bluuebunny/crossref_metadata_2025_split huggingface dataset:
92 ‘Greenprint’ for integrated care clinics—the hub and spoke model
Authors: Murphy D E , Geoghegan J , Reddin C , McCleane F , Neachtain M Ni , Mannion K , Shiel E , O'Malley K , Lynch Amy , Okon M , Okpaje B , Griffith V , Hanrahan C , Loughlin E , Robinson S , Murphy R , Waters R , Costello M , Canavan M 
Published: September 2023

Abstract

Background
Climate change is a major public health crisis requiring attention at an individual, local and national policy level. Transport is the largest source of energy related carbon emissions in Ireland. The development of integrated care occurs alongside climate emergency. Care previously delivered in hospital outpatients, or a central ‘hub’ is now being delivered in integrated care clinics, ‘spokes’. We aimed to assess the environmental impact of transport to integrated care clinics compared to travel to hospital clinic.

Methods
Geriatric Medicine Integrated Care attendances from January 2023 to March 2023 were included. Distance from the patient’s home address to the location of Integrated Care Clinic (spoke), and to the affiliated hospital (hub) were recorded in kilometres. For the primary analysis we have not considered staff travel as there was heterogeneity in number of staff per clinic and distance travelled per staff member. Where more than one route was available, the shortest distance was recorded. Carbon emissions were estimated based on kilometres travelled by a standard new passenger car.

Results
Among 206 clinic attendances, the mean distance to ‘spoke’ clinic was 16.06 km (15.98). The mean distance to the ‘hub’ clinic was 39.29 km (17.82). The estimated total distance travelled by patients to integrated care clinics was 3293.45 km, whereas the distance which would have been travelled to ‘hub’ clinics was 8055.85 km. Total carbon emissions for 3 month travel to ‘spoke’ clinics were estimated at 371 kg, compared to 907 kg to the ‘hub’.

Conclusion
The development of integrated care services, which provides necessary care to older adults, may also have an environmental advantage. Healthcare’s contribution to climate change action is another incentive to invest in integrated care services.
102 Decision making around Eating and Drinking with Acknowledged Risk (EDAR)
Authors: Donders-Seóighe C 
Published: September 2023

Abstract

Background
Life expectancy in Ireland has increased, leading to older adults with increasingly complex health needs, including dysphagia. Reportedly, dysphagia affects 30% of older adults in hospital and 68% of nursing home residents. Speech and Language Therapists (SLT) in a large teaching hospital, identified a need to develop a pathway or policy to help guide decision making around older adults who wish to eat and drink despite the presence of Dysphagia.
Methods: A comprehensive literature review compared different approaches to the management of Eating and Drinking with Acknowledged Risk (EDAR), exploring the following questions: (1) Should eating and drinking with acknowledged risk be outlined in a policy?, (2) Should it include a capacity assessment?, (3) Who is the final decision maker?, (4) What is the optimal timing of a conversation around this subject? The evidence was presented to relevant stakeholders from disciplines where EDAR arose most often e.g. other SLT’s, Geriatric medicine, General surgery and Palliative Care.

Results
Given the need for patient-centred care, there was a preference for a care pathway, as opposed to a policy for EDAR. General consensus was that the patient should be the final decision maker, with senior medical support. Optimal timing for EDAR decisions can be complex: Hospital SLTs struggle with limited time resources, acute illness can affect patient’s ability to engage, or a patient might benefit from a swallow rehab program first. Community therapists work in isolation and might lack medical support. Nursing home residents have least access to SLT and often lack any opportunity to discuss EDAR.

Conclusion
The EDAR approach varies from traditional SLT practices. It can evoke strong opinions, especially around final decision making. Timing of discussions around EDAR presents with unique challenges in different healthcare settings. A care pathway in the acute setting can streamline decision making, support SLTs, and allow for individual patient choice.
198 How comprehensive is our Comprehensive Geriatric Assessment in clinical practice?
Authors: Dennehy K , Lynch A , Reddin C , Costello M , Canavan M , Murphy R 
Published: September 2023

Abstract

Background
No gold standard exists for what should be included within a Comprehensive Geriatric Assessment (CGA). Consensus is that a CGA assessment should assess physical, functional, psychological and social well-being. We sought to examine the specific content of CGA that are being delivered across integrated care teams in Ireland.

Methods
We completed a cross sectional study of what domains are included in different integrated care CGA proformas. All operational leads for each integrated care hub were contacted and invited to share their local CGA. We examined what components across the domains of physical, psychological, functional and social assessment were included.

Results
We examined 16 different CGAs. The median length of a CGA was 14 pages (range: 4–28 pages). Common areas in all CGAs included assessments of frailty, cognition, mobility, falls, continence and social assessment, but there was variability in how these assessments were carried out. The Rockwood Clinical frailty scale the most common diagnostic tool for frailty (15/16 CGAs) with sarcopenia assessed in 75% of CGAs. The 4AT tool was used in 56% of CGAs, with a more detailed tool (e.g MMSE or MOCA) used in 56% of CGAs. Mood was assessed in 15 CGAs, sleep assessed in 10 CGAs and pain assessed in 7 CGAs. The widest variability was in the social assessment section with inconsistent assessments of caregiver strain (completed in 50%) and assessments of formal advanced care supports such as enduring power of attorney included in 44% of CGAs. Sexual health was not explicitly addressed in any CGA.

Conclusion
While there is considerable overlap with the core components of a CGA across integrated care sites there is significant variability across individual sites. Our results highlight the opportunity for consensus building across different integrated care teams to harmonise the delivery of CGA.
237 Drug–drug interactions and the risk of adverse drug reaction hospital admissions in the older population: a prospective cohort study
Authors: Hughes J E , Moriarty F , Cahir C , Bennett K E 
Published: September 2023

Abstract

Background
Drg–Drg Interactions (DDIs) can lead to medication-related harm; the older population is at greatest risk. We estimate DDI prevalence and the average causal effect of DDI exposure on adverse drug reaction (ADR)-related hospital admission in an older (≥65 years) population admitted acutely to hospital in Ireland. We also examine the effect of DDI exposure on health-related quality of life (HRQoL) and Length of Stay (LoS) in hospital.

Methods
Prospectively collected (2016–17) data from the Adverse Drg Reactions in an Ageing PopulaTion cohort were used (N = 798). Medication (current/recently-discontinued/over-the-counter) and objective clinical data (e.g. renal function) were available. DDIs (which may result in a life-threatening event/permanent detrimental effect) were identified using the BNF and Stockley’s. Causal inference models were developed using directed acyclic graphs. HRQoL was measured using the EQ-5D-5L. Multivariable logistic regression was performed using SAS (v9.4).

Results
N = 782 patients using ≥2drugs were included, mean age = 80.9(±7.5); 52.2% female; 92.2% polypharmacy (≥5drugs); 45.1% had an ADR-related hospital admission. N = 316 (40.4% [95% Confidence Interval (CI):37.0–43.9]) patients with at least one DDI at hospital admission. After controlling for confounding, the average causal effect of DDI exposure on ADR-related hospital admission was Odds Ratio (OR) = 1.2 [95% CI: 0.9–1.6]. This risk was significantly increased for patients exposed to DDIs which increase bleeding risk (OR: 2.0 [1.3–3.1]); for aspirin-warfarin (OR: 2.8 [1.4–5.7]) and esomeprazole-escitalopram (OR: 3.2 [1.1–10.3] DDIs. Patients with a DDI had a lower HRQoL (mean EQ-5D: 0.49 [±0.39]) compared to those with none (mean EQ-5D: 0.58 [±0.41], p = 0.08). Patients with an ADR-related hospitalisation and DDI had a significantly greater LoS in hospital (8 [Interquartile Range:5–17] days) compared to those with no DDI (6[Interquartile Range: 3–13] days, p = 0.02).

Conclusion
DDIs are prevalent among older adults on acute admission to hospital, and increase the risk of ADR-related hospitalisation, significantly for patients with DDIs that increase bleeding risk. Patients with a DDI had lower HRQoL, and prolonged LOS in hospital.
257 Chronic pain is associated with mobility impairment and falls among community-dwelling older people: data from TILDA
Authors: Lalor P , Swanton A , Lavan A , Kenny R A , Briggs R 
Published: September 2023

Abstract

Background
Chronic pain is prevalent among older people in Ireland and can have a profound impact on health outcomes. The aim of this study is to assess the relationship between chronic pain and mobility impairment and falls risk in a population-representative sample of older people.

Methods
Participants ≥70 years at TILDA Wave 1 were asked ‘Are you often troubled with pain?’ and if yes, were then asked ‘How bad is it most of the time? Mild, moderate, or severe?’. Mobility was assessed with Timed Up and Go (TUG). Data was collected on falls and unexplained falls (falls not due to a slip/trip, with no apparent cause) within the last 12 months. Linear regression models, reporting β-coefficients, assessed the independent relationship between chronic pain and TUG; logistic regression models, reporting Odds Ratios (OR) and 95% Confidence Intervals (95% CI) assessed the association with falls.

Results
Over 1/3 of participants reported chronic pain as follows: mild (10%, 221/2,308); moderate (17%, 396/2,308) and severe (10%, 222/2,308). Participants with moderate (TUG: 12.67 [95% CI 11.83–13.51]) and severe chronic pain (TUG 13.98 [95% CI 12.32–15.64]) had a prolonged TUG, compared to those who were pain-free (TUG 10.94 [95% CI 10.61–11.25]). In fully-adjusted linear regression models, both moderate (β = 1.11 [95% CI 0.28–1.93]; p = 0.008) and severe pain (β = 1.63 [95% CI 0.48–2.77]; p = 0.005) were independently associated with prolonged TUG. Participants with chronic pain also had a higher likelihood of total (OR 1.30 [95% CI 1.00–1.6]); p = 0.049) and unexplained falls (OR 1.81 [95% CI 1.18–2.76]; p = 0.006) in fully-adjusted models.

Conclusion
Chronic pain confers significant limitations on mobility among older people: participants with severe pain take on average 3 seconds longer to complete the TUG. Further, chronic pain is associated with falls, particularly unexplained falls, highlighting the need to assess and treat pain as part of the comprehensive geriatric assessment.
343 Sustainability of area-based, community-driven post-diagnostic support services for people with dementia: evidence from a mixed-methods study
Authors: Pierce M , Golden J 
Published: September 2023

Abstract

Background
Supporting people with dementia to live at home in their communities post-diagnosis is a goal of national and international policy. Local area-based, community driven services can play a key role in supporting people with dementia post-diagnosis, and have demonstrated their role in helping to move the existing care system to a personalised model. Sustaining such services over the long-term can be a struggle. This study aimed to understand the factors affecting the sustainability of dementia post-diagnostic support services, how these can best be addressed, and what are the lessons for policymakers and others.

Methods
This mixed-methods study of one area-based, community driven dementia post-diagnostic service was conducted between September 2022 and February 2023. Qualitative methods were used to explore the perspectives of 47 study participants on the value of the service and its sustainability. The study included focus groups (n = 2) with service staff, interviews with people with dementia (n = 8), family carers (n = 16) and national and locally-based stakeholders (n = 16), and a review of seven years of service activity and expenditure data.

Results
The study found that the service was widely regarded as a valuable addition to the dementia care landscape, in high demand, well integrated into the service landscape and an important resource for other services. A range of factors were found to affect service sustainability including funding levels, resource allocation mechanisms, working relationships between key organisations, managerial change, organisational restructuring, staff capacity and strategic planning.

Conclusion
Despite demonstrated value to dementia care landscape, service sustainability cannot be taken for granted. Strategies that will help sustain dementia post-diagnostic services in the long-term need to be adopted. The results will be of interest to policy-makers and a range of other actors involved in planning, implementing and supporting post-diagnostic services as well as service users and healthcare professionals.
Analysis of Complications in Patients With a History of Cannabis Use and Tobacco Use Undergoing Implant-Based Breast Reconstruction
Authors: Garoosi Kassra , Lee Nayun , Tuano Krystle R , Lee Elliot L H , Cohen Justin , Winocour Julian , Mathes David W , Iorio Matthew L , Kaoutzanis Christodoulos 
Published: September 2023

Abstract

Background
There is limited information regarding the perioperative effects of marijuana in breast reconstructive surgeries.

Objectives
The objective of this study was to explore the association between a history of cannabis use and postoperative complications in the setting of implant-based breast reconstruction.

Methods
Two databases, TriNetX and PearlDiver, were queried for patients undergoing implant-based breast reconstruction. Patients were divided into 4 groups based on active ICD-10 diagnostic codes: (1) cannabis use only, (2) tobacco use only, (3) cannabis and tobacco use, and (4) neither cannabis nor tobacco use. Associations with postoperative complications were analyzed with a logistic regression test.

Results
TriNetX search revealed that 327 patients had an active diagnosis of cannabis use only and 1118 had an active diagnosis of tobacco use only. Patients in the cannabis only cohort had a significantly increased risk of developing surgical site infection. Patients in the tobacco only cohort had significantly increased risk of developing wound dehiscence, need for debridement, and surgical site infection. The PearlDiver search included 472 patients who had an active diagnosis of both cannabis and tobacco use and 17,361 patients with a diagnosis of tobacco use only. Patients with a diagnosis of cannabis and tobacco use had a significantly increased risk of developing postoperative complications including surgical site infection, wound dehiscence, need for incision and drainage, and debridement.

Conclusions
Patients undergoing implant-based breast reconstruction with an active diagnosis of cannabis with or without tobacco use were at increased risk of developing postoperative complications, and the risk was even higher in patients using both tobacco and cannabis.

Level of Evidence: 3
Analyzing the Impact of Social and Psychiatric Factors in Patients Who Undergo Body Contouring Procedures
Authors: Glenney Anne E , Mocharnuk Joseph W , Humar Pooja , Zhang Casey , Rubin J Peter , Gusenoff Jeffrey A 
Published: September 2023

Abstract

Background
As the prevalence of obesity increases, the number of patients seeking body contouring procedures after bariatric surgery for massive weight loss is increasing. Although the positive impact of bariatric surgery on physical and emotional health is well-described, few studies have reported on the psychosocial well-being of patients undergoing body contouring procedures. Psychosocial well-being can impact patient satisfaction and maintenance of weight loss, and is an important area to study.

Objective
The aim of this study was to characterize social and psychiatric factors of patients undergoing body contouring surgery, and to evaluate their impact on maintenance of weight loss.

Methods
A retrospective review was performed of patients who presented to a single institution for body contouring procedures between 2002 and 2018. Demographic details, medical history, psychosocial support, and operative details were collected. Univariate analysis and multinomial logistic regressions were performed with R statistical software (version 1.3.1093).

Results
A total of 1187 patients underwent at least 1 body contouring procedure during the study time frame. Mean BMI at presentation was 31.21 ± 10.49 kg/m2. Patients diagnosed with obesity at age 18 or older had significantly greater odds of suffering from generalized anxiety disorder (odds ratio [OR] 1.08 [95% CI, 1.02-1.15], P = .008). Patients with spousal support had 1.93 times higher odds of having maintained postbariatric weight loss at their 6-month follow-up (OR 1.93 [95% CI, 1.84-2.01], P = .028).

Conclusions
Social support and age of obesity diagnosis impact psychological well-being and maintenance of weight loss following body contouring procedures.

Level of Evidence: 3
Enhanced tight junction in Caco-2 cells by the pretreatment with Lactobacillus johnsonii strain MG
Authors: Bai Yuying , Miyanaga Kazuhiko , Yamamoto Naoyuki 
Published: September 2023

ABSTRACT
We investigated roles of Lactobacillus johnsonii MG (MG) isolated from mice with interaction with tight junction on gut barrier function with Caco-2 cell model. Pretreatment with MG enhanced barrier function and showed protective effect against Enterococcus faecium provided damage. MG treatment increased the gene expressions of transcriptional regulator NFKB and major tight junction protein, ZO-1.
The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference
Authors: Haag Julia , Hübner Lukas , Kozlov Alexey M , Stamatakis Alexandros 
Published: September 2023

Abstract

Summary
Maximum likelihood (ML) is a widely used phylogenetic inference method. ML implementations heavily rely on numerical optimization routines that use internal numerical thresholds to determine convergence. We systematically analyze the impact of these threshold settings on the log-likelihood and runtimes for ML tree inferences with RAxML-NG, IQ-TREE, and FastTree on empirical datasets. We provide empirical evidence that we can substantially accelerate tree inferences with RAxML-NG and IQ-TREE by changing the default values of two such numerical thresholds. At the same time, altering these settings does not significantly impact the quality of the inferred trees. We further show that increasing both thresholds accelerates the RAxML-NG bootstrap without influencing the resulting support values. For RAxML-NG, increasing the likelihood thresholds ϵLnL and ϵbrlen to 10 and 103, respectively, results in an average tree inference speedup of 1.9 ± 0.6 on Data collection 1, 1.8 ± 1.1 on Data collection 2, and 1.9 ± 0.8 on Data collection 2 for the RAxML-NG bootstrap compared to the runtime under the current default setting. Increasing the likelihood threshold ϵLnL to 10 in IQ-TREE results in an average tree inference speedup of 1.3 ± 0.4 on Data collection 1 and 1.3 ± 0.9 on Data collection 2.

Availability and implementation
All MSAs we used for our analyses, as well as all results, are available for download at https://cme.h-its.org/exelixis/material/freeLunch_data.tar.gz. Our data generation scripts are available at https://github.com/tschuelia/ml-numerical-analysis.
Immuno-metabolic signaling in leishmaniasis: insights gained from mathematical modeling
Authors: Khandibharad Shweta , Singh Shailza 
Published: September 2023

Abstract

Motivation
Leishmaniasis is a global concern especially in underdeveloped and developing subtropical and tropical regions. The extent of infectivity in host is majorly dependent on functional polarization of macrophages. Classically activated M1 macrophage can eliminate parasite through production of iNOS and alternatively activated M2 macrophages can promote parasite growth through by providing shelter and nutrients to parasite. The biological processes involved in immune signaling and metabolism of host and parasite might be responsible for deciding fate of parasite.

Results
Using systems biology approach, we constructed two mathematical models and inter-regulatory immune-metabolic networks of M1 and M2 state, through which we identified crucial components that are associated with these phenotypes. We also demonstrated how parasite may modulate M1 phenotype for its growth and proliferation and transition to M2 state. Through our previous findings as well as from recent findings we could identify SHP-1 as a key component in regulating the immune-metabolic characterization of M2 macrophage. By targeting SHP-1 at cellular level, it might be possible to modulate immuno-metabolic mechanism and thereby control parasite survival.

Availability and implementation
Mathematical modeling is implemented as a workflow and the models are deposited in BioModel database. FactoMineR is available at: https://github.com/cran/FactoMineR/tree/master.
ChromNetMotif: a Python tool to extract chromatin-sate marked motifs in a chromatin interaction network
Authors: Soibam Benjamin 
Published: September 2023

Abstract

Motivation
Analysis of network motifs is crucial to studying the robustness, stability, and functions of complex networks. Genome organization can be viewed as a biological network that consists of interactions between different chromatin regions. These interacting regions are also marked by epigenetic or chromatin states which can contribute to the overall organization of the chromatin and proper genome function. Therefore, it is crucial to integrate the chromatin states of the nodes when performing motif analysis in chromatin interaction networks. Even though there has been increasing production of chromatin interaction and genome-wide epigenetic modification data, there is a lack of publicly available tools to extract chromatin state-marked motifs from genome organization data.

Results
We develop a Python tool, ChromNetMotif, offering an easy-to-use command line interface to extract chromatin-state-marked motifs from a chromatin interaction network. The tool can extract occurrences, frequencies, and statistical enrichment of the chromatin state-marked motifs. Visualization files are also generated which allow the user to interpret the motifs easily. ChromNetMotif also allows the user to leverage the features of a multicore processor environment to reduce computation time for larger networks. The output files generated can be used to perform further downstream analysis. ChromNetMotif aims to serve as an important tool to comprehend the interplay between epigenetics and genome organization.

Availability and implementation
ChromNetMotif is available at https://github.com/lncRNAAddict/ChromNetworkMotif.