bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in the proportion of the segregating genome shared between full-sibling cattle and sheep
Authors: Kenny David , Berry Donagh P. , Pabiou Thierry , Rafter Pierce
Published: April 2023

The construction of covariance matrices that account for the genetic relationships among individuals, using pedigree or genotype data, is integral to genetic evaluations, which are now routinely used in the field of animal breeding. The objective of the present study was to estimate the standard deviation in the proportion of the segregating genome that is shared between pairs of full-sibling cattle and sheep independently. Post edits, genotype data comprising 46,069 autosomal single nucleotide polymorphisms (SNPs) were available for 4532 unique full-sibling sheep pairs, as well as for their respective parents. Post edits, genotypes from 50,493 autosomal SNPs were also available for 10,000 unique full-sibling cattle pairs, as well as their respective parents. Genomic relationship matrices were constructed for the sheep and cattle populations, separately. After accounting for both parental genomic inbreeding and the genomic relationship between both parents, the standard deviation in full-sibling cattle and sheep genomic relationships was 0.040 and 0.037 units, respectively. In addition, the intercept value from a linear regression model which regressed each full-sibling genomic relationship on both sire and dam inbreeding, as well as the genomic relationship between the parents, was 0.499 (0.001) for sheep and 0.500 (0.001) for cattle, conforming to the expectation that full-siblings, on average, share 50% of their segregating genome.
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis
Authors: Li He , Yang Lei , Wang Yuanyuan , Wang Lingchan , Chen Gang , Zhang Li , Wang Dongchang
Published: April 2023

Background

The TP53 tumor suppressor gene is one of the most mutated genes in lung adenocarcinoma (LUAD) and plays a vital role in regulating the occurrence and progression of cancer. We aimed to elucidate the association between TP53 mutations, response to immunotherapies and the prognosis of LUAD.

Methods

Genomic, transcriptomic, and clinical data of LUAD were downloaded from The Cancer Genome Atlas (TCGA) dataset. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, gene set enrichment analysis (GSEA). Gene set variation analysis (GSVA) were performed to determine the differences in biological pathways. A merged protein–protein interaction (PPI) network was constructed and analyzed. MSIpred was used to analyze the correlation between the expression of the TP53 gene, tumor mutation burden (TMB) and tumor microsatellite instability (MSI). CIBERSORT was used to calculate the abundance of immune cells. Univariate and multivariate Cox regression analyses were used to determine the prognostic value of TP53 mutations in LUAD.

Results

TP53 was the most frequently mutated in LUAD, with a mutational frequency of 48%. GO and KEGG enrichment analysis, GSEA, and GSVA results showed a significant upregulation of several signaling pathways, including PI3K-AKT mTOR (P < 0.05), Notch (P < 0.05), E2F target (NES = 1.8, P < 0.05), and G2M checkpoint (NES = 1.7, P < 0.05). Moreover, we found a significant correlation between T cells, plasma cells, and TP53 mutations (R2 < 0.01, P = 0.040). Univariate and multivariate Cox regression analyses revealed that the survival prognosis of LUAD patients was related to TP53 mutations (Hazard Ratio (HR) = 0.72 [95% CI, 0.53 to 0.98], P < 0.05), cancer status (P < 0.05), and treatment outcomes (P < 0.05). Lastly, the Cox regression models showed that TP53 exhibited good power in predicting three- and five-year survival rates.

Conclusions

TP53 may be an independent predictor of response to immunotherapy in LUAD, and patients with TP53 mutations have higher immunogenicity and immune cell infiltration.
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis
Authors: Hosseini-Gerami Layla , Higgins Ixavier Alonzo , Collier David A. , Laing Emma , Evans David , Broughton Howard , Bender Andreas
Published: April 2023

Background

Elucidating compound mechanism of action (MoA) is beneficial to drug discovery, but in practice often represents a significant challenge. Causal Reasoning approaches aim to address this situation by inferring dysregulated signalling proteins using transcriptomics data and biological networks; however, a comprehensive benchmarking of such approaches has not yet been reported. Here we benchmarked four causal reasoning algorithms (SigNet, CausalR, CausalR ScanR and CARNIVAL) with four networks (the smaller Omnipath network vs. 3 larger MetaBase™ networks), using LINCS L1000 and CMap microarray data, and assessed to what extent each factor dictated the successful recovery of direct targets and compound-associated signalling pathways in a benchmark dataset comprising 269 compounds. We additionally examined impact on performance in terms of the functions and roles of protein targets and their connectivity bias in the prior knowledge networks.

Results

According to statistical analysis (negative binomial model), the combination of algorithm and network most significantly dictated the performance of causal reasoning algorithms, with the SigNet recovering the greatest number ofdirect targets. With respect to the recovery ofsignalling pathways, CARNIVAL with the Omnipath network was able to recover the most informative pathways containing compound targets, based on the Reactome pathway hierarchy. Additionally, CARNIVAL, SigNet and CausalR ScanR all outperformed baseline gene expression pathway enrichment results. We found no significant difference in performance between L1000 data or microarray data, even when limited to just 978 ‘landmark’ genes. Notably, all causal reasoning algorithms also outperformed pathway recovery based on input DEGs, despite these often being used for pathway enrichment. Causal reasoning methods performance was somewhat correlated with connectivity and biological role of the targets.

Conclusions

Overall, we conclude that causal reasoning performs well at recovering signalling proteins related to compound MoA upstream from gene expression changes by leveraging prior knowledge networks, and that the choice of network and algorithm has a profound impact on the performance of causal reasoning algorithms. Based on the analyses presented here this is true for both microarray-based gene expression data as well as those based on the L1000 platform.
PyAGH: a python package to fast construct kinship matrices based on different levels of omic data
Authors: Zhao Wei , Qadri Qamar Raza , Zhang Zhenyang , Wang Zhen , Pan Yuchun , Wang Qishan , Zhang Zhe
Published: April 2023

Background

Construction of kinship matrices among individuals is an important step for both association studies and prediction studies based on different levels of omic data. Methods for constructing kinship matrices are becoming diverse and different methods have their specific appropriate scenes. However, software that can comprehensively calculate kinship matrices for a variety of scenarios is still in an urgent demand.

Results

In this study, we developed an efficient and user-friendly python module, PyAGH, that can accomplish (1) conventional additive kinship matrces construction based on pedigree, genotypes, abundance data from transcriptome or microbiome; (2) genomic kinship matrices construction in combined population; (3) dominant and epistatic effects kinship matrices construction; (4) pedigree selection, tracing, detection and visualization; (5) visualization of cluster, heatmap and PCA analysis based on kinship matrices. The output from PyAGH can be easily integrated in other mainstream software based on users’ purposes. Compared with other softwares, PyAGH integrates multiple methods for calculating the kinship matrix and has advantages in terms of speed and data size compared to other software. PyAGH is developed in python and C +  + and can be easily installed by pip tool. Installation instructions and a manual document can be freely available from https://github.com/zhaow-01/PyAGH.

Conclusion

PyAGH is a fast and user-friendly Python package for calculating kinship matrices using pedigree, genotype, microbiome and transcriptome data as well as processing, analyzing and visualizing data and results. This package makes it easier to perform predictions and association studies processes based on different levels of omic data.
Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing
Authors: Steensma Marije J. , Lee Y. L. , Bouwman A. C. , Pita Barros C. , Derks M. F.L. , Bink M. C.A.M. , Harlizius B. , Huisman A. E. , Crooijmans R. P.M.A. , Groenen M. A.M. , Mulder H. A. , Rochus C. M.
Published: April 2023

Background

De novo mutations arising in the germline are a source of genetic variation and their discovery broadens our understanding of genetic disorders and evolutionary patterns. Although the number of de novo single nucleotide variants (dnSNVs) has been studied in a number of species, relatively little is known about the occurrence of de novo structural variants (dnSVs). In this study, we investigated 37 deeply sequenced pig trios from two commercial lines to identify dnSVs present in the offspring. The identified dnSVs were characterised by identifying their parent of origin, their functional annotations and characterizing sequence homology at the breakpoints.

Results

We identified four swine germline dnSVs, all located in intronic regions of protein-coding genes. Our conservative, first estimate of the swine germline dnSV rate is 0.108 (95% CI 0.038–0.255) per generation (one dnSV per nine offspring), detected using short-read sequencing. Two detected dnSVs are clusters of mutations. Mutation cluster 1 contains a de novo duplication, a dnSNV and a de novo deletion. Mutation cluster 2 contains a de novo deletion and three de novo duplications, of which one is inverted. Mutation cluster 2 is 25 kb in size, whereas mutation cluster 1 (197 bp) and the other two individual dnSVs (64 and 573 bp) are smaller. Only mutation cluster 2 could be phased and is located on the paternal haplotype. Mutation cluster 2 originates from both micro-homology as well as non-homology mutation mechanisms, where mutation cluster 1 and the other two dnSVs are caused by mutation mechanisms lacking sequence homology. The 64 bp deletion and mutation cluster 1 were validated through PCR. Lastly, the 64 bp deletion and the 573 bp duplication were validated in sequenced offspring of probands with three generations of sequence data.

Conclusions

Our estimate of 0.108 dnSVs per generation in the swine germline is conservative, due to our small sample size and restricted possibilities of dnSV detection from short-read sequencing. The current study highlights the complexity of dnSVs and shows the potential of breeding programs for pigs and livestock species in general, to provide a suitable population structure for identification and characterisation of dnSVs.
Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data
Authors: Ruiz-Ceja Karla Alejandra , Capasso Dalila , Pinelli Michele , Del Prete Eugenio , Carrella Diego , di Bernardo Diego , Banfi Sandro
Published: April 2023

Background

Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedures fail to detect pathogenic sequence variants in coding regions of known IRD disease genes in about 30–40% of patients. One of the possible explanations for this missing heritability is the presence of yet unidentified transcripts of known IRD genes. Here, we aimed to define the transcript composition of IRD genes in the human retina by a meta-analysis of publicly available RNA-seq datasets using an ad-hoc designed pipeline.

Results

We analysed 218 IRD genes and identified 5,054 transcripts, 3,367 of which were not previously reported. We assessed their putative expression levels and focused our attention on 435 transcripts predicted to account for at least 5% of the expression of the corresponding gene. We looked at the possible impact of the newly identified transcripts at the protein level and experimentally validated a subset of them.

Conclusions

This study provides an unprecedented, detailed overview of the complexity of the human retinal transcriptome that can be instrumental in contributing to the resolution of some cases of missing heritability in IRD patients.
Development and usability of a hospital standardized ADL ratio (HSAR) for elderly patients with cerebral infarction: a retrospective observational study using administrative claim data from 2012 to 2019 in Japan
Authors: Onishi Ryo , Hatakeyama Yosuke , Hirata Koki , Matsumoto Kunichika , Seto Kanako , Wu Yinghui , Kitazawa Takefumi , Hasegawa Tomonori
Published: April 2023

Background

Maintenance of activities of daily living (ADL) during acute hospitalization is an important treatment goal, especially for elderly inpatients with diseases that often leave disabilities, such as cerebral infarction. However, studies assessing risk-adjusted ADL changes are limited. In this study, we developed and calculated a hospital standardized ADL ratio (HSAR) using Japanese administrative claims data to measure the quality of hospitalization care for patients with cerebral infarction.

Methods

This study was designed as a retrospective observational study using the Japanese administrative claim data from 2012 to 2019. The data of all hospital admissions with a primary diagnosis of cerebral infarction (ICD-10, I63) were used. The HSAR was defined as the ratio of the observed number of ADL maintenance patients to the expected number of ADL maintenance patients multiplied by 100, and ratio of ADL maintenance patients was risk-adjusted using multivariable logistic regression analyses. The c-statistic was used to evaluate the predictive accuracy of the logistic models. Changes in HSARs in each consecutive period were assessed using Spearman’s correlation coefficient.

Results

A total of 36,401 patients from 22 hospitals were included in this study. All variables used in the analyses were associated with ADL maintenance, and evaluations using the HSAR model showed predictive ability with c-statistics (area under the curve, 0.89; 95% confidence interval, 0.88–0.89).

Conclusions

The findings indicated a need to support hospitals with a low HSAR because hospitals with high/low HSAR were likely to produce the same results in the subsequent periods. HSAR can be used as a new quality indicator of in-hospital care and may contribute to the assessment and improvement of the quality of care.
Strategies to increase HIV testing among men who have sex with men and transgender women: an integrative review
Authors: Rocha Gustavo Machado , Cândido Raissa Carolina Fonseca , de Carvalho Nathália Pacífico , Carvalho Emilly Gabrielly Araujo , Costa Alícia Amanda Moreira , Machado Ives Vieira , da Cruz Pimenta Marcos Paulo , de Paula Júnior José Anastácio , Guimarães Mark Drew Crosland , de Pádua Cristiane Aparecida Menezes
Published: April 2023

Background

Men who have sex with men (MSM) and transgender women (TGW) are disproportionately affected by HIV, with much higher incidence and prevalence rates than in the general population in different countries. There are several barriers to testing among MSM and TGW, such as low risk perception, anticipation of HIV-related stigma, discrimination of sexual orientation, in addition to difficulties related to care and access to health services. Therefore, analyzing the available evidence of the effectiveness of strategies for scaling up HIV testing among key populations is essential to point out potential knowledge gaps which may need to be addressed and develop public health policies to promote testing and early diagnosis of HIV infection.

Methods

An integrative review was carried out to evaluate strategies for scaling up HIV testing in these populations. Search strategy was performed on eight electronic databases, without language restriction. We included clinical trials, quasi-experimental studies, and non-randomized studies. Study selection and data extraction were both performed independently by pairs and disagreements were solved by a third revisor. The screening of the studies was carried out through the selection of titles/abstracts and the reading of the full texts of the pre-selected studies based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Data extraction was performed using a structured form.

Results

Thirty-seven publications referring to 35 studies were included, mostly being carried out in the United States of America and Australia. No studies were found evaluating disaggregated data on TGW. The studies were grouped into four types of intervention strategies: self-test distribution system (n = 10), organization of health services (n = 9), peer education (n = 6), and social marketing campaign (n = 10). Strategies that focused on the first three groups, combined or not, were more effective in increasing HIV testing among MSM.

Conclusions

Considering the diversity of interventions and the methodological heterogeneity of the included studies, strategies especially involving self-test distribution systems, associated with new information and communication technologies, should be evaluated in different communities and social contexts. Research evaluating specific studies on TGW population is still needed.
Clinical outcomes of antimicrobial resistance in cancer patients: a systematic review of multivariable models
Authors: Danielsen Anders Skyrud , Franconeri Léa , Page Samantha , Myhre Anders Eivind , Tornes Ragnhild Agathe , Kacelnik Oliver , Bjørnholt Jørgen Vildershøj
Published: April 2023

Background

Infections are major causes of disease in cancer patients and pose a major obstacle to the success of cancer care. The global rise of antimicrobial resistance threatens to make these obstacles even greater and hinder continuing progress in cancer care. To prevent and handle such infections, better models of clinical outcomes building on current knowledge are needed. This internally funded systematic review (PROSPERO registration: CRD42021282769) aimed to review multivariable models of resistant infections/colonisations and corresponding mortality, what risk factors have been investigated, and with what methodological approaches.

Methods

We employed two broad searches of antimicrobial resistance in cancer patients, using terms associated with antimicrobial resistance, in MEDLINE and Embase through Ovid, in addition to Cinahl through EBSCOhost and Web of Science Core Collection. Primary, observational studies in English from January 2015 to November 2021 on human cancer patients that explicitly modelled infection/colonisation or mortality associated with antimicrobial resistance in a multivariable model were included. We extracted data on the study populations and their malignancies, risk factors, microbial aetiology, and methods for variable selection, and assessed the risk of bias using the NHLBI Study Quality Assessment Tools.

Results

Two searches yielded a total of 27,151 unique records, of which 144 studies were included after screening and reading. Of the outcomes studied, mortality was the most common (68/144, 47%). Forty-five per cent (65/144) of the studies focused on haemato-oncological patients, and 27% (39/144) studied several bacteria or fungi. Studies included a median of 200 patients and 46 events. One-hundred-and-three (72%) studies used a p-value-based variable selection. Studies included a median of seven variables in the final (and largest) model, which yielded a median of 7 events per variable. An in-depth example of vancomycin-resistant enterococci was reported.

Conclusions

We found the current research to be heterogeneous in the approaches to studying this topic. Methodological choices resulting in very diverse models made it difficult or even impossible to draw statistical inferences and summarise what risk factors were of clinical relevance. The development and adherence to more standardised protocols that build on existing literature are urgent.
Network analysis of polymicrobial chronic wound infections in Masanga, Sierra Leone
Authors: Sandmann Sarah , Nunes Jonathan Vas , Grobusch Martin P. , Sesay Maxwell , Kriegel Martin A. , Varghese Julian , Schaumburg Frieder
Published: April 2023

Background

Chronic wounds are frequently colonized or infected with multiple bacterial or fungal species, which can both promote or inhibit each other. Network analyses are helpful to understand the interplay of these species in polymicrobial infections. Our aim was to analyse the network of bacterial and fungal species in chronic wounds.

Methods

Swabs (n = 163) from chronic wound infections (Masanga, Sierra Leone, 2019–2020) were screened for bacterial and fungal species using non-selective agars. Some of these wounds were suspected but not confirmed Buruli ulcer. Species identification was done with MALDI-TOF mass spectrometry. Network analysis was performed to investigate co-occurrence of different species within one patient. All species with n ≥ 10 isolates were taken into account.

Results

Of the 163 patients, 156 had a positive wound culture (median of three different species per patient; range 1–7). Pseudomonas aeruginosa (n = 75) was the dominating species with frequent co-detections of Klebsiella pneumoniae (21 cases; OR = 1.36, 95%CI: 0.63–2.96, p = 0.47), Staphylococcus aureus (14 cases; OR = 1.06, 95%CI: 0.44–2.55, p = 1) and Proteus mirabilis (13 cases; OR = 0.84, 95%CI: 0.35–1.99, p = 0.69).

Conclusion

The culturome of chronic wounds in Sierra Leonean patients is highly diverse and characterized by the co-occurrence of P. aeruginosa, K. pneumoniae and S. aureus.
Fungal infection profile in critically ill COVID-19 patients: a prospective study at a large teaching hospital in a middle-income country
Authors: Negm Essamedin M. , Mohamed Mohamed Sorour , Rabie Rehab A. , Fouad Walaa S. , Beniamen Ahmed , Mosallem Ahmed , Tawfik Ahmed E. , Salama Hussein M.
Published: April 2023

Background

Critically ill COVID-19 patients are highly susceptible to opportunistic fungal infection due to many factors, including virus-induced immune dysregulation, host-related comorbidities, overuse and misuse of antibiotics or corticosteroids, immune modulator drugs, and the emergencies caused by the pandemic. This study aimed to assess the incidence, identify the potential risk factors, and examine the impact of fungal coinfection on the outcomes of COVID-19 patients admitted to the intensive care unit (ICU).

Methods

A prospective cohort study including 253 critically ill COVID-19 patients aged 18 years or older admitted to the isolation ICU of Zagazig University Hospitals over a 4-month period from May 2021 to August 2021 was conducted. The detection of a fungal infection was carried out.

Results

Eighty-three (83) patients (32.8%) were diagnosed with a fungal coinfection. Candida was the most frequently isolated fungus in 61 (24.1%) of 253 critically ill COVID-19 patients, followed by molds, which included Aspergillus 11 (4.3%) and mucormycosis in five patients (1.97%), and six patients (2.4%) diagnosed with other rare fungi. Poor diabetic control, prolonged or high-dose steroids, and multiple comorbidities were all possible risk factors for fungal coinfection [OR (95% CI) = 10.21 (3.43–30.39), 14.1 (5.67–35.10), 14.57 (5.83–33.78), and 4.57 (1.83–14.88), respectively].

Conclusion

Fungal coinfection is a common complication of critically ill COVID-19 patients admitted to the ICU. Candidiasis, aspergillosis, and mucormycosis are the most common COVID-19-associated fungal infections and have a great impact on mortality rates.
PET-CT detection of local residual laryngeal carcinoma after definitive (chemo)radiotherapy
Authors: Sistonen Heli J. , Ilmarinen Taru , Atula Timo , Aro Katri , Schildt Jukka , Markkola Antti
Published: April 2023

Background

Positron emission tomography and computed tomography (PET-CT) is currently recommended in evaluating the treatment response after (chemo)radiotherapy ([C]RT). In the larynx, post-treatment changes and physiological uptake make image interpretation more challenging compared to other head and neck sites. Previous research has not addressed imaging factors specifically in the larynx that would help in distinguishing the residual disease and explain the unique challenges of that anatomic area. The study cohorts are small and heterogenous. Our objective was to investigate the ability of PET-CT in diagnosing local residual laryngeal carcinoma, and to uncover imaging factors that could be used in differentiating the residual disease from post-treatment and physiological changes. In the same study cohort, we also aimed to uncover prognostic factors for local residual or recurrent disease.

Methods

Our retrospective study cohort included 73 patients with T2-T4 laryngeal carcinoma undergoing (C)RT with curative intention, and post-treatment non-contrast-enhanced PET-CT at 2–6 months. Findings were compared between local residual and non-residual disease. Local residual disease was defined as a persistent tumor growth with no evidence of remission in between, confirmed by biopsy, and evident within 6 months from the end of RT. PET-CT was evaluated using a 3-step scale: negative, equivocal, and positive.

Results

Nine (12%) had a local residual tumor and 11 (15%) developed local recurrence, based on the biopsy. The median follow-up of surviving patients was 64 months (range, 28–174). In univariate analysis, primary tumor diameter greater than 2.4 cm (median value), and vocal cord fixation were prognostic for local residual or recurrent disease. Sensitivity, specificity, PPV, and NPV were 100%, 75%, 36%, and 100%, respectively, when the equivocal interpretation was grouped with the positive interpretation. All local residuals, and 28% (18/64) non-residuals, had a primary tumor area SUVmax of over 4.0 (p < 0.001). CT showed a persistent mass at the primary tumor area in 56% of residuals, and in 23% of non-residuals (p > 0.05). By combining SUVmax>4.0 and mass, specificity improved to 91%.

Conclusions

NPV of post-treatment PET-CT in laryngeal carcinoma is high, but equivocal and positive results have low PPV and require further diagnostics. All local residuals had SUVmax over 4.0. The combination of SUVmax over 4.0 and mass on CT increased specificity, but the sensitivity was low.
Association between axial length and HDL in children: a hospital-based cross-sectional study
Authors: Zheng Qingqing , Hong Chaoyang , Peng Yaling , He Ting , Lai Yuan , Tan Lingtong , Shen Ting
Published: April 2023

Background

To analyze the relationship between axial length and levels of high-density lipoprotein (HDL) cholesterol in children.

Methods

A retrospective, hospital-based cross-sectional research with 69 right eyes from 69 children who underwent health examination by Zhejiang Provincial People’s Hospital was carried out. The participants were split into three groups: Group A (axial length < = 23 mm), Group B (axial length 23–24 mm), and Group C (axial length > 24 mm). Demographic epidemiological information, blood biochemical parameters and ophthalmic characteristics including refractive status and ocular geometric parameters were obtained and analyzed.

Results

69 right eyes from 69 patients (25 males and 44 females) with a median age of 10.00 years old (IQR: 8.00–11.00 years) were included in the study. Within Group A, there were a total of 17 individuals; Group B consisted of 22 individuals; Group C included 30 individuals. The mean axial length of three groups was 22.148(0.360), 23.503(0.342) and 24.770(0.556) mm, respectively (p < 0.0001). The mean HDL levels were significantly different in three groups are 1.824(0.307), 1.485(0.253) and 1.507 (0.265) mmol/L, respectively. By applying a Pearson Coefficient, we evaluated the association between axial length and HDL and discovered that there was a statistically significant (p = 0.00025) and adverse (R = -0.43) association between axial length and HDL.

Conclusions

We concluded from our study that there was a significantly inverse relationship between axial length and the levels of HDL in children.
Determinants of clinical outcome and length of stay in acute care forensic psychiatry units
Authors: D’Orta Isabella , Weber Kerstin , Herrmann François R. , Giannakopoulos Panteleimon
Published: April 2023

Criminological and sociodemographic variables, such as previous criminal convictions, increased risk of violence, early onset of mental disorder, antisocial personality, psychosis and low social support, have all been related to longer length of stay (LoS) and poorer outcome in long stay forensic services. The factors impacting on LoS and clinical response in acute care specialized units are poorly documented. To address this issue, we examined the psychiatric records of all cases admitted between January 1st and December 31th 2020 in the sole acute ward for detained persons located in the central prison of the Geneva County, Switzerland. Information on judicial status included pre-trial versus sentence execution, previous incarcerations, and age of the first incarceration. Sociodemographic data included age, gender, marital status, and education attainment. Previous inpatient stays prior to incarceration were recorded. All of the ICD-10 clinical diagnoses were made by two independent, board-certified psychiatrists blind to the scope of the study. The standardized assessment was based on the HoNOS (Health of Nation Outcome Scales) at admission and discharge, HONOS-secure at admission, HCR-20 (Historical Clinical Risk 20) version 2, PCL-R (Psychopathy Checklist Revised), and SAPROF (Structured Assessment of Protective Factors). Stepwise forward multiple linear regression models predicting the LoS and delta HONOS respectively were built with the above mentioned parameters. The selected variables were then used in univariate and multivariable regression models. Higher HCR-scores (mainly on clinical items), and longer LoS were related to higher delta HONOS scores. In contrast, cases in pre-trial detention showed a worst clinical outcome. In multivariable models, all three variables remained independent predictors of the clinical outcome and explained 30.7% of its variance. Only education and diagnosis of borderline personality were related to the LoS and explained 12.6% of its variance in multivariable models. Our results suggest that the use of acute wards specialized in forensic psychiatry are mainly useful for patients with prior inpatient care experience, and higher violence risk during sentence execution. In contrast, they seem to be less performant for persons in pre-trial detention that could benefit from less restrictive clinical settings.
Involving supermarkets in health promotion interventions in the Danish Project SoL. A practice-oriented qualitative study on the engagement of supermarket staff and managers
Authors: Winkler Lise L. , Toft Ulla , Glümer Charlotte , Bloch Paul , Buch-Andersen Tine , Christensen Ulla
Published: April 2023

Background

Supermarkets have been suggested as relevant settings for environmental and educational initiatives encouraging healthier shopping and eating decisions, but in the literature, limited attention has been paid to the context, perspectives, and everyday practices of supermarket staff. The aim of this study was to examine the engagement of supermarket staff in a health promotion project from a practice-oriented perspective.

Methods

The study was based on qualitative data collected in the supermarket setting of Project SoL; a community-based health promotion project in Denmark. We conducted 26 in-depth interviews with store managers and other key staff members in seven participating supermarkets. In addition, we collected data on planning, implementation, and perceptions of supermarket staff of in-store interventions and other project-related activities. These field data included short telephone interviews, observational notes, photos, and audiotapes of meetings. Data were analysed from the perspective of practice theory.

Results

Although supermarket staff found community-based health promotion meaningful to engage in, the study observed that their engagement was challenged by a business mindset, practical routines and structural requirements favouring sales promotion over health promotion. Nevertheless, there were also examples of how health promotion activities and ways of thinking were successfully incorporated in everyday staff practices during and after Project SoL.

Conclusions

Our findings point to both potentials and challenges for using supermarkets as settings for health promotion. The voluntary engagement of supermarket staff in community-based health projects cannot stand alone but should be supplemented by more long-lasting strategies and policies regulating this and other food environments. Context-sensitive and practice-oriented analyses in local food environments could inform such strategies and policies to make sure they target unwanted elements and practices and not just individual behavior.
Association between serum uric acid levels and bone mineral density in patients with osteoporosis: a cross-sectional study
Authors: Xu Min-zhe , Lu Ke , Yang Xu-feng , Ye Yao-wei , Xu Si-ming , Shi Qin , Gong Ya-qin , Li Chong
Published: April 2023

Background

The results of studies exploring the association between serum uric acid (SUA) and bone mineral density (BMD) have been controversial and inconsistent. We thus sought to explore whether SUA levels were independently associated with BMD in patients with osteoporosis (OP).

Methods

This cross-sectional analysis was conducted using prospectively obtained data from the Affiliated Kunshan Hospital of Jiangsu University database pertaining to 1,249 OP patients that were hospitalized from January 2015 – March 2022. BMD was the outcome variable for this study, while baseline SUA levels were the exposure variable. Analyses were adjusted for a range of covariates including age, gender, body mass index (BMI) and a range of other baseline laboratory and clinical findings.

Results

SUA levels and BMD were independently positively associated with one another in OP patients. Following adjustment for age, gender, BMI, blood urae nitrogen (BUN), and 25(OH)D levels, a 0.0286 g/cm2 (β, 0.0286; 95% confidence interval [CI], 0.0193—0.0378, P < 0.000001) increase in BMD was observed per 100 μmol/L rise in SUA levels. A non-linear association between SUA and BMD was also observed for patients with a BMI < 24 kg/m2, with a SUA level inflection point at 296 μmol/L in the adjusted smoothed curve.

Conclusions

These analyses revealed SUA levels to be independently positively associated with BMD in OP patients, with an additional non-linear relationship between these two variables being evident for individuals of normal or low body weight. This suggests that SUA levels may exert a protective effect on BMD at concentrations below 296 μmol/L in normal- and low-weight OP patients, whereas SUA levels above this concentration were unrelated to BMD.
“I am accustomed to something in my body causing pain”: a qualitative study of knee replacement non-improvers’ stories of previous painful and stressful experiences
Authors: Sellevold Vibeke Bull , Olsen Unni , Lindberg Maren Falch , Steindal Simen A. , Aamodt Arild , Lerdal Anners , Dihle Alfhild
Published: April 2023

Background

Approximately 20% of total knee arthroplasty patients experience persistent postsurgical pain one year after surgery. No qualitative studies have explored previous stories of painful or stressful life experiences in patients experiencing persistent postsurgical pain after total knee replacement. This study aimed to explore stories of previous painful or stressful experiences in life in a cohort of patients that reported no improvement in pain one year after total knee arthroplasty.

Methods

The study employed an explorative-descriptive qualitative design. Data was collected through semi-structured interviews five to seven years after surgery, with patients who reported no improvement in pain-related interference with walking 12 months after total knee replacement. The data was analyzed using qualitative content analysis.

Results

The sample consisted of 13 women and 10 men with a median age of 67 years at the time of surgery. Prior to surgery, six reported having at least one chronic illness and 16 reported having two or more painful sites. Two main themes were identified in the data analysis: Painful years - the burden of living with long lasting pain, and the burden of living with psychological distress.

Conclusions

The participants had severe long lasting knee pain as well as long lasting pain in other locations, in addition to experiences of psychologically stressful life events before surgery. Health personnel needs to address the experience and perception of pain and psychological struggles, and how it influences patients’ everyday life including sleeping routines, work- and family life as well as to identify possible vulnerability for persistent postsurgical pain. Identifying and assessing the challenges enables personalized care and support, such as advice on pain management, cognitive support, guided rehabilitation, and coping strategies both pre-and post-surgery.
Dental care for older adults in home health care services - practices, perceived knowledge and challenges among Norwegian dentists and dental hygienists
Authors: Uhlen-Strand Marte-Mari , Hovden Ewa Alicja Szyszko , Schwendicke Falk , Ansteinsson Vibeke Elise , Mdala Ibrahimu , Skudutyte-Rysstad Rasa
Published: April 2023

Background

Providing dental services to dependent older adults might be challenging because of physical and cognitive decline. The present study aimed to explore current practices, knowledge, and experienced challenges related to the treatment of older adults in home health care services (HHCS) among dentists and dental hygienists in Norway.

Methods

An electronic questionnaire survey was distributed to Norwegian dentists and dental hygienists, inquiring about background characteristics, current practices, self-perceived knowledge, and challenges when providing oral health care for older HHCS patients.

Results

Four hundred and sixty-six dentists and 244 dental hygienists treating older HHCS patients responded to the survey. The majority were female (n=620; 87.3%) and worked in the public dental service (PDS) (n=639; 90%). When older HHCS adults attended the dental practice, the treatments provided were most frequently aimed at relieving acute oral problems, although dental hygienists reported to focus on improving oral health more often than dentists. Dentists reported to have more self-perceived knowledge than dental hygienists regarding patients with complex treatment needs, cognitive or physical impairment. Exploratory Factor Analysis (EFA) was carried out on the 16 items related to challenges, three factors were extracted and Structural Equation Models (SEMs) were performed. Challenges related to dental care for older HHCS adults were related to time, practical organization and communication. Variation within these categories was associated with sex, graduation year and country, as well as time used per patient and work sector, but not with professional status.

Conclusions

The results indicate that dental care for older HHCS patients is time-demanding and more often aimed at relieving symptoms than improving oral health. A substantial proportion of dentists and dental hygienists in Norway lack confidence when providing dental care for frail elderly.
Machine learning prediction of mortality in Acute Myocardial Infarction
Authors: Oliveira Mariana , Seringa Joana , Pinto Fausto José , Henriques Roberto , Magalhães Teresa
Published: April 2023

Background

Acute Myocardial Infarction (AMI) is the leading cause of death in Portugal and globally. The present investigation created a model based on machine learning for predictive analysis of mortality in patients with AMI upon admission, using different variables to analyse their impact on predictive models.

Methods

Three experiments were built for mortality in AMI in a Portuguese hospital between 2013 and 2015 using various machine learning techniques. The three experiments differed in the number and type of variables used. We used a discharged patients’ episodes database, including administrative data, laboratory data, and cardiac and physiologic test results, whose primary diagnosis was AMI.

Results

Results show that for Experiment 1, Stochastic Gradient Descent was more suitable than the other classification models, with a classification accuracy of 80%, a recall of 77%, and a discriminatory capacity with an AUC of 79%. Adding new variables to the models increased AUC in Experiment 2 to 81% for the Support Vector Machine method. In Experiment 3, we obtained an AUC, in Stochastic Gradient Descent, of 88% and a recall of 80%. These results were obtained when applying feature selection and the SMOTE technique to overcome imbalanced data.

Conclusions

Our results show that the introduction of new variables, namely laboratory data, impacts the performance of the methods, reinforcing the premise that no single approach is adapted to all situations regarding AMI mortality prediction. Instead, they must be selected, considering the context and the information available. Integrating Artificial Intelligence (AI) and machine learning with clinical decision-making can transform care, making clinical practice more efficient, faster, personalised, and effective. AI emerges as an alternative to traditional models since it has the potential to explore large amounts of information automatically and systematically.
Awareness of and subjective needs for post-discharge healthcare services among older adult patients
Authors: Yen Hsin-Yen , Liu Doresses , Chi Mei-Ju , Huang Hao-Yun
Published: April 2023

Background

Increasing patient awareness of post-discharge care resources is an effective strategy to reduce rehospitalization rates and medical costs. Therefore, the purpose of this study was to explore hospitalized older adult patients’ awareness of and subjective demands for post-discharge healthcare services.

Methods

A cross-sectional study design was conducted from November 2018 to May 2020. STROBE statement was completed. Participants were inpatients over 65 years of age in the general ward of a medical center in northern Taiwan. A questionnaire was used to collect data by face-to-face interviews. Two hundred and twelve participants were recruited. Home nursing care, home rehabilitation, home respiratory therapy, home services, assistive devices rental, and transportation were the main post-discharge healthcare services in this study.

Results

Overall, 83.5% of older adult patients were aware of and 55.7% of the older adult patients demanded at least one post-discharge healthcare services. Logistic regression results found that, patients experiencing moderate to severe disability and cognitive impairment, and those hospitalized in the past year had significantly higher demands for services.

Conclusions

Developing post-discharge healthcare services for older adult patients provides continuous patient-centered services for assisting patients and their families in adapting to the transition period of the post-acute stage. Satisfying these demands is beneficial for older adult patients and their families, as well as for reducing readmissions and medical costs.
A systematic review on clinical guidelines of home health care in heart failure patients
Authors: Hashemlu Leila , Esmaeili Roghayeh , Bahramnezhad Fatemeh , Rohani Camelia
Published: April 2023

Background

“Guidelines for the care of heart failure patients at home support safe and effective evidence-based practice. The aims of the present study were: [1] to identify guidelines addressing the care at home for adults with heart failure and [2] evaluate the quality of the guidelines and the extent to which they address eight components of home-based HF disease management.”

Methods

A systematic review was conducted of articles published between 1st of January 2000 to 17th of May 2021 using the databases of PubMed, Web of Science, Scopus, Embase, Cochrane, and nine specific websites for guideline development organisations. Clinical guidelines for HF patients with recommendations relevant to care provision at home were included. The results were reported according to the Preferred Reporting Items for Systematic Reviews (PRISMA-2020) criteria. The quality of included guidelines was evaluated using the Appraisal of Guidelines for Research and Evaluation-II (AGREE-II) by two authors independently. Guidelines were evaluated for their coverage of eight components of HF care at home, consisting of integration, multi-disciplinary care, continuity of care, optimized treatment, patient education, patient and partner participation, care plans with clear goals of care, self-care management and palliative care.

Results

Ten HF guidelines, including two nursing-focused guidelines and eight general guidelines were extracted from 280 studies. After evaluation of quality by AGREE-II, two guidelines obtained the highest score: “NICE” and the “Adapting HF guideline for nursing care in home health care settings. Five guidelines addressed all eight components of care at home while the others had six or seven.

Conclusions

This systematic review identified ten guidelines addressing care at home for patients with HF. The highest quality guidelines most relevant to the care at home of patients with HF are the “NICE” and “Adapting HF guideline for nursing care in home health care settings” and would be most appropriate for use by home healthcare nurses.
Indoleacrylic acid produced by Parabacteroides distasonis alleviates type 2 diabetes via activation of AhR to repair intestinal barrier
Authors: Liu Deliang , Zhang Shaobao , Li Siju , Zhang Qian , Cai Ying , Li Pei , Li Hao , Shen Baochun , Liao Qiongfeng , Hong Yanjun , Xie Zhiyong
Published: April 2023

Background

Anti-inflammatory therapy is an effective strategy in the treatment of type 2 diabetes (T2D). Studies found that inflammatory responses in vivo were strongly associated with defects in the mucosal barrier function of the gut epithelium. While some microbial strains could help repair the intestinal mucosa and maintain the integrity of the intestinal barrier, the specific mechanisms remain to be fully elucidated. The present study investigated the effects of Parabacteroides distasonis (P. distasonis) on the intestinal barrier and the inflammation level in T2D rats and explored the specific mechanisms.

Results

By analyzing the intestinal barrier function, the inflammatory conditions, and the gut microbiome, we found that P. distasonis could attenuate insulin resistance by repairing the intestinal barrier and reducing inflammation caused by the disturbed gut microbiota. We quantitatively profiled the level of tryptophan and indole derivatives (IDs) in rats and fermentation broth of the strain, demonstrating that indoleacrylic acid (IA) was the most significant factor correlated with the microbial alterations among all types of endogenous metabolites. Finally, we used molecular and cell biological techniques to determine that the metabolic benefits of P. distasonis were mainly attributed to its ability to promote IA generation, active the aryl hydrocarbon receptor (AhR) signaling pathway, and increase the expression level of interleukin-22 (IL-22), thus enhancing the expression of intestinal barrier-related proteins.

Conclusions

Our study revealed the effects of P. distasonis in the treatment of T2D via intestinal barrier repairment and inflammation reduction and highlighted a host-microbial co-metabolite indoleacrylic acid that could active AhR to perform its physiological effects. Our study provided new therapeutic strategies for metabolic diseases by targeting the gut microbiota and tryptophan metabolism.