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The Journal of Chemical Physics Apr 2024HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been...
HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade.
PubMed: 38651814
DOI: 10.1063/5.0196638 -
Antimicrobial Resistance and Infection... Apr 2024Widespread inappropriate use of antimicrobial substances drives resistance development worldwide. In long-term care facilities (LTCF), antibiotics are among the most...
BACKGROUND
Widespread inappropriate use of antimicrobial substances drives resistance development worldwide. In long-term care facilities (LTCF), antibiotics are among the most frequently prescribed medications. More than one third of antimicrobial agents prescribed in LTCFs are for urinary tract infections (UTI). We aimed to increase the number of appropriate antimicrobial treatments for UTIs in LTCFs using a multi-faceted antimicrobial stewardship intervention.
METHODS
We performed a non-randomized cluster-controlled intervention study. Four LTCFs of the Geriatric Health Centers Graz were the intervention group, four LTCFs served as control group. The main components of the intervention were: voluntary continuing medical education for primary care physicians, distribution of a written guideline, implementation of the project homepage to distribute guidelines and videos and onsite training for nursing staff. Local nursing staff recorded data on UTI episodes in an online case report platform. Two blinded reviewers assessed whether treatments were adequate.
RESULTS
326 UTI episodes were recorded, 161 in the intervention group and 165 in the control group. During the intervention period, risk ratio for inadequate indication for treatment was 0.41 (95% CI 0.19-0.90), p = 0.025. In theintervention group, the proportion of adequate antibiotic choices increased from 42.1% in the pre-intervention period, to 45.9% during the intervention and to 51% in the post-intervention period (absolute increase of 8.9%). In the control group, the proportion was 36.4%, 33.3% and 33.3%, respectively. The numerical difference between intervention group and control group in the post-intervention period was 17.7% (difference did not reach statistical significance). There were no significant differences between the control group and intervention group in the safety outcomes (proportion of clinical failure, number of hospital admissions due to UTI and adverse events due to antimicrobial treatment).
CONCLUSIONS
An antimicrobial stewardship program consisting of practice guidelines, local and web-based education for nursing staff and general practitioners resulted in a significant increase in adequate treatments (in terms of decision to treat the UTI) during the intervention period. However, this difference was not maintained in the post-intervention phase. Continued efforts to improve the quality of prescriptions further are necessary.
TRIAL REGISTRATION
The trial was registered at ClinicalTrials.gov NCT04798365.
Topics: Aged; Humans; Anti-Bacterial Agents; Anti-Infective Agents; Antimicrobial Stewardship; Long-Term Care; Nursing Homes; Urinary Tract Infections
PubMed: 38627795
DOI: 10.1186/s13756-024-01397-2 -
International Journal of Gynecological... May 2024To determine if reviewer experience impacts the ability to discriminate between human-written and ChatGPT-written abstracts.
OBJECTIVE
To determine if reviewer experience impacts the ability to discriminate between human-written and ChatGPT-written abstracts.
METHODS
Thirty reviewers (10 seniors, 10 juniors, and 10 residents) were asked to differentiate between 10 ChatGPT-written and 10 human-written (fabricated) abstracts. For the study, 10 gynecologic oncology abstracts were fabricated by the authors. For each human-written abstract we generated a ChatGPT matching abstract by using the same title and the fabricated results of each of the human generated abstracts. A web-based questionnaire was used to gather demographic data and to record the reviewers' evaluation of the 20 abstracts. Comparative statistics and multivariable regression were used to identify factors associated with a higher correct identification rate.
RESULTS
The 30 reviewers discriminated 20 abstracts, giving a total of 600 abstract evaluations. The reviewers were able to correctly identify 300/600 (50%) of the abstracts: 139/300 (46.3%) of the ChatGPT-generated abstracts and 161/300 (53.7%) of the human-written abstracts (p=0.07). Human-written abstracts had a higher rate of correct identification (median (IQR) 56.7% (49.2-64.1%) vs 45.0% (43.2-48.3%), p=0.023). Senior reviewers had a higher correct identification rate (60%) than junior reviewers and residents (45% each; p=0.043 and p=0.002, respectively). In a linear regression model including the experience level of the reviewers, familiarity with artificial intelligence (AI) and the country in which the majority of medical training was achieved (English speaking vs non-English speaking), the experience of the reviewer (β=10.2 (95% CI 1.8 to 18.7)) and familiarity with AI (β=7.78 (95% CI 0.6 to 15.0)) were independently associated with the correct identification rate (p=0.019 and p=0.035, respectively). In a correlation analysis the number of publications by the reviewer was positively correlated with the correct identification rate (r28)=0.61, p<0.001.
CONCLUSION
A total of 46.3% of abstracts written by ChatGPT were detected by reviewers. The correct identification rate increased with reviewer and publication experience.
Topics: Humans; Abstracting and Indexing; Female; Peer Review, Research; Writing; Gynecology; Surveys and Questionnaires; Publishing
PubMed: 38627032
DOI: 10.1136/ijgc-2023-005162 -
Brain & Spine 2024To evaluate the clinical 10 year outcome of patients treated with percutaneous vertebroplasty for vertebral compression fractures and to determine the incidence of new...
OBJECTIVES
To evaluate the clinical 10 year outcome of patients treated with percutaneous vertebroplasty for vertebral compression fractures and to determine the incidence of new fractures in this time interval, as well as the mortality of the patients who underwent this procedure.
METHODS
All patients undergoing vertebroplasty for vertebral compression fractures between May 2007 until July 2008 were prospectively followed up at 10 years postoperatively. Patients were assessed for radiologic outcome and self-reported outcome parameters (PROs). Gathered parameters remained unmodified to the initial ones analyzing QoL improvement (EQ5D 3L and NASS score) and pain alleviation (VAS, NRS). Mortality was defined as an additional endpoint. Exclusion criteria include additional instrumentation, use of additional devices such as kyphoplasty balloons/stentoplasty, cognitive impairment, insufficient radiological documentation or absent re-consent.
RESULTS
Of 280 patients who underwent vertebroplasty, 49 (17.5%) were available for re-assessment with a mean follow-up of 10.5 years (9.9-11.1). Thirty patients (10.7%) were assessed clinically and radiologically, 16 (5.7%) in written form and three (1.1%) by phone only. A total of 186 (66.4%) died during the follow up period. Out of the remaining 45 patients, 27 patients declined participation, eight couldn't participate due to cognitive impairment, four had insufficient radiologic documentation. Six patients were lost to follow-up. At 10 years, patients reported a consistently improved quality of life (EQ-5D; p < 0.01) and global satisfaction. Vertebroplasty demonstrated a substantial and enduring effect on alleviating back pain over 10 years (p < 0.001). 26 (53%) patients experienced a new fracture since the initial procedure.
CONCLUSION
A decade following vertebroplasty, patients continue to demonstrate a quality of life and pain level comparable to short and medium-term assessments, with a significant difference from baseline measurements. More than half (53%) of the patients participating at last follow-up experienced new fractures during this interim period. The cohort as a whole has been impacted by an elevated mortality rate over the time period.
PubMed: 38618227
DOI: 10.1016/j.bas.2024.102783 -
Genes To Cells : Devoted To Molecular &... Jun 2024Identifying key genes from a list of differentially expressed genes (DEGs) is a critical step in transcriptome analysis. However, current methods, including Gene...
Identifying key genes from a list of differentially expressed genes (DEGs) is a critical step in transcriptome analysis. However, current methods, including Gene Ontology analysis and manual annotation, essentially rely on existing knowledge, which is highly biased depending on the extent of the literature. As a result, understudied genes, some of which may be associated with important molecular mechanisms, are often ignored or remain obscure. To address this problem, we propose Clover, a data-driven scoring method to specifically highlight understudied genes. Clover aims to prioritize genes associated with important molecular mechanisms by integrating three metrics: the likelihood of appearing in the DEG list, tissue specificity, and number of publications. We applied Clover to Alzheimer's disease data and confirmed that it successfully detected known associated genes. Moreover, Clover effectively prioritized understudied but potentially druggable genes. Overall, our method offers a novel approach to gene characterization and has the potential to expand our understanding of gene functions. Clover is an open-source software written in Python3 and available on GitHub at https://github.com/G708/Clover.
Topics: Software; Humans; Gene Expression Profiling; Alzheimer Disease; Transcriptome; Computational Biology; Gene Ontology
PubMed: 38602264
DOI: 10.1111/gtc.13119 -
Bioinformatics (Oxford, England) May 2024Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in...
MOTIVATION
Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in information, phylogeneticists need new tools and skills to manipulate and analyze these data. To facilitate these tasks and encourage reproducibility, the community is increasingly moving toward automated workflows.
RESULTS
Here we present pipesnake, a phylogenomics pipeline written in Nextflow for the processing, assembly, and phylogenetic estimation of genomic data from short-read sequences. pipesnake is an easy to use and efficient software package designed for this next era in phylogenetics.
AVAILABILITY AND IMPLEMENTATION
pipesnake is publicly available on GitHub at https://github.com/AusARG/pipesnake and accompanied by documentation and a wiki/tutorial.
Topics: Software; Phylogeny; Genomics
PubMed: 38597877
DOI: 10.1093/bioinformatics/btae195 -
BMC Emergency Medicine Apr 2024Medication-related problems are an important cause of emergency department (ED) visits, and medication errors are reported in up to 60% of ED patients. Procedures such... (Observational Study)
Observational Study
BACKGROUND
Medication-related problems are an important cause of emergency department (ED) visits, and medication errors are reported in up to 60% of ED patients. Procedures such as medication reconciliation and medication review can identify and prevent medication-related problems and medication errors. However, this work is often time-consuming. In EDs without pharmacists, medication reconciliation is the physician's responsibility, in addition to the primary assignments of examining and diagnosing the patient. The aim of this study was to identify how much time ED physicians spend on medication-related tasks when no pharmacists are present in the EDs.
METHODS
An observational time-and-motion study of physicians in three EDs in Northern Norway was conducted using Work Observation Method by Activity Timing (WOMBAT) to collect and time-stamp data. Observations were conducted in predefined two-hour observation sessions with a 1:1 relationship between observer and participant, during Monday to Friday between 8 am and 8 pm, from November 2020 to October 2021.
RESULTS
In total, 386 h of observations were collected during 225 observation sessions. A total of 8.7% of the physicians' work time was spent on medication-related tasks, of which most time was spent on oral communication about medications with other physicians (3.0%) and medication-related documentation (3.2%). Physicians spent 2.2 min per hour on medication reconciliation tasks, which includes retrieving medication-related information directly from the patient, reading/retrieving written medication-related information, and medication-related documentation. Physicians spent 85.6% of the observed time on non-medication-related clinical or administrative tasks, and the remaining time was spent standby or moving between tasks.
CONCLUSION
In three Norwegian EDs, physicians spent 8.7% of their work time on medication-related tasks, and 85.6% on other clinical or administrative tasks. Physicians spent 2.2 min per hour on tasks related to medication reconciliation. We worry that patient safety related tasks in the EDs receive little attention. Allocating dedicated resources like pharmacists to contribute with medication-related tasks could benefit both physicians and patients.
Topics: Humans; Physicians; Medication Errors; Patient Safety; Time and Motion Studies; Emergency Service, Hospital
PubMed: 38594615
DOI: 10.1186/s12873-024-00974-3 -
BMJ Open Quality Apr 2024Early skin-to-skin contact (SSC) at birth has been shown to improve neonatal outcomes due to enhanced cardiorespiratory stability, thermoregulation and breastfeeding...
BACKGROUND
Early skin-to-skin contact (SSC) at birth has been shown to improve neonatal outcomes due to enhanced cardiorespiratory stability, thermoregulation and breastfeeding success.
LOCAL PROBLEM
The practice of early SSC was virtually non-existent in our delivery room (DR).
METHODS AND INTERVENTIONS
The study was conducted in a newly established tertiary care teaching hospital in Western Rajasthan, India. We aimed to improve the median duration of early SSC from 0 min to at least 60 min over 24 weeks in our DR. A quality improvement (QI) team was formed, and all inborn infants ≥35 weeks born vaginally from 9 March 2017 were included. Using the tools of point-of-care QI, we found the lack of standard operating procedure, lack of knowledge among nursing staff regarding early SSC, routine shifting of all infants to radiant warmer, the practice of prioritising birthweight documentation and vitamin K administration as the major hindrances to early SSC. Various change ideas were implemented and tested sequentially through multiple plan-do-study-act (PDSA) cycles to improve the duration of early SSC. Interventions included framing a written policy for SSC, sensitising the nursing staff and resident doctors, actively delaying the alternate priorities, making early SSC a shared responsibility among paediatricians, obstetricians, nursing staff and family members, and continuing SSC in the recovery area of the DR complex.
RESULTS
The duration of early SSC increased from 0 to 67 min without any additional resources. The practice of SSC got well established in the system as reflected by a sustained improvement of 63 min and 72 min, respectively, at the end of 2 months and 4 years after study completion.
CONCLUSION
Using the QI approach, we established and sustained the practice of early SSC for more than 60 min in our unit by using system analysis and testing change ideas in sequential PDSA cycles.
Topics: Infant, Newborn; Infant; Child; Humans; Pregnancy; Female; Quality Improvement; Kangaroo-Mother Care Method; India; Vitamin K; Time Factors
PubMed: 38589043
DOI: 10.1136/bmjoq-2023-002408 -
Joint Commission Journal on Quality and... Mar 2024Communication failures are among the most common causes of harmful medical errors. At one Comprehensive Cancer Center, patient handoffs varied among services. The...
BACKGROUND
Communication failures are among the most common causes of harmful medical errors. At one Comprehensive Cancer Center, patient handoffs varied among services. The authors describe the implementation and results of an Organization-wide project to improve handoffs and implement an evidence-based handoff tool across all inpatient services.
METHODS
The research team created a task force composed of members from 22 hospital services-advanced practice providers (APPs), trainees, some faculty members, electronic health record (EHR) staff, education and training specialists, and nocturnal providers. Over two years, the task force expanded to include consulting services and Anesthesiology. Factors contributing to ineffective handoffs were identified and organized into categories. The EHR I-PASS tool was used to standardize handoff documentation. Training was provided to staff on its use, and compliance was monitored using a customized dashboard. I-PASS champions in each service were responsible for the rollout of I-PASS in their respective services. The data were reported quarterly to the Quality Assessment and Performance Improvement (QAPI) governing committee. Provider handoff perception was assessed through the biennial Institution-wide safety culture survey.
RESULTS
All fellows, residents, APPs, and physician assistants were trained in the use of I-PASS, either online or in person. Adherence to the I-PASS written tool improved from 41.6% in 2019 to 70.5% in 2022 (p < 0.05), with improvements seen in most services. The frequency of updating I-PASS elements and the action list in the handoff tool also increased over time. The handoff favorability score on the safety culture survey improved from 38% in 2018 to 59% in 2022.
CONCLUSION
The implementation approach developed by the Provider Handoff Task Force led to increased use of the I-PASS EHR tool and improved safety culture survey handoff favorability.
PubMed: 38584053
DOI: 10.1016/j.jcjq.2024.03.004 -
Molecular Medicine Reports Jun 2024Following the publication of this paper, the authors requested that the paper be retracted, specifically on account of deficiencies that were identified both in the...
Following the publication of this paper, the authors requested that the paper be retracted, specifically on account of deficiencies that were identified both in the documentation of patient records and in written consent pertaining to the data presented in Fig. 1. After having considered the authors' request, the Editor of has agreed that this paper should be retracted from the Journal. All the authors are in agreement with the decision to retract this paper. The Editor apologizes to the readership for any inconvenience caused. [Molecular Medicine Reports 24: 724, 2021; DOI: 10.3892/mmr.2021.12363].
PubMed: 38577946
DOI: 10.3892/mmr.2024.13212