bluuebunny/crossref_metadata_2025 huggingface dataset:
Preventable deaths involving falls in England and Wales, 2013–22: a systematic case series of coroners’ reports
Authors: Song Kaiyang , Portwood Clara , Jindal Jessy , Launer David , France Harrison , Hey Molly , Richards Georgia , Dernie Francesco
Published: October 2023

Background

Falls in older people are common, leading to significant harm including death. Coroners have a duty to report cases where action should be taken to prevent future deaths, but dissemination of their findings remains poor.

Objective

To identify preventable fall-related deaths, classify coroner concerns and explore organisational responses.

Design

A retrospective systematic case series of coroners’ Prevention of Future Deaths (PFD) reports, from July 2013 (inception) to November 2022.

Setting

England and Wales.

Methods

Reproducible data collection methods were used to web-scrape and read PFD reports. Demographic information, coroner concerns and responses from organisations were extracted and descriptive statistics used to synthesise data.

Results

Five hundred and twenty-seven PFDs (12.5% of PFDs) involved a fall that contributed to death. These deaths predominantly affected older people (median 82 years) in the community (72%), with subsequent death in hospital (70.8%). A high proportion of cases experienced fractures (51.6%), major bleeding (35.9%) or head injury (38.7%). Coroners frequently raised concerns regarding falls risks assessments (20.9%), failures in communication (20.3%) and documentation issues (17.5%). Only 56.7% of PFDs received a response from organisations to whom they were addressed. Organisations tended to produce new protocols (58.5%), improve training (44.6%) and commence audits (34.3%) in response to PFDs.

Conclusions

One in eight preventable deaths in England and Wales involved a fall. Addressing concerns raised by coroners should improve falls prevention and care following falls especially for older adults, but the poor response rate may indicate that lessons are not being learned. Wider dissemination of PFD findings may help reduce preventable fall-related deaths in the future.
New horizons in the diagnosis and management of dehydration
Authors: Frith James
Published: October 2023

Hydration is a fundamental aspect of clinical practice and yet it is an under-researched topic, particularly in older people, leading to many areas of uncertainty. There are two types of dehydration; hypertonic, which is a water deficit, and isotonic, which is a deficit of both water and salt. Individual clinical signs and bedside tests are poor diagnostic tools, making dehydration difficult to identify. However, the diagnostic value of a holistic clinical approach is not known. The gold-standard clinical test for dehydration is serum osmolality, but this cannot diagnose isotonic dehydration and may delay diagnosis in acute situations. Salivary osmolality point-of-care testing is a promising and rapid new diagnostic test capable of detecting both hypertonic and isotonic dehydration in older people, but further evidence to support its clinical utility is needed. Daily fluid requirements may be less than previously thought in adults, but the evidence specific to older people remains limited. Hydration via the subcutaneous route is safer and easier to initiate than the intravenous route but is limited by infusion speed and volume. Prompting older adults more frequently to drink, offering a wider selection of drinks and using drinking vessels with particular features can result in small increases in oral intake in the short-term. The ongoing clinically-assisted hydration at end of life (CHELsea II) trial will hopefully provide more evidence for the emotive issue of hydration at the end of life.
Considerations for Use of Blood-Based Biomarkers in Epidemiologic Dementia Research
Authors: Hayes-Larson Eleanor , Ackley Sarah F , Turney Indira C , La Joie Renaud , Mayeda Elizabeth Rose , Glymour M Maria ,   for the Alzheimer's Disease Neuroimaging Initiative
Published: October 2023

Dementia represents a growing public health burden with large social, racial, and ethnic disparities. The etiology of dementia is poorly understood, and the lack of robust biomarkers in diverse, population-representative samples is a barrier to moving dementia research forward. Existing biomarkers and other measures of pathology—derived from neuropathology, neuroimaging, and cerebrospinal fluid samples—are commonly collected from predominantly White and highly educated samples drawn from academic medical centers in urban settings. Blood-based biomarkers are noninvasive and less expensive, offering promise to expand our understanding of the pathophysiology of dementia, including in participants from historically excluded groups. Although largely not yet approved by the Food and Drug Administration or used in clinical settings, blood-based biomarkers are increasingly included in epidemiologic studies on dementia. Blood-based biomarkers in epidemiologic research may allow the field to more accurately understand the multifactorial etiology and sequence of events that characterize dementia-related pathophysiological changes. As blood-based dementia biomarkers continue to be developed and incorporated into research and practice, we outline considerations for using them in dementia epidemiology, and illustrate key concepts with Alzheimer’s Disease Neuroimaging Initiative (2003–present) data. We focus on measurement, including both validity and reliability, and on the use of dementia blood-based biomarkers to promote equity in dementia research and cognitive aging.

This article is part of a Special Collection on Mental Health.
Evaluating Mixtures of Urinary Phthalate Metabolites and Serum Per-/Polyfluoroalkyl Substances in Relation to Adolescent Hair Cortisol: The HOME Study
Authors: Sears Clara G , Liu Yun , Lanphear Bruce P , Buckley Jessie P , Meyer Jerrold , Xu Yingying , Chen Aimin , Yolton Kimberly , Braun Joseph M
Published: October 2023

Results of toxicological studies indicate that phthalates and per-/polyfluoroalkyl substances (PFAS), 2 classes of endocrine-disrupting chemicals, may alter the functioning of the hypothalamic-pituitary-adrenocortical (HPA) axis. We evaluated the associations of urinary phthalate metabolites and serum PFAS during gestation and childhood with adolescent hair cortisol concentrations (pg/mg hair) at age 12 years, an integrative marker of HPA axis activity (n = 205 mother-child pairs; Cincinnati, Ohio; enrolled 2003–2006). We used quantile-based g-computation to estimate associations between mixtures of urinary phthalate metabolites or serum PFAS and hair cortisol. We also examined whether associations of individual phthalate metabolites or PFAS with cortisol varied by the timing of exposure. We found that a 1-quartile increase in all childhood phthalate metabolites was associated with 35% higher adolescent hair cortisol (phthalate mixture ψ = 0.13; 95% confidence interval: 0.03, 0.22); these associations were driven by monoethyl phthalate, monoisobutyl phthalate, and monobenzyl phthalate. We did not find evidence that phthalate metabolites during gestation or serum PFAS mixtures were related to adolescent hair cortisol concentrations. We found suggestive evidence that higher childhood concentrations of individual PFAS were related to higher and lower adolescent hair cortisol concentrations. Our results suggest that phthalate exposure during childhood may contribute to higher levels of chronic HPA axis activity.
Evidential meta-model for molecular property prediction
Authors: Ham Kyung Pyo , Sael Lee
Published: October 2023

Motivation

The usefulness of supervised molecular property prediction (MPP) is well-recognized in many applications. However, the insufficiency and the imbalance of labeled data make the learning problem difficult. Moreover, the reliability of the predictions is also a huddle in the deployment of MPP models in safety-critical fields.

Results

We propose the Evidential Meta-model for Molecular Property Prediction (EM3P2) method that returns uncertainty estimates along with its predictions. Our EM3P2 trains an evidential graph isomorphism network classifier using multi-task molecular property datasets under the model-agnostic meta-learning (MAML) framework while addressing the problem of data imbalance.

 

Our results showed better prediction performances compared to existing meta-MPP models. Furthermore, we showed that the uncertainty estimates returned by our EM3P2 can be used to reject uncertain predictions for applications that require higher confidence.

Availability and implementation

Source code available for download at https://github.com/Ajou-DILab/EM3P2.
iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion
Authors: Wu Yiming , Qian Bing , Wang Anqi , Dong Heng , Zhu Enqiang , Ma Baoshan
Published: October 2023

Motivation

Gene regulatory networks (GRNs) are a way of describing the interaction between genes, which contribute to revealing the different biological mechanisms in the cell. Reconstructing GRNs based on gene expression data has been a central computational problem in systems biology. However, due to the high dimensionality and non-linearity of large-scale GRNs, accurately and efficiently inferring GRNs is still a challenging task.

Results

In this article, we propose a new approach, iLSGRN, to reconstruct large-scale GRNs from steady-state and time-series gene expression data based on non-linear ordinary differential equations. Firstly, the regulatory gene recognition algorithm calculates the Maximal Information Coefficient between genes and excludes redundant regulatory relationships to achieve dimensionality reduction. Then, the feature fusion algorithm constructs a model leveraging the feature importance derived from XGBoost (eXtreme Gradient Boosting) and RF (Random Forest) models, which can effectively train the non-linear ordinary differential equations model of GRNs and improve the accuracy and stability of the inference algorithm. The extensive experiments on different scale datasets show that our method makes sensible improvement compared with the state-of-the-art methods. Furthermore, we perform cross-validation experiments on the real gene datasets to validate the robustness and effectiveness of the proposed method.

Availability and implementation

The proposed method is written in the Python language, and is available at: https://github.com/lab319/iLSGRN.
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites
Authors: Jiao Shihu , Ye Xiucai , Ao Chunyan , Sakurai Tetsuya , Zou Quan , Xu Lei
Published: October 2023

Motivation

The rapid and extensive transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global health emergency, affecting millions of people and causing an immense socioeconomic impact. The identification of SARS-CoV-2 phosphorylation sites plays an important role in unraveling the complex molecular mechanisms behind infection and the resulting alterations in host cell pathways. However, currently available prediction tools for identifying these sites lack accuracy and efficiency.

Results

In this study, we presented a comprehensive biological function analysis of SARS-CoV-2 infection in a clonal human lung epithelial A549 cell, revealing dramatic changes in protein phosphorylation pathways in host cells. Moreover, a novel deep learning predictor called PSPred-ALE is specifically designed to identify phosphorylation sites in human host cells that are infected with SARS-CoV-2. The key idea of PSPred-ALE lies in the use of a self-adaptive learning embedding algorithm, which enables the automatic extraction of context sequential features from protein sequences. In addition, the tool uses multihead attention module that enables the capturing of global information, further improving the accuracy of predictions. Comparative analysis of features demonstrated that the self-adaptive learning embedding features are superior to hand-crafted statistical features in capturing discriminative sequence information. Benchmarking comparison shows that PSPred-ALE outperforms the state-of-the-art prediction tools and achieves robust performance. Therefore, the proposed model can effectively identify phosphorylation sites assistant the biomedical scientists in understanding the mechanism of phosphorylation in SARS-CoV-2 infection.

Availability and implementation

PSPred-ALE is available at https://github.com/jiaoshihu/PSPred-ALE and Zenodo (https://doi.org/10.5281/zenodo.8330277).
Evaluation of haplotype-aware long-read error correction with hifieval
Authors: Guo Yujie , Feng Xiaowen , Li Heng
Published: October 2023

The PacBio High-Fidelity (HiFi) sequencing technology produces long reads of >99% in accuracy. It has enabled the development of a new generation of de novo sequence assemblers, which all have sequencing error correction (EC) as the first step. As HiFi is a new data type, this critical step has not been evaluated before. Here, we introduced hifieval, a new command-line tool for measuring over- and under-corrections produced by EC algorithms. We assessed the accuracy of the EC components of existing HiFi assemblers on the CHM13 and the HG002 datasets and further investigated the performance of EC methods in challenging regions such as homopolymer regions, centromeric regions, and segmental duplications. Hifieval will help HiFi assemblers to improve EC and assembly quality in the long run.

Availability and implementation

The source code is available at https://github.com/magspho/hifieval.
Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information
Authors: Jiao Peishun , Wang Beibei , Wang Xuan , Liu Bo , Wang Yadong , Li Junyi
Published: October 2023

Motivation

In recent years, there has been a breakthrough in protein structure prediction, and the AlphaFold2 model of the DeepMind team has improved the accuracy of protein structure prediction to the atomic level. Currently, deep learning-based protein function prediction models usually extract features from protein sequences and combine them with protein–protein interaction networks to achieve good results. However, for newly sequenced proteins that are not in the protein–protein interaction network, such models cannot make effective predictions. To address this, this article proposes the Struct2GO model, which combines protein structure and sequence data to enhance the precision of protein function prediction and the generality of the model.

Results

We obtain amino acid residue embeddings in protein structure through graph representation learning, utilize the graph pooling algorithm based on a self-attention mechanism to obtain the whole graph structure features, and fuse them with sequence features obtained from the protein language model. The results demonstrate that compared with the traditional protein sequence-based function prediction model, the Struct2GO model achieves better results.

Availability and implementation

The data underlying this article are available at https://github.com/lyjps/Struct2GO.
Performance of large language model artificial intelligence on dermatology board exam questions
Authors: Park Lily , Ehlert Brittany , Susla Lyudmyla , Lum Zachary C , Lee Patrick K
Published: October 2023

Our study attempted to assess the performance of two large language models: Open AI's ChatGPT and Google's Bard on dermatology board exam-style questions. Based on our study, Google Bard outperformed ChatGPT and achieved the highest scores in general dermatology among dermatology disciplines.
Leucine-rich repeat kinase 2 promotes the development of experimental severe acute pancreatitis
Authors: Otsuka Yasuo , Hara Akane , Minaga Kosuke , Sekai Ikue , Kurimoto Masayuki , Masuta Yasuhiro , Takada Ryutaro , Yoshikawa Tomoe , Kamata Ken , Kudo Masatoshi , Watanabe Tomohiro
Published: October 2023

Translocation of gut bacteria into the pancreas promotes the development of severe acute pancreatitis (SAP). Recent clinical studies have also highlighted the association between fungal infections and SAP. The sensing of gut bacteria by pattern recognition receptors promotes the development of SAP via the production of proinflammatory cytokines; however, the mechanism by which gut fungi mediate SAP remains largely unknown. Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that regulates innate immunity against fungi via Dectin-1 activation. Here, we investigated the role of LRRK2 in SAP development and observed that administration of LRRK2 inhibitors attenuated SAP development. The degree of SAP was greater in Lrrk2 transgenic (Tg) mice than in control mice and was accompanied by an increased production of nuclear factor-kappaB-dependent proinflammatory cytokines. Ablation of the fungal mycobiome by anti-fungal drugs inhibited SAP development in Lrrk2 Tg mice, whereas the degree of SAP was comparable in Lrrk2 Tg mice with or without gut sterilization by a broad range of antibiotics. Pancreatic mononuclear cells from Lrrk2 Tg mice produced large amounts of IL-6 and TNF-α upon stimulation with Dectin-1 ligands, and inhibition of the Dectin-1 pathway by a spleen tyrosine kinase inhibitor protected Lrrk2 Tg mice from SAP. These data indicate that LRRK2 activation is involved in the development of SAP through proinflammatory cytokine responses upon fungal exposure.
Outcomes of patients with early calcific aortic valve disease detected by clinically indicated echocardiography
Authors: Moore Matthew K , Jones Gregory T , Whalley Gillian , Prendergast Bernard , Williams Michael J A , Coffey Sean
Published: October 2023

Aims

Previous studies have demonstrated relatively slow rates of progression of early calcific aortic valve disease (CAVD), which encompasses aortic sclerosis (ASc) and mild aortic stenosis (AS). The potential evolution to clinically significant AS is unclear, and we therefore examined the long-term outcomes of patients with ASc and mild AS detected at the time of clinically indicated echocardiography.

Methods and results

Data from initial clinically indicated echocardiograms performed between 2010 and 2018 in patients aged ≥18 years were extracted and linked to nationally collected outcome data. Those with impaired right or left systolic ventricular function or other significant left-sided valve disease were excluded. A time to first event analysis was performed with a composite primary outcome of cardiovascular death and aortic valve intervention (AVI). Of the 13 313 patients, 8973 had no CAVD, 3436 had ASc, and 455 had mild AS. The remainder had moderate or worse stenosis. Over a median follow-up period of 4.2 (interquartile range 1.8–6.7) years (and after adjustment for age and sex), those with ASc were at greater risk of the primary outcome [hazard ratio (HR) 2.9, 95% confidence interval (CI) 2.1–4.0] and need for AVI (HR 26.8, 95% CI 9.1–79.1) compared with those with no CAVD. Clinical event rates accelerated after ∼5 years in those with mild AS.

Conclusion

Patients with ASc are >25 times more likely to require AVI than those with no CAVD, and follow-up echocardiography should be considered within 3–4 years in those with mild AS.
Blood pressure control in hypertensive sleep apnoea patients of the European Sleep Apnea Database cohort - effects of positive airway pressure and antihypertensive medication
Authors: Svedmyr Sven , Hedner Jan , Bailly Sebastien , Fanfulla Francesco , Hein Holger , Lombardi Carolina , Ludka Ondrej , Mihaicuta Stefan , Parati Gianfranco , Pataka Athanasia , Schiza Sophia , Tasbakan Sezai , Testelmans Dries , Zou Ding , Grote Ludger ,   European Sleep Apnea Database (ESADA) study group, P Steiropoulos , J Verbraecken , E Petiet , Trakada Georgia , I Fietze , T Penzel , Ludka Ondrej , I Bouloukaki , S Schiza , W T McNicholas , S Ryan , R L Riha , J A Kvamme , L Grote , J Hedner , D Zou , Hertegonne Katrien , Pevernagie Dirk , S Bailly , J L Pépin , R Tamisier , H Hein , O K Basoglu , M S Tasbakan , J Buskova , P Joppa , R Staats , Testelmans Dries , Gouveris Haralampos , K Ludwig , C Lombardi , G Parati , M R Bonsignore , Fanfulla Francesco , M Drummond , M van Zeller , W Randerath , Treml Marcel , Z Dogas , R Pecotic , A Pataka , U Anttalainen , T Saaresranta , P Sliwinski
Published: October 2023

Aims

We analysed longitudinal blood pressure (BP) data from hypertensive obstructive sleep apnoea (OSA) patients in the European Sleep Apnea Database cohort. The study investigated the interaction between positive airway pressure (PAP)-induced BP change and antihypertensive treatment (AHT).

Methods and results

Hypertensive patients with AHT [monotherapy/dual therapy n = 1283/652, mean age 59.6 ± 10.7/60.6 ± 10.3 years, body mass index (BMI) 34.2 ± 6.5/34.8 ± 7.0 kg/m2, apnoea–hypopnoea index 46 ± 25/46 ± 24 n/h, proportion female 29/26%, respectively] started PAP treatment. Office BP at baseline and 2- to 36-month follow-up were assessed. The interaction between AHT drug classes and PAP on BP was quantified and the influences of age, gender, BMI, co-morbidities, BP at baseline, and study site were evaluated. Following PAP treatment (daily usage, 5.6 ± 1.6/5.7 ± 1.9 h/day), systolic BP was reduced by −3.9 ± 15.5/−2.8 ± 17.7 mmHg in mono/dual AHT and diastolic BP by −3.0 ± 9.8/−2.7 ± 10.8 mmHg, respectively, all P < 0.0001. Systolic and diastolic BP control was improved following PAP treatment (38/35% to 54/46% and 67/67% to 79/74%, mono/dual AHT, respectively). PAP treatment duration predicted a larger BP improvement in the monotherapy group. Intake of renin–angiotensin blockers [angiotensin converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB)] alone or in any AHT combination was associated with better BP control. The AHT-dependent BP improvement was independent of confounders.

Conclusion

In this pan-European OSA patient cohort, BP control improved following initiation of PAP. Longer PAP treatment duration, was associated with a favourable effect on BP. Our study suggests that ACEI/ARB, alone or in combination with other drug classes, provides a particularly strong reduction of BP and better BP control when combined with PAP in OSA.
Future burden of myocardial infarction in Australia: impact on health outcomes between 2019 and 2038
Authors: Abebe Tamrat Befekadu , Morton Jedidiah I , Ilomaki Jenni , Ademi Zanfina
Published: October 2023

Background

Myocardial infarction (MI) remains a major health burden in Australia. Yet the future burden of MI has not been extensively studied for the Australian population.

Methods and results

A multistate lifetable model was constructed to estimate the lifetime risk of MI and project the health burden of MI for the Australian population aged between 40 and 100 years over a 20-year period (2019–2038). Data for the model were primarily sourced from the Victorian-linked dataset and supplemented with other national data. The lifetime risk of MI at age 40 was estimated as 24.4% for males and 13.2% for females in 2018. From 2019 to 2038, 891 142 Australians were projected to develop incident MI. By 2038, the model estimated there would be 702 226 people with prevalent MI, 51 262 incident non-fatal MI, and 3717 incident fatal MI; these numbers represent a significant increase compared to the 2019 estimates, with a 27.0% (148 827), 62.0% (19 629), and 104.7% (1901) rise, respectively. Projected years of life lived (YLL) (5% discount) accrued by the Australian population was 174 795 232 (84 356 304 in males and 90 438 928 in females), with 7 657 423 YLL among people with MI (4 997 009 in males and 2 660 414 in females).

Conclusion

The burden of MI was projected to increase between 2019 and 2038 in Australia. The outcomes of the model provide important information for decision-makers to prioritize population-wide prevention strategies to reduce the burden of MI.
Three-dimensional changes in the cranial base associated with soft-diet feeding
Authors: Murata Yuka , Tanikawa Chihiro , Shiraishi Yuki , Inubushi Toshihiro , Kono Kana , Kamioka Hiroshi , Yamashiro Takashi
Published: October 2023

Background

Masticatory activity affects the morphology of the maxillo-mandibular complex, however, its influence on the cranial base remains to be elucidated. The recent integration of quantitative morphometric analysis with 3D imaging enabled a comprehensive and high-resolution morphological characterization of the craniofacial complex. We aimed to investigate the influence of masticatory activity on the morphology of the growing cranial base by three-dimensional (3D) geometric morphometric approach using micro-CT.

Methods

The micro-CT data was reanalyzed to illustrate the 3D shape of the cranial base, and wireframe models were generated by connecting landmarks on the images. In the original study, mice were fed a soft diet (SD) of powdered pellets or a conventional hard diet (HD) for 6 weeks from 3 to 9 weeks of age, immediately after weaning. A principal component (PC) analysis analyzed shape variations and assessed their significance, while canonical variate (CV) analysis facilitated the comparison and differentiation of groups based on shape, unveiling meaningful shape distinctions.

Results

Three PCs were extracted that significantly separated the SD and HD groups among those explaining variations in shape. These PCs were related to the length of the sphenoid bone, the width of the anterior part of the sphenoid bone, and the length of the cranial base. Furthermore, one CV effectively distinguished SD from HD, and CV analysis showed that the sphenoid was shortened in the length and narrowed at the border of the temporal bone in SD mice.

Conclusions

Masticatory loading affects the skeletal development of the cranial base. The morphology of the sphenoid bone was affected in both the sagittal and transverse axes.
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods
Authors: Kanduri Chakravarthi , Scheffer Lonneke , Pavlović Milena , Rand Knut Dagestad , Chernigovskaya Maria , Pirvandy Oz , Yaari Gur , Greiff Victor , Sandve Geir K
Published: October 2023

Background

Machine learning (ML) has gained significant attention for classifying immune states in adaptive immune receptor repertoires (AIRRs) to support the advancement of immunodiagnostics and therapeutics. Simulated data are crucial for the rigorous benchmarking of AIRR-ML methods. Existing approaches to generating synthetic benchmarking datasets result in the generation of naive repertoires missing the key feature of many shared receptor sequences (selected for common antigens) found in antigen-experienced repertoires.

Results

We demonstrate that a common approach to generating simulated AIRR benchmark datasets can introduce biases, which may be exploited for undesired shortcut learning by certain ML methods. To mitigate undesirable access to true signals in simulated AIRR datasets, we devised a simulation strategy (simAIRR) that constructs antigen-experienced-like repertoires with a realistic overlap of receptor sequences. simAIRR can be used for constructing AIRR-level benchmarks based on a range of assumptions (or experimental data sources) for what constitutes receptor-level immune signals. This includes the possibility of making or not making any prior assumptions regarding the similarity or commonality of immune state–associated sequences that will be used as true signals. We demonstrate the real-world realism of our proposed simulation approach by showing that basic ML strategies perform similarly on simAIRR-generated and real-world experimental AIRR datasets.

Conclusions

This study sheds light on the potential shortcut learning opportunities for ML methods that can arise with the state-of-the-art way of simulating AIRR datasets. simAIRR is available as a Python package: https://github.com/KanduriC/simAIRR.
Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications
Authors: Shrestha Prasansah , Karmacharya Jayram , Han So-Ra , Lee Jun Hyuck , Oh Tae-Jin
Published: October 2023

Bacteria possess diverse metabolic and genetic processes, resulting in the inability of certain bacteria to degrade trehalose. However, some bacteria do have the capability to degrade trehalose, utilizing it as a carbon source, and for defense against environmental stress. Trehalose, a disaccharide, serves as a carbon source for many bacteria, including some that are vital for pathogens. The degradation of trehalose is carried out by enzymes like trehalase (EC 3.2.1.28) and trehalose phosphorylase (EC 2.4.1.64/2.4.1.231), which are classified under the glycoside hydrolase families GH37, GH15, and GH65. Numerous studies and reports have explored the physiological functions, recombinant expression, enzymatic characteristics, and potential applications of these enzymes. However, further research is still being conducted to understand their roles in bacteria. This review aims to provide a comprehensive summary of the current understanding of trehalose degradation pathways in various bacteria, focusing on three key areas: (i) identifying different trehalose-degrading enzymes in Gram-positive and Gram-negative bacteria, (ii) elucidating the mechanisms employed by trehalose-degrading enzymes belonging to the glycoside hydrolases GH37, GH15, and GH65, and (iii) discussing the potential applications of these enzymes in different sectors. Notably, this review emphasizes the bacterial trehalose-degrading enzymes, specifically trehalases (GH37, GH15, and GH65) and trehalose phosphorylases (GH65), in both Gram-positive and Gram-negative bacteria, an aspect that has not been highlighted before.
Earnings per share
Authors: Crowe Jonathan , Bradshaw Tony
Published: October 2023

This chapter addresses earnings per share (EPS), one of the key ratios that equity investors will use to assess the performance of a company and the return to them. IAS 33 Earnings per Share is the standard used in the calculation of earnings per share. The chapter explains the significance of basic and diluted EPS as a measure of financial performance. It then provides the calculation of basic and diluted EPS for a variety of situations, including changes in share capital, and where share options and convertible financial instruments exist. Finally, it imparts the way to present EPS on the face of the statement of profit or loss and the disclosure requirements.
Inventories
Authors: Maynard Jennifer
Published: October 2023

This chapter considers the measurement, valuation, and reporting of inventories. International Accounting Standard (IAS) 2 Inventories deals with the issue of measurement, to ensure consistency of approach, which is discussed in detail in the chapter. Current asset is defined as well as the illustration of the significance of inventories in companies' financial statements. The chapter introduces the key valuation principle for inventories, the lowering of cost, and net realizable value and the cost methods of first in, first out. It closes with a discussion detailing net realizable value and disclosures in financial statements.
Liabilities
Authors: Maynard Jennifer
Published: October 2023

This chapter examines liabilities, particularly, provisions and contingent liabilities. It references the International Accounting Standard (IAS) 37 Provisions, Contingent Liabilities and Contingent Assets, which specifies when a provision for liabilities should be recognized, gives guidance as to its measurement, and addresses what should happen in increasing cases of uncertainty. The chapter begins with the definition of a liability. It then goes on to discuss the accounting treatments of contingent liabilities, contingent assets, operating losses, restructuring, and onerous contracts. IAS 10 Events after the Reporting Period, the standard that addresses the issue of as to what extent a company should change its financial statements as a result of what happens after the statement of financial position date, is discussed in detail in the latter part of the chapter.
Employee benefits and share-based payments
Authors: Crowe Jonathan , Bradshaw Tony
Published: October 2023

This chapter covers accounting and reporting for both short- and long-term employee benefits, particularly on the key issues of defined benefit pension plans and share-based payments. It starts with the introduction of the different types of employee benefits including bonuses, holiday pay, sick pay, retirement benefit plans, and defined benefit plans. Then it considers the accounting treatments for those benefits. The different share-based payment arrangements, and how they are accounted for and disclosed in financial statements, are also discussed extensively. The International Accounting Standard (IAS) 19 Employee Benefits is the financial reporting standard which deals with all employee remuneration and defined benefit plans, except for share-based remuneration. The International Financial Reporting Standard (IFRS) 2 Share-based Payment is the standard for the recognition of the expense of the share-based schemes and sets out how the expense is measured and the disclosures required for the many different types of schemes which exist.
Framing Business Ethics Corporate Responsibility, Stakeholders, and Citizenship
Authors: Crane Andrew , Matten Dirk , Glozer Sarah , Spence Laura J.
Published: October 2023

This chapter focuses on the ways of framing business ethics in the context of the corporation being part of a wider society. It investigates why corporations have social responsibilities, then explains corporate social responsibility in terms of its levels, strategies, and outcomes. The chapter also offers an overview of concepts such as stakeholder theory. This leads on to an analysis of key contemporary concepts such as corporate accountability and corporate citizenship, which give important conceptual space for understanding business ethics beyond its traditional boundaries. The chapter then evaluates the implications of applying these theories and concepts to different international contexts. Ultimately, the chapter argues that, although this is a more recent interpretation of business ethics to have emerged from the literature, it still can be analyzed in a number of different ways and it can be extremely useful for framing some of the problems of business ethics in the global economy.
Government, Regulation, and Business Ethics
Authors: Crane Andrew , Matten Dirk , Glozer Sarah , Spence Laura J.
Published: October 2023

This chapter talks about government and regulation. The government as a stakeholder, as the chapter defines it, is a very multifaceted group. The chapter unfolds the government at various levels, functions, and areas. It investigates problems such as corruption and corporate lobbying, and explores the shifting relationships between regulation, government, and business, emphasizing the increasingly important role played by corporations in the governance of the global economy. By describing the ethical issues and problems faced in business–government relations, the chapter evaluates the shifts in these issues and problems in the context of globalization. Ultimately, the chapter looks at the changing role of business and CSOs in the regulatory process as well as the role of governmental regulation in achieving potentially sustainable solutions.
Conclusions and Future Perspectives
Authors: Crane Andrew , Matten Dirk , Glozer Sarah , Spence Laura J.
Published: October 2023

This chapter sums up the role, meaning, and importance of business ethics, including emergent themes. It identifies the emerging themes of gender and other inequalities, alternative business models, and digitalization. The chapter also tackles the influence of globalization on business ethics and the value of the notion of sustainability. It then shifts to explain the role and significance of stakeholders as a whole for ethical management, and presents the implications of corporate citizenship thinking for business ethics. Ultimately, the chapter discusses the contribution of normative ethical theories to business ethics. It then considers the potential conflicts between different stakeholder groups, and draws conclusions about the future relevance of business ethics issues.
Introduction to the Statement of Profit or Loss
Authors: Carey Mary , Knowles Cathy
Published: October 2023

This chapter focuses on the statement of profit or loss. It looks into the differences between cash and profits of a business in line with sales and purchases. The chapter argues that double-entry bookkeeping is necessary to know whether a trial balance would turn into a statement of profit or loss. It lists assets, liabilities, capital, income, expenses, and drawings as types of accounts. A trial balance is drawn up at the end of a fiscal period as it is used to prepare the financial statements. Next, the chapter explores the difference between capital expenditure and revenue expenditure. It includes the equation for calculating gross profit and cost of sales.
Company Accounts
Authors: Carey Mary , Knowles Cathy
Published: October 2023

This chapter explains company accounts. It discusses the process of filing a statement of financial position, a statement of profit or loss, and a statement of comprehensive income for a limited company. In addition, the chapter highlights the purpose of a statement of changes in equity. It explores the concept of operating profit, retained profit, and shareholders' equity. Additionally, interest and dividends are paid to providers of capital to a company. The chapter notes that the equity of a company consists of ordinary share capital and all the reserves such as share premium and retained profits. It references goodwill and brands as examples of intangible assets.
Capital Structure and Investment Ratios
Authors: Carey Mary , Knowles Cathy
Published: October 2023

This chapter discusses capital structure and investment ratios. It notes how capital structure ratios consider the origin of the long-term funds of the business, while investment ratios look at how company shares are performing and how they are returned. The chapter explains the advantages and disadvantages of gearing and interest cover which are the key ratios of capital structures. It also explores the equations for dividend yield, price to earnings ratio, and earnings per share dividend cover. Next, the chapter looks into the limitations of ratio analysis in line with the nature of the business and broader economic environment.
Costs and Break-Even Analysis
Authors: Carey Mary , Knowles Cathy
Published: October 2023

This chapter looks at cost and break-even analysis. It cites the difference between management accounting and financial accounting. Management accounting is the financial and non-financial information generated for business managers to help them in their daily operations. Next, the chapter gives the equation to calculate fixed and variable costs via the high-low method. It uses break-even analysis as a tool for decision making. As the chapter shows, the break-even point is where neither a profit nor a loss is made. The chapter also explores contribution, the break-even point, and margin of safety before enumerating the limitations of break-even analysis.
Absorption and Activity-Based Costing
Authors: Carey Mary , Knowles Cathy
Published: October 2023

This chapter explores absorption and activity-based costing. It notes the importance of overheads when costing products. The chapter uses equations to calculate a simple blanket overhead rate and a simple activity-based cost. It uses absorption costing methods to fully cost out a range of products. The chapter also cites the limitations of traditional costing methods. It includes the under recovery and over recovery of overheads costs which are indirect costs to a business that cannot be linked directly with a product. Towards the end, the chapter includes the process of going through costs being collected by manufacturing departments by referencing cost allocation, apportion, and reapportion of indirect costs.
The Statement of Financial Position
Authors: Scott Peter
Published: October 2023

This chapter presents the elements that make up the statement of financial position. It first defines what constitutes an asset and a liability and explains how equity is calculated. Then it proceeds to the construction of simple statements of financial position from available data. Finally, the chapter briefly considers how new transactions affect the statement of financial position.
The Statement of Cash Flows
Authors: Scott Peter
Published: October 2023

This chapter looks at the statement of cash flows, which presents users of financial information with details of cash inflows and outflows for an accounting period. It shows how the statement of cash flows links together the statement of profit or loss and the statement of financial position to demonstrate changes in an entity's financial position over each accounting period arising from operating, investing, and financing activities. The use of the direct and indirect method of preparing statements of cashflows is also demonstrated. Finally, the chapter provides a list and description of the conventions upon which accounting is based.
SMRT–AgRenSeq-d in potato (Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5
Authors: Wang Yuhan , Brown Lynn H , Adams Thomas M , Cheung Yuk Woon , Li Jie , Young Vanessa , Todd Drummond T , Armstrong Miles R , Neugebauer Konrad , Kaur Amanpreet , Harrower Brian , Oome Stan , Wang Xiaodan , Bayer Micha , Hein Ingo
Published: October 2023

Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT–AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR–AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT–RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT–AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT–AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
Pulmonary valve reconstruction for acquired pulmonary regurgitation in patients with treated congenital heart disease
Authors: Jussli-Melchers Jill , Hansen Jan Hinnerk , Scheewe Jens , Attmann Tim , Eide Martin , Logoteta Jana , Dütschke Peter , Salehi Ravesh Mona , Uebing Anselm , Voges Inga
Published: October 2023

OBJECTIVES

Pulmonary valve regurgitation is a common problem after relief of right ventricular outflow tract (RVOT) obstruction with a transannular patch. Pulmonary valve replacement with a homograft or xenograft is the routine treatment. Longevity of biological valves and the availability of homografts are limited. Alternatives to restore RVOT competence are evaluated. The goal of this study was to present intermediate-term results for pulmonary valve reconstruction (PVr) in patients with severe regurgitation.

METHODS

PVr was performed in 24 patients (August 2006‒July 2018). We analysed perioperative data, pre- and postoperative cardiac magnetic resonance (CMR) imaging studies, freedom from valve replacement and risk factors for pulmonary valve dysfunction.

RESULTS

The underlying diagnoses were tetralogy of Fallot (n = 18, 75%), pulmonary stenosis (n = 5, 20.8%) and the double outlet right ventricle post banding procedure (n = 1, 4.2%). The median age was 21.5 (14.8–23.7) years. Main (n = 9, 37.5%) and branch pulmonary artery procedures (n = 6, 25%) and surgery of the RVOT (n = 16, 30.2%) were often part of the reconstruction. The median follow-up after the operation was 8.0 (4.7–9.7) years. Freedom from valve failure was 96% at 2 and 90% at 5 years. The mean longevity of the reconstructive surgery was 9.9 years (95% confidence interval: 8.8–11.1 years). CMR before and 6 months after surgery showed a reduction in the regurgitation fraction [41% (33–55) vs 20% (18–27) P = 0.00] and of the indexed right ventricular end-diastolic volume [156 ml/m2 (149–175) vs 116 ml/m2 (100–143), P = 0.004]. Peak velocity across the pulmonary valve (determined by CMR) half a year after surgery was 2.0, unchanged.

CONCLUSIONS

PVr can be achieved with acceptable intermediate-term results and may delay pulmonary valve replacement.
Perioperative discordance in mesothelioma cell type after pleurectomy/decortication—a possible detrimental effect of neoadjuvant chemotherapy due to epithelial to mesenchymal transition?
Authors: Ventura Luigi , Lee Michelle , Baranowski Ralitsa , Hargrave Joanne , Sheaff Michael , Waller David
Published: October 2023

OBJECTIVES

The goal was to evaluate the accuracy of preoperative histological assessment and the factors affecting the accuracy and the subsequent effect on postoperative survival after surgical treatment for malignant pleural mesothelioma (MPM).

METHODS

We analysed the perioperative course of patients who underwent surgery for MPM in a single institution over a 5-year period. The primary end point was to evaluate the proportion of histological discordance between preoperative assessment and postoperative histological diagnosis. The secondary end point was to evaluate its prognostic effect on postoperative survival after surgical treatment.

RESULTS

One-hundred and twenty-nine patients were included in this study. Histological discordance between preoperative assessment and postoperative histological diagnosis was found in 27 of 129 patients (20.9%): epithelial to biphasic/sarcomatoid (negative discordance) in 24 and biphasic to epithelial (positive discordance) in 3 (P-value < 0.001). All 24 patients who exhibited epithelial-to-mesenchymal transition (EMT) had received neoadjuvant chemotherapy (P-value: 0.006). In the 34 patients who underwent upfront surgery, only 1 case (2.9%) of EMT was identified (P-value: 0.127). EMT was not associated with a less invasive method of biopsy (P-value: 0.058) or with the volume or maximum diameter of the biopsy (P-value: 0.358 and 0.518, respectively), but it was significantly associated with the receipt of neoadjuvant chemotherapy (P-value: 0.006). At a median follow-up of 17 months (IQR: 11.0–28.0), 50 (39%) patients are still alive. Overall survival was significantly reduced in those patients who received neoadjuvant chemotherapy and who exhibited discordance (EMT) compared to those who did not: 11 (95% CI: 6.2–15.8) months versus 19 (95% CI: 14.2–23.8) months (P-value < 0.001). In addition, there was no difference in overall survival between those who received neoadjuvant chemotherapy and those who had upfront surgery: 16 (95% CI: 2.5–19.5) months versus 30 (95% CI: 11.6–48.4) months (P-value: 0.203).

CONCLUSIONS

The association of neoadjuvant chemotherapy with perioperative histological discordance can be explained by EMT, which leads to worse survival. Therefore, there is an argument for the preferential use of upfront surgery in the treatment of otherwise resectable MPM.