract
Background
Mid-regional pro-atrial natriuretic peptide (MR-proANP) is a useful biomarker in outpatients with type 2 diabetes (T2D) to diagnose heart failure (HF). Elevated B-type natriuretic peptides are included in the definition of HF with preserved ejection fraction (HFpEF) but little is known about the prognostic value of including A-type natriuretic peptides (MR-proANP) in the evaluation of patients with T2D.

Methods
We prospectively evaluated the risk of incident cardiovascular (CV) events in outpatients with T2D (n = 806, mean ± standard deviation age 64 ± 10 years, 65% male, median [interquartile range] duration of diabetes 12 [6–17] years, 17.5% with symptomatic HFpEF) according to MR-proANP levels and stratified according to HF-status including further stratification according to a prespecified cut-off level of MR-proANP.

Results
A total of 126 CV events occurred (median follow-up 4.8 [4.1–5.3] years). An elevated MR-proANP, with a cut-off of 60 pmol/l or as a continuous variable, was associated with incident CV events (p < 0.001). Compared to patients without HF, patients with HFpEF and high MR-proANP (≥ 60 pmol/l; median 124 [89–202] pmol/l) and patients with HF and reduced ejection fraction (HFrEF) had a higher risk of CV events (multivariable model; hazard ratio (HR) 2.56 [95% CI 1.64–4.00] and 3.32 [1.64–6.74], respectively). Conversely, patients with HFpEF and low MR-proANP (< 60 pmol/l; median 46 [32–56] pmol/l) did not have an increased risk (HR 2.18 [0.78–6.14]).

Conclusions
Patients with T2D and HFpEF with high MR-proANP levels had an increased risk for CV events compared to patients with HFpEF without elevated MR-proANP and compared to patients without HF, supporting the use of MR-proANP in the definition of HFpEF from a prognostic point-of-view.