HIS-based electronic documentation can significantly reduce the time from biopsy to final report for prostate tumours and supports quality management as well as clinical research

<p>Abstract</p> <p>Background</p> <p>Timely and accurate information is important to guide the medical treatment process. We developed, implemented and assessed an order-entry system to support documentation of prostate histologies involving urologists, pathologists and physicians in private practice.</p> <p>Methods</p> <p>We designed electronic forms for histological prostate biopsy reports in our hospital information system (HIS). These forms are created by urologists and sent electronically to pathologists. Pathological findings are entered into the system and sent back to the urologists. We assessed time from biopsy to final report (TBF) and compared pre-implementation phase (paper-based forms) and post-implementation phase. In addition we analysed completeness of the electronic data.</p> <p>Results</p> <p>We compared 87 paper-based with 86 electronic cases. Using electronic forms within the HIS decreases time span from biopsy to final report by more than one day per patient (p < 0.0001). Beyond the optimized workflow we observed a good acceptance because physicians were already familiar with the HIS. The possibility to use these routine data for quality management and research purposes is an additional important advantage of the electronic system.</p> <p>Conclusion</p> <p>Electronic documentation can significantly reduce the time from biopsy to final report of prostate biopsy results and generates a reliable basis for quality management and research purposes.</p

Design of paddle shifts for formula student

Táto bakalárska práca sa zabýva návrhom a výrobou podvolantových radiacich pák pre Formulu Student. V teoretickej časti sa zaoberá zhrnutím poznatkov o dnešných mechanizmoch radenia, aditívnych technológiách výroby a spôsoboch optimalizácie hmotnosti súčiastok. V konštrukčnej časti sa zaoberá konkrétnymi riešeniami tejto problematiky, pričom najväčší dôraz bol kladený na nízku hmotnosť a vysokú tuhosť celého mechanizmu.This bachelor thesis concerns design of paddle shifters for Formula Student. It deals in theoretical part with knowledge of today’s shifting mechanisms, additive manufacturing technologies and ways of weight optimization of parts. In design section, it covers with actual solutions of this problems, whereas the most important target was to minimalize mass and maximize stiffness of the whole mechanism.

Mapping Turnaround Times (TAT) to a Generic Timeline: A Systematic Review of TAT Definitions in Clinical Domains

<p>Abstract</p> <p>Background</p> <p>Assessing turnaround times can help to analyse workflows in hospital information systems. This paper presents a systematic review of literature concerning different turnaround time definitions. Our objectives were to collect relevant literature with respect to this kind of process times in hospitals and their respective domains. We then analysed the existing definitions and summarised them in an appropriate format.</p> <p>Methods</p> <p>Our search strategy was based on Pubmed queries and manual reviews of the bibliographies of retrieved articles. Studies were included if precise definitions of turnaround times were available. A generic timeline was designed through a consensus process to provide an overview of these definitions.</p> <p>Results</p> <p>More than 1000 articles were analysed and resulted in 122 papers. Of those, 162 turnaround time definitions in different clinical domains were identified. Starting and end points vary between these domains. To illustrate those turnaround time definitions, a generic timeline was constructed using preferred terms derived from the identified definitions. The consensus process resulted in the following 15 terms: admission, order, biopsy/examination, receipt of specimen in laboratory, procedure completion, interpretation, dictation, transcription, verification, report available, delivery, physician views report, treatment, discharge and discharge letter sent. Based on this analysis, several standard terms for turnaround time definitions are proposed.</p> <p>Conclusion</p> <p>Using turnaround times to benchmark clinical workflows is still difficult, because even within the same clinical domain many different definitions exist. Mapping of turnaround time definitions to a generic timeline is feasible.</p

Benchmarking of 4C-seq pipelines based on real and simulated data

"jats:sec" "jats:title"Motivation"/jats:title" "jats:p"With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data are complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published."/jats:p" "/jats:sec" "jats:sec" "jats:title"Results"/jats:title" "jats:p"We conducted a benchmarking study on 66 4C-seq samples from 20 datasets, and developed a novel 4C-seq simulation software, Basic4CSim, to allow for detailed comparisons of 4C-seq algorithms on 50 simulated datasets with 10–120 samples each. Simulations and benchmarking were adapted to address different characteristics of 4C-seq data. Simulated data were compared with published samples to validate simulation settings. We identified differences between 4C-seq algorithms in terms of precision, recall, interaction structure, and run time, and observed general trends. Novel differential pipeline versions of single-sample based 4C-seq algorithms were included in the benchmarking. While no single tool was optimally suited for both near-cis and far-cis, and both single-sample and differential analyses, choosing a high-performing algorithm variant did improve results considerably. For near-cis scenarios, r3Cseq, peakC and FourCSeq offered high precision, while fourSig demonstrated high overall F1 scores in far-cis analyses. Finally, 4C-seq simulations may aid in the development of improved analysis algorithms."/jats:p" "/jats:sec" "jats:sec" "jats:title"Availability and implementation"/jats:title" "jats:p"Basic4CSim is available at https://github.com/walter–ca/Basic4CSim."/jats:p" "/jats:sec" "jats:sec" "jats:title"Supplementary information"/jats:title" "jats:p"Supplementary data are available at Bioinformatics online."/jats:p" "/jats:sec Document type: Articl

Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities

Motivation: The analysis of a number of different genetic features like copy number (CN) variation, gene expression (GE) or loss of heterocygosity has considerably increased in recent years, as well as the number of available datasets. This is particularly due to the success of microarray technology. Thus, to understand mechanisms of disease pathogenesis on a molecular basis, e.g. in cancer research, the challenge of analyzing such different data types in an integrated way has become increasingly important. In order to tackle this problem, we propose a new procedure for an integrated analysis of two different data types that searches for genes and genetic regions which for both inputs display strong equally directed deviations from the reference median. We employ this approach, based on a modified correlation coefficient and an explorative Wilcoxon test, to find DNA regions of such abnormalities in GE and CN (e.g. underexpressed genes accompanied by a loss of DNA material). Results: In an application to acute myeloid leukemia, our procedure is able to identify various regions on different chromosomes with characteristic abnormalities in GE and CN data and shows a higher sensitivity to differences in abnormalities than standard approaches. While the results support various findings of previous studies, some new interesting DNA regions can be identified. In a simulation study, our procedure also shows more reliable results than standard approaches. Availability: Code and data available as R packages edira and ediraAMLdata from http://www.statistik.tu-dortmund.de/~schaefer/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Assessing and Improving the Usability of the Medical Data Models Portal

Case report forms (CRF) specify data definitions and encodings for data to be collected in clinical trials. To enable exchange of data definitions and in this way to avoid creation of variants of CRF for similar study designs, the Medical Data Model portal (MDM) has been developed since 2011. This work aims at studying the usability of the MDM portal. We identify issues that hamper its adoption by researchers in order to derive measurements for improving it. We selected relevant tools (e.g. Nibbler, Hotjar, SUPR-Q) for usability testing and generated a structured test protocol. More specifically, the portal was assessed by means of a static analysis, user analysis (n=10), a usability test (n=10) and statistical evaluations. Regarding accessibility and technology, the static code analysis resulted in high scores. Presentation of information and functions as well as interaction with the portal still has to be improved: The results show that only limited functions of the webpage are used regularly and some user navigation errors occur due to the portal's design. In total, six major problems were identified which will be addressed in future. A continuous evaluation using the same structured test protocol allows to continuously measure the website quality, to compare it after changes have been implemented and in this way, to realise a continuous improvement. The effort for a repeated evaluation of the same evaluation with 10 persons is estimated with 10 hours

Using electronic health records to support clinical trials: a report on stakeholder engagement for EHR4CR

Background. The conduct of clinical trials is increasingly challenging due to greater complexity and governance requirements as well as difficulties with recruitment and retention. Electronic Health Records for Clinical Research (EHR4CR) aims at improving the conduct of trials by using existing routinely collected data, but little is known about stakeholder views on data availability, information governance, and acceptable working practices. Methods. Senior figures in healthcare organisations across Europe were provided with a description of the project and structured interviews were subsequently conducted to elicit their views. Results. 37 structured interviewees in Germany, UK, Switzerland, and France indicated strong support for the proposed EHR4CR platform. All interviewees reported that using the platform for assessing feasibility would enhance the conduct of clinical trials and the majority also felt it would reduce workloads. Interviewees felt the platform could enhance trial recruitment and adverse event reporting but also felt it could raise either ethical or information governance concerns in their country. Conclusions. There was clear support for EHR4CR and a belief that it could reduce workloads and improve the conduct and quality of trials. However data security, privacy, and information governance issues would need to be carefully managed in the development of the platform

Is the ACSM and FRIEND Metabolic Equations Valid for Assessing Cardiorespiratory Fitness Among 18-34 Aged Men? : Preliminary Results

Topics in Exercise Science and Kinesiology Volume 2: Issue 1, Article 2, 2021. Metabolic equations, such as ACSM and FRIEND, are used worldwide to indirectly measure the VO2max in adults, but lack of accuracy seems to occur. 30 men of 18-34 years old performed a maximal incremental test on a treadmill during which direct VO2max measurements was taken and then have been compared to ACSM and FRIEND metabolic equations. Point of application #1: Better evaluation and exercise prescription among athletic populations. Point of application #2: Act in prevention among sedentary and symptomatic populations. Point of application #3: Improve the assessment of physiological need associated with work tasks, personal protective equipment and the physical preparation of the tactical personnel

Effects of Muscle Fatigue, Creep, and Musculoskeletal Pain on Neuromuscular Responses to Unexpected Perturbation of the Trunk: A Systematic Review

Introduction: Trunk neuromuscular responses have been shown to adapt under the influence of muscle fatigue, as well as spinal tissue creep or even with the presence of low back pain (LBP). Despite a large number of studies exploring how these external perturbations affect the spinal stability, characteristics of such adaptations remains unclear. Aim: The purpose of this systematic review was to assess the quality of evidence of studies investigating trunk neuromuscular responses to unexpected trunk perturbation. More specifically, the targeted neuromuscular responses were trunk muscle activity reflex and trunk kinematics under the influence of muscle fatigue, spinal creep, and musculoskeletal pain. Methods: A research of the literature was conducted in Pubmed, Embase, and Sport-Discus databases using terms related to trunk neuromuscular reflex responses, measured by electromyography (baseline activity, reflex latency, and reflex amplitude) and/or trunk kinematic, in context of unexpected external perturbation. Moreover, independent variables must be either trunk muscle fatigue or spinal tissue creep or LBP. All included articles were scored for their electromyography methodology based on the “Surface Electromyography for the Non-Invasive Assessment of Muscles (SENIAM)” and the “International Society of Electrophysiology and Kinesiology (ISEK)” recommendations whereas overall quality of articles was scored using a specific quality checklist modified from the Quality Index. Meta-analysis was performed on reflex latency variable. Results: A final set of 29 articles underwent quality assessments. The mean quality score was 79%. No effect of muscle fatigue on erector spinae reflex latency following an unexpected perturbation, nor any other distinctive effects was found for back muscle fatigue and reflex parameters. As for spinal tissue creep effects, no alteration was found for any of the trunk reflex variables. Finally, the meta-analysis revealed an increased erector spinae reflex latency in patients with chronic LBP in comparison with healthy controls following an unexpected trunk perturbation. Conclusion: The literature provides some evidence with regard to trunk adaptions in a context of spinal instability. However, most of the evidence was inconclusive due to a high methodological heterogeneity between the studies