bluuebunny/crossref_metadata_2025 huggingface dataset:
Sexy fingers: Pheromones in the glands of male dendrobatid frogs
Authors: Almeida Diana Abondano , Twomey Evan , Vargas‐Salinas Fernando , Meyer Carmen , Schulte Lisa M.
Published: July 2024

Many animals exchange chemicals during courtship and mating. In some amphibians, sexual chemical communication is mediated by pheromones produced in male breeding glands that are transferred to the female's nostrils during mating. This has been mostly studied in salamanders, despite frogs having similar glands and courtship behaviours suggestive of chemical communication. In Neotropical poison frogs (Dendrobatidae and Aromobatidae), males of many species develop breeding glands in their fingers, causing certain fingers to visibly swell. Many also engage in cephalic amplexus, whereby the male's swollen fingers are placed in close contact with the female's nares during courtship. Here, we investigate the possible roles of swollen fingers in pheromone production using whole‐transcriptome sequencing (RNAseq). We examined differential gene expression in the swollen versus non‐swollen fingers and toes of two dendrobatid species, Leucostethus brachistriatus and Epipedobates anthonyi, both of which have specialised mucous glands in finger IV, the latter of which has cephalic amplexus. The overwhelming pattern of gene expression in both species was strong upregulation of sodefrin precursor‐like factors (SPFs) in swollen fingers, a well‐known pheromone system in salamanders. The differentially expressed SPF transcripts in each species were very high (>40), suggesting a high abundance of putative protein pheromones in both species. Overall, the high expression of SPFs in the swollen fingers in both species, combined with cephalic amplexus, supports the hypothesis that these traits, widespread across members of the subfamilies Colostethinae and Hyloxalinae (ca. 141 species), are involved in chemical signalling during courtship.
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)
Authors: Schneider Katharina , Steward Rachel A. , Celorio‐Mancera Maria de la Paz , Janz Niklas , Moberg Dick , Wheat Christopher W. , Nylin Sören
Published: July 2024

Generalist plant‐feeding insects are characterised by a broad host repertoire that can comprise several families or even different orders of plants. The genetic and physiological mechanisms underlying the use of such a wide host range are still not fully understood. Earlier studies indicate that the consumption of different host plants is associated with host‐specific gene expression profiles. It remained, however, unclear if and how larvae can alter these profiles in the case of a changing host environment. Using the polyphagous comma butterfly (Polygonia c‐album) we show that larvae can adjust their transcriptional profiles in response to a new host plant. The switch to some of the host plants, however, resulted in a larger transcriptional response and, thus, seems to be more challenging. At a physiological level, no correspondence for these patterns could be found in larval performance. This suggests that a high transcriptional but also phenotypic flexibility are essential for the use of a broad and diverse host range. We furthermore propose that host switch tests in the laboratory followed by transcriptomic investigations can be a valuable tool to examine not only plasticity in host use but also subtle and/or transient trade‐offs in the evolution of host plant repertoires.
Why Black Grassroots Museums Matter
Authors: McClaurin Irma
Published: July 2024

Traditional Museums have dominated the American landscape, but there exist hundreds of “Black Grassroots Museum” that are preserved by what African Diaspora museum specialist, Deborah Johnson‐Simon, calls “kulture keepers;” these are everyday folk who dedicate themselves to protect and preserve the artifacts and stories of Black survival, ingenuity, resistance, and resiliency inside their homes, churches, or in community spaces, lest we forget.
Transformative justice to support truth and reconciliation within nurse–midwifery education
Authors: Altman Molly R. , Sherley Clare , Lazarus Judy , Kantrowitz‐Gordon Ira , Ward Teresa M.
Published: July 2024

Nursing education holds a history framed in white supremacy and whiteness. Efforts to employ antiracist strategies have been hindered, largely due to an inability for faculty to acknowledge and hold accountability for racialized harms that occur within nursing educational structures. A nurse–midwifery program in the Pacific Northwest United States uncovered harm that impacted students and identified a need to respond and hold accountability. Guided by the framework of Transformative Justice, a truth and reconciliation process was implemented as a first step to better address racism within nursing and nurse–midwifery education. This paper describes the process to support other institutions in their work to address harms within nursing education.
Quiet quitting: Obedience a minima as a form of nursing resistance
Authors: Domingue Jean‐Laurent , Lauzier Kim , Foth Thomas
Published: July 2024

In this article, we provide a philosophical and ethical reflection about quiet quitting as a tool of political resistance for nurses. Quiet quitting is a trend that gained traction on TikTok in July 2022 and emerged as a method of resistance among employees facing increasing demands from their workplaces at the detriment of their personal lives. It is characterised by employees refraining from exceeding the basic requirements outlined in their job descriptions. To understand why quiet quitting can be a tool of resistance useful for nurses, we first draw on Frédéric Gros' concept of ‘surplus obedience’ and Michael Lipsky's notion of ‘routines and simplification strategies’ to highlight the ethical implications associated with nurses engaging in and sustaining harmful systems, such as the neoliberal healthcare system. Leaning again on Gros, we then propose that ‘obedience a minima’, a concept akin to quiet quitting, can serve as a method of ethical nursing resistance. After describing what the concept entails, we provide a discussion emphasising the potential of obedience a minima as a one method, among many, that can be leveraged by nurses to challenge and resist a system that prioritises financial considerations over patient wellbeing. The article concludes by reflecting on the ethical nature of resistance in the context of nursing, that is the act of obeying oneself and refraining from participating in systems that are detrimental to the lives of Others.
Exploring suitability to electrical storm ablation in patients in waiting list for heart transplantation: A single center experience
Authors: Gigli Lorenzo , Preda Alberto , Varrenti Marisa , Baroni Matteo , Vargiu Sara , Guarracini Fabrizio , Ammirati Enrico , Mazzone Patrizio
Published: July 2024

Electrical storm (ES) is among the most fearsome events in patients in waiting list for heart transplantation (HT) and catheter ablation (CA) demonstrated to be effective in reduce the arrhythmic burden. However, selection criteria for CA suitability in this specific population have never been addressed before. We retrospectively enrolled 36 patients (mean age 51 ± 8 years; 83% men) waiting HT referred to our department for ES resistant to antiarrhythmic drugs and percutaneous stellate ganglion blockade. Twenty patients were judged suitable for VT ablation according to specific criteria including absence of increased arrhythmic burden secondary to volume overload and hemodynamic decompensation; expected CA outcome favorable due to etiology of the cardiomyopathy, no need for coronary revascularization and technical feasibility of the procedure. The pre‐emptive use of mechanical circulatory supports (MCS) were discussed integrating the PAINESD score with additional clinical and hemodynamic parameters. Acute procedural success was accounted in 85% of cases with only two major complications. The CA group reported lower length of in‐hospital stay after CA suitability evaluation (56 ± 17 vs. 131 ± 64 days, p = .004). Furthermore, at a mean follow‐up of 703 ± 145 days, this group showed reduction of ventricular arrhythmia (VA) recurrence leading to implantable cardioverter defibrillator shock (4 vs. 8, p = .051) and underwent HT with a lower level of urgency (0 vs. 6 patients needed for UNOS1 status upgrade). Respectively, one patient of the CA group and two patients of the conservative group died (p = .839). At the end of follow‐up, eight patients underwent heart transplantation (p = .964) while four patients underwent Left Ventricular Assist device (LVAD) implantation (p = .440). This pilot study should be a proof for further studies exploring CA of VAs as a possible bridge therapy to HT.
Acute Kidney Injury Requiring Dialysis After Pediatric Heart Transplant
Authors: Lipman Amy R. , Lytrivi Irene D. , Fernandez Hilda E. , Lynch Aine M. , Yu Miko E. , Stevens Jacob S. , Mohan Sumit , Husain Syed Ali
Published: July 2024

Background

Acute kidney injury (AKI) is a common complication of pediatric heart transplant, with a subset of patients developing severe AKI requiring dialysis (AKI‐D). We aimed to identify the epidemiology, risk factors, and outcomes of postoperative AKI‐D in pediatric heart transplant recipients.

Methods

We retrospectively identified all pediatric first‐time, single‐organ heart transplants at our institution from 2014 to 2022. Postoperative AKI was defined as AKI within 2 weeks of transplant. Unadjusted and adjusted logistic regression were used to identify characteristics associated with AKI‐D, and unadjusted time‐to‐event analyses were used to determine the association between AKI‐D and survival free of kidney failure.

Results

Among 177 patients included, 116 (66%) developed postoperative AKI of any stage, including 13 (7%) who developed AKI‐D with median time from transplant to dialysis initiation of 6 days (IQR 3–13). In adjusted models, increased cardiopulmonary bypass time (OR 1.19, 95% CI 1.04–1.37, per 15 min increase in bypass time) and higher weight at transplant were associated with higher odds of AKI‐D, whereas patient demographics and pretransplant kidney function were not associated with AKI‐D. AKI‐D was associated with greater mortality during initial hospitalization (46% vs. 1%, p < 0.001) and a lower rate of survival free of kidney failure.

Conclusions

The incidence of AKI‐D after pediatric heart transplant was 7%, with extended cardiopulmonary bypass time associated with postoperative AKI‐D even in adjusted models. Further research is needed to improve the prediction and management of AKI‐D in this population.
A causal modeler's guide to double effect reasoning
Authors: Rothfus Gerard J.
Published: July 2024

Trolley problems and like cases are often thought to show the inadequacy of purely consequentialist moral theories. In particular, they are often taken to reveal that consequentialists unduly neglect the moral significance of the causal structure of decision problems. To precisify such critiques and one sort of deontological morality they motivate, I develop a formal modeling framework within which trolley problems can be represented as suitably supplemented structural causal models and various consequentialist and double effect‐inspired moral theories can be viewed as disagreeing over the inputs of a common decision rule.
Does leadership promote a cleaner climate?
Authors: Mideksa Torben
Published: July 2024

The Paris Agreement encourages developed countries to lead in reducing emissions. Using a model of national emissions, I examine whether leadership improves global welfare. The results suggest that leadership reduces global emissions when the leader's abatement generates cost‐reducing spillover effects or conveys private information about abatement costs. With spillover effects, the leader abates more to incentivize a greater reduction of emissions by followers. Under private information, the leader abates more to signal the abatement cost. If it has to choose between transparency and no transparency, the leader commits to transparency despite this being inefficient. Besides, I find sequential abatement stable against unilateral deviation.
Omniphobic PTFE based Hollow Fiber Membrane with ZnO Nanoparticles Deposition via Universal Spray Technique
Authors: Wan Zulkifli W. M. Z. , Othman M. H. D. , Pauzan M. A. B. , Hisam N. A. S. M. , Jaffar F. H.
Published: July 2024

This investigation aimed to enhance the hydrophobicity of a polytetrafluoroethylene (PTFE) hollow fiber membrane, transforming it into an omniphobic surface. This was achieved by coating the membrane with a mixture of zinc oxide nanoparticles (ZnO-NPs) and polyvinylidene fluoride-cohexafluoropropylene (PVDF-HFP) using the universal spray technique. The membrane's morphology and performance were evaluated based on the number of spray cycles, which influenced the coating thickness on the membrane surface. The spraying process was varied up to 4 cycles to determine the membrane with the most effective deposition of ZnO NPs in terms of water contact angle and liquid entry pressure (LEPw). Results indicated that the membrane spray-coated up to 4 cycles, denoted as PTFE-4, exhibited a rough hierarchical re-entrant morphology, imparting omniphobic characteristics. The optimized membrane demonstrated a high water contact angle of 170° and a liquid entry pressure of 2.6 bar. Fourier-transform infrared (FTIR) and energy dispersive analysis of X-rays (EDX) confirmed the successful chemical integration of ZnO NPs onto the commercial membrane. This research holds significance for the future of membrane distillation in treating wastewater containing low surface tension pollutants.
Book Review Carbon Membrane Technology Fundamentals and Applications
Authors: Lai Li Sze
Published: July 2024

Carbon membrane has shown great advantages with high separation performance, especially under high temperature and pressure condition with its strong mechanical and chemical stabilities, as well as well-defined pores structures [1]. An overview of the fundamental aspect and industrial application of carbon membrane is thus important to demonstrate the potential development of the membrane. This recent published book summarized both aspects in two parts. For the first part, the formation, state-of-art of the performance, characterization and transport mechanism of carbon membranes were discussed. For the second part, the application of carbon membrane in biogas upgrading, natural gas sweetening, hydrogen purification, micro-, ultra- or nanofiltration and other applications were reported. Subsequently, future perspectives of the carbon membrane were also analysed. In short, the book offers a thorough discussion on the fundamentals and applications of carbon membrane towards a sustainable development, which is a valuable resource for both academic and industrial researchers.
THE IMPACT OF DIGITAL TRANSFORMATION ON NIGERIAN SMALL AND MEDIUM-SIZED ENTERPRISES (SMES) IN THE GLOBAL BUSINESS LANDSCAPE
Authors: Unegbu Hyginus C.O. , Yawas D.S. , Dan-asabe B.
Published: July 2024

Small and Medium-sized Enterprises (SMEs) are pivotal economic entities, and their adaptability in an evolving global business landscape is integral to sustainable growth. This study delves into the profound influence of digital transformation on Nigerian SMEs, offering a comprehensive analysis of the extent to which digitalization shapes their competitiveness, operations, and associated challenges. Employing a quantitative research approach, data from a diverse sample of Nigerian SMEs is collected to assess the relationship between digital transformation and SME outcomes. Demographically, the surveyed SMEs portray a multifaceted distribution across various industries, business sizes, geographic locations, annual revenues, and years in operation. A substantial proportion actively integrates digital tools and technologies into their operations, underscoring their recognition of the strategic value of digitalization. Perceived benefits of digital transformation encompass amplified operational efficiency, extended market access, innovation, elevated customer satisfaction, cost savings, and streamlined internal processes. However, challenges, notably financial constraints, a dearth of digital skills among employees, and regulatory barriers, reflect the multifaceted nature of obstacles faced by SMEs in their digital transformation journey. The study establishes a significant relationship between digital transformation and SME competitiveness. SMEs acknowledge its role in amplifying their global market reach, augmenting their competitiveness on a global scale, strengthening their competitive position within industries, nurturing international partnerships, expanding market share, and enhancing brand visibility in global markets. In essence, this research posits that digital transformation plays an indispensable role in the growth and competitiveness of Nigerian SMEs within the global business landscape. The findings serve as a cornerstone for informed decisions, strategies, and interventions to augment the digital capabilities of Nigerian SMEs, fostering their resilience and competitiveness in an increasingly digital world.
Role of adaptor protein complexes in generating functionally distinct synaptic vesicle pools
Authors: Asmerian Hrach , Alberts Jacob , Sanetra Anna M. , Diaz Alexia J. , Silm Katlin
Published: July 2024

The synaptic vesicle (SV) cycle ensures the release of neurotransmitters and the replenishment of SVs to sustain neuronal activity. Multiple endocytosis and sorting pathways contribute to the recapture of the SV membrane and proteins after fusion. Adaptor protein (AP) complexes are among the critical components of the SV retrieval machinery. The canonical clathrin adaptor AP2 ensures the replenishment of most SVs across many neuronal populations. An alternative AP1/AP3‐dependent process mediates the formation of a subset of SVs that differ from AP2 vesicles in molecular composition and respond preferentially during higher frequency firing. Furthermore, recent studies show that vesicular transporters for different neurotransmitters depend to a different extent on the AP3 pathway and this affects the release properties of the respective neurotransmitters. This review focuses on the current understanding of the AP‐dependent molecular and functional diversity among SVs. We also discuss the contribution of these pathways to the regulation of neurotransmitter release across neuronal populations.

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Analytic Modeling of Two-Dimensional Transient Heat Conduction With Heat Source Under Mixed Boundary Constraints by Symplectic Superposition
Authors: Xu Dian , Li Jinbao , Wang Zixuan , Xiong Sijun , He Qianqiang , Li Rui
Published: July 2024

Many studies have been conducted on two-dimensional (2D) transient heat conduction, but analytic modeling is still uncommon for the cases with complex boundary constraints due to the mathematical challenge. With an unusual symplectic superposition method (SSM), this paper reports new analytic solutions to 2D isotropic transient heat conduction problems with heat source over a rectangular region under mixed boundary constraints at an edge. With the Laplace transform, the Hamiltonian governing equation is derived. The applicable mathematical treatments, e.g., the variable separation and the symplectic eigenvector expansion in the symplectic space, are implemented for the fundamental solutions whose superposition yields the ultimate solutions. Benchmark results obtained by the present method are tabulated, with verification by the finite element solutions. Instead of the conventional Euclidean space, the present symplectic-space solution framework has the superiority on rigorous derivations without predetermining solution forms, which may be extended to more issues with the complexity caused by mixed boundary constraints.
Quantifying the resonant photoemission of radiation damaged Pu
Authors: Tobin J. G. , Yu S.-W. , Chung B. W.
Published: July 2024

The resonant photoelectron spectroscopy (ResPes) of new and aged δ-Pu(Ga) is reassessed by using the small oxygen contaminant peaks as an independent and quantitative check upon conventional cross-photon-energy normalization. Good agreement is found between the measured oxygen intensities and the atomic cross section calculations. Consistent with earlier analyses, the radiation induced damage in the aged samples is found to compress and sharpen the 5f peaks. This is associated with increased localization of the 5f bands, corresponding to the 5f density of states calculations that show a narrowing of 5f bandwidth with cluster size diminishment.
Coupling a torque rheometer with an ultrasonic velocity profiler for evaluating multiphase fluids in oscillatory shear flows
Authors: Ohie Kohei , Yoshida Taiki , Tasaka Yuji
Published: July 2024

We propose a torque rheometer coupled with an ultrasonic velocity profiler (UVP) for evaluating multiphase fluids as bulk rheology in oscillatory shear flows. The rheometer mainly consists of wide-gap coaxial cylinders, where the outer cylinder is sinusoidally oscillated and the inner cylinder is fixed to a torque sensor for measuring the wall shear stress. Based on Cauchy’s equation of motion, the spatiotemporal distribution of the shear stress is obtained from the velocity information and the wall shear stress as a boundary condition. This rheometer was applied to a carboxymethyl cellulose aqueous solution and compared with a standard torque-type rheometer. The results of the evaluated viscoelastic properties agreed well with each other, indicating the validity of the proposed rheometry. To further investigate the applicability of the rheometer to multiphase fluids, suspensions of solid spherical particles with a diameter of 220μm with volume fraction of 0.8–3.4% were measured, which are out of the applicable ranges of the standard rheometer. For volume fractions up to 3% where the UVP measurement is available, the relative viscosity agrees well with a theoretical formula. This indicates the applicability of the method to examine multiphase fluids.
Draft genome of
Bacillus subtilis
strain YB955, prophage-cured derivative of strain 168
Authors: Perez Ryan King , Chavez Rios Jocelyn Sofia , Grifaldo Jessica , Regner Kurt , Pedraza-Reyes Mario , Robleto Eduardo A.
Published: July 2024

We report the genome sequence of
Bacillus subtilis
strain YB955, a prophage-cured strain used as a model in DNA repair, bacterial physiology, and mutagenesis studies. The assembled and annotated draft genome contains 4,031 coding genes, 5 rRNAs, and 73 tRNAs. Compared to 168, YB955 has a 134,402 bp deletion.
Draft genome sequence of
Collimonas
sp. strain H4R21, an effective mineral-weathering bacterial strain isolated from the beech rhizosphere
Authors: E. Morin , S. Uroz , R. Kumar , M.W. Rey , J. Pham , F. Akum , J. H. J. Leveau
Published: July 2024

We present the draft genome sequence of
Collimonas
sp. strain H4R21, isolated from the rhizosphere of
Fagus sylvatica
in the forest experimental site of Montiers (France). This genome features coding capacity for plant growth promotion, such as the ability to solubilize minerals, to produce siderophores and antifungal secondary metabolites.
Whole-genome sequence of
Enterobacter hormaechei
, isolate
jjbc
recovered from the gut of
Plutella xylostella
feeding on cabbage
Authors: Mugo-Kamiri Loretta , Schäfer Lea , Wennmann Jörg T. , Herniou Elisabeth A. , Raymond Ben
Published: July 2024

We present the whole-genome sequence of
Enterobacter hormaechei
(previously
Enterobacter cloacae
) obtained from long and short reads. It is a dominant gut symbiont of the notorious crop pest
Plutella xylostella
, highly prevalent in lepidopteran midguts and a useful model for the evolution of resistance to antimicrobials.
Metagenome-assembled bacterial genomes derived from various aging flue-cured tobacco samples
Authors: Li Minghou , Dong Yingjie , Liu Chen , Liu Haoran , Wang Zhen , Ma Jingru , Wang Xinhui , Zhang Xiaojun
Published: July 2024

We recovered 16 bacterial metagenome-assembled genomes from 11 flue-cured tobacco samples with different aging stage and various geographic origins. Their sizes range from 2.3 M to 5.4 M, with GC contents of 43.17%–74.45%, completeness of 78.80%–99.25%, and contamination of 0.47%–8.56%.
Draft genome sequence of multidrug-resistant
Kurthia gibsonii
strain Hakim RU_BHWE isolated from sewage water in Bangladesh
Authors: Romance M. , Polash Md. Arif-Uz-Zaman , Zahan Nusrat , Raihan Jafor , Ali Md. Sumon , khan Muhib Ullah , Sarker Subir , Haque Md. Hakimul
Published: July 2024

We have sequenced the genome of Kurthia
gibsonii
strain Hakim RU_BHWE, isolated from sewage water. The assembled genome consists of 2.891 Mb with 58.6883× coverage, presenting an average GC content of 36.60%. This genome includes 8 CRISPR arrays, 3 prophages, 3 antibiotic resistance genes, and 12 virulence factor genes.
Whole-genome sequences of
Helicobacter pylori
isolated from patients with high risk of gastric cancer in the Andes of Nariño, Colombia
Authors: Guzman Kevin Andres , Daza Angi Paola , Gomez Rudy Viviana , Montenegro Lidia Madeline , Pazos Alvaro
Published: July 2024

We sequenced the complete genomes of 16
Helicobacter pylori
isolates obtained from patients residing in Nariño, Colombia. These isolates were collected from patients presenting various gastric lesions classified according to the Correa cascade classification. The genomic characterization of these isolates provides valuable insights into the structure, composition, and pathogenicity.
Beav: a bacterial genome and mobile element annotation pipeline
Authors: Jung Jewell M. , Rahman Arafat , Schiffer Andrea M. , Weisberg Alexandra J.
Published: July 2024

Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional
Agrobacterium
-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at
https://github.com/weisberglab/beav
.

IMPORTANCE

Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
Advancing COVID-19 diagnostics: rapid detection of intact SARS-CoV-2 using viability RT-PCR assay
Authors: Veugen Judith M. J. , Schoenmakers Tom , van Loo Inge H. M. , Haagmans Bart L. , Leers Mathie P. G. , Lamers Mart M. , Lucchesi Mayk , van Bussel Bas C. T. , van Mook Walther N. K. A. , Nuijts Rudy M. M. A. , Savelkoul Paul H. M. , Dickman Mor M. , Wolffs Petra F. G.
Published: July 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). Commonly used methods for both clinical diagnosis of SARS-CoV-2 infection and management of infected patients involve the detection of viral RNA, but the presence of infectious virus particles is unknown. Viability PCR (v-PCR) uses a photoreactive dye to bind non-infectious RNA, ideally resulting in the detection of RNA only from intact virions. This study aimed to develop and validate a rapid v-PCR assay for distinguishing intact and compromised SARS-CoV-2. Propidium monoazide (PMAxx) was used as a photoreactive dye. Mixtures with decreasing percentages of intact SARS-CoV-2 (from 100% to 0%) were prepared from SARS-CoV-2 virus stock and a clinical sample. Each sample was divided into a PMAxx-treated part and a non-PMAxx-treated part. Reverse transcription-PCR (RT-PCR) using an in-house developed SARS-CoV-2 viability assay was then applied to both sample sets. The difference in intact SARS-CoV-2 was determined by subtracting the cycle threshold (
Ct
) value of the PMAxx-treated sample from the non-PMAxx-treated sample. Mixtures with decreasing concentrations of intact SARS-CoV-2 showed increasingly lower delta
Ct
values as the percentage of intact SARS-CoV-2 decreased, as expected. This relationship was observed in both high and low viral load samples prepared from cultured SARS-CoV-2 virus stock, as well as for a clinical sample prepared directly from a SARS-CoV-2 positive nasopharyngeal swab. In this study, a rapid v-PCR assay has been validated that can distinguish intact from compromised SARS-CoV-2. The presence of intact virus particles, as determined by v-PCR, may indicate SARS-CoV-2 infectiousness.

IMPORTANCE

This study developed a novel method that can help determine whether someone who has been diagnosed with coronavirus disease 2019 (COVID-19) is still capable of spreading the virus to others. Current tests only detect the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, but cannot tell whether the particles are still intact and can thus infect cells. The researchers used a dye that selectively blocks the detection of damaged virions and free RNA. They showed that this viability PCR reliably distinguishes intact SARS-CoV-2 capable of infecting from damaged SARS-CoV-2 or free RNA in both cultured virus samples and a clinical sample. Being able to quickly assess contagiousness has important implications for contact tracing and safely ending isolation precautions. This viability PCR technique provides a simple way to obtain valuable information, beyond just positive or negative test results, about the actual risk someone poses of transmitting SARS-CoV-2 through the air or surfaces they come into contact with.
Recurrent steroid-responsive polyserositis of unclear aetiology: a possible post-COVID-19 phenomenon
Authors: Rossi Peter , Wilkinson Michael , Choong Jamie , Ninan Jem
Published: July 2024

A previously healthy male patient presented with relapsing serous effusions affecting the pleural, pericardial and peritoneal membranes, along with thrombocytopaenia, following infection with COVID-19. An extensive workup was performed to rule out potential causes of polyserositis, including an infectious disease screen, autoantibody testing and imaging; however, no clear other cause was found. He exhibited a robust response to high-dose corticosteroid therapy but experienced several recurrences on tapering of treatment. His clinical course and treatment response were most suggestive of an autoimmune or autoinflammatory cause of polyserositis, though without confirmation of a specific underlying diagnosis. This report builds on existing literature on a possible link between COVID-19 and polyserositis.
Deep learning-based image quality assessment for optical coherence tomography macular scans: a multicentre study
Authors: Tang Ziqi , Wang Xi , Ran An Ran , Yang Dawei , Ling Anni , Yam Jason C , Zhang Xiujuan , Szeto Simon K H , Chan Jason , Wong Cherie Y K , Hui Vivian W K , Chan Carmen K M , Wong Tien Yin , Cheng Ching-Yu , Sabanayagam Charumathi , Tham Yih Chung , Liew Gerald , Anantharaman Giridhar , Raman Rajiv , Cai Yu , Che Haoxuan , Luo Luyang , Liu Quande , Wong Yiu Lun , Ngai Amanda K Y , Yuen Vincent L , Kei Nelson , Lai Timothy Y Y , Chen Hao , Tham Clement C , Heng Pheng-Ann , Cheung Carol Y
Published: July 2024

Aims

To develop and externally test deep learning (DL) models for assessing the image quality of three-dimensional (3D) macular scans from Cirrus and Spectralis optical coherence tomography devices.

Methods

We retrospectively collected two data sets including 2277 Cirrus 3D scans and 1557 Spectralis 3D scans, respectively, for training (70%), fine-tuning (10%) and internal validation (20%) from electronic medical and research records at The Chinese University of Hong Kong Eye Centre and the Hong Kong Eye Hospital. Scans with various eye diseases (eg, diabetic macular oedema, age-related macular degeneration, polypoidal choroidal vasculopathy and pathological myopia), and scans of normal eyes from adults and children were included. Two graders labelled each 3D scan as gradable or ungradable, according to standardised criteria. We used a 3D version of the residual network (ResNet)-18 for Cirrus 3D scans and a multiple-instance learning pipline with ResNet-18 for Spectralis 3D scans. Two deep learning (DL) models were further tested via three unseen Cirrus data sets from Singapore and five unseen Spectralis data sets from India, Australia and Hong Kong, respectively.

Results

In the internal validation, the models achieved the area under curves (AUCs) of 0.930 (0.885–0.976) and 0.906 (0.863–0.948) for assessing the Cirrus 3D scans and Spectralis 3D scans, respectively. In the external testing, the models showed robust performance with AUCs ranging from 0.832 (0.730–0.934) to 0.930 (0.906–0.953) and 0.891 (0.836–0.945) to 0.962 (0.918–1.000), respectively.

Conclusions

Our models could be used for filtering out ungradable 3D scans and further incorporated with a disease-detection DL model, allowing a fully automated eye disease detection workflow.
Rapid review method series: interim guidance for the reporting of rapid reviews
Authors: Stevens Adrienne , Hersi Mona , Garritty Chantelle , Hartling Lisa , Shea Beverley J , Stewart Lesley A , Welch Vivian Andrea , Tricco Andrea C
Published: July 2024

Rapid reviews (RRs) are produced using abbreviated methods compared with standard systematic reviews (SR) to expedite the process for decision-making. This paper provides interim guidance to support the complete reporting of RRs. Recommendations emerged from a survey informed by empirical studies of RR reporting, in addition to collective experience. RR producers should use existing, robustly developed reporting guidelines as the foundation for writing RRs: notably Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 (PRISMA 2020; reporting for SRs), but also preferred reporting items for overviews of reviews (PRIOR) items (reporting for overviews of SRs) where SRs are included in the RR. In addition, a minimum set of six items were identified for RRs: three items pertaining to methods and three addressing publication ethics. Authors should be reporting what a priori-defined iterative methods were used during conduct, what distinguishes their RR from an SR, and knowledge user (eg, policymaker) involvement in the process. Explicitly reporting deviations from standard SR methods, including omitted steps, is important. The inclusion of publication ethics items reflects the predominance of non-journal published RRs: reporting an authorship byline and corresponding author, acknowledging other contributors, and reporting the use of expert peer review. As various formats may be used when packaging and presenting information to decision-makers, it is practical to think of complete reporting as across a set of explicitly linked documents made available in an open-access journal or repository that is barrier-free. We encourage feedback from the RR community of the use of these items as we look to develop a consolidated list in the development of PRISMA-RR.
Novel machine learning algorithm in risk prediction model for pan-cancer risk: application in a large prospective cohort
Authors: Wu Xifeng , Tu Huakang , Hu Qingfeng , Tsai Shan Pou , Ta-Wei Chu David , Wen Chi-Pang
Published: July 2024

Objective

To develop and validate machine-learning models that predict the risk of pan-cancer incidence using demographic, questionnaire and routine health check-up data in a large Asian population.

Methods and analysis

This study is a prospective cohort study including 433 549 participants from the prospective MJ cohort including a male cohort (n=208 599) and a female cohort (n=224 950).

Results

During an 8-year median follow-up, 5143 cancers occurred in males and 4764 in females. Compared with Lasso-Cox and Random Survival Forests, XGBoost showed superior performance for both cohorts. The XGBoost model with all 155 features in males and 160 features in females achieved an area under the curve (AUC) of 0.877 and 0.750, respectively. Light models with 31 variables for males and 11 variables for females showed comparable performance: an AUC of 0.876 (95% CI 0.858 to 0.894) in the overall population and 0.818 (95% CI 0.795 to 0.841) in those aged ≥40 years in the male cohort and an AUC of 0.746 (95% CI 0.721 to 0.771) in the overall population and 0.641 (95% CI 0.605 to 0.677) in those aged ≥40 years in the female cohort. High-risk individuals have at least ninefold higher risk of pan-cancer incidence compared with low-risk groups.

Conclusion

We developed and internally validated the first machine-learning models based on routine health check-up data to predict pan-cancer risk in the general population and achieved generally good discriminatory ability with a small set of predictors. External validation is warranted before the implementation of our risk model in clinical practice.
Suicide in Hong Kong during the COVID-19 pandemic: an observational study
Authors: Bai Anying , Li Jinjian , Pan Yuhang , Jiang Yu
Published: July 2024

Introduction

The COVID-19 pandemic has exacerbated suicide risk factors in Hong Kong, which faces economic shocks and strict travel restrictions due to its unique economic structure and geographical location. However, there is a scarcity of reliable empirical evidence regarding the relationship between the pandemic and suicide mortality. This study examines whether changes in the suicide rate align with COVID-19 situations and anti-COVID-19 policy events in Hong Kong, focusing on vulnerable population groups based on demographic and socioeconomic characteristics.

Methods

Suicide data spanning 1 January 2019 to 31 December 2022 were sourced from the Hong Kong Suicide Press Database. Case-level data were aggregated monthly by district. Population-weighted Poisson regression with district-level fixed effects was employed to analyse suicide patterns and their association with COVID-19 developments. Robustness checks and demographic-based heterogeneity analysis were conducted, distinguishing suicide risk among different population groups.

Results

A total of 4061 suicide cases were analysed, encompassing deaths and attempts. The first wave of the pandemic saw a 30% decline in suicide cases compared with the 2019 average, while the second and fifth waves witnessed increases of 33% and 51% in suicide rates, respectively. Older adults and individuals with lower socioeconomic status were particularly susceptible to the adverse effects, as evidenced by a significant rise in suicides during the fifth wave.

Conclusions

The findings underscore the importance of targeted interventions to address the mental health needs of vulnerable populations during pandemics, highlighting the impact of COVID-19 situations and antipandemic policies on the suicide rate.
Monitoring the progress and impact of a multicountry, interdisciplinary research project on childhood stunting: the UKRI GCRF Action Against Stunting Hub MEL protocol
Authors: D M Dinesh Yadav , Tata Darius Tetsa , Jobarteh Modou Lamin , Ndulu Ndolo Rose , Banjara Santosh Kumar , Augustine Little Flower , Manne Munikumar , Kulkarni Bharati , Diop Assana , Tairou Fassiatou , Fatou Ndiaye Diop Camara , Faye Babacar , Fahmida Umi , Htet Min Kyaw , Zahra Nur L , Sudibya Arienta R P , Naab Francis , Harder Marie K , Knott Chelsey Victoria , Waddington Hugh Sharma , Heffernan Claire
Published: July 2024

Introduction

Monitoring, Evaluation and Learning (MEL) is an integral part of research, programme and policy development and implementation. However, MEL methods used to monitor and evaluate interdisciplinary research projects are often informal and under-reported. This article describes the MEL protocol of the UKRI GCRF Action Against Stunting Hub (AASH).

Methods and analysis

The AASH conducts interdisciplinary research into childhood stunting in India, Indonesia and Senegal across 23 distinct work packages. Project-specific MEL framework and methods will be implemented. A logframe will be developed to monitor and evaluate the research activities across the field sites including the number of participants recruited, questionnaires, measurements and procedures completed. MEL dashboards using Tableau and Glasscubes will be used to track and report progress, milestones and outcomes of the project. Dashboard outputs will be reported as numbers and percentages, with additional graphs/charts for easy visualisation. A ‘learning’ framework will be developed to outline appropriate pipelines for the dissemination of the research findings. This includes a theory of change explicating the overarching ambitions of the project in influencing policy, practice and research, and strategic engagement of relevant stakeholders to evaluate knowledge, attitudes and best practices for impactful engagement and dissemination of the research findings.

Ethics and dissemination

Ethical approval was granted by the Ethics Committee of the London School of Hygiene & Tropical Medicine (17915/RR/17513); National Institute of Nutrition (ICMR)–Ministry of Health and Family Welfare, Government of India (CR/04/I/2021); Health Research Ethics Committee, University of Indonesia and Cipto Mangunkusumo Hospital (KET-887/UN2.F1/ETIK/PPM.00.02/2019); and the National Ethics Committee for Health Research (CNERS), Senegal (Protocole SEN19/78). Findings from this work will be published in peer-reviewed journals, presented in conferences and disseminated to policy makers and research communities.
Clinical features and associated factors of impaired ventilatory efficiency: findings from the ECOPD study in China
Authors: Deng Zhishan , Wu Fan , Wan Qi , Dai Cuiqiong , Lu Lifei , Peng Jieqi , Zhou Kunning , Wu Xiaohui , Tang Gaoying , Huang Suyin , Cai Guannan , Huang Peiyu , Wang Zihui , Zheng Youlan , Yang Huajing , Zhao Ningning , Xiao Shan , Wen Xiang , Sun Ruiting , Yang Changli , Huang Yongqing , Chen Rongchang , Zhou Yumin , Ran Pixin
Published: July 2024

Background

Impaired ventilatory efficiency during exercise is a predictor of mortality in chronic obstructive pulmonary disease. However, little is known about the clinical features and associated factors of impaired ventilatory efficiency in China.

Methods

We conducted a cross-sectional community-based study in China and collected demographic and clinical information, cardiopulmonary exercise testing, spirometry, and CT data. Impaired ventilatory efficiency was defined by a nadir ventilatory equivalent for CO2production above the upper limit of normal. Multivariable linear and logistic regression models were used to explore the clinical features and associated factors of impaired ventilatory efficiency.

Results

The final analyses included 941 subjects, 702 (74.6%) of whom had normal ventilatory efficiency and 239 (25.4%) had impaired ventilatory efficiency. Participants with impaired ventilatory efficiency had more chronic respiratory symptoms, poorer lung function and exercise capacity, and more severe emphysema (natural logarithm transformation of the low-attenuation area of the lung with attenuation values below −950 Hounsfield units, logLAA−950: 0.19±0.65 vs −0.28±0.63, p<0.001) and air trapping (logLAA−856: 1.03±0.65 vs 0.68±0.70, p<0.001) than those with normal ventilatory efficiency. Older age (60–69 years, OR 3.10 (95% CI 1.33 to 7.21), p=0.009 and 70–80 years, OR 6.48 (95% CI 2.56 to 16.43), p<0.001 vs 40–49 years) and smoking (former, OR 3.19 (95% CI 1.29 to 7.86), p=0.012; current, OR 4.27 (95% CI 1.78 to 10.24), p=0.001 vs never) were identified as high risk factors of impaired ventilatory efficiency.

Conclusions

Impaired ventilatory efficiency was associated with poorer respiratory characteristics. Longitudinal studies are warranted to explore the progression of individuals with impaired ventilatory efficiency.
Concealed firearm carrying laws and defensive firearm use in public locations of US metropolitan areas, 1986–2004
Authors: Koper Christopher S , Lu Yi-Fang , Dong Beidi
Published: July 2024

Objectives

There has been extensive debate in the USA as to how laws regulating the carrying of concealed firearms affect crime and public safety. This study examines whether US state laws making it easier for civilians to obtain permits to carry concealed handguns in public increase defensive gun uses against violent threats and attacks in public.

Methods

We used National Crime Victimization Survey data from 39 metropolitan statistical areas (MSAs) in the USA over a 19-year period (1986–2004) to examine whether laws making it easier for civilians to obtain concealed carry permits are linked to higher levels of defensive gun use against violence in public spaces of metropolitan areas. Bivariate χ2tests and multivariate logistic regression models (controlling for actor and situational characteristics) were used with 7196 public incidents to examine whether the likelihood of the victim using a gun against an attacker(s) varied based on the type of concealed carry law in the MSA at the time of the incident.

Results

The prevalence of self-defensive gun use in this sample was not clearly related to the passage of permissive gun carrying laws. Although defensive gun use was more common in MSAs with permissive gun carrying laws, this difference was not consistently related in magnitude or statistical significance to the passage of those laws or the length of time they had been in effect.

Conclusions

Permissive concealed carry permit laws do not produce evident increases in self-defensive gun uses against crime in public locations.