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Bioinformatics (Oxford, England) Jun 2021Microscopy images of stained cells and tissues play a central role in most biomedical experiments and routine histopathology. Storing colour histological images...
MOTIVATION
Microscopy images of stained cells and tissues play a central role in most biomedical experiments and routine histopathology. Storing colour histological images digitally opens the possibility to process numerically colour distribution and intensity to extract quantitative data. Among those numerical procedures are colour deconvolution, which enable decomposing an RGB image into channels representing the optical absorbance and transmittance of the dyes when their RGB representation is known. Consequently, a range of new applications become possible for morphological and histochemical segmentation, automated marker localization and image enhancement.
AVAILABILITY AND IMPLEMENTATION
Colour deconvolution is presented here in two open-source forms: a MATLAB program/function and an ImageJ plugin written in Java. Both versions run in Windows, Macintosh and UNIX-based systems under the respective platforms. Source code and further documentation are available at: https://blog.bham.ac.uk/intellimic/g-landini-software/colour-deconvolution-2/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Color; Coloring Agents; Image Enhancement; Image Processing, Computer-Assisted; Microscopy; Software
PubMed: 32997742
DOI: 10.1093/bioinformatics/btaa847 -
Acta Medico-historica Adriatica : AMHA Dec 2021In the general trend of nationalization after 1945, many pharmacies in our area were destroyed, relocated or repurposed. During these events, their interiors changed,...
In the general trend of nationalization after 1945, many pharmacies in our area were destroyed, relocated or repurposed. During these events, their interiors changed, and the inventory was damaged or destroyed. The aim of this paper is to research the historiography of pharmacy by reconstructing the chronology of the Joanović pharmacy as well as the Public Pharmacy of the town of Debeljača until it moved out of the building where the pharmacy was founded. Descriptive research covers the periods before the First World War, between the two World Wars and after the Second World War. The data presented in this paper are the result of interdisciplinary research related to the study of the historiography of the Joanović pharmacy as well as the Public Pharmacy of the town of Debeljača. This paper is based on unpublished documents (database of the pharmacy Joanović and the Publik Pharmacy of the town of Debeljača), as well as on the statements and written statements of Mrs. Mila Đorđević born Joanović and pharmacist Ivan Šimić as documents from the author’s personal archive. Methods of documentation analysis and desk analysis of secondary data were used. In the Joanović Pharmacy, almost semi-industrial production of cosmetic and perfumery products was developed, as well as the production of flavors for the production of alcoholic and non-alcoholic beverages. After the forced purchase, a biochemical laboratory was formed in the newly established National Pharmacy, which provided a large number of various laboratory services. The results of this study could be used in further study of the historiography of pharmacy research of the goods that pharmacies offered to consumers.
Topics: Pharmaceutical Services; Pharmacies; Pharmacy
PubMed: 35333015
DOI: 10.31952/amha.19.2.3 -
Advanced Biology Apr 2024The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering...
The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering toolkits enables the rapid design of genetic bioparts and genetically modified organisms. Although various software solutions assist with specific design tasks and challenges, lab internal documentation and ensuring compliance with governmental regulations on biosafety assessment of the generated organisms remain the responsibility of individual academic researchers. This results in inconsistent and redundant documentation regimes and a significant time and labor burden. GMOCU (GMO documentation) is a standardized semi-automatic user-oriented software approach -written in Python and freely available- that unifies lab internal data documentation on genetic parts and genetically modified organisms (GMOs). It automatizes biological risk evaluations and maintains a shared up-to-date inventory of bioparts for team-wide data navigation and sharing. GMOCU further enables data export into customizable formats suitable for scientific publications, official biosafety documents, and the research community.
Topics: Software; Risk Assessment; Documentation; Government Regulation
PubMed: 38263723
DOI: 10.1002/adbi.202300529 -
PeerJ 2022Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the...
BACKGROUND
Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.
METHODS
This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.
RESULTS
Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, F scores, and S scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.
AVAILABILITY
Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
Topics: Software; Algorithms; Molecular Sequence Annotation; Proteins; Databases, Protein
PubMed: 35186498
DOI: 10.7717/peerj.12931 -
Lakartidningen Oct 2023The scientific documentation of prehospital emergency care in Sweden is slowly expanding. The first thesis on the value of a mobile coronary care unit was defended in...
The scientific documentation of prehospital emergency care in Sweden is slowly expanding. The first thesis on the value of a mobile coronary care unit was defended in 1982. Since then, at least 106 theses have been defended at 15 educational institutes in Sweden. The theses can be divided into nine different themes, of which acute disease and prognostic factors (n = 30) is the most common, followed in order of frequency by caring, assessment and decision (n = 18), patient and next of kin perspective (n = 14), trauma (n = 1 1), competence, learning, and education (n = 10), care needs, cooperation, and prioritization (n = 10), disaster (n = 7), workers' health and environment (n = 3), and ethics and values (n = 3). The University of Gothenburg had the highest number of theses defended (n = 28), followed by the Karolinska Institute (n = 24) and the University of Umeå (n = 10). The theses were written by 64 nurses, 36 physicians, two public health specialists, one physiotherapist, one priest, one social worker, and one statistician.
Topics: Humans; Emergency Medical Services; Documentation; Sweden
PubMed: 37860864
DOI: No ID Found -
Journal of Pediatric Surgery Apr 2022I-PASS is a validated and standardized hand-off protocol shown to reduce medical error and improve hand-off efficiency in the pediatric medical population. Our aim was...
BACKGROUND
I-PASS is a validated and standardized hand-off protocol shown to reduce medical error and improve hand-off efficiency in the pediatric medical population. Our aim was to evaluate the feasibility, effectiveness, accuracy and resident satisfaction of implementing I-PASS on a pediatric surgery service.
METHODS
A prospective intervention Quality Improvement (QI approved) study was utilized to evaluate resident written and verbal hand-offs before and after implementation of I-PASS on a pediatric surgery service at a tertiary center. Anonymous surveys were completed by residents following each observation. Results were analyzed using T or Mann-Whitney U Tests and Chi Square.
RESULTS
A total of 49 written tools and 50 verbal hand-offs were compared pre-and post I-PASS implementation. With I-PASS, increased written accuracy was observed in the documentation of the patient summary (p < 0.05). Accuracy in the verbal hand-off of illness severity, patient summary, contingency plan, action list and synthesis also improved (p < 0.05); but duration of hand-off increased (p < 0.01). Post implementation surveys of residents demonstrated an increased understanding of patient management (p < 0.05).
CONCLUSION
Implementing I-PASS on a pediatric surgery service with modifications catered to surgical patients, improved the effectiveness and accuracy of written and verbal patient hand-offs and increased provider satisfaction and preparedness.
LEVEL OF EVIDENCE
Level II.
Topics: Child; Communication; Humans; Internship and Residency; Medical Errors; Patient Handoff; Prospective Studies
PubMed: 34911653
DOI: 10.1016/j.jpedsurg.2021.11.015 -
Journal of Multidisciplinary Healthcare 2023Adverse incidents in nursing home (NH) may occur as the result of inadequate monitoring for signs of unobservable initial complications, medical errors, improper nursing...
INTRODUCTION
Adverse incidents in nursing home (NH) may occur as the result of inadequate monitoring for signs of unobservable initial complications, medical errors, improper nursing interventions, lack of communication, and inadequate reporting.
PURPOSE
This study explores incident types, causes, handling, and documentation in Indonesian NHs through a qualitative approach.
PATIENTS AND METHODS
In-depth interviews were conducted with 23 NH staff members, including managers, nurses, and support staff.
RESULTS
Five themes and 17 sub-themes emerged, with falls and resident-to-resident abuse as common adverse incidents. Causes included older adults' conditions, environment, and misunderstanding. Follow-up action included first aid, hospital referrals, and assertive communication. Adverse incidents were actively reported through verbal and written reports or WhatsApp groups. Reports and documentation remain unstructured, however, as there were no standard operating procedures regarding incident reporting, documentation, and the types of adverse incidents that staff should report.
CONCLUSION
Improvements in management, documentation, and reporting adverse incidents are highlighted in this research. Practitioners, nurses, and social workers should develop guidelines for handling, reporting, and documenting adverse incidents in NHs.
PubMed: 37964796
DOI: 10.2147/JMDH.S436766 -
AORN Journal Sep 2019Surgical instrument decontamination requires the collective input of facility leaders, OR staff members, and sterile processing department personnel. Individual...
Surgical instrument decontamination requires the collective input of facility leaders, OR staff members, and sterile processing department personnel. Individual accountability can ensure that instruments are cleaned according to the manufacturers' written instructions for use, appropriate regulations, and facility policies. Information about the instrument decontamination process-from point of use to sterilization-should help enable perioperative nurses to advocate for and participate in the appropriate implementation of the necessary process steps. Sterile processing department leaders should develop policies and procedures for decontamination of surgical instruments and devices and the various accountabilities for the process steps. They also should help provide education for their staff members and complete required documentation. This article reviews the steps of instrument cleaning and decontamination and provides a framework to help perioperative leaders and educators facilitate these steps in their work environments, prevent instrument damage, and help ensure safe patient care.
Topics: Central Supply, Hospital; Disinfection; Humans; Leadership; Perioperative Nursing; Personnel, Hospital; Surgical Instruments
PubMed: 31465566
DOI: 10.1002/aorn.12784 -
Improving feedback students receive on documentation during the obstetrics and gynecology clerkship.AJOG Global Reports Nov 2022Students need feedback on written documentation to optimize their long-term development of this important clinical skill. The culture in surgical specialties does not...
BACKGROUND
Students need feedback on written documentation to optimize their long-term development of this important clinical skill. The culture in surgical specialties does not always prioritize feedback regarding this skill.
OBJECTIVE
This study aimed to examine the effectiveness of 2 specific forms to improve the quantity and quality of feedback to students about their medical documentation.
STUDY DESIGN
In a multiphase quality improvement project, medical students were surveyed after the obstetrics and gynecology clerkship regarding their experience of receiving feedback on written notes. The proportions of students who received feedback on notes and those rating the feedback as meaningful were measured before and after the implementation of a required, formative feedback card. In phase 2, students were randomized to use a simplified feedback card or the original detailed card, and outcomes were compared. This study was conducted at the Medical University of South Carolina, a tertiary care academic medical center. The participants included third-year medical students that completed their 6-week obstetrics and gynecology clerkship.
RESULTS
Before the intervention, of 82 students, 70 (85%) and 55 (67%) received feedback on written notes in the inpatient and outpatient settings, respectively, which increased to 99.6% (254/255) and 98.5% (251/255) (<.001) after the implementation of any feedback card. Moreover, the proportion of students who felt the feedback helped them improve their clinical documentation skills increased from 72% to 90% (<.001) with the use of a feedback card. These improvements were noted in all clinical units within the clerkship. There was no difference (=.3) in outcomes between the simplified and detailed cards.
CONCLUSION
A formative card is a simple, cost-effective, low-resource intervention that can increase both the quantity and quality of written note feedback that students receive during their obstetrics and gynecology clerkship. A less detailed card achieved comparable outcomes and increased faculty satisfaction.
PubMed: 36311295
DOI: 10.1016/j.xagr.2022.100117 -
Urogynecology (Philadelphia, Pa.) Mar 2024The price range, insurance coverage, and side effect burden of overactive bladder medications is broad and varied. An internal quality improvement project was undertaken...
IMPORTANCE
The price range, insurance coverage, and side effect burden of overactive bladder medications is broad and varied. An internal quality improvement project was undertaken to improve patient ability to access and ultimately adhere to preferred medication therapy for treatment of overactive bladder.
OBJECTIVE
Our objective was to increase the percentage of patients per month at an academic Urogynecology practice who receive their preferred overactive bladder medication from baseline 39.5% to 45%.
STUDY DESIGN
Data were extracted via Epic report. Manual chart review and calls to patients and/or pharmacy were completed to obtain status of medication access and reasons why medications were not taken. A targeted intervention was implemented with creation of a written document to help guide patients with options to decrease prescription costs. After this document was embedded into Epic after visit summary documentation, a repeat analysis was performed.
RESULTS
The most common barrier to medication access was cost; specifically, the medication was not covered and a prior authorization was not initiated. Before the intervention, more than 60% of patients did not persist with their initially prescribed overactive bladder medication at a 6-month follow-up interval from office visit. Following implementation of a cost-navigation guide, persistence increased to 45.5% at a 3-month follow-up interval.
CONCLUSIONS
A targeted intervention on cost navigation of prescriptions can have a positive effect on patient access and persistence of using overactive bladder medications. Our practice continues to use our prescription navigation handout.
Topics: Humans; Urinary Bladder, Overactive
PubMed: 38484255
DOI: 10.1097/SPV.0000000000001493