bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deformed wing virus genotypes A and B do not elicit immunologically different responses in naïve honey bee hosts
Authors: Norton Amanda M , Buchmann Gabriele , Ashe Alyson , Watson Owen T , Beekman Madeleine , Remnant Emily J 
Published: August 2023

ABSTRACTDeformed wing virus(DWV), in association withVarroa destructor, is currently the leading factor associated with global honey bee deaths. With the exception of Australia, the virus and mite have a near global distribution, making it difficult to separate the effect of one from the other. Over time, the prevalence of the two main DWV genotypes (DWV-A and DWV-B) has changed, leading to the suggestion that the two strains elicit a different immune response by the host, the western honey beeApis mellifera. Here we use a honey bee population naïve to both the mite and the virus to investigate if honey bees show a different immunological response to DWV genotypes. We examined the expression of 19 immune genes by RT-qPCR and comprehensively analysed the small RNA response in honey bees after experimental injection with DWV-A and DWV-B. We found no evidence to indicate that DWV-A and DWV-B elicit a different immune response in honey bees. We found that RNA interference genes are up-regulated during DWV infection and that the small interfering RNA (siRNA) response is proportional to viral loads, yet does not inhibit the virus from accumulating to high loads. We also found that the siRNA response towards DWV was weaker than the response to another honey bee pathogen,Black queen cell virus. This suggests that DWV is comparatively better at evading antiviral host defences. There was no evidence for the production of virus-derived PIWI-RNAs in response to DWV infection. In contrast to previous studies, and in the absence ofV.destructor, we found no evidence that DWV has an immunosuppressive effect in honey bees. Overall, our results advance our understanding of the immunological effect DWV elicits in honey bees.
Investigation of the reasons for delayed presentation in proliferative diabetic retinopathy patients
Authors: Zhao Meng , Chandra Aman , Liu Lin , Zhang Lin , Xu Jun , Li Jipeng 
Published: August 2023

AbstractAimTo investigate reasons for delayed presentation in patients with proliferative diabetic retinopathy (PDR).MethodsA questionnaire was designed to investigate consecutive PDR patients with delayed presentation who visited our center between January 2021 and December 2021. The questionnaire was divided into four sections: knowledge regarding diabetic retinopathy (DR), attitude toward DR treatment, difficulties adhering to follow-up plans, and medical care. The systemic disease status and severity of DR were recorded. Logistic analysis was undertaken to investigate DR treatment refusal and delay factors.ResultsA total of 157 patients were included in this study, with an average age of 50.0 ± 11.6 years. The overall glycemic control was poor, with a median glycated hemoglobin level (HbA1c) of 7.8% (IQR 2.5%). Among the 157 eyes, most required vitrectomy intervention (144, 91.7%); 17 developed neovascular glaucoma (NVG), while only 13 required additional photocoagulation. Among the 36 patients with undiagnosed DM, the reason for delayed DR presentation was a lack of awareness of DM status among these patients (36 cases, 100.0%). Most of the patients with a known history of DM exhibited inadequate DR knowledge (29, 24.0%), believed their good visual acuity did not require DR screening (98, 81.0%), and had poorly controlled diabetes (113, 93.3%). Factors related to refusing DR treatment were patients with an inability to receive regular diabetes treatment in internal medicine clinics (OR 6.78, 95% CI 1.73-26.59, p=0.006), patients who could not tolerate discomfort during ophthalmic examination and treatment (OR 15.15, 95% CI 2.70-83.33, p<0.001), and patients who did not have any retinal abnormalities detected and were not informed about the need for regular screening (OR 2.05, 95% CI 1.36-3.09, p<0.001).ConclusionsThis study investigated the factors contributing to delayed presentation among patients with PDR. Many individuals in the delayed population were found to have undiagnosed DM. Among patients already aware of their DM status, reasons for delay included insufficient knowledge about DR, negative attitudes toward screening and treatment, and difficulties seeking medical care in real-life situations.Furthermore, there needed to be more improvements in the detection, treatment, and follow-up of DR by internal medicine practitioners and ophthalmologists.
AutoHiC: a deep-learning method for automatic and accurate chromosome-level genome assembly
Authors: Jiang Zijie , Peng Zhixiang , Luo Yongjiang , Bie Lingzi , Wang Yi 
Published: August 2023

AbstractAn accurate genome at the chromosome level is the key to unraveling the mysteries of gene function and unlocking the mechanisms of disease. Irrespective of the sequencing methodology adopted, Hi-C aided scaffolding serves as a principal avenue for generating genome assemblies at the chromosomal level. However, the results of such scaffolding are often flawed and require extensive manual refinement. In this paper, we introduce AutoHiC, an innovative deep learning-based tool designed to identify and rectify genome assembly errors. Diverging from conventional approaches, AutoHiC harnesses the power of high-dimensional Hi-C data to enhance genome continuity and accuracy through a fully automated workflow and iterative error correction mechanism. AutoHiC was trained on Hi-C data from more than 300 species (approximately five hundred thousand interaction maps) in DNA Zoo and NCBI. Its confusion matrix results show that the average error detection accuracy is over 90%, and the area under the precision-recall curve is close to 1, making it a powerful error detection capability. The benchmarking results demonstrate AutoHiC’s ability to substantially enhance genome continuity and significantly reduce error rates, providing a more reliable foundation for genomics research. Furthermore, AutoHiC generates comprehensive result reports, offering users insights into the assembly process and outcomes. In summary, AutoHiC represents a breakthrough in automated error detection and correction for genome assembly, effectively promoting more accurate and comprehensive genome assemblies.
A multifaceted suite of metrics for comparative myoelectric prosthesis controller research
Authors: Williams Heather E. , Shehata Ahmed W. , Cheng Kodi Y. , Hebert Jacqueline S. , Pilarski Patrick M. 
Published: August 2023

AbstractUpper limb robotic (myoelectric) prostheses are technologically advanced, but challenging to use. In response, substantial research is being done to develop user-specific prosthesis controllers that can predict a person’s intended movements. Most studies that test and compare new controllers rely on simple assessment measures such as task scores (e.g., number of objects moved across a barrier) or duration-based measures (e.g., overall task completion time). These assessment measures, however, fail to capture valuable details about: the quality of device arm movements; whether these movements match users’ intentions; the timing of specific wrist and hand control functions; and users’ opinions regarding overall device reliability and controller training requirements. In this work, we present a comprehensive and novel suite of myoelectric prosthesis control evaluation metrics that better facilitates analysis of device movement details—spanning measures of task performance, control characteristics, and user experience. As a case example of their use and research viability, we applied these metrics in real-time control experimentation. Here, eight participants without upper limb impairment compared device control offered by a deep learning-based controller (recurrent convolutional neural network-based classification with transfer learning, or RCNN-TL) to that of a commonly used controller (linear discriminant analysis, or LDA). The participants wore a simulated prosthesis and performed complex functional tasks across multiple limb positions. Analysis resulting from our suite of metrics identified 16 instances of a user-facing problem known as the “limb position effect”. We determined that RCNN-TL performed the same as or significantly better than LDA in four such problem instances. We also confirmed that transfer learning can minimize user training burden. Overall, this study contributes a multifaceted new suite of control evaluation metrics, along with a guide to their application, for use in research and testing of myoelectric controllers today, and potentially for use in broader rehabilitation technologies of the future.
MAGinator enables strain-level quantification ofde novoMAGs
Authors: Zachariasen Trine , Russel Jakob , Petersen Charisse , Vestergaard Gisle A. , Shah Shiraz , Turvey Stuart E. , Sørensen Søren J. , Lund Ole , Stokholm Jakob , Brejnrod Asker , Thorsen Jonathan 
Published: August 2023

AbstractMotivationMetagenomic sequencing has provided great advantages in the characterization of microbiomes, but currently available analysis tools lack the ability to combine strain-level taxonomic resolution and abundance estimation with functional profiling of assembled genomes. In order to define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes.ResultsHere, we present MAGinator, a freely available tool, tailored for the profiling of shotgun metagenomics datasets. MAGinator providesde novoidentification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes as well as genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences within subspecies MAGs.Availability and implementationMAGinator is available as a Python module athttps://github.com/Russel88/MAGinatorContactTrine Zachariasen,trine_zachariasen@hotmail.com
Cool temperature acclimation in toxigenicMicrocystis aeruginosaPCC 7806 and its non-toxigenic mutant
Authors: Stark Gwendolyn F. , Martin Robbie M. , Smith Laura E. , Wei Bofan , Hellweger Ferdi L. , Bullerjahn George S. , McKay R. Michael L. , Boyer Gregory L. , Wilhelm Steven W. 
Published: August 2023

AbstractForMicrocystis aeruginosaPCC 7806, temperature decreases from 26° C to 19° C double the microcystin quota per cell during growth in continuous culture. Here we tested whether this increase in microcystin providedM. aeruginosaPCC 7806 with a fitness advantage during colder-temperature growth by comparing cell concentration, cellular physiology, and the transcriptomics-inferred metabolism to a non-toxigenic mutant strainM. aeruginosaPCC 7806 ΔmcyB. Photo-physiological data combined with transcriptomic data revealed metabolic changes in the mutant strain during growth at 19° C, which included increased electron sinks and non-photochemical quenching. Increased gene expression was observed for a glutathione-dependent peroxiredoxin during cold treatment, suggesting compensatory mechanisms to defend against reactive oxygen species are employed in the absence of microcystin in the mutant. Our observations highlight the potential selective advantages of a longer-term defensive strategy in management of oxidative stress (i.e.,making microcystin)vsthe shorter-term proactive strategy of producing cellular components to actively dissipate or degrade oxidative stress agents.ImportanceThrough comparisons of a microcystin-producing wildtype strainM. aeruginosaPCC 7806 and a non microcystin-producing mutant,M. aeruginosaPCC 7806ΔmcyB, our observations highlight defensive (microcystin production)vsactive (production of degradation enzymes and increased electron sinks) strategies for dealing with cold-temperature induced oxidative stress as well as associated physiological changes. This work increases our understanding of microcystin’s intracellular function, and the role it may play in bloom ecology. In combination with other studies, this work begins to experimentally establish a mechanistic foundation to better understand cold-to-warm seasonal transitions from toxigenic to non-toxigenic strains frequently observedin situ.
β1 integrins regulate cellular behaviors and cardiomyocyte organization during ventricular wall formation
Authors: Miao Lianjie , Castillo Micah , Lu Yangyang , Xiao Yongqi , Liu Yu , Burns Alan R , Kumar Ashok , Gunaratne Preethi , Michael DiPersio C. , Wu Mingfu 
Published: August 2023

AbstractAimsThe mechanisms regulating the cellular behavior and cardiomyocyte organization during ventricular wall morphogenesis are poorly understood. Cardiomyocytes are surrounded by extracellular matrix (ECM) and interact with ECM via integrins. This study aims to determine whether and how β1 integrins regulate cardiomyocyte behavior and organization during ventricular wall morphogenesis in the mouse.Methods and ResultsWe applied mRNA deep sequencing and immunostaining to determine the expression repertoires of α/β integrins and their ligands in the embryonic heart. Integrin β1 subunit (β1) and some of its ECM ligands are asymmetrically distributed and enriched in the luminal side of cardiomyocytes, while fibronectin surrounds cardiomyocytes, creating a network for them.Itgb1, which encodes the β1 integrin subunit, was deleted viaNkx2.5Cre/+to generate myocardial-specificItgb1knockout (B1KO) mice. B1KO hearts display an absence of trabecular zone but a thicker compact zone. The abundances of hyaluronic acid and versican are not significantly different. Instead, fibronectin, a ligand of β1, was absent in B1KO. We examined cellular behaviors and organization via various tools. B1KO cardiomyocytes display a random cellular orientation and fail to undergo perpendicular cell division, be organized properly, and establish the proper tissue architecture to form trabeculae. The reduction of Notch1 activation was not the cause of the abnormal cellular organization in B1KO hearts. Mosaic clonal lineage tracing shows thatItgb1regulates cardiomyocyte transmural migration and proliferation autonomously.Conclusionsβ1 is asymmetrically localized in the cardiomyocytes, and its ECM ligands are enriched in the luminal side of the myocardium and surrounding cardiomyocytes. β1 integrins are required for cardiomyocytes to attach to the ECM network. This engagement provides structural support for cardiomyocytes to maintain shape, undergo perpendicular division, and establish cellular organization. Deletion ofItgb1, leading to ablation of β1 integrins, causes the dissociation of cardiomyocytes from the ECM network and failure to establish tissue architecture to form trabeculae.
NRF2 Dysregulation in Mice Leads to Inadequate Beta-Cell Mass Expansion during Pregnancy and Gestational Diabetes
Authors: Baumel-Alterzon Sharon , Tse Isabelle , Heidery Fatema , Garcia-Ocaña Adolfo , Scott Donald K. 
Published: August 2023

ABSTRACTThe late stages of the mammalian pregnancy are accompanied with increased insulin resistance due to the increased glucose demand of the growing fetus. Therefore, as a compensatory response to maintain the maternal normal blood glucose levels, maternal beta-cell mass expands leading to increased insulin release. Defects in beta-cell adaptive expansion during pregnancy can lead to gestational diabetes mellitus (GDM). Although the exact mechanisms that promote GDM are poorly understood, GDM strongly associates with impaired beta-cell proliferation and with increased levels of reactive oxygen species (ROS). Here, we show that NRF2 levels are upregulated in mouse beta-cells at gestation day 15 (GD15) concomitant with increased beta-cell proliferation. Importantly, mice with tamoxifen-induced beta-cell-specific NRF2 deletion display inhibition of beta-cell proliferation, increased beta-cell oxidative stress and elevated levels of beta-cell death at GD15. This results in attenuated beta-cell mass expansion and disturbed glucose homeostasis towards the end of pregnancy. Collectively, these results highlight the importance of NRF2-oxidative stress regulation in beta-cell mass adaptation to pregnancy and suggest NRF2 as a potential therapeutic target for treating GDM.
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Authors: Bantele Susanne , Mordini Irene , Biran Alva , Alcaraz Nicolas , Wenger Alice , Krietenstein Nils , Groth Anja , Lukas Jiri 
Published: August 2023

AbstractUpon DNA breakage, a genomic locus undergoes alterations in 3-D chromatin architecture to facilitate signaling and repair. While cells possess mechanisms to repair damaged DNA, it is unknown whether the surrounding chromatin is restored to its naïve state. We show that a single DNA double-strand break (DSB) within a topologically-associated domain (TAD) harboring conformation-sensitive genes causes lasting chromatin alterations, which persist after completion of DNA repair and feature structural changes, chromatin compaction and loss of local RNA species. Unexpectedly, these newly-acquired features of post-repair chromatin are transmitted to daughter cells and manifest as heritable impairments of gene expression. These findings uncover a hitherto concealed dimension of DNA breakage, which we term post-repair chromatin fatigue, and which confers heritable impairment of gene function beyond DNA repair.
A bibliometric analysis of library automation software research from 2001-2022: evidence from the Web of Science (WoS)
Authors: Naveed Muhammad , Ali Nusrat , Khan Shakeel Ahmad , Shahzad Khurram 
Published: August 2023

Purpose
The purpose of this study is to conduct a bibliometric analysis to discover the published information on the subject of “Library Automation Software.”

Design/methodology/approach
This study is based on bibliometric research to analyze the growth of literature on the subject area “Library Automation Software.” The data were retrieved from the leading database Web of Science to analyze the scholarly publications on the topic during 2001–2022. To analyze the bibliometric data on the subject, the VOSviewer, Biblioshiny and MS Excel software were used.

Findings
Results manifest that the topic of “Library Management Systems” has been greatly used by several authors as a title to publish their research work. The USA emerged as the most productive country. The most used keywords to retrieve literature on the topic were “Library Automation,” “Library Management Systems,” “KOHA,” “Integrated Library Systems” and “Open Source Software.”

Originality/value
To the best of the authors’ knowledge, this is the first bibliometric study in Pakistan that has been conducted to measure the productivity of literature at the international level on library automation.
Safeguarding human rights to health: a systematic review of supply chain impediments to safe medicines in developing nations
Authors: Loomba Arvinder P.S. 
Published: August 2023

Purpose
A key feature of human rights in health is access to safe, effective and affordable medicines. Pharmacovigilance is advocated for monitoring intended/unintended effects of medicines to assure their safety. The purpose of this paper is to synthesize knowledge about supply chain impediments to safe medicines in developing nations and contribute to future development of research in this field.

Design/methodology/approach
This paper conducts a structured literature review based on Preferred Reporting Items for the Systematic Reviews and Meta-Analyses guidelines. It aims at profiling supply chain impediments to safe medicines in developing nations by reviewing 46 recent pharmacovigilance-specific papers published between 2005 and 2020.

Findings
Analysis of reviewed articles identified criticality of supply chain impediments that affect constituents across pharmaceutical in developing nations, which still struggle to maintain robust national pharmacovigilance systems due to lack of awareness, policy and practices.

Research limitations/implications
Research results can be applied by pharmaceutical industry decision-makers and drug safety professionals in developing nations. Because the review is qualitative in nature, its implication ought to be tested after actual implementation.

Practical implications
This review can help identify underinvestigated impediments and methods to aid in developing new pharmacovigilance knowledge areas in developing nation context.

Social implications
The review uncovers gaps in global health equity dialogue in developing nations. It also recognizes that macrolevel supply chain impediments exist due to unfair disease burden and health inequities in developing nations.

Originality/value
The paper examines supply chain impediments to safe medicines in developing nations with insights for future pharmacovigilance research. Identifying and classifying supply chain impediments through this review is the first step toward creating effective interventions for these impediments to safe medicines.
Thermo-elastohydrodynamic lubrication performance study of step seal under transient condition
Authors: Wei Jian , Sun XiaoYue , Tian Jing , Liu CaiHong 
Published: August 2023

Purpose
This paper aims to study the impact of transient velocity changes on sealing performance during reciprocating sealing processes.

Design/methodology/approach
Establish a model of transient mixed lubrication, solve the transient Reynolds equation, consider the effect of temperature rise at the seal interfaces, and determine the behavior of the seal interfaces, such as film thickness and fluid pressure. Evaluation with friction and leakage rate, calculate the variation of sealing performance with reciprocating velocity under different working conditions, and verify it through bench experiments.

Findings
Within a reciprocating stroke, the frictional force decreases with increasing velocity, and the frictional force of the outstroke is greater than that of the instroke; at the time of the stroke transition, the fluid pressure is smallest and the rough peak contact pressure is greatest. At present, the dynamic pressure effect of fluids is the largest, and the friction force also increases, which increases the risk of material wear and failure. Friction and leakage increase with increasing pressure and root mean square roughness. As temperature increases, friction increases and leakage decreases. In studying the performance variations of seal components through a reciprocating sealing experiment, it was found that the friction force decreases with increasing velocity, which is consistent with the calculated results and more similar to the calculated results considering the temperature rise.

Originality/value
This study provides a reference for the study of transient sealing performance.