bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeted deletion of Pf prophages from diversePseudomonas aeruginosaisolates impacts quorum sensing and virulence traits
Authors: Schmidt Amelia K. , Schwartzkopf Caleb M. , Pourtois Julie D. , Burgener Elizabeth , Faith Dominick R. , Joyce Alex , Lamma Tyrza , Kumar Geetha , Bollyky Paul L. , Secor Patrick R.
Published: November 2023

Pseudomonas aeruginosais an opportunistic bacterial pathogen that commonly causes medical hardware, wound, and respiratory infections. Temperate filamentous Pf phages that infectP. aeruginosaimpact numerous bacterial virulence phenotypes. Most work on Pf phages has focused on strain Pf4 and its hostP. aeruginosaPAO1. Expanding from Pf4 and PAO1, this study explores diverse Pf strains infectingP. aeruginosaclinical isolates. We describe a simple technique targeting the Pf lysogeny maintenance gene,pflM(PA0718), that enables the effective elimination of Pf prophages from diverseP. aeruginosahosts. This study also assesses the effects different Pf phages have on host quorum sensing, biofilm formation, virulence factor production, and virulence. Collectively, this research not only introduces a valuable tool for Pf prophage elimination from diverseP. aeruginosaisolates, but also advances our understanding of the complex relationship betweenP. aeruginosaand filamentous Pf phages.

Importance

Pseudomonas aeruginosais an opportunistic bacterial pathogen that is frequently infected by filamentous Pf phages (viruses) that integrate into its chromosome, affecting behavior. While prior work has focused on Pf4 and PAO1, this study investigates diverse Pf strains in clinical isolates. A simple method targeting the deletion of the Pf lysogeny maintenance genepflM(PA0718) effectively eliminates Pf prophages from clinical isolates. The research evaluates the impact Pf prophages have on bacterial quorum sensing, biofilm formation, and virulence phenotypes. This work introduces a valuable tool to eliminate Pf prophages from clinical isolates and advances our understanding ofP. aeruginosaand filamentous Pf phage interactions.
Challenges in estimating species age from phylogenetic trees
Authors: Calderón del Cid Carlos , Hauffe Torsten , Carrillo Juan D. , Warnock Rachel C. M. , Silvestro Daniele
Published: November 2023

Aim

Species age, the elapsed time since origination, can give an insight into how species longevity might influence eco-evolutionary dynamics and has been hypothesized to influence extinction risk. Traditionally, species ages have been measured in the fossil record. However, recently, numerous studies have attempted to estimate the ages of extant species from the branch lengths of time-calibrated phylogenies. This approach poses problems because phylogenetic trees contain direct information about species identity only at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction, and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from the comparison between phylogenetic age and other traits, such as extinction risk.

Innovation

For bifurcating speciation, which is the default assumption in most analyses, we propose a probabilistic approach to improve the estimation of species ages, based on the properties of a birth-death process. We show that our model can reduce the error by one order of magnitude under cases of high extinction and high percentage of unsampled extant species.

Main conclusion

Our results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcate, it is possible to obtain better approximations of species age by combining information from branch lengths with the expectations of a birth-death process.
Statistical Analysis Plan for the INTIMET study (Insulin Resistance in Type 1 Diabetes Managed with Metformin)
Authors: Snaith Jennifer R , Olsen Nick , Greenfield Jerry R
Published: November 2023

This document provides the full statistical analysis plan (SAP) for the INTIMET study (Insulin Resistance in Type 1 Diabetes Managed with Metformin), a randomised double-blinded placebo-controlled trial, designed to evaluate the effect of metformin on insulin resistance and cardiometabolic health in type 1 diabetes. This trial was prospectively registered within the Australian and New Zealand Clinical Trials Registry (ACTRN12619001440112). The study protocol has previously been published (Snaith JR et al, Diabetic Medicine 2021).
The overlooked first intercostal ligament: Does it help to stabilize the Weberian apparatus?
Authors: Leyhr Jake , Haitina Tatjana , Bird Nathan C.
Published: November 2023

The Weberian apparatus is a novel hearing adaptation that facilitates increased hearing sensitivity in otophysan fishes. The apparatus is a complex system composed of modifications to anterior vertebral elements, the inner ear, and the swim bladder. A critical piece of the system that often receives minor attention are the various ligaments that bridge these three regions. Most famous of the ligaments is the interossicular ligament, which connects the weberian ossicle chain (scaphium-intercalarium-tripus). Several other ligaments are present, including the suspensor (tripus to parapophysis 4) and the triple ligament (tripus-os suspensorium-tunica externa). Here, by combining diffusible iodine-based contrast enhancement (DICE) and propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SRμCT) with classic histological methods we shine new light on the first intercostal ligament (ICL1) and discuss its potential function in relation to the Weberian apparatus. ICL1 is nearly absent from the cypriniform literature, typically only mentioned in a general discussion together with other intercostal ligaments. This study examines the development and structure of ICL1 comparatively with the other definitive Weberian ligaments in the zebrafish (Danio rerio). We provide a comprehensive view of development, three-dimensional shape, and composition to generate hypotheses regarding potential functions of ICL1 within the greater Weberian apparatus. Given new detail presented herein regarding the structure of ICL1, modifications to rib 5 and parapophysis 4 for ICL1 attachment, and the alignment of ICL1 with the os suspensorium, we propose a supportive (anchoring) role of ICL1 to aid in minimizing non-optimal movement of the structures of the fourth vertebra, thereby allowing the focus of vibrations anteriorly to the ossicle chain with minimal signal loss in zebrafish and other species with similar Weberian apparatus morphologies. We conclude that ICL1 should be included in future analyses of Weberian apparatus function where ligaments are addressed.
Microcephaly with a disproportionate hippocampal reduction, stem cell loss and neuronal lipid droplet symptoms inTrappc9KO mice
Authors: Aljuraysi Sultan , Platt Mark , Pulix Michela , Poptani Harish , Plagge Antonius
Published: November 2023

Mutations of the humanTRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 9(TRAPPC9) cause a neurodevelopmental disorder characterised by microcephaly and intellectual disability. Trappc9 constitutes a subunit specific to the intracellular membrane-associated TrappII complex. The TrappII complex interacts with Rab11 and Rab18, the latter being specifically associated with lipid droplets (LDs). Here we used non-invasive imaging to characteriseTrappc9knock-out (KO) mice as a model of the human hereditary disorder. KOs developed postnatal microcephaly with many grey and white matter regions being affected.In vivoMRI identified a disproportionately stronger volume reduction in the hippocampus, which was associated with a significant loss of Sox2-positive neural stem and progenitor cells. Diffusion Tensor imaging indicated a reduced organisation or integrity of white matter areas.Trappc9KOs displayed behavioural abnormalities in several tests related to exploration, learning and memory. Trappc9-deficient primary hippocampal neurons accumulated a larger LD volume per cell following Oleic Acid stimulation, and the coating of LDs by Perilipin-2 was much reduced. Additionally,Trappc9KOs developed obesity, which was significantly more severe in females than in males. Our findings indicate that, beyond previously reported Rab11-related vesicle transport defects, dysfunctions in LD homeostasis might contribute to the neurobiological symptoms of Trappc9 deficiency.
Analytic hierarchy process (AHP) assessment of Kuwait mega construction projects' complexity
Authors: AlKheder Sharaf , Al Otaibi Hajar , Al Baghli Zahra , Al Ajmi Shaikhah , Alkhedher Mohammad
Published: November 2023

Purpose

Megaproject's construction is essential for the development and economic growth of any country, especially in the developing world. In Kuwait, megaprojects are facing many restrictions that discourage their execution causing a significant delay in bidding, design, construction and operation phases with the execution quality being affected. The objective of this study is to develop a complexity measurement model using analytic hierarchy process (AHP) for megaprojects in Kuwait, with a focus on the New Kuwait University multi-billion campus Shadadiyah (College of Social Science, Sharia and Law (CSSL)) as a case study.

Design/methodology/approach

The study applies a hybrid fuzzy analytic hierarchy process (FAHP) method to compare the results with those obtained using the conventional AHP method. This can facilitate the project management activities during the different stages of construction. Data were collected based on the results of a two-round Delphi questionnaire completed by seniors and experts of the selected project.

Findings

It was found that project modeling methodology was responsible for complexity. It was grouped under several categories that include technological, goal, organizational, environmental and cultural complexities. The study compares complexity degrees assessed by AHP and FAHP methods. “Technological Complexity” scores highest in both methods, with FAHP reaching 7.46. “Goal Complexity” follows closely behind, with FAHP. “Cultural Complexity” ranks third, differing between methods, while “Organizational” and “Environmental Complexity” consistently score lower, with FAHP values slightly higher. These results show varying complexity levels across dimensions. Assessing and understanding such complexities were essential toward the completion of such megaprojects.

Originality/value

The contribution of this study is on providing the empirical evidential knowledge for the priority over construction complexities in a developing country (Kuwait) in the Middle East.
Understanding how ethical claims in advertising affect subjective ambivalence toward buying ethical products
Authors: Toti Jean-François , Sánchez Romero Andrea Milena
Published: November 2023

Purpose

The purpose of this paper is to examine the effect of subjective ambivalence on ethical consumption behaviors and the role of ethical claims in reducing feelings of ambivalence toward buying ethical products.

Design/methodology/approach

The authors conducted two studies. In study 1, the authors carried out an online survey with a sample of 230 French consumers. The authors applied structural equation modeling with Amos to test the relationships among skepticism, ambivalence and ethical consumption behaviors. Study 2 is an experimental design in which the authors manipulated ethical claims (low – few ethical arguments vs. high – many ethical arguments) in advertising (176 French panelists). The authors tested the relationships among consumer ethical sensitivity, perceived brand ethicality, skepticism, ambivalence and intention to purchase an ethical product, depending on ethical claims in advertising.

Findings

Study 1 shows that skepticism toward advertising of ethical products amplifies feelings of ambivalence and that ambivalence reduces consumers’ willingness to adopt ethical consumption behaviors. Study 2 shows that strong claims in advertising of ethical products reduce skepticism toward advertising of ethical products and feelings of ambivalence toward buying an ethical product through perceived brand ethicality, with consumers’ ethical sensitivity positively moderating these relationships.

Research limitations/implications

The two studies explore only one form of ambivalence (i.e. subjective), and the experimental study focuses on a single category of products.

Practical implications

The findings highlight the difficulties in promoting ethical products. Consumers need to know if a product is “really” ethical, as they may feel ambivalent toward that product. This paper shows that strong ethical claims in advertising ethical products significantly help to overcome this barrier.

Originality/value

Based on attribution theory and persuasion models, this research reveals how ethical claims in advertising affect feelings of ambivalence, which negatively influence consumers’ willingness to adopt ethical consumption. In addition, it follows a holistic approach to ethical consumption behaviors to explore consumers’ ambivalence.
Social representations of retirement: a study with professors from public higher education institutions
Authors: Vasconcelos da Nóbrega Cléverson , Helal Diogo Henrique
Published: November 2023

Purpose

The article aims at analyzing the social representations of retirement in two different groups of professors – pre-retired and retired – from a public higher education institution. The goal is to explore the experiences, reflections, beliefs, and attitudes originated from the transition to retirement.

Design/methodology/approach

The research, of exploratory and descriptive nature, was guided by the Social Representation Theory (SRT) and took a qualitative approach. 16 professors were interviewed, 8 in each group (pre-retired and retired professors), using semi-structured interviews that followed a script designed to discover the main aspects of the transition to retirement.

Findings

Three figurative cores were raised – the financial aspect, the centrality of work, and the will to continue contributing, and the unpreparedness for retirement – and testimonies have shown heterogeneous representations. The study observed that although relevant, the bonus for continued services is not the main determinant for professors to continue working in the university.

Originality/value

The results of this study indicate the need to treat retirement as a complex and multidimensional process, offering a fresh perspective on the social representations of retirement in the academic context. The use of the Social Representation Theory to explore these perspectives adds to the originality of the approach, highlighting the multifaceted nature of the retirement process in this specific professional group.
Budgeting changes and success: abandonment, reform or stability in Finnish manufacturing firms?
Authors: Kihn Lili-Anne
Published: November 2023

Purpose

The need to change budgeting has been frequently debated. Drawing on the literature on management accounting and budgeting change, this study aims to explore changes in budgeting and whether experienced success of budgeting varied with time and budget type. Changes in the use of the following budget types were investigated: fixed, revised, rolling, flexible and hybrid budgets.

Design/methodology/approach

This study uses a mixed research methodology. Survey data was collected from the same business units of large Finnish manufacturing firms in 2004 (Time 1) and 2016/2017 (Time 2) (N = 28). In addition, some of the respondents of the latter survey were interviewed in 2023 (Time 3).

Findings

Almost all business units were found to have remained loyal to budgeting. However, changes in budget types were not uncommon and varied considerably. Overall, the use of fixed budgets continued strongly, the use of revised and hybrid budgets declined, and the use of rolling budgets increased over time. Moreover, the joint use of budgets declined. The perceived success of budgetary processes was, initially, weakened by the use of fixed budgets and, later, by the use of revised budgets. The interview data further illustrates some of the patterns of, and reasons behind, the changes.

Originality/value

Longitudinal analysis of change in the same business units was useful in revealing the patterns of change in budgeting and on relationships between the variables analysed over time. Further research could be carried out using more extensive case studies in companies or sector-focused surveys longitudinally.
The impact of environmental, social and governance (ESG) scores on stock market: evidence from G7 countries
Authors: Kevser Mustafa , Tunçel Mert Baran , Gürsoy Samet , Zeren Feyyaz
Published: November 2023

Purpose

This study aims to examine the effect of environmental, social and corporate governance (ESG) scores on stock markets for the period from February 2018 to December 2022 for G7 countries. Even though ESG is an established area of investigation, prior research has paid inadequate attention to the nexus of ESG scores and stock markets in G7 (Germany, USA, UK, Italy, France, Japan and Canada) countries.

Design/methodology/approach

This study covers G7 countries and uses a data set, which includes ESG scores and stock market returns from reporting channels including financial websites, and international indexes, between February 2018 and December 2022. Cross-section dependency and homogeneity tests were used with Konya (2006) panel causality test to investigate the relations of ESG scores and stock markets, and the research also conducted a separate analysis for each sub-dimension. Homogeneity/heterogeneity tests were also carried out in the research.

Findings

The findings suggest that causality from ESG scores to stock market (DAX) was determined only for Germany. Accordingly, it is understood that German companies have started to implement corporate social responsibility and ESG practices in their management strategies and reporting. These findings offer important implications for those who are considering investing in G7 countries, whether or not to consider ESG scores.

Originality/value

In this context, the research contributes to the existing literature on the relationships between ESG scores and stock markets, which are seen as a vital tool to meet the expectations of stakeholders.
Pain scoring systems in hospitalized horses with ocular disease
Authors: Jodzio Dayna , DeNotta Sally , Plummer Caryn , Sanchez Chris
Published: November 2023

Background

Pain recognition in hospitalized horses is challenging, and the utility of pain scoring systems in horses with ocular disease has not been well‐described.

Hypothesis/Objectives

Evaluate the horse grimace scale (HGS) and behavior pain score (BPS) in hospitalized horses with ocular disease. We hypothesized that HGS and BPS would be associated with different clinical progressions.

Animals

Privately owned horses hospitalized for ocular disease between September 2018 and September 2020.

Methods

Retrospective observational study. The HGS and BPS were recorded daily throughout hospitalization. Clinical progressions were categorized as: (a) discharge from hospital after medical treatment, (b) ophthalmic surgery (eg, keratectomy, conjunctival flap, amniotic membrane transplantation, corneal transplant), or (c) enucleation. Temporal trends in HGS and BPS were assessed using linear regression. Correlations among slope, intercept, and progression were determined using the Kruskal‐Wallis test.

Results

Of 65 horses that met inclusion criteria, 29 (45%) were discharged after exclusively medical management, 28 (43%) underwent ophthalmic surgery, and 8 (12%) underwent enucleation. Two horses (3%) had 2 ophthalmic surgeries performed. The BPS scores at admission were higher in horses that were managed medically than in those that underwent enucleation (P = .01). Horses requiring enucleation had higher increases in HGS (P = .02) and BPS (P = .01) during hospitalization than horses that were medically managed and a higher increase in BPS (P = .04) than horses that required ophthalmic surgery.

Conclusions and Clinical Importance

Pain scoring may represent a useful tool for monitoring progression and response to treatment in hospitalized horses with ocular disease.
Quantifying dimensional change in stochastic portfolio theory
Authors: Bayraktar Erhan , Kim Donghan , Tilva Abhishek
Published: November 2023

In this paper, we develop the theory of functional generation of portfolios in an equity market with changing dimension. By introducing dimensional jumps in the market, as well as jumps in stock capitalization between the dimensional jumps, we construct different types of self‐financing stock portfolios (additive, multiplicative, and rank‐based) in a very general setting. Our study explains how a dimensional change caused by a listing or delisting event of a stock, and unexpected shocks in the market, affect portfolio return. We also provide empirical analyses of some classical portfolios, quantifying the impact of dimensional change in portfolio performance relative to the market.
Experimental Study on Performance of a Solar Thermal-Driven Vapor Absorption System Integrated With Hot Thermal Energy Storage for Milk Chilling
Authors: Sharma Dinesh Kumar , Sharma Dilip , Ali Ahmed Hamza H.
Published: November 2023

Solar thermal-driven vapor absorption system has proven to be a feasible and viable cooling source. However, most reported installations for milk chilling applications are equipped with an auxiliary heater that consumes significant electricity/gas, making it economically unviable. In this study, the experimental investigation of the performance of a solar-powered vapor absorption chiller has been reported for milk chilling applications as per standard ISO 5708–2 II. It has been identified that the performance of the vapor absorption chiller is quite uncertain and underperforming while operated with the heat directly fed through the evacuated tube compound parabolic concentrator solar field due to diurnal and seasonal variations of solar radiation intensity. Therefore, hot thermal energy storage integration has been studied and analyzed in this study. The performance of the vapor absorption chiller has improved significantly with the use of hot thermal energy storage in the solar circuit as the coefficient of performance (COP) of the vapor absorption chiller improved up to 0.4, which was earlier around 0.25. Further, hot thermal energy storage provides better thermal management to increase the productivity and performance of the vapor absorption chiller, and the cooling time for the first milking is 2 h and 45 min. The performance of the vapor absorption chiller enhanced further up to 0.52 when supplied heat entirely with thermal energy storage. The energy efficiency ratio has a maximum value of 6.1, with an average of 4.3, whereas the thermal COP has an average of 0.35 and a maximum value of 0.52 when run with thermal energy storage alone.
Performance Evaluation of Micro-Textured Inserts Coupled With Solid Lubricants During the Sustainable Dry Machining of Inconel 825
Authors: Nayak Jyoti Prakash , Chetan
Published: November 2023

In this research work, the turning of Inconel 825 has been carried out using uncoated and coated laser-textured hard tungsten carbide (WC) cutting inserts. The efficacy of uncoated textured inserts has been tried to improve by impregnating them with micro-sized MoS2 and nano-TiC powder paste. The results of coated and uncoated textured inserts have been compared with the plain uncoated tungsten carbide insert. The use of solid lubricant-impregnated textured tools and coated textured tools has significantly reduced the cutting forces and chip–tool interface friction as compared to plain and normal textured tools. Upon the SEM analysis, high adhesion over the rake face of the plain tool has been observed. The excessive adhesion over the rake surface has been observed over the normal textured tool due to the derivative cutting phenomena. The use of MoS2 and nano-TiC-impregnated textured tools has significantly reduced the material adhesion over the rake surface by eliminating the derivative cutting effect. The use of AlTiSiN-coated textured tools has also restricted the extent of work material adhesion over the rake surface of the cutting insert.
Impact of the DC intensity and electrode distance on pulsed-DC powder-pack boride layer growth kinetics
Authors: Campos-Silva I. , Castillo-Vela L. E. , Mejía-Caballero I. , Rosales-Lopez J. L. , Olivares-Luna M. , Chaparro-Pérez K. D. , Espino-Cortes F. P. , González-Carmona J. M.
Published: November 2023

In this study, novel findings were obtained regarding the influence of current intensity and electrode distance on the growth of the FeB-Fe2B layer during pulsed-DC powder pack boriding (PDCPB). Boride layer formation was carried out on AISI 1018 and AISI 4140 steels at 900 °C for 2700 s, considering current intensities ranging from 2.5 to 7.5 A and electrode distances of 10, 15, and 20 mm for each current intensity. The growth of the FeB-Fe2B layer was enhanced as the current intensity/electrode distance increased. This was related to the contribution of electromigration, the amount of powder mixture (used during the PDCPB) between electrodes, and Joule heating. Analysis of variance was performed on borided steels to assess the impact of the current intensity/electrode distance on the boride layer growth. The results revealed weight coefficients of approximately 50% for current intensity, around 40% for electrode distance, and a combined contribution of both variables of no more than 3.5%. Finally, multiple regression analyses were conducted to estimate boride layer thickness expressions as a function of the independent variables. The model results demonstrated a 5% error when compared to the experimental boride layer thickness.
DLG1 promotes the antiviral innate immune response by inhibiting p62-mediated autophagic degradation of IKKε
Authors: Chang Huasong , Wu Hao , Hou Peili , Aizaz Muhammad , Yang Rukun , Xiang Aibiao , Qi Wenjing , He Hongbin , Wang Hongmei
Published: November 2023

Discs large membrane-associated guanylate kinase (MAGUK) scaffold protein 1 (DLG1) plays important roles in cell contact and migration, but its role in antiviral innate immunity is not clear. In this study, the role of DLG1 in the antiviral innate immune response and its impact on type-I interferon (IFN-I) signaling were investigated. DLG1 plays a critical role in promoting the IFN-I response by inhibiting the autophagic degradation of the innate immune adaptor IκB kinase epsilon (IKKε). As a result, DLG1 effectively suppresses negative-stranded RNA virus replication, including that of viruses such as vesicular stomatitis virus, Sendai virus, and bovine ephemeral fever virus. DLG1 was found to enhance the production of IFN-β and IFN-stimulated genes, leading to the attenuation of virus propagation. Mechanistically, DLG1 competitively binds to the E3 ubiquitin ligase March2, preventing the ubiquitination and subsequent degradation of IKKε. Notably, March2 specifically catalyzes K27-linked polyubiquitination of IKKε. The interaction between March2 and IKKε is mediated by the transmembrane domain of March2 and the C-terminal domain of IKKε. Furthermore, p62 acts as a cargo receptor, recognizing ubiquitinated IKKε for eventual autophagic degradation, whereas the process is blocked by DLG1. Additionally, the results demonstrated a significant decrease in DLG1 mRNA and protein levels upon negative-stranded RNA virus infection. Overall, these findings provide insights into the molecular mechanisms by which DLG1 promotes IFN-I production by regulating IKKε expression to inhibit viral replication.

IMPORTANCE

The type-I interferon (IFN-I) signaling pathway is the first line of antiviral innate immunity. It must be precisely regulated against virus-induced damage. The tightly regulated mechanisms of action of host genes in the antiviral innate immune signaling pathway are still worth studying. Here, we report a novel role of DLG1 in positively regulating the IκB kinase epsilon (IKKε)-mediated IFN-I signaling response against negative-stranded RNA virus replication, whereas the RNA virus inhibits the expression of DLG1 for immune escape. Importantly, the E3 ligase March2 interacts with and promotes K27-linked polyubiquitination of IKKε, and p62 is a cargo receptor that recognizes ubiquitinated IKKε for eventual autophagic degradation. Together, the current findings elucidate the role of DLG1 in the antiviral IFN-I signaling pathway and viral infection repression.
Draft genome sequence of
Yarrowia lipolytica
NRRL Y-64008, an oleaginous yeast capable of growing on lignocellulosic hydrolysates
Authors: Jagtap Sujit Sadashiv , Liu Jing-Jing , Walukiewicz Hanna E. , Riley Robert , Ahrendt Steven , Koriabine Maxim , Cobaugh Kelly , Salamov Asaf , Yoshinaga Yuko , Ng Vivian , Daum Chris , Grigoriev Igor V. , Slininger Patricia J. , Dien Bruce S. , Jin Yong-Su , Rao Christopher V.
Published: November 2023

Yarrowia lipolytica
is an oleaginous yeast that produces high titers of fatty acid-derived biofuels and biochemicals. It can grow on hydrophobic carbon sources and lignocellulosic hydrolysates. The genome sequence of
Y. lipolytica
NRRL Y-64008 is reported to aid in its development as a biotechnological chassis for producing biofuels and bioproducts.
Metagenome-assembled genomes of the GU0601 sample (the Han River, South Korea)
Authors: Jang YeongJun , Kang Jae-Shin , Bae Eun Hee , Lee JunMo
Published: November 2023

We generated metagenome sequences of the GU0601 sample collected from the Han River and constructed metagenome-assembled genomes (MAGs) to identify their bacterial composition. We identified six MAGs belonging to Alphaproteobacteria, Cyanobacteria, and Flavobacteria.
The heat shock protein Hsc70-3 mediates an anti-apoptotic response critical for
Plasmodium
evasion of
Anopheles gambiae
immunity
Authors: Alves e Silva Thiago Luiz , Canepa Gaspar E. , Sweeney Brendan , Hessab Alvarenga Patricia , Zhao Ming , Vega-Rodríguez Joel , Molina-Cruz Alvaro , Barillas-Mury Carolina
Published: November 2023

The mosquito immune system limits
Plasmodium
infection and malaria transmission.
Plasmodium falciparum
evades the mosquito defense response by expressing the surface protein
P. falciparum
P47 (Pfs47) that inhibits midgut epithelial nitration by interacting with the mosquito midgut P47 receptor (P47Rec). However, the mechanism by which P47Rec suppresses caspase-mediated nitration is unknown. Here, we show that epithelial invasion by Pfs47 knockout parasites is followed by an extrusion of cells undergoing caspase-mediated apoptosis, which triggers the release of hemocyte-derived microvesicles (HdMv’s), known to promote complement activation and ookinete lysis. In contrast, invasion by
P. falciparum
parasites that express Pfs47 accelerates the extrusion of damaged cells and disrupts caspase activation and HdMv release. The
Anopheles gambiae
heat shock protein 70 cognate 3 (Hsc70-3), the ortholog of
Drosophila
binding immunoglobulin protein, was identified as a molecular partner of P47Rec. Silencing of Hsc70-3 promotes lysis of Pfs47 wild-type parasites through a caspase S2-dependent mechanism. The interaction of P47Rec activates a Hsc70-3-mediated anti-apoptotic response that prevents caspase activation. The interaction of P47Rec with Hsc70-3 is necessary for
P. falciparum
to evade the mosquito early immune responses that target the ookinete stage.

IMPORTANCE

Malaria transmission by
Anopheles gambiae
mosquitoes is very effective, in part because the parasite expresses a surface protein called Pfs47 that allows it to evade the mosquito immune system. Here we investigate how this protein changes the response of mosquito midgut epithelial cells to invasion by the parasite. Pfs47 is known to interact with P47Rec, a mosquito midgut receptor. We found that Pf47Rec inhibits caspase-mediated apoptosis by interacting with the Hsc70-3. This disrupts nitration of midgut epithelial cells invaded by the parasite and the release of hemocyte-derived microvesicles, which are critical for effective activation of the mosquito complement system that eliminates the parasite.
Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia
Authors: Gaudino Maria , Salem Elias , Ducatez Mariette F. , Meyer Gilles
Published: November 2023

Bovine Astroviruses (BAstV) are small single-stranded, positive-sense RNA viruses that have been historically associated with the infection of the enteric tract in cattle, causing outbreaks of diarrhea, especially in young immunologically naive calves. Long neglected, BAstV have recently regained interest as they have been associated with several nonsuppurative encephalitis cases in cattle as well as in other species. Yet, the difficulty in isolating the virus in conventional cell cultures prevents a full understanding of BAstV tropism and pathogenesis in this species. Here, we describe the metagenomic identification of BAstV in the respiratory tract of calves affected by respiratory distress in French farms. BastV were prevalently detected in the lower respiratory tract of sick calves; however, molecular testing of further cohorts of respiratory samples highlighted their presence also in nasal swabs. Phylogenetic analyses revealed two divergent clades for neurotropic and enteric BAstV, suggesting that their tropism is likely to be strain-specific. BAstV detected in the respiratory tract of calves with respiratory disease were genetically related to enteric strains already described in cattle in Asia, displaying between 85% and 95% nucleotide identity. In addition, the sequences from France belonged to the clade of BAstV identified in yaks, roe deer, and camelids, underlining the interspecies transmission potential of the virus. More studies are warranted to understand if BAstV have a potential role in the onset of bovine respiratory disease.

IMPORTANCE

Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease.
Differences in injury and concussion rates in a cohort of Canadian female and male youth Rugby Union: a step towards targeted prevention strategies
Authors: Shill Isla J , West Stephen W , Sick Stacy , Schneider Kathryn J , Wiley J Preston , Hagel Brent E , Black Amanda M , Emery Carolyn A
Published: November 2023

Objective

To examine differences in match and training musculoskeletal injury and concussion rates and describe mechanisms of concussion while considering previous playing experience in female and male Canadian high school Rugby Union (‘rugby’) players.

Methods

A 2-year prospective cohort study was completed in a high school league (n=361 females, 421 player-seasons; n=429 males, 481 player-seasons) in Calgary, Canada over the 2018 and 2019 rugby playing seasons. Baseline testing was completed at the start of each season and injury surveillance and individual player participation through session attendance was documented to quantify individual-level player exposure hours. Injury incidence rates (IRs) and incidence rate ratios (IRRs) were calculated using Poisson regression, offset by player exposure hours and clustered by team.

Results

Overall match IR for females was 62% higher than males (overall IRR=1.62, 95% CI: 1.20 to 2.18) and the overall training IR was twice as high for females (overall IRR=2.15, 95% CI: 1.40 to 3.32). The female match concussion IR was 70% higher than the males (concussion IRR=1.70, 95% CI: 1.08 to 2.69). Females had a 75% greater tackle-related IR compared with males (IRR=1.75, 95% CI: 1.20 to 2.56). Additionally, female tacklers had a twofold greater rate of injury compared with male tacklers (IRR=2.17, 95% CI: 1.14 to 4.14). Previous playing experience was not associated with tackle-related injury or concussion IRs.

Conclusion

The rate of injury and concussion was significantly higher in females within this Canadian high school cohort. These results emphasise the need for development, implementation and evaluation of female-specific injury and concussion prevention strategies to reduce injury and concussion in female youth rugby.
Trends and risk of recurrent preterm birth in pregnancy cohorts in rural Bangladesh, 1990–2019
Authors: Aktar Shaki , Nu U Tin , Rahman Monjur , Pervin Jesmin , Rahman Syed Moshfiqur , El Arifeen Shams , Persson Lars Åke , Rahman Anisur
Published: November 2023

Introduction

A history of preterm birth reportedly increases the risk of subsequent preterm birth. This association has primarily been studied in high-income countries and not in low-income settings in transition with rapidly descending preterm birth figures. We evaluated the population-based trends of preterm births and recurrent preterm births and the risk of preterm birth recurrence in the second pregnancy based on prospectively studied pregnancy cohorts over three decades in Matlab, Bangladesh.

Methods

A population-based cohort included 72 160 live births from 1990 to 2019. We calculated preterm birth and recurrent preterm birth trends. We assessed the odds of preterm birth recurrence based on a subsample of 14 567 women with live-born singletons in their first and second pregnancies. We used logistic regression and presented the associations by OR with a 95% CI.

Results

The proportion of preterm births decreased from 25% in 1990 to 13% in 2019. The recurrent preterm births had a similar, falling pattern from 7.4% to 3.1% across the same period, contributing 27% of the total number of preterm births in the population. The odds of second pregnancy preterm birth were doubled (OR 2.18; 95% CI 1.96 to 2.43) in women with preterm birth compared with the women with term birth in their first pregnancies, remaining similar over the study period. The lower the gestational age at the first birth, the higher the odds of preterm birth in the subsequent pregnancy (test for trend p<0.001).

Conclusion

In this rural Bangladeshi setting, recurrent preterm births contributed a sizeable proportion of the total number of preterm births at the population level. The increased risk of recurrence remained similar across three decades when the total proportion of preterm births was reduced from 25% to 13%.
Improving early infant diagnosis for HIV-exposed infants using unmanned aerial vehicles for blood sample transportation in Conakry, Guinea: a comparative cost-effectiveness analysis
Authors: Inghels Maxime , Mee Paul , Diallo Oumou Hawa , Cissé Mohamed , Nelson David , Tanser Frank , Asghar Zahid , Koita Youssouf , Laborde-Balen Gabrièle , Breton Guillaume
Published: November 2023

Background

Early infant diagnosis (EID) for HIV-exposed infants is essential due to high mortality during the first months of their lives. In Conakry (Guinea), timely EID is difficult as traffic congestion prevents the rapid transport of blood samples to the central laboratory. We investigated the cost-effectiveness of transporting EID blood samples by unmanned aerial vehicles (UAV), also known as drones.

Methods and findings

Using Monte Carlo simulations, we conducted a cost-effectiveness comparative analysis between EID blood samples transportation by on-demand UAV transportation versus the baseline scenario (ie, van with irregular collection schedules) and compared with a hypothetic on-demand motorcycle transportation system. Incremental cost-effectiveness ratio (ICER) per life-year gained was computed. Simulation models included parameters such as consultation timing (eg, time of arrival), motorcycle and UAV characteristics, weather and traffic conditions. Over the 5-year period programme, the UAV and motorcycle strategies were able to save a cumulative additional 834.8 life-years (585.1–1084.5) and 794.7 life-years (550.3–1039.0), respectively, compared with the baseline scenario. The ICER per life-year gained found were US$535 for the UAV strategy versus baseline scenario, US$504 for the motorcycle strategy versus baseline scenario and US$1137 per additional life-year gained for the UAV versus motorcycle strategy. Respectively, those ICERs represented 44.8%, 42.2% and 95.2% of the national gross domestic product (GDP) per capita in Guinea—that is, US$1194.

Conclusion

Compared with the baseline strategy, both transportation of EID blood samples by UAVs or motorcycles had a cost per additional life-year gained below half of the national GDP per capita and could be seen as cost-effective in Conakry. A UAV strategy can save more lives than a motorcycle one although the cost needed per additional life-year gained might need to consider alongside budget impact and feasibility considerations.
Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
Authors: Khan Waqasuddin , Kabir Furqan , Kanwar Samiah , Aziz Fatima , Muneer Sahrish , Kalam Adil , Rajab Ali Mehdia Nadeem , Ansari Nadia , Vanaerschot Manu , Ahyong Vida , Fahsbender Liz , Kalantar Katrina , Black Allison , Glascock Abigail , Gil Juliana , Ayscue Patrick , Tato Cristina , Jehan Fyezah , Nisar Imran
Published: November 2023

Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associated with sequencing—equipment and running consumables have created an opportunity for broader adoption. During the COVID-19 pandemic, rapid diagnostics development and DNA sequencing revolutionised the ability to diagnose and sequence SARS-CoV-2 rapidly. Socioeconomic inequalities substantially impact the ability to sequence SARS-CoV-2 strains and undermine a developing country’s pandemic preparedness. Low- and middle-income countries face additional challenges in establishing, maintaining and expanding genomic surveillance. We present our experience of establishing a genomic surveillance system at the Aga Khan University, Karachi, Pakistan. Despite being at a leading health sciences research institute in the country, we encountered significant challenges. These were related to collecting standardised contextual data for SARS-CoV-2 samples, procuring sequencing reagents and consumables, and challenges with library preparation, sequencing and submission of high-quality SARS-CoV-2 genomes. Several technical roadblocks ensued during the implementation of the genomic surveillance framework, which were resolved in collaboration with our partners. High-quality genome sequences were then deposited on open-access platforms per the best practices. Subsequently, these efforts culminated in deploying Pakistan’s first SARS-CoV-2 phyllo surveillance map as a Nextstrain build. Our experience offers lessons for the successful development of Genomic Surveillance Infrastructure in resource-limited settings struck by a pandemic.
Household food insecurity during the COVID-19 pandemic and associated socioeconomic demographic factors in Papua New Guinea: evidence from the Comprehensive Health and Epidemiological Surveillance System
Authors: Silas Vinson D , Pomat William , Jorry Ronny , Emori Rebecca , Maraga Seri , Kue Lydia , Berry Noel , Aga Tess , Luu Hung N , Ha Toan H , Okely Anthony D , Pham Bang N
Published: November 2023

Introduction

The COVID-19 pandemic had an unprecedented impact on global food security, but little is known about the impact on food security at the household level. We examined the prevalence and socioeconomic demographic factors for household food insecurity during the COVID-19 pandemic in Papua New Guinea.

Methods

Household socioeconomic demographic data from the Comprehensive Health and Epidemiological Surveillance System were collected from six main provinces in 2020 (37880 participants) and compared with the 2018 data (5749 participants). The prevalence of household food insecurity was estimated and stratified by household socioeconomic demographic characteristics. Multinomial logistic regression was conducted to estimate adjusted OR (aOR) and 95% CI of risk factors.

Results

The overall prevalence of household food insecurity increased from 11% in 2018 to 20% in 2020, but varied across provinces, with the highest level reported in Central Province (35%) and the lowest level in East New Britain Province (5%).

Food shortages were 72% less likely among urban residents than those living in rural areas (aOR 0.28 (95% CI 0.21 to 0.36)). The risk of food insecurity was 53% higher among adults aged 25+ years with primary education (grades 3–8) than those with university education (aOR 1.53 (95% CI 1.09 to 2.13)). People from households in the poorest wealth quintiles were 80% more likely to report food shortage than those from the richest wealth quintile (aOR 1.78 (95% CI 1.29 to 2.45).

Conclusion

The study provides evidence to develop policy and intervention to deal with food insecurity in emergency situations in the future.
A systematic review of the indirect impacts of COVID-19 on sexual and reproductive health services and outcomes in humanitarian settings
Authors: Singh Lucy , Abbas Sarah Mohammedahmed , Roberts Bayard , Thompson Niamh , Singh Neha S
Published: November 2023

Background

Humanitarian settings, particularly those in low-income and middle-income countries (LMICs), present increased sexual and reproductive health (SRH) challenges for individuals and health systems. Previous infectious disease outbreaks in such settings have negatively impacted SRH services and outcomes, as fragmented health systems are further overstretched. The COVID-19 pandemic has magnified the SRH challenges in LMIC humanitarian settings on an unprecedented scale. However, understanding of the impacts of COVID-19 is lacking. This review aimed to understand how the COVID-19 pandemic has impacted SRH service coverage, utilisation and outcomes in LMIC humanitarian settings, to inform current and future humanitarian research, programming and practice.

Methods

A systematic review methodology was followed using Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting standards. Three search fields related to humanitarian settings, SRH and COVID-19 were applied, and limited to LMIC settings only. Three bibliographic databases and nine grey literature sources were searched. Articles meeting inclusion criteria at full-text screening were critically appraised using standardised tools. Data extraction was undertaken on included articles and analysed through narrative synthesis.

Results

In total, 7742 citations were screened and 42 were included in the review. All included studies were cross-sectional. The quality was mostly medium to high. Narrative synthesis identified the reduced provision of, and access to, SRH services, and increased morbidity including sexual and gender-based violence and unplanned pregnancies. Impacts on service uptake varied across and within settings. Adaptations to improve SRH service access including telemedicine were reported; however, implementation was hindered by resource constraints.

Conclusions

The COVID-19 pandemic has indirectly negatively impacted SRH at the individual and health system levels in LMIC humanitarian settings. Further research on the impacts on service uptake is required. SRH programmers should target interventions to meet the increased SRH needs identified. Policy-makers must incorporate SRH into emergency preparedness and response planning to mitigate indirect impacts on SRH in future outbreaks.