bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct RNA sequencing of theEscherichia coliepitranscriptome uncovers alterations under heat stress
Authors: Barrios Sebastian Riquelme , Camus Leonardo Vasquez , Cusack Siobhan A. , Burdack Korinna , Petrov Dimitar Plamenov , Yeşiltaç-Tosun G. Nur , Kaiser Stefanie , Giehr Pascal , Jung Kirsten
Published: July 2024

Modifications of RNA, known as the epitranscriptome, affect gene expression, translation, and splicing in eukaryotes, with implications for developmental processes, cancer, and viral infections. In prokaryotes, regulation at the level of the epitranscriptome is still poorly understood. Here, we used Nanopore direct RNA sequencing ofEscherichia colito study RNA modifications and their changes under heat stress. With a single sequencing reaction, we detected most known modification types in rRNA, tRNA, and mRNA. RNA sequencing was complemented by a multifaceted approach that included mass spectrometry, deletion mutants, single-nucleotide PCR, andin vitromethylation. Known m5C and m6A sites in the rRNA were confirmed, but these types of modifications could not be localized in the mRNA. In response to heat stress, levels of m5C, m6A, and m6,6A increased in the 16S rRNA. Sequencing and mass spectrometry data demonstrated a decrease in tRNA modification abundance in the anticodon loop at 45 °C. In general, mRNA modifications at 37 °C were enriched in the coding regions of genes associated with general metabolism and RNA processing, which shifted to genes involved in cell wall synthesis and membrane transport under heat stress. This study provides new insights into the complexity of post-transcriptional regulation in bacteria.

GRAPHICAL ABSTRACT
Biotin based Northern Blotting (BiNoB): A Robust and Efficient Alternative
Authors: Madhry Deeksha , Roy Riya , Verma Bhupendra
Published: July 2024

Advancements in sequencing technology have led to the emergence of diverse types of regulatory RNAs. Differential transcript levels regulate cellular processes and influence disease severity. Identifying these variations through reliable methods is crucial for understanding their regulatory roles and disease mechanisms. Northern blotting, which used to be considered the gold standard for differential expression analysis, poses challenges due to various limitations associated with RNA quality, integrity, radioactivity, reagents, and the expenses associated with it. In this study, we employed a biotin-based Northern blotting approach, BiNoB, which offers advantages over traditional methods. In this study, we comprehensively targeted various RNA types, making this technique a versatile tool for RNA detection. Additionally, we conducted a comparison between 3’-end labeled probes, which were labeled in-house, and 5’-end labeled probes, which were commercially obtained. Remarkably, the results revealed significantly increased sensitivity with 3’-end labeled probes. Furthermore, we prepared an in-house buffer and compared its performance with the commercially available ULTRAhyb buffer, which exhibited comparable sensitivity, indicating that the in-house buffer is a cost-effective alternative. Intriguingly, our findings showed that as little as 1µg of total RNA proved to be adequate for the detection of small RNAs like tRNAs and their derived fragments.
Evaluating the utility of ChatGPT to convert clinic letters into patient friendly language
Authors: Cork Simon C. , Hopcroft Keith
Published: July 2024

Communication with patients in language they understand leads to greater comprehension of treatment and diagnoses but can be time consuming for clinicians. Here we sought to investigate the utility of ChatGPT to translate clinic letters into language patients understood, without loss of clinical information. Twenty-three letters from a range of specialities were translated, resulting in no loss of clinical information. Subjective analysis from patient representatives revealed significantly increased understanding of treatment and diagnoses, increased satisfaction, and a significant decrease in the requirement to seek medical assistance in understanding their content when compared to original letters written to clinicians. Overall, we conclude that ChatGPT can be used to translate clinic letters into patient friendly language, and that these letters are preferred by patients.
Ongoing and planned Randomized Controlled Trials of AI in medicine: An analysis of Clinicaltrials.gov registration data
Authors: Andreoletti Mattia , Senkalfa Berkay , Blasimme Alessandro
Published: July 2024

The integration of Artificial Intelligence (AI) technologies into clinical practice holds significant promise for revolutionizing healthcare. However, the realization of this potential requires rigorous evaluation and validation of AI applications to ensure their safety, efficacy, and clinical significance. Despite increasing awareness of the need for robust testing, the majority of AI-related Randomized Controlled Trials (RCTs) so far have exhibited notable limitations, impeding the generalizability and proper integration of their findings into clinical settings. To understand whether the field is progressing towards more robust testing, we conducted an analysis of the registration data of ongoing and planned RCTs of AI in medicine available in theClinicaltrials.govdatabase. Our analysis highlights several key trends and challenges. Effectively addressing these challenges is essential for advancing the field of medical AI and ensuring its successful integration into clinical practice.
scKEPLM: Knowledge enhanced large-scale pre-trained language model for single-cell transcriptomics
Authors: Li Yang , Qiao Guanyu , Wang Guohua
Published: July 2024

The success of large-scale pre-trained language models in the Natural Language Processing (NLP) domain has encouraged their adoption in genomics and single-cell biology. Developing pre-trained models using the rapidly growing single-cell transcriptomic data helps to unravel the intricate language of cells. However, current single-cell pre-trained models primarily focus on learning gene and cell representations from extensive gene expression data, failing to fully comprehend the biological significance of the gene expression patterns and cell types they identify, which leads to limited interpretability and transferability. We propose scKEPLM, a knowledge-enhanced single-cell pre-training language model integrates a biology knowledge graph into the single-cell transcriptome pre-training process. scKEPLM covers over 41 million single-cell RNA sequences and 8.9 million gene relations. Through parallel pre-training of single-cell transcriptome sequences and genetic knowledge, combined with a Gaussian cross-attention mechanism, scKEPLM precisely aligns cell semantics with genetic information, to learn more accurate and comprehensive representations of single-cell transcriptomes. The introduction of knowledge enhancement has improved the identification of important genes in cells by scKEPLM, and greatly enriched the understanding of cell function and disease mechanism. The scKEPLM model has achieved state-of-the-art performance in more than 12 downstream tasks, including gene annotation, cell annotation, and drug response prediction, demonstrating strong generalization and transferability. Further exploration of the model’s interpretability demonstrates its adaptability to variations in gene expression patterns within cells under various physiological or pathological conditions.
Relativistic head-on collisions of
U(1)
gauged
Q
-balls
Authors: Kinach Michael P. , Choptuik Matthew W.
Published: July 2024

We investigate the collision dynamics of U(1) gauged Q-balls by performing high-resolution numerical simulations in axisymmetry. Focusing on the case of relativistic head-on collisions, we consider the effects of the initial velocity, relative phase, relative charge, and electromagnetic coupling strength on the outcome of the collision. We find that the collision dynamics can depend strongly on these parameters; most notably, electromagnetic effects can significantly alter the outcome of the collision when the gauge coupling is large. When the gauge coupling is small, we find that the dynamics generally resemble those of ordinary (nongauged) Q-balls.

Published by the American Physical Society
2024
Estimates on the convergence of expansions at finite baryon chemical potentials
Authors: Wen Rui , Yin Shi , Fu Wei-jie
Published: July 2024

Convergence of three different expansion schemes at finite baryon chemical potentials, including the conventional Taylor expansion, the Padé approximants, and the T′ expansion proposed recently in lattice QCD simulations, have been investigated in a low energy effective theory within the functional renormalization group approach. It is found that the convergence of the T′ expansion and the Padé approximants is consistent with the conventional Taylor expansion, within the expansion orders considered in this work. Furthermore, we find that the consistent regions of the three different expansions are in agreement with the convergence radius of the Lee-Yang edge singularities.

Published by the American Physical Society
2024
Hairy black holes by spontaneous symmetry breaking
Authors: Latosh Boris , Park Miok
Published: July 2024

We study hairy black hole solutions in Einstein(-Maxwell)-scalar-Gauss-Bonnet theory. The complex scalar coupling function includes quadratic and quartic terms, so the gravitational action has a U(1) symmetry. We argued that when the effective mass of the scalar field is at the critical value, the black holes without hairs transform into hairy black holes in a symmetry-broken vacuum via spontaneous symmetry breaking. These hairy black holes are stable under scalar perturbations, and the Goldstone bosons are trivial. Moreover, we found that the spontaneous symmetry breaking associated with local U(1) is unlikely to occur in this theory.

Published by the American Physical Society
2024
Fracton Infrared Triangle
Authors: Pérez Alfredo , Prohazka Stefan , Seraj Ali
Published: July 2024

In theories with conserved dipole moment, isolated charged particles (fractons) are immobile, but dipoles can move. We couple these dipoles to the fracton gauge theory and analyze the universal infrared structure. This uncovers an observable double kick memory effect which we relate to a novel dipole soft theorem. Together with their asymptotic symmetries this constitutes the first realization of an infrared triangle beyond Lorentz symmetry. This demonstrates the robustness of these IR structures and paves the way for their investigation in condensed matter systems and beyond.

Published by the American Physical Society
2024
Deterministic discrete-time quantum walk search on complete bipartite graphs
Authors: Peng Fangjie , Li Meng , Sun Xiaoming
Published: July 2024

Searching via quantum walk is a topic that has been extensively studied. Most previous results provide approximate solutions, while in this paper we prove an algorithm that can find a marked vertex certainly. We adopt the coined discrete-time quantum walk (DTQW) model with adjusted operators and prove that, on complete bipartite graphs, when parameters are set properly, coined DTQW can deterministically find a marked vertex, i.e., the success probability is exactly 1. Before this paper there have been results of an alternating continuous-time quantum walk method that achieve deterministic spatial search, but this paper provides a deterministic quantum spatial search result via DTQW, while maintaining a quadratic speedup compared to classical algorithms. We also provide the quantum circuit implementation.

Published by the American Physical Society
2024
Financial reporting quality dynamics in India: the role of IFRS convergence and corporate governance
Authors: Gomes Lorraine Rayelle , Costa Juao C.
Published: July 2024

Purpose

This paper aims to investigate the impact of International Financial Reporting Standards (IFRS) convergence on value relevance and earnings management for Indian listed firms while also exploring whether the relationship is moderated by the firms’ corporate governance structures.

Design/methodology/approach

Corporate governance (CG) scores of 573 listed firms were calculated by using a self-constructed index for a period of 7 years (2014–2015 to 2020–2021). Static and dynamic panel models with generalized method of moments (GMM) estimators were used to test the conditional hypothesis that the impact of the Indian IFRS converged standards (Indian Accounting Standards [IndAS]) on information quality is affected by the firm’s corporate governance strength.

Findings

The estimates reveal that the positive effect of corporate governance scores on the value relevance of earnings reduces in the presence of IFRS, whereas the interaction of both the variables on book values remains insignificant. Secondly, the use of IndAS reduces discretionary accruals, but corporate governance does not have a significant moderating effect within the equation.

Practical implications

The results offer an interesting perspective into the debate on IFRS consequences and the role of internal institutional frameworks. It provides preliminary evidence suggesting that although corporate governance improves the value relevance of earnings, it may not be entirely effective in reducing the management of earnings.

Originality/value

To the best of the authors’ knowledge, it is the first study in India to provide empirical findings on the role played by corporate governance mechanisms in explaining the relationship between IFRS convergence and accounting information quality. The analysis accounts for modelling issues such as endogeneity and autocorrelation by using dynamic panel models and instrumental variables.
Investment efficiency, ESG performance and corporate performance: evidence from Chinese listed enterprises
Authors: Gao Daquan , Li Songsong , Zhou Yan
Published: July 2024

Purpose

This study aims to propose a moderated mediation model to investigate the moderating effects of environmental, social and governance (ESG) performance on the relationship between inefficient investment and firm performance and the mediating effect of firms that participate in institutional research on the relationship between investment efficiency and performance. This study also analyses the heterogeneity of the corporate nature, intensity of industrial research and development (R&D), industrial competition and regional marketization.

Design/methodology/approach

This study uses a panel data fixed-effects model to conduct a regression analysis of 1,918 Chinese listed firms from 2016 to 2020. A Fisher’s permutation test is used to examine the differences between state-owned and nonstate-owned firms.

Findings

Inefficient investment negatively impacts corporate performance and higher ESG performance exacerbates this effect by attracting more institutional research which reveals more problems. State-owned enterprises perform significantly better than nonstate-owned enterprises in terms of ESG transformation. Industrial R&D intensity, competition and regional marketization also mitigate the negative effects of inefficient investment on corporate performance.

Practical implications

This study suggests that companies should consider inefficient investments that arise from agency issues in corporate ESG transformation. In addition, state-owned enterprises in ESG transformation should take the lead to achieve sustainable development more efficiently. China should balance regional marketization, encourage enterprises to increase R&D intensity, reduce industry concentration, encourage healthy competition and prevent market monopolies.

Originality/value

This study combines the agency and stakeholder theories to reveal how inefficient investments that arise from agency issues inhibit value creation in ESG initiatives.
Transforming stench to scent – the case of Phool.Co.
Authors: Tiwari Neha , Gupta Vibhuti , Sharma Sheetal
Published: July 2024

Learning outcomes

After completion of the case study, students will be able to decipher key concepts underpinning sustainable entrepreneurship and its application in the recognition and exploitation of sustainable business opportunities, decipher the application of circular economy business models, understand the pivots to achieve the billion-dollar valuation and analyse the strategies for value creation during the pivoting journey of a startup.

Case overview/synopsis

The case study traces the journey of Phool.Co, a sustainable biomaterial startup based in a Tier II city of Kanpur located in the state of Uttar Pradesh, India, by Ankit Agarwal in 2017. Agarwal started with the vision of providing solution to the effects of water pollution and environmental damage. Ganga is not just a river, rather it is the symbol of cultural and religious faith in India. Although the river Ganga is considered a deity in India, it is one of the most polluted rivers. Every year 8,000,000 metric tonnes of waste flowers are dumped into the sacred river to pollute it further. The pollution poses grave dangers to the health and livelihood of millions of Indians. Phool.Co is a sustainable enterprise that has pioneered flower cycling technology. The dumped flowers are recycled to produce organic incense sticks, Florafoam, and “Fleather – the organic alternative to leather”. The case study traces the genesis of Phool.Co and its approach towards sustainability in the context of the circular economy. The case study primarily explores the pivot points for a startup to enter the unicorn club in the present context. To achieve the desired valuation, Agarwal must decide to rethink its business model. Will franchise model work for Phool.Co? Should Agarwal scale up with commercialization of Florafoam to capitalize the opportunity in packaging industry? Vegan leather is a nascent market and how will the consumers respond to Fleather is a pertinent question. The case study attempts to explore the challenges encountered in augmenting the valuation of sustainable enterprises.

Complexity academic level

This case study is suitable for graduate and postgraduate students enrolled in courses related to entrepreneurship, innovation and sustainability. The case study is of intermediate-level difficulty. There are no specific prerequisites to understand the case.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 3: Entrepreneurship.
Analysing FDI inflow effects on CO2 emissions: a comparative study of OECD and BRICS nations with PHH and PHE models
Authors: Sreenu Nenavath
Published: July 2024

Purpose

The purpose of this study is to explore the correlation between foreign direct investment (FDI) and carbon dioxide (CO2) emissions in emerging economies, with a particular emphasis on Brazil, Russia, India, China and South Africa (BRICS) countries along with 10 the Organization for Economic Cooperation and Development nations.

Design/methodology/approach

This study uses quantitative research methods and econometric analysis to investigate the relationship between FDI inflows and CO2 emissions in selected countries. Specifically, the research concentrates on assessing the impact of FDI on CO2 emissions within the BRICS countries. By examining data spanning from 2000 to 2003, the study aims to shed light on the interaction between economic integration and environmental sustainability dynamics on a global scale.

Findings

The results of this study highlight notable contributors to CO2 emissions within the BRICS countries, identifying Switzerland, Denmark and the UK as significant sources. These findings support the notion of a pollution haven, underscoring the influence of FDI in moulding environmental outcomes in developing economies.

Research limitations/implications

Drawing from the study’s outcomes, suggestions are put forth to foster sustainable development strategies. It is recommended that BRICS nations prioritize the attraction of environmentally aware FDI to bolster efforts aimed at mitigating environmental harm.

Originality/value

This study adds to the ongoing discussion surrounding sustainable development by offering a concentrated analysis of how FDI influences CO2 emissions within BRICS countries. Its novelty lies in questioning traditional assumptions about environmental accountability and emphasizing the necessity for cooperative endeavours between emerging and developed economies to effectively tackle global environmental issues.
Energy poverty and developments in finance, economic complexity and economic conditions
Authors: Ashena Malihe , Shahpari Ghazal
Published: July 2024

Purpose

Energy poverty presents substantial challenges for both developed and developing nations, with the latter experiencing more pronounced adverse effects due to issues related to the provision and equitable access of energy resources. This study aims to provide a deep understanding of how financial development, economic complexity and government expenditures can impact energy poverty.

Design/methodology/approach

This research employs generalized method of moments (GMM) estimation on panel data to investigate the economic determinants of energy poverty in 31 developing countries from 2000 to 2020. For a comprehensive analysis, the proxies for energy poverty include access to electricity, access to clean fuels and energy consumption.

Findings

The findings suggest that while financial development cannot facilitate access to clean fuels in developing countries, it contributes to an increase in energy access and consumption. Another finding is that energy poverty can be alleviated by enhancing economic complexity since economic complexity can result in increased access to electricity and increased use of clean energy sources. Furthermore, the results underscore the pivotal role of government expenditures, surpassing the influence of financial development. In other words, government expenditures have the potential to significantly improve energy poverty across all three indices.

Originality/value

This is a pioneering research that seeks to examine some economic dynamics including, financial development and economic complexity on energy poverty and provide valuable guidance for policymakers aiming to promote sustainable energy development with respect to economic dynamics.
Access to environmental information in Sweden in the context of principles of good administration
Authors: Azam Monirul
Published: July 2024

Purpose

This paper aims to examine how Sweden, as a member state of the European Union (EU), has implemented the EU Directive on Public Access to Environmental Information (AEI directive) in the context of the principles of good administration.

Design/methodology/approach

This paper adopts the EU law methodology, as this paper mainly examines the implementation of the EU AEI directive by the member states and, as an EU member state, how Sweden used procedural autonomy to implement the EU directive at the national level. The EU law methodology further guides how national laws are to be interpreted considering obligations under the EU law. This paper further applies a comparative review to determine the differences in the approaches used by the AEI directive and relevant Swedish national laws to facilitate access to environmental information.

Findings

Despite Sweden used a minimalist approach rather than maximal harmonization while implementing the AEI directive at the national level, the Swedish model of the accessibility and availability of environmental information is fully compliant with the principles of good administration. The Swedish approach has an enormous effect on promoting access to environmental information as an integral part of good governance and fundamental rights.

Research limitations/implications

It was not possible to perform a comparative review of court cases on relevant issues from different EU member states.

Practical implications

Access to environmental information could be a tool for environmental democracy and sustainable development.

Social implications

Access to environmental information could contribute to more public engagement and participation in environmental decision making and hence could make developmental projects more inclusive to meet societal objectives.

Originality/value

This study makes a unique contribution by evaluating access to environmental information in the context of the principles of good administration under EU law.
Emerging technologies and higher education libraries: a bibliometric analysis of the global literature
Authors: Mitha Sara Bibi , Omarsaib Mousin
Published: July 2024

Purpose

This paper explores emerging technologies in higher education libraries indexed in the Web of Science core collection and Scopus for the periods between 1994 and 2024 (January 18, 2024).

Design/methodology/approach

Data from Web of Science (WoS) and Scopus databases were collected and combined using RStudio software. Once this was completed using RStudio, the combined Scopus and Web of Science Excel file was uploaded into Biblioshiny, an interactive web interface. The data was then categorized to illustrate contributions from authors, journals, countries and academic institutions across the globe.

Findings

Results and findings related to publication growth trends, annual growth, core journals, impact and productivity of authors, most cited documents, collaborations, network mapping and country contributions on emerging technologies and higher education libraries are presented.

Research limitations/implications

This topic requires further exploration as academic librarians are fast becoming integrated into the teaching and learning agenda of institutions globally.

Practical implications

Higher education libraries and library schools to promote the teaching identity of academic librarians by helping them improve their pedagogical and digital skills for online teaching.

Social implications

Library and information science schools need to fast track the integration of emerging technologies into the curriculum. Higher education libraries should consider the training of staff in order to keep abreast of emerging technologies. Library management must frame their policies and strategies in order to promote the use of emerging technologies in higher education libraries.

Originality/value

The current study is novel in that it explores emerging technologies and higher education libraries using combined data from Scopus and Web of Science. The topic of emerging technologies and higher education libraries is still developing and therefore is in its infancy. The research is useful for researchers, library management and library schools in the higher education sector globally.
Predictors and mediators of work-related stress among Hong Kong police officers: a quantitative secondary survey data analysis
Authors: Cheung Yuen-kiu , Li Jessica C.M. , Zhu Shimin
Published: July 2024

Purpose

The aim of this study is to examine predictors and mediators of work-related stress among Hong Kong police officers.

Design/methodology/approach

Quantitative secondary survey data were used, based on surveys collected from 335 police officers in Hong Kong between May and June in 2020.

Findings

It was found that operational stressors were directly and positively related to work-related stress among Hong Kong police officers. The more the operational stressors, the more the work-related stress. It was also found that internal procedural justice had an indirect effect on work-related stress via work engagement among Hong Kong police officers. More internal procedural justice fostered an increased work engagement, causing less work-related stress.

Research limitations/implications

Given that the nature of secondary cross-sectional survey data, causal relationships are difficult to make.

Originality/value

Results from this study contribute to the expansion of the job demands-resources model (the JD-R model). This study used structural equation modelling (SEM) for quantitative secondary survey data analysis, providing a more accurate understanding of this topic. This study provides insights into how to formulate relevant measures to reduce work-related stress in policing occupation.
An extended TOE framework for local government technology adoption for citizen participation: insights for city digital twins for collaborative planning
Authors: Adade David , de Vries Walter Timo
Published: July 2024

Purpose

This study aims to understand and explain factors that influence how, when and under which conditions local governments adopt digital technologies for citizen collaboration. It discusses what these findings mean for city digital twin adoption.

Design/methodology/approach

This research uses the systematic literature review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) process to collect and evaluate evidence needed to answer the research questions. It uses the technology–organisation–environment (TOE) framework and proposes an additional dimension: “stakeholders” as the analytical framework.

Findings

Critical influential factors identified include the technology dimension: security and privacy; organisation dimension: top management support; environment dimension: political influence; and stakeholders’ dimension: technological experience.

Research limitations/implications

This research extends the TOE framework and comprehensively analyses those factors which relate to citizens but significantly impact local government’s decision to adopt digital tools for collaboration purposes. This research posits that in the context of local government technology adoption for collaboration, both the organisation and stakeholders’ dimensions are critical.

Social implications

This research contributes to the government-citizen discourse and provides a constructive understanding of technological transformation in collaborative planning. The findings are helpful for local governments, researchers and geospatial industries as they offer a critical understanding of digital technology adoption, particularly city digital twins, for collaborative planning.

Originality/value

This study extends the TOE framework to include aspects relating to citizens. It provides a nuanced understanding of the influential factors and intricacies of technology adoption by local governments for citizen collaboration. It also discusses relevant issues of city digital twins’ adoption by local governments for citizen participation.
Analysis of the privacy‐performance tradeoff of reference testing in Forensic Investigative Genetic Genealogy
Authors: Hu Yuchen , Wein Lawrence M.
Published: July 2024

During an investigation using Forensic Investigative Genetic Genealogy, which is a novel approach for solving violent crimes and identifying human remains, reference testing—when law enforcement requests a DNA sample from a person in a partially constructed family tree—is sometimes used when an investigation has stalled. Because the people considered for a reference test have not opted in to allow law enforcement to use their DNA profile in this way, reference testing is viewed by many as an invasion of privacy and by some as unethical. We generalize an existing mathematical optimization model of the genealogy process by incorporating the option of reference testing. Using simulated versions of 17 DNA Doe Project cases, we find that reference testing can solve cases more quickly (although many reference tests are required to substantially hasten the investigative process), but only rarely (<1%) solves cases that cannot otherwise be solved. Through a mixture of mathematical and computational analysis, we find that the most desirable people to test are at the bottom of a path descending from an ancestral couple that is most likely to be related to the target. We also characterize the rare cases where reference testing is necessary for solving the case: when there is only one descending path from an ancestral couple, which precludes the possibility of identifying an intersection (e.g., marriage) between two descendants of two different ancestral couples.
A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral‐associated Halomonas meridiana
Authors: Liu Tianlang , Gao Xinyu , Chen Ran , Tang Kaihao , Liu Ziyao , Wang Pengxia , Wang Xiaoxue
Published: July 2024

The coral reef microbiome plays a vital role in the health and resilience of reefs. Previous studies have examined phage therapy for coral pathogens and for modifying the coral reef microbiome, but defence systems against coral‐associated bacteria have received limited attention. Phage defence systems play a crucial role in helping bacteria fight phage infections. In this study, we characterized a new defence system, Hma (HmaA‐HmaB‐HmaC), in the coral‐associated Halomonas meridiana derived from the scleractinian coral Galaxea fascicularis. The Swi2/Snf2 helicase HmaA with a C‐terminal nuclease domain exhibits antiviral activity against Escherichia phage T4. Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Additionally, HmaA homologues are present in ~1000 bacterial and archaeal genomes. The high frequency of HmaA helicase in Halomonas strains indicates the widespread presence of these phage defence systems, while the insertion of defence genes in the hma region confirms the existence of a defence gene insertion hotspot. These findings offer insights into the diversity of phage defence systems in coral‐associated bacteria and these diverse defence systems can be further applied into designing probiotics with high‐phage resistance.
Fast mvSLOUCH: Multivariate Ornstein–Uhlenbeck‐based models of trait evolution on large phylogenies
Authors: Bartoszek Krzysztof , Tredgett Clarke John , Fuentes‐González Jesualdo , Mitov Venelin , Pienaar Jason , Piwczyński Marcin , Puchałka Radosław , Spalik Krzysztof , Voje Kjetil Lysne
Published: July 2024

The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models.

Taking advantage of it, we redesigned the R package mvSLOUCH.

Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein–Uhlenbeck processes.

The results of our analysis demonstrate the ability of the modelling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.
Infringement of clinical pharmacist's authority
Authors: Mawardi Fitriana , Lestari Ayuningtyas S. , Kusnanto Hari , Sasongko Elsa P. S. , Hilmanto Dany
Published: July 2024

Clinical pharmacists are healthcare practitioners who have advanced education and training in comprehensive medication management. Clinical pharmacists work with other members of the healthcare team to manage particular medications or disease states. Even though clinical pharmacists are members of healthcare teams, there are still many cases of challenge in the interprofessional relationship with other healthcare team members, especially related to drug management. Increasing interprofessional communication between physicians and clinical pharmacists within the healthcare system could enhance the role of clinical pharmacists. Earlier studies reported that physicians were comfortable with pharmacists detecting and preventing prescription errors, but were uncomfortable with them recommending drug therapy to patients. Acceptance of pharmacists’ suggestions by prescribers is a necessary component of the evaluation of clinical pharmacy services. The role of clinical pharmacists could be improved by increasing interprofessional communication between doctors and clinical pharmacists in the healthcare system.
PGD: Shared gene linking polycystic ovary syndrome and endometrial cancer, influencing proliferation and migration through glycometabolism
Authors: Chen Jia‐ming , Chen Wei‐Hong , Wang Zhi‐yi , Zhou Liang‐Yu , Lin Qiu‐ya , Huang Qiao‐yi , Zheng Ling‐tao , You Hui‐jie , Lin Shu , Shi Qi‐yang
Published: July 2024

The relationship among polycystic ovary syndrome (PCOS), endometrial cancer (EC), and glycometabolism remains unclear. We explored shared genes between PCOS and EC, using bioinformatics to unveil their pathogenic connection and influence on EC prognosis. Gene Expression Omnibus datasets GSE226146 (PCOS) and GSE196033 (EC) were used. A protein–protein interaction (PPI) network was constructed to identify the central genes. Candidate markers were screened using dataset GSE54250. Differences in marker expression were confirmed in mouse PCOS and human EC tissues using RT‐PCR and immunohistochemistry. The effect of PGD on EC proliferation and migration was explored using Ki‐67 and Transwell assays. PGD's impact on the glycometabolic pathway within carbon metabolism was assessed by quantifying glucose content and lactic acid production. R software identified 31 common genes in GSE226146 and GSE196033. Gene Ontology functional classification revealed enrichment in the “purine nucleoside triphosphate metabolism process,” with key Kyoto Encyclopedia of Genes and Genomes pathways related to “carbon metabolism.” The PPI network identified 15 hub genes. HK2, NDUFS8, PHGDH, PGD, and SMAD3 were confirmed as candidate markers. The RT‐PCR analysis validated distinct HK2 and PGD expression patterns in mouse PCOS ovarian tissue and human EC tissue, as well as in normal and EC cells. Transfection experiments with Ishikawa cells further confirmed PGD's influence on cell proliferation and migration. Suppression of PGD expression impeded glycometabolism within the carbon metabolism of EC cells, suggesting PGD as a significant PCOS risk factor impacting EC proliferation and migration through modulation of single carbon metabolism. These findings highlight PGD's pivotal role in EC onset and prognosis.
Smell loss is associated with cognitive impairment in amyotrophic lateral sclerosis patients
Authors: Huang Xin , Wu Jieying , Zhang Nan , Teng Jinghong , Yang Qiong , Zhang Yingshuang , Yin Tielun , Zhou Wen , Fan Dongsheng , Ye Shan
Published: July 2024

Background

Smell loss significantly impacts the quality of life in patients. However, there is limited research on smell loss in individuals with amyotrophic lateral sclerosis (ALS), and the correlation between smell loss and cognitive impairment is unclear. This study aimed to investigate the correlation between smell loss and cognition impairment in ALS patients.

Methods

The study included 216 ALS patients. The Edinburgh Cognitive and Behavioural ALS Screen (ECAS) and smell identification test specifically for the Chinese population (CSIT) were administered to evaluate participants' cognitive and olfactory function, respectively.

Results

After covarying for age, sex, BMI, education level, degree of hunger, dietary bias, eagerness for food, stress, smoking status, alcohol consumption, and upper respiratory tract infection (URTI) or rhinitis, CSIT scores were significantly correlated with ECAS scores (r = 0.162, p = 0.028), especially the ALS‐specific scores (r = 0.158, p = 0.031). Even after excluding patients with URTI or rhinitis, the results were similar. CSIT scores were significantly correlated with ECAS scores (r = 0.224, p = 0.011), especially the ALS‐specific scores (r = 0.205, p = 0.019).

Conclusion

In patients with ALS, smell loss is significantly correlated with cognitive impairment, particularly frontotemporal dysfunction. Cognitive dysfunction may lead to worse olfactory performance in ALS patients.
Outcomes with low dose anti‐thymocyte globulin based graft versus host disease prophylaxis after mismatched unrelated donor allogeneic hematopoietic cell transplantation
Authors: Chalchal Hafsah , Dhir Vinita , Masurekar Ashish , Atkins Harold , Bredeson Christopher , Kennah Michael , Kekre Natasha , Allan David , Vasudevan Nampoothiri Ram
Published: July 2024

Background

Anti‐thymocyte globulin (ATG) based graft versus host disease (GVHD) prophylaxis is widely used for mismatched unrelated donor allogeneic hematopoietic cell transplantation (HCT) although optimal dose remains unclear. Although recent literature suggested improved outcomes with PTCy‐based regimens when compared to ATG‐based regimens these studies used doses of ATG ≥5 mg/kg. Thus, we analyzed outcomes of HLA 9/10 MMUD allogeneic HCTs using lower‐dose ATG‐based regimens at our center.

Methods

We retrospectively analyzed outcomes of HLA 9/10 MMUD allogeneic HCTs using lower dose ATG‐based regimens for all adults undergoing allogeneic HCT at The Ottawa Hospital from 2015 to 2022. Data regarding demographics, conditioning regimen, dose of ATG, rates of GVHD, duration of remission, and survival, were collected and analyzed.

Results

Seventy‐seven (n = 77) patients (males 62.3%; median age 50 years) underwent allogeneic HCT from MMUD. Majority(81%; n = 63) received 2.5 mg/kg of rabbit ATG and remaining 18.2% (n = 14) received 4.5 mg/kg. Grade II‐IV acute GVHD occurred in 24.7% (n = 19) while any chronic GVHD occurred in 32.5% (n = 25) patients. After a median follow‐up of 21 months, relapse occurred in 28.6% of patients. Two‐year OS, GRFS, CIR, and NRM were 60.6%, 45.3%, 16.9%, and 18.2% respectively. Dose of ATG (2.5 mg/kg vs. 4.5 mg/kg) was not associated with outcomes in either univariate or multivariate analyses.

Conclusions

When compared to published studies using ATG doses ≥5 mg/kg, GVHD prophylaxis using lower dose ATG may potentially lead to improved outcomes in patients undergoing MMUD allogeneic HCT. Further studies are needed to directly compare lower dose ATG to PTCy‐based regimens to determine ideal GVHD prophylaxis for these patients.
Treatment response amplitude and timing in chronic inflammatory demyelinating polyneuropathy with routine care: Study of a UK cohort
Authors: Rajabally Yusuf A. , Min Young Gi , Nazeer Kabir K. , Englezou Christina
Published: July 2024

Background and purpose

The amplitude, timing, and determinants of improvement with available treatments are uncertain in chronic inflammatory demyelinating polyneuropathy (CIDP). Our primary objective was to quantify categorized outcomes with routine care.

Methods

We retrospectively studied treatment response within 36 months from initiation in 112 consecutive subjects with CIDP. Response was classified into a proposed new "CIDP treatment‐response category" (CT‐RC), based on achieved endpoints. Determinants of the CT‐RC, of timing of maximum improvement, and of treatment discontinuation were ascertained.

Results

The CT‐RC demonstrated high concurrent validity with current outcome measures. Thirty‐six subjects (32.1%) achieved a “complete response,” 37 (33%) a “good partial response,” 10 (8.9%) a “moderate partial response,” and 15 (13.4%) a “poor partial response.” Fourteen subjects (12.5%) were “nonresponsive.” The CT‐RC was independently predicted only by age. Mean time to maximum improvement was 12.1 months (range = 1–36) and was not associated with any pretreatment covariate. Treatment discontinuation occurred in 24 of 62 (38.2%) partial responders and was only associated with shorter pretreatment disease duration. Nonresponders were older and received a similar number of treatments compared to responders.

Conclusions

CT‐RC classification indicates persistent disability in >60% of treatment responders in CIDP. Timing of maximum improvement is variable, frequently delayed, and unpredictable. Treatment withdrawal without deterioration is achievable in approximately 40% of subjects and may be more likely with prompt treatment. Treatment withdrawal in partial responders and limited escalation in nonresponders suggest implication of physician‐ and patient‐related factors in suboptimal response. More effective treatments/treatment methods and better understanding of other factors influencing response are needed in CIDP.
An EEMD‐LSTM, SVR, and BP decomposition ensemble model for steel future prices forecasting
Authors: Wu Sen , Wang Wei , Song Yanan , Liu Shuaiqi
Published: July 2024

The forecasting of steel futures prices is important for the steel futures market, even for the steel industry. We propose a decomposition ensemble model that incorporates the Ensemble Empirical Mode Decomposition (EEMD), Long Short‐Term Memory (LSTM), Support Vector Regression (SVR), and Back Propagation (BP) neural network to forecast steel futures prices. The forecasting procedures are as follows: (1) The price data are initially decomposed into several relatively independent Intrinsic Mode Functions (IMFs) and a residue using EEMD. (2) The IMFs are then reconstructed as components representing short‐term, medium‐term, and long‐term frequencies via fine‐to‐coarse. (3) LSTM, SVR, and BP neural network are utilized to forecast the short‐term, medium‐term, and long‐term reconstructed components, respectively. (4) The prediction results for each component are simply added to the final prediction results. The accuracy of the proposed model is compared with several benchmark models by experiments and evaluated by some prediction evaluation indexes. The experimental results show that our model outperforms other models in terms of forecast accuracy, confirming its strong predictive capabilities. This study provides some suggestions for investment and decision making by participants in the steel futures market. It may promote the smooth operation of the steel futures market and shed some light on the operation of the steel industry.
Functional and structural neuroretinal disorders in HIV Controllers. Prospective cohort study
Authors: Ruiz‐Bilbao Susana , Videla Sebastian , Pascual Ester , Soler Montse , Jordi Puig , Grizolli Stefano , Negredo Eugènia , Castellvi‐Manent Jordi
Published: July 2024

Objective

To estimate the prevalence and cumulative incidence of neuro‐retinal‐disorders (NRD) in HIV‐controllers.

Design

Prospective, single‐centre, cohort study of people living with HIV (PLWH): elite‐controllers, long‐term‐non‐progressors and early diagnosed.

Methods

The study compared “HIV‐controllers” (including elite‐controllers and long‐term‐non‐progressors), who were not on antiretroviral therapy (ART), and “HIV‐treatment” (HIV‐infected subjects with a recent diagnosis and on ART). A matched cohort of “non‐HIV subjects” was created. NRD was defined as at least one altered (not normal) ophthalmological parameter (functional or structural). Functional (visual acuity, contrast sensitivity, chromatic vision, visual field) and structural parameters (ganglion cells, macular nerve fibre layer, peripapillary nerve fibre layers, vascular calibre) as well as quality of life (Medical Outcomes Study‐HIV Short Form‐30) were assessed.

Results

Between March 2012 and November 2015, the study included all HIV‐controllers (16 elite‐controllers, 1 long‐term‐non‐progressor), 11 HIV‐treatment and 16 non‐HIV. Prevalence of NRD at baseline was 88.2% (15/17, 95% CI: 65.7%–96.7%), 90.9% (10/11, 95% CI: 62.3%–98.4%) and 56.3% (9/16, 95% CI: 33.2%–76.9%), respectively. Cumulative incidence at 3 years was 50% (1/2), 100% (1/1) and 33.3% (2/6), respectively. None of the participants manifested ocular clinical symptoms. Three years later, prevalence of NRD was 92.3% (12/13, 95% CI: 66.7%–98.6%), 75% (6/8, 95% CI: 40.9%–92.9%) and 50.0% (7/14, 95% CI: 26.8%–73.2%), respectively. Contrast sensitivity and structural parameters were globally the most affected among PLWH. Quality of life (total score) [median (interquartile range)] at baseline and 3 years was 82 (71–89) and 74 (63.5–79.25) in HIV‐controllers and 80 (73–88) and 88 (83–92) in HIV‐treatment.

Conclusions

HIV‐controllers and those individuals on ART presented a higher percentage of NRD than non‐HIV. Our results suggest that NRD could be a biomarker of ocular aging among PLWH.