bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of stacked proportional bar graphs (“Grotta bars”) to visualize functional outcome distributions in observational neurology research
Authors: Forrest Meghan R. , Weissgerber Tracey L. , Lieske Emma S. , Tamayo Cuartero Elena , Fischer Elena , Jones Lydia , Piccininni Marco , Rohmann Jessica L.
Published: July 2024

Background and Objectives

Stacked proportional bar graphs (nicknamed “Grotta bars”) are commonly used to visualize functional outcome scales in stroke research and are also used in other domains of neurological research. In observational studies that present adjusted effect estimates, Grotta bars can mislead readers if they show unadjusted, confounded comparisons. In a sample of recent observational neurology studies with confounding-adjusted effect estimates, we aimed to determine the frequency with which Grotta bars were used to visualize functional outcomes and how often unadjusted Grotta bars were presented without an accompanying adjusted version. We also assessed the methods used to generate adjusted Grotta bars.

Methods

In this meta-research study, we systematically examined all observational studies published in the top 15 Clinical Neurology journals between 2020-2021 with an ordinal functional outcome and confounding-adjusted effect estimate. We determined whether at least one comparison using Grotta bars was present, whether the visualized comparisons were adjusted, and which adjustment strategies were applied to generate these graphs.

Results

250 studies met all inclusion criteria. Of these, 93 (37.2%) used Grotta bars to depict functional outcome scale distributions, with 73 (81.7%) presenting only Grotta bars without model-based adjustment. Amongst the 17 studies that presented Grotta bars adjusted using a model, the adjustment strategies included propensity score matching (n=10; 58.8%), regression (n=6; 35.3%), and inverse probability weighting (n=1; 5.9%). Most studies with Grotta bars (n=87; 87.9%) were stroke studies.

Discussion

Grotta bars were most often used in stroke research within our sample. Papers that present adjusted associations for functional outcomes commonly showed only unadjusted Grotta bars, which alone may be misleading for causal questions. In observational research, Grotta bars are most informative if an adjusted version, aligning with adjusted effect estimates, is presented directly alongside the unadjusted version. Based on our findings, we offer recommendations to help authors generate informative Grotta bars and facilitate correct interpretation for readers.
Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters
Authors: Madrigal Jennifer , Schubert Heidi L. , Sdano Matthew A. , McCullough Laura , Connell Zaily , Formosa Tim , Hill Christopher P.
Published: July 2024

Phosphorylation-dependent binding of theS. cerevisiaeSpt6p tSH2 domain (Spt6ptSH2) to the Rbp1p subunit of RNA polymerase II supports efficient transcription. Here, we report that Spt6ptSH2also binds the HECT-family E3 ubiquitin ligase Tom1p, a homolog of human HUWE1. Tom1p/HUWE1 have been implicated in targeting many small basic proteins for degradation, including excess ribosomal subunits and histones, although the mechanism of substrate recognition is not known. Our cryo-EM data revealed that Tom1p can adopt a compact α-solenoidal “basket” similar to the previously described structure of HUWE1, with the central cavity partially occupied by a disordered acidic domain. Sub-regions of this acidic domain supported binding to Spt6p or histones/nucleosomesin vitro, and the histone-binding region was important for Tom1p functionin vivo. We also visualized Tom1p in more extended forms, and speculate that transitions among these forms could be important for substrate selection and ubiquitylation. Genomic analyses provided additional support for the previously observed role for Tom1p in maintaining ribosomal protein pools, and also demonstrated a role in maintaining chromatin structure near genes. This suggests that the interaction with Spt6ptSH2affects substrate specificity by anchoring Tom1p to localized environments where histone ubiquitylation alters chromatin architecture.
Comparative vitreous proteomic profiling of proliferative diabetic retinopathy and diabetic with no-retinopathy subjects implicates impaired autophagy in DR pathogenesis
Authors: Sharma Sarmeela , Hameed Shahna Shahul , Vishwakarma Sushma , Chhablani Jay , Tyagi Mudit , Narayanan Raja , Pappuru Rajeev R , Swarup Ghanshyam , Chakrabharti Subhabrata , Kaur Inderjeet
Published: July 2024

Purpose

Diabetic retinopathy (DR) is a neurovascular complication of diabetes (DM) causing the loss of neurons (ganglion cells) in the retina. The disease etiology and potential pathogenic mechanisms in this disease remains unclear. In the present study, we aimed to further understand the key and novel pathogenic mechanisms involved in DR pathogenesis by taking cues from our global proteomics data.

Methodology

The study was approved by the institutional review board (IRB) of LVPEI, Hyderabad, India. Vitreous humour samples (PDR; n=3, DM; n=3, Control; n=3) were collected from patients undergoing vitrectomy and subjected to LC-MS-MS analysis. The acquired raw data were searched against the human vitreous proteome and was further analysed by various bioinformatic and proteomic tools. Western blotting and IHC was performed to validate crucial pathways. Blood samples from patients (DM, PDR & NPDR) and controls (n=50); cadaveric retinas from diabetic and non-diabetic donors (n=10) and epiretinal membranes (ERM, n=10) from DR cases and controls were collected and RNA was isolated. Quantitative expression of genes involved in autophagy were performed. ɅɅCT was compared across different categories and significance estimated using a student t-test.

Result

A total of 1079 proteins were identified with 16 completely novel proteins in eye proteome. Top pathways identified were autophagy, inflammation, LXR/RXR activation (lipid metabolism), ROS generation by macrophages, apoptosis and protein degradation. Regulatory proteins identified were associated with cell death, phagocytic activation, angiogenesis and apoptosis. Autophagy inducers such as ROS was found to be accumulated in the DR vitreous. TREM2, microglial receptor was identified as a novel protein in PDR vitreous. The expression ofTREM2, anautophagy-associated gene was significantly (p-value = 0.05) upregulated in all categories as compared to control (NDM and/or NDM/No-DR). TREM2 protein also seemed to colocalise with microglial marker F4/80 in retinal tissues and intense expression was observed near the blood vessels in case of PDR retina. Other autophagy-associated markers were also differentially regulated in DR as compared to controls.

Conclusion

This study emphasises on the strong role of autophagy pathways and its associated genes in the development of DR.
A cost-effective and scalable approach for DNA extraction from FFPE tissues
Authors: Geisenberger Christoph , Chimal Edgar , Jurmeister Philipp , Klauschen Frederick
Published: July 2024

Genomic profiling of cancer plays an increasingly vital role for diagnosis and therapy planning. In addition, research of novel diagnostic applications such as DNA methylation profiling requires large training and validation cohorts. Currently, most diagnostic cases processed in pathology departments are stored as formalin-fixed and paraffin embedded tissue blocks (FFPE). Consequently, there is a growing demand for high-throughput extraction of nucleic acids from FFPE tissue samples. While proprietary kits are available, they are expensive and offer little flexibility. Here, we present ht-HiTE, a high-throughput implementation of a recently published and highly efficient DNA extraction protocol. This approach enables manual and automated processing of 96-well plates with a liquid handler, offers two options for purification and utilizes off-the-shelf reagents. Finally, we show that methylation profiles obtained from DNA processed with ht-HiTE are of equivalent quality as compared to a manual, kit-based approach.
Jasmonic acid signalling is targeted by a smut fungal Tin2-fold effector
Authors: Gul Summia , Mendoza-Rojas Gabriel , Heßler Natascha , Galle Stefanie , Smits Sander H.J. , Altegoer Florian , Göhre Vera
Published: July 2024

In plants, jasmonate signaling is a hub integrating environmental cues with growth and development. Due to its role in balancing defense responses against pathogens, it is a target of effector proteins from various pathogens. Here, we characterized the fungal effector protein Tue1 from the Brassicaceae smut fungusThecaphora thlaspeos.T. thlaspeosnaturally infectsArabis hirsutabut can also colonize the non-hostArabidopsis thaliana. In planta, the fungal protein Tue1 hijacks the plant importin-α dependent nuclear transporter to reach the plant nucleus. It interacts with jasmonate ZIM domain 10 (JAZ10) proteins of bothA. thalianaandAr. hirsuta. Structure-guided analysis of Tue1 suggests that it binds the Jas motif of JAZ10 indicating a role in stabilization or binding competition with proteins like MYC3 and COI1. A subset of jasmonate-responsive genes is differentially regulated duringT. thlaspeosinfection, proposing a link of the Tue1 function to infection. Tue1 share structural similarity to the Tin2-fold family recently described in the corn smutUstilago maydis. Our study therefore suggests that this structural effector family is expanded across fungal pathogens, although future studies have to reveal whether targeting JAZ-repressors is a conserved mechanism or specifically acquired as an adaptation to its perennial host.
Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics
Authors: VanBelzen Jake , Sakelaris Bennet , Brickner Donna Garvey , Marcou Nikita , Riecke Hermann , Mangan Niall , Brickner Jason H.
Published: July 2024

Chromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNAin vivo. The occupancy of transcription factors (TFs) from ChIP-seq agrees well with an alternative method, chromatin endogenous cleavage (ChEC-seq2). However, ChIP-seq and ChEC-seq2 reveal strikingly different patterns of enrichment of yeast RNA polymerase II. We hypothesized that this reflects distinct populations of RNAPII, some of which are captured by ChIP-seq and some of which are captured by ChEC-seq2. RNAPII association with enhancers and promoters - predicted from biochemical studies - is detected well by ChEC-seq2 but not by ChIP-seq. Enhancer/promoter bound RNAPII correlates with transcription levels and matches predicted occupancy based on published rates of enhancer recruitment, preinitiation assembly, initiation, elongation and termination. The occupancy from ChEC-seq2 allowed us to develop a stochastic model for global kinetics of RNAPII transcription which captured both the ChEC-seq2 data and changes upon chemical-genetic perturbations to transcription. Finally, RNAPII ChEC-seq2 and kinetic modeling suggests that a mutation in the Gcn4 transcription factor that blocks interaction with the NPC destabilizes promoter-associated RNAPII without altering its recruitment to the enhancer.
Default Mode Network activation at task switches reflects mental task-set structure
Authors: Zhou Ashley X. , Duncan John , Mitchell Daniel J.
Published: July 2024

Recent findings challenge traditional views of the Default Mode Network (DMN) as purely task-negative or self-oriented, showing increased DMN activity during demanding switches between externally-focused tasks (Crittenden et al., 2015; Smith et al., 2018; Zhou et al., 2024). However, it is unclear what modulates the DMN at switches, with transitions within a stimulus domain activating DMN regions in some studies but not others. Differences in the number of tasks suggest that complexity or structure of the set of tasks may be important. In this fMRI study, we examined whether the DMN’s response to task switches depends on the complexity of the active set of tasks, manipulated by the number of tasks in a run, or abstract task groupings based on instructional order. Core DMN activation at task switches was unaffected by the number of currently relevant tasks. Instead, it depended on the order in which groups of tasks had been learnt. Multivariate decoding revealed that Core DMN hierarchically represents individual tasks, task domains, and higher-order task groupings based on instruction order. We suggest that, as the complexity of instructions increases, rules are increasingly organized into higher-level chunks, and Core DMN activity is highest at switches between chunks.
Near-Unity Indistinguishability of Single Photons Emitted from Dissimilar and Independent Atomic Quantum Nodes
Authors: Hoffet Félix , Lowinski Jan , Heller Lukas , Padrón-Brito Auxiliadora , de Riedmatten Hugues
Published: July 2024

Generating indistinguishable photons from independent nodes is an important challenge for the development of quantum networks. In this work, we demonstrate the generation of highly indistinguishable single photons from two dissimilar atomic quantum nodes. One node is based on a fully blockaded cold Rydberg ensemble and generates on-demand single photons. The other node is a quantum repeater node based on a Duan-Lukin-Cirac-Zoller quantum memory and emits heralded single photons after a controllable memory time that is used to synchronize the two sources. We demonstrate an indistinguishability of 94.6±5.2% for a temporal window including 90% of the photons. This advancement opens new possibilities for interconnecting quantum repeater and processing nodes with high-fidelity Bell state measurement without sacrificing its efficiency.

Published by the American Physical Society
2024
Innovative strategic multicriteria decision-making selection model of infrastructures projects delivery systems using multiobjective optimization, case of Egypt
Authors: Nouh Meshref Ahmed , Elkasaby Elsayed , Wageh Omnia
Published: July 2024

Purpose

To help decision-makers choose appropriate infrastructure project delivery systems (IPDS) and keep up with the construction industry’s rapid growth, this study aims to develop a goal optimization technique.This looks into team integration, large production and optimum sustainability. The suggested approach for meeting several infrastructure project objectives is flexible and expandable. This research overcomes the significant discrepancy between the construction industry’s progress and the rate at which project delivery methods evolve.

Design/methodology/approach

This study examined pertinent literature to choose an appropriate project delivery method and gave information on several elements that affect that decision. After optimization using a genetic algorithm (GA), a Pareto front of solutions has been found. The three construction goals of sustainability, mass production and team integration are all met by the chosen best solution. The four most popular possibilities for studying the suggested approach are five primary categories, each of which has 22 variables, and the weight of each variable was established using Simo’s procedure. This is optimized, demonstrating the accuracy of the optimization model.

Findings

Sustainability, mass production and team integration are the major goals of selecting the finest IPDS. The Pareto-optimal solutions discovered through analysis demonstrated that the created GA is reliable and generates solid outcomes. In fact, it enables decisions that were based on a single criterion to be overturned. The process has therefore demonstrated its efficacy in identifying the ideal answer. First integrated project delivery (IPD), second design-build (DB), third design-bid-build (DBB) and last construction manager at risk (CMR) are the best options. The weight of the aims function has found these rankings to be satisfactory.

Practical implications

The findings demonstrate that the suggested strategy can lead to optimization, providing the government with a wide range of options for attaining certain project objectives. The ability of this study to evaluate the combined effects of three objectives in choosing the best IPDS, the production of optimal selection solutions (IPDS), which can help with better decision-making when many objectives are present, and the flexibility and extendibility of the suggested approach for achieving priorities in infrastructure projects are what make it unique. This approach was able to select IPDS to meet developments in the construction project.

Originality/value

To confirm the validity of the GA, the factor of error was calculated, which is equal to 1.7599e-08.
Research visualization trends in research data management (RDM): a bibliometric analysis
Authors: Shah Naimat Ullah , Ali Nusrat , Hamid Aamir , Khan Muhammad Ajmal
Published: July 2024

Purpose

This study aims to examine research visualization trends in research data management (RDM), analyzing factors such as contributions, publications, document types, authors and research areas, emphasizing the dynamic nature of RDM research in the scholarly landscape.

Design/methodology/approach

The study analyzed citation histories for 1,401 publications from 2001 to 2021 in the Web of Science database, extracting no restrictions on document type or language. Literature visualization tools such as Biblioshiny, VOSviewer, ScientoPy and MS Excel were used. The researchers explored institutional collaborations, data-centric trends and RDM frontiers.

Findings

The majority of RDM research is conducted by librarians and information scientists. Research on RDM has increased over the past 21 years, peaking in 2019. Among universities, Sheffield and Pittsburgh have the most productivity in RDM research, and the USA is the most productive country. Most productive authors are Aleixandre-Benavent-R and Da Silva Jr. RDM; however, improvement is still needed, especially at academic universities.

Originality/value

This study provides valuable insights into the published literature on RDM and identifies patterns of collaboration among researchers in RDM.
Short-term rentals and residential rents: evidence from a regulation in Santa Monica
Authors: Chaves Fonseca Cayrua
Published: July 2024

Purpose

This study aims to investigate the relationship between Airbnb and long-term residential rents, using Santa Monica, California, as a case study. In 2015, Santa Monica adopted the home sharing ordinance (HSO), a stringent regulation aimed at restricting short-term rentals (STR). This research examines the implications of this ordinance on the local housing market.

Design/methodology/approach

The synthetic control method (SCM) is applied to a panel data set comprising Airbnb listings and residential rents from multiple cities in Los Angeles County. This approach is used to estimate the causal effects of Santa Monica’s HSO on two outcomes: Airbnb listings and residential rents.

Findings

The empirical results show a 60% reduction in Airbnb listings in Santa Monica within two years of implementing the ordinance. Despite this significant decrease, the effect of the regulation on rents was not significant. Suggestive evidence indicates that the ordinance’s ineffectiveness in increasing the number of houses allocated to long-term tenants may have contributed to its negligible impact on rental rates.

Originality/value

To the best of the author’s knowledge, this research is the first to use the SCM for evaluating the impact of STR regulations. It offers crucial insights to policymakers on regulating platforms like Airbnb. The study reveals a scenario where a marked decrease in Airbnb activity did not lower residential rents, highlighting the need for context-specific evaluations in understanding the housing market’s dynamics. Additionally, these findings are valuable for investors considering the implications of regulatory changes in the STR sector.
Export Potential Index for Textile Industry (EPIT) model proposal with structural equation modelling and application
Authors: Kırkın Metin , Aktepe Adnan , Toklu Bilal
Published: July 2024

Purpose

The aim of this study is to develop a new multidimensional index to measure export potential of textile firms by using firm-level data.

Design/methodology/approach

After a conceptual model, a structural equation model is developed with five dimensions and 27 observed variables based on resource-based view theory. The measurement model is solved by Linear Structural Relations (LISREL) with maximum likelihood algorithm by using data collected from 454 textile firms in Türkiye.

Findings

In this study, a new multidimensional index that measures export potential of textile firms is developed. With the proposed model, the export potential of textile firms can be calculated numerically with the five dimensions: Resources, Dynamism, Knowledge, Innovation and Sustainability. The comparison of the output of the proposed model with the control variable, firm’s actual export values, shows a significantly high success ratio of 90.76%.

Research limitations/implications

The model is applicable for textile firms at different export levels, regions and sub-sectors. The Export Potential Index for Textile Industry model is verified by using Turkish textile industry data. The robustness of the model may be increased by verifying the model by using some other countries data. This model can be implemented to other industrial sectors with some modification of the dimensions and variables.

Practical implications

The proposed model will contribute to the firms by calculating their export potential in five dimensions with their own variables numerically. The model will help firms to develop strategies to increase their export potential and to the governmental and industrial organizations to develop incentives policies.

Originality/value

This paper fills the gap in the literature by proposing a multidimensional index that determines a firm’s export potential numerically by using firm-level data.
Directional connectedness between the electricity prices and natural gas prices: evidence from Alberta’s electricity market
Authors: Oviedo-Gómez Andrés , Londoño-Hernández Sandra Milena , Manotas-Duque Diego Fernando
Published: July 2024

Purpose

This study aims to assess volatility spillovers and directional connectedness between electricity (EPs) and natural gas prices (GPs) in the Canadian electricity market, based on a hydrothermal power generation market strongly dependent on exogenous variables such as fossil fuel prices and climatology factors.

Design/methodology/approach

The methodology is divided into two stages. First, a quantile vector autoregression model is used to evaluate the direction and magnitude of the influence between natural gas and electricity prices through different quantiles of their distributions. Second, a cross-quantilogram is estimated to measure the directional predictability between these prices. The data set consists of daily electricity and natural gas prices between January 2015 and December 2023.

Findings

The main finding shows that electricity prices are pure shock receivers of volatility from natural gas prices for the different quantiles. In this way, natural gas price fluctuations explain 0.20%, 0.98% and 22.72% of electricity price volatility for the 10th, 50th and 90th quantiles, respectively. On the other hand, a significant and positive correlation is observed in the high quantiles of the electricity prices for any natural gas price value.

Originality/value

The study described the risk to the electricity market caused by nonrenewable source price fluctuations and provided evidence for designing regulatory policies to reduce its exposure in Alberta, Canada. It also allows us to understand the importance of natural gas in the energy transition process and define it as the fundamental determinant of the electricity market dynamic.
Effect of ozone treatment on phenylpropanoid metabolism in harvested cantaloupes
Authors: Ren Jie , Li Xiaoxue , Dong Chenghu , Zheng Pufan , Zhang Na , Ji Haipeng , Yu Jinze , Lu Xiaohui , Li Mo , Chen Cunkun , Liang Liya
Published: July 2024

Phenylpropanoid metabolism plays an important role in cantaloupe ripening and senescence, but the mechanism of ozone regulation on phenylpropanoid metabolism remains unclear. This study investigated how ozone treatment modulates the levels of secondary metabolites associated with phenylpropanoid metabolism, the related enzyme activities, and gene expression in cantaloupe. Treating cantaloupes with 15 mg/m3 of ozone after precooling can help maintain postharvest hardness. This treatment also enhances the production and accumulation of secondary metabolites, such as total phenols, flavonoids, and lignin. These metabolites are essential components of the phenylpropanoid metabolic pathway, activating enzymes like phenylalanine ammonia‐lyase, cinnamate 4‐hydroxylase, 4CL, chalcone synthase, and chalcone isomerase. The results of the transcriptional expression patterns showed that differential gene expression related to phenylpropanoid metabolism in the peel of ozone‐treated cantaloupes was primarily observed during the middle and late storage stages. In contrast, the pulp exhibited significant differential gene expression mainly during the early storage stage. Furthermore, it was observed that the level of gene expression in the peel was generally higher than that in the pulp. The correlation between the relative amount of gene changes in cantaloupe, activity of selected enzymes, and concentration of secondary metabolites could be accompanied by positive regulation of the phenylpropanoid metabolic pathway. Therefore, ozone stress induction positively enhances the biosynthesis of flavonoids in cantaloupes, leading to an increased accumulation of secondary metabolites. Additionally, it also improves the postharvest storage quality of cantaloupes.
Virulence factors of Salmonella spp. isolated from free‐living grass snakes Natrix natrix
Authors: Pawlak Aleksandra , Małaszczuk Michał , Dróżdż Mateusz , Bury Stanisław , Kuczkowski Maciej , Morka Katarzyna , Cieniuch Gabriela , Korzeniowska‐Kowal Agnieszka , Wzorek Anna , Korzekwa Kamila , Wieliczko Alina , Cichoń Mariusz , Gamian Andrzej , Bugla‐Płoskońska Gabriela
Published: July 2024

Salmonellosis associated with reptiles is a well‐researched topic, particularly in China and the United States, but it occurs less frequently in Europe. The growth of the human population and changes in the environment could potentially increase the interaction between humans and free‐living reptiles, which are an unidentified source of Salmonella species. In this study, we sought to explore this issue by comparing the microbiota of free‐living European grass snakes, scientifically known as Natrix natrix, with that of captive banded water snakes, or Nerodia fasciata. We were able to isolate 27 strains of Salmonella species from cloacal swabs of 59 N. natrix and 3 strains from 10 N. fasciata. Our findings revealed that free‐living snakes can carry strains of Salmonella species that are resistant to normal human serum (NHS). In contrast, all the Salmonella species strains isolated from N. fasciata were sensitive to the action of the NHS, further supporting our findings. We identified two serovars from N. natrix: Salmonella enterica subspecies diarizonae and S. enterica subspecies houtenae. Additionally, we identified three different virulotypes (VT) with invA, sipB, prgH, orgA, tolC, iroN, sitC, sifA, sopB, spiA, cdtB and msgA genes, and β‐galactosidase synthesised by 23 serovars. The identification of Salmonella species in terms of their VT is a relatively unknown aspect of their pathology. This can be specific to the serovar and pathovar and could be a result of adaptation to a new host or environment.
Rapid, easy, sensitive, low‐cost and on‐site detection of environmental DNA and RNA using CRISPR‐Cas13
Authors: Yang Jiwei , Matsushita Shoma , Xia Fei , Yoshizawa Susumu , Iwasaki Wataru
Published: July 2024

Environmental DNA (eDNA) monitoring of species distribution has become a critical tool in ecology, conservation biology and fisheries for identifying the presence and distribution of diverse organisms, including important, threatened and invasive species. However, eDNA detection still has room for improvement in sensitivity, requiring time‐consuming real‐time polymerase chain reaction (qPCR) steps and costly machines.

In this study, we report a CRISPR‐Cas13‐based method for rapid, easy, sensitive, low‐cost and on‐site detection of eDNA. The assay for the detection of common carp (Cyprinus carpio) and medaka (Oryzias latipes) nucleic acid employs a two‐step process, starting with recombinase polymerase amplification (RPA) and followed by cleavage using Cas13 nuclease, to effectively identify mitochondrial DNA or RNA.

Our results showed that the Cas13‐based method has a higher sensitivity than the qPCR‐based method in detecting tiny amounts of eDNA. When combined with reverse transcription of environmental RNA (eRNA), our method increased detection sensitivity by approximately one order of magnitude. Cas13‐based detection could achieve on‐site detection of eDNA using a quick nucleic acid extraction solution and lateral flow strips.

Cas13‐based detection of eDNA and eRNA requires minimal training efforts and can be performed in 1 h, without the need for centrifugation and qPCR machines. The portability of the Cas13‐based method, along with its accuracy and relative ease in designing primers and CRISPR RNA (crRNA), underscores its potential to broaden the application of eDNA and eRNA in various fields, including biodiversity conservation.
The impact of a mega‐fire on tree hollow loss and nest box occupancy by secondary cavity‐nesting cockatoos
Authors: Berris Karleah Kyrene , Barth Michael , Welz Torran
Published: July 2024

Tree hollows are important structural habitat features for secondary cavity‐nesting birds, however, there has been limited research on how fire severity and frequency affect hollow abundance. Following a mega‐fire on Kangaroo Island during the 2019–2020 Australian bushfire season, we conducted an opportunistic post‐fire assessment of the fate of 144 monitored hollows in Eucalyptus cladocalyx and Eucalyptus leucoxylon trees used by endangered glossy black‐cockatoos (Calyptorhynchus lathami halmaturinus) and yellow‐tailed black‐cockatoos (Zanda funerea). We investigated the relationship between burn severity, inter‐fire interval, tree species and landscape position on the likelihood of tree hollow loss. We also compared the occupancy of nest boxes by both cockatoo species in fire‐affected catchments pre‐fire (2015–2017; 59 nest boxes) and post‐fire (2020–2022; 52 nest boxes). Surveys revealed that 64.4% of monitored tree hollows within the burnt area were destroyed, as were the trees that contained them. Most monitored tree hollows (76.9%) were in areas that had not experienced fire in >50 years prior to the 2019–2020 fires. Tree hollow loss in 2020 was 29 times greater than the mean annual loss of 1.6% recorded in the 22 years prior. Burn severity, inter‐fire interval, landscape matrix and tree species were poor predictors of hollow loss. However, increasing distance from forest edge slightly increased the probability of hollow loss. Post‐fire, the proportion of nest boxes used for nesting by glossy black‐cockatoos per annum increased to 0.70 ± 0.09, compared to 0.50 ± 0.03 pre‐fire. However, the proportion of nest boxes used for nesting by yellow‐tailed black‐cockatoos per annum remained similar (post‐fire 0.32 ± 0.12; pre‐fire 0.28 ± 0.05). The mega‐fires on Kangaroo Island in 2019–2020 resulted in tree hollow loss on a much larger scale than recorded in the 22 years prior, and subsequently, nest boxes have become an important resource for the endangered glossy black‐cockatoo.
Trastuzumab deruxtecan versus trastuzumab emtansine in Asian patients with HER2‐positive metastatic breast cancer
Authors: Iwata Hiroji , Xu Binghe , Kim Sung‐Bae , Chung Wei‐Pang , Park Yeon Hee , Kim Min Hwan , Tseng Ling‐Ming , Chung Chi‐Feng , Huang Chiun‐Sheng , Kim Jee Hyun , Chiu Joanne Wing Yan , Yamashita Toshinari , Li Wei , Egorov Anton , Nishijima Soichiro , Nakatani Shunsuke , Nishiyama Yuji , Sugihara Masahiro , Cortés Javier , Im Seock‐Ah
Published: July 2024

The global phase 3 DESTINY‐Breast03 study (ClinicalTrials.gov; NCT03529110) showed statistically significant and clinically meaningful improvements in progression‐free survival (PFS) and overall survival (OS) with trastuzumab deruxtecan (T‐DXd) over trastuzumab emtansine (T‐DM1) in patients with human epidermal growth factor receptor 2 (HER2)‐positive metastatic breast cancer (mBC) previously treated with trastuzumab and a taxane. Here, we report a subgroup analysis of Asian patients enrolled in DESTINY‐Breast03. In total, 309 patients (149 in the T‐DXd arm and 160 in the T‐DM1 arm) from Asian countries and regions were randomized. At data cutoff (July 25, 2022), the median duration of follow‐up in the Asian subpopulation was 29.0 months with T‐DXd and 26.0 months with T‐DM1. The PFS (determined by blinded independent central review) hazard ratio was 0.30 (95% confidence interval 0.22–0.41) favoring T‐DXd over T‐DM1 (median PFS 25.1 vs. 5.4 months). Median OS was not reached in the T‐DXd arm and was 37.7 months in the T‐DM1 arm. The median treatment duration was 15.4 months with T‐DXd and 5.5 months with T‐DM1. The incidence of grade ≥3 drug‐related treatment‐emergent adverse events was similar between both treatment arms (49.0% vs. 46.5%) and was consistent with the overall DESTINY‐Breast03 population. Adjudicated drug‐related interstitial lung disease or pneumonitis occurred in 12.9% of patients treated with T‐DXd and 2.5% treated with T‐DM1, with a higher incidence in Japanese patients; none of these were grade ≥4 events. These efficacy and safety data reinforce the favorable benefit–risk profile of T‐DXd in HER2‐positive mBC, including in the Asian subgroup.
Keratin 17 and Collagen type 1 genes: Esophageal cancer molecular marker discovery and evaluation
Authors: Pan Huiwen , Hong Jie , Shao Aizhong , Zhao Zhiguo , Ding Guowen , Fang Zhijie , Chen Keping , Zhu Jingfeng
Published: July 2024

One hundred eighty pairs of tissues of esophageal squamous cell carcinoma (ESCC) were tested by the transcriptome sequencing in order to explore etiology factors. The chi‐square test and correlation analysis demonstrated that the relative expression levels of keratin 17 (KRT17) and collagen type I α1 chain (COL1A1) were significantly higher in EC with diabetes. Expression of KRT17 was correlated with blood glucose (r = 0.204, p = 0.001) and tumor size (r = −0.177, p = 0.038) in patients. COL1A1 correlated with age (r = −0.170, p = 0.029) and blood glucose levels (r = 0.190, p = 0.015). Experimental results of qRT‐PCR: KRT17 and COL1A1 genes were highly expressed in ESCC (p < 0.05). When the two genes were used as a combination test, the positive detection rate of EC was 90.6%, and the ROC curve had greater power. The KRT17 and COL1A1 genes had the potential to be biomarkers for the diagnosis of ESCC.
SARS‐CoV‐2‐Infektionen bei Patienten mit Psoriasis in Deutschland: Daten aus den deutschen Registern PsoBest und CoronaBest
Authors: López María José Valencia , Meineke Anna , Stephan Brigitte , Rustenbach Stephan Jeff , Kis Anne , Thaçi Diamant , Mrowietz Ulrich , Reich Kristian , Staubach‐Renz Petra , von Kiedrowski Ralph , Bogena Henriette , Augustin Matthias
Published: July 2024

Einleitung

Es gibt nur wenige Daten über die Merkmale von SARS‐CoV‐2‐Infektionen bei deutschen Patienten mit Psoriasis oder Psoriasisarthritis (PsA). Diese Studie analysiert die COVID‐19‐Prävalenz und den Schweregrad der Symptome bei diesen Patienten.

Patienten und Methodik

Die Teilnehmer der deutschen Register PsoBest und CoronaBest wurden im Februar 2022 befragt und deskriptiv ausgewertet.

Ergebnisse

4818 Patienten mit einem Durchschnittsalter von 56,4 Jahren wurden in die Analyse einbezogen. Positive SARS‐CoV‐2‐Tests wurden von 737 (15,3%) Patienten gemeldet. Die am häufigsten berichteten akuten Symptome waren Müdigkeit (67,3%), Husten (58,8%) und Kopfschmerzen (58,3%). Länger anhaltende Symptome nach der akuten Phase von COVID‐19 wurden von 231 der 737 Patienten angegeben. Bei den meisten Patienten (92,9%) wurde die systemische Behandlung für ihre Psoriasis oder PsA während der Pandemie nicht geändert. Positiv auf SARS‐CoV‐2 getestete Patienten waren im Durchschnitt jünger und hatten häufiger Änderungen in der Therapie der Psoriasis als negativ getestete Patienten (8,5% vs. 5,4%).

Schlussfolgerungen

In dieser Kohorte von Patienten mit Psoriasis oder PsA, die sich einer systemischen Behandlung unterzogen, waren SARS‐CoV‐2‐Infektionen häufig, wenn auch weniger häufig als in der deutschen Allgemeinbevölkerung. Bei den Patienten wurden keine Risikosignale für schwerere COVID‐19‐Erkrankungen oder erhöhte Infektionsraten beobachtet. Außerdem blieben die systemischen Therapien weitgehend unverändert, so dass keine Risiken auf diese Therapien zurückgeführt werden können.
Qatar's multifaceted humanitarian role in Afghanistan since August 2021
Authors: Milton Sansom , Elkahlout Ghassan
Published: July 2024

Motivation

Qatar's humanitarian role in Afghanistan, a less‐explored example of a non‐traditional actor, is crucial in understanding international responses to geopolitical crises. Examining Qatar's involvement provides insights into the complex dynamics of humanitarian assistance, diplomatic efforts, and post‐crisis challenges.

Purpose

The study examines Qatar's multifaceted role in Afghanistan since 2021, highlighting its impact as a non‐traditional actor in complex humanitarian operations and diplomacy.

Approach and methods

The research combines a desk review of online sources, academic literature, reports, non‐governmental organization documents, and media articles with first‐hand observations and informal stakeholder interviews. It also analyses international aid statistics from the United Nations Office for the Coordination of Humanitarian Affairs' Financial Tracking Service and the Organisation for Economic Co‐operation and Development's Development Assistance Committee.

Findings

Qatar emerged as a key humanitarian player in Afghanistan, adopting a whole‐of‐society approach. Its efforts encompassed emergency relief, evacuations, educational support, and humanitarian diplomacy, effectively bridging the Taliban with international actors after the takeover.

Policy implications

This research highlights the impactful role of non‐traditional donors, as seen with Qatar in Afghanistan, emphasizing their potential in complex humanitarian scenarios. The study advocates recognizing and leveraging the unique capabilities of smaller states and non‐traditional actors in humanitarian responses, promoting capacity building to harness their institutional agility and societal resources effectively.
Evaluation of the prognostic value of papillary muscle‐free strain in patients with hypertrophic cardiomyopathy
Authors: Koyuncu Atilla , Yildiz Cennet , Oflar Ersan , Mavi Busra , Ertugrul Abdulcelil Sait , Ocal Lutfi , Gürsoy Mustafa Ozan , Kahveci Gokhan
Published: July 2024

Background

The prognosis of hypertrophic cardiomyopathy (HCM) varies from mild disease with a normal life expectancy to heart failure and sudden cardiac death (SCD). The identification of patients who are at high risk for SCD remains challenging.

Aims

In this study, we evaluated the prognostic value of papillary muscle‐free strain in HCM patients.

Methods and Results

Seventy‐nine patients with a diagnosis of HCM were included in this study. Patients were divided into low/intermediate‐risk (n = 57) and high‐risk (n = 22) groups. Two‐dimensional (2‐D) echocardiography and strain imaging were performed for each patient. The mean age of the study population was 53.85 ± 15.88 years; 47 (59.5%) of them were male. During a mean follow‐up duration of 74.45 ± 17.03 months, 12 patients died. A comparison of the low‐intermediate and high‐SCD risk groups revealed that patients in the high‐SCD risk group had greater maximal wall thickness, interventricular septum thickness, posterior wall thickness, and left ventricular mass index (LVMI) and lower (less negative) global longitudinal, anterolateral papillary muscle (ALPM) and posteromedial papillary muscle (PMPM) free strain. Additionally, a history of syncope and ICD implantation were found to be more common in patients with high SCD risk scores. The SCD risk score was positively correlated with the global longitudinal strain, ALPM‐free strain, and PMPM‐free strain (r = .528, r = .658, and r = .600, respectively; p < .001 for all). Our results showed that the LVMI, presence of syncope, global longitudinal strain, and ALPM‐free strain were predictors of death.

Conclusions

Decreased papillary muscle‐free strain values might have prognostic value in patients with HCM.
Weather patterns determine success rates of two biocontrol agents on Cytisus scoparius in the USA
Authors: Bode Robert Frederick , Cervantez Olivia
Published: July 2024

To be effective, a biocontrol agent must survive and persist in the same habitat as the target species and reduce target population growth. When multiple biocontrol agents are used against a single invasive species, they may each perform better under a subset of the habitat in which the target lives. This complementarity allows for a more consistent level of control and a higher resilience to environmental variability. Two species that feed on the same plant tissues would compete, but niche partitioning in the native range may be replicated when both species are introduced to the invasive range. When biocontrol agents are released, they may self‐sort to perform best in their respective niches. We hypothesized that two biocontrol agents—Scotch broom seed beetle, Bruchidius villosus (Fabricius) (Coleoptera: Chrysomelidae) and Scotch broom seed weevil, Exapion fuscirostre (Fabricius) (Coleoptera: Brentidae)—that both feed on seeds of the invasive legume Scotch broom, Cytisus scoparius L. Link (Fabaceae), would be impacted differently by different weather conditions and plant traits, and would show different success rates at field sites with different conditions. We used a 5‐year study to reveal that the two biocontrol agents are not uniformly distributed in the field and that weather and plant factors influence their success. We confirmed that weather conditions of the previous year influenced biocontrol agent attack rate and found that weather patterns at a field site may predict the impact of each biocontrol agent.
Effects of co‐administration of lamotrigine on valproate transfer across the placenta and its brain entry in developing Genetic Absence Epilepsy Rats from Strasbourg (GAERS)
Authors: Qiu Fiona , Huang Yifan , Dziegielewska Katarzyna M. , Habgood Mark D. , Saunders Norman R.
Published: July 2024

During development, embryos and foetuses may be exposed to maternally ingested antiseizure medications (ASM), valproate and lamotrigine, essential in some patients to control their epilepsy symptoms. Often, the two drugs are co‐administered to reduce required doses of valproate, a known potential teratogen. This study used Genetic Absence Epilepsy Rat from Strasbourg to evaluate transfer of valproate and lamotrigine across late gestation placenta and their entry into cerebrospinal fluid (CSF) and brain of developing rats, in mono‐ and combination therapies. Animals at embryonic day (E) 19, postnatal day (P) 0, 4 and 21, and adults were administered valproate (30 mg/kg) or lamotrigine (6 mg/kg) with their respective [3H]‐tracers, either alone or in combination. In chronic experiments, females consumed valproate‐containing diet from 2 weeks prior to mating until offspring were used at E19 and P0. Drugs were injected 30 min before blood, CSF and brain samples were collected from terminally anaesthetised animals. Radioactivity in samples was measured. In acute monotherapy brain entry of valproate was higher in foetal than postnatal animals, correlating with its plasma protein binding. Brain entry of lamotrigine was not age‐dependent. Combination therapy enhanced entry of lamotrigine into the adult brain but had no effects on brain and CSF entry of valproate. Following chronic valproate exposure, placental transfer of valproate decreased in combination therapy; however, foetal brain entry increased. Results suggest that during pregnancy, the use of combination therapy of valproate and lamotrigine may mitigate overall foetal exposure to valproate but potential risks to foetal brain development are less clear.
Molecular mechanisms of spinal cord injury repair across vertebrates: A comparative review
Authors: Jiang Ying , Cai Yang , Yang Ning , Gao Si , Li Qingwei , Pang Yue , Su Peng
Published: July 2024

In humans and other adult mammals, axon regeneration is difficult in axotomized neurons. Therefore, spinal cord injury (SCI) is a devastating event that can lead to permanent loss of locomotor and sensory functions. Moreover, the molecular mechanisms of axon regeneration in vertebrates are not very well understood, and currently, no effective treatment is available for SCI. In striking contrast to adult mammals, many nonmammalian vertebrates such as reptiles, amphibians, bony fishes and lampreys can spontaneously resume locomotion even after complete SCI. In recent years, rapid progress in the development of next‐generation sequencing technologies has offered valuable information on SCI. In this review, we aimed to provide a comparison of axon regeneration process across classical model organisms, focusing on crucial genes and signalling pathways that play significant roles in the regeneration of individually identifiable descending neurons after SCI. Considering the special evolutionary location and powerful regenerative ability of lamprey and zebrafish, they will be the key model organisms for ongoing studies on spinal cord regeneration. Detailed study of SCI in these model organisms will help in the elucidation of molecular mechanisms of neuron regeneration across species.
TRAF2 associates with cullin neddylation complex assembly
Authors: Wang Tiantian , Zhang Qi , Xu Yu , Yan Rong , Pan Yuting , Xuan Ying , Shen Mengzhen , Chen Xianzhi , Zhu Hongyan , Ke Xisong , Qu Yi , Zhang Xue
Published: July 2024

Cullin‐based RING ligases (CRLs) comprise the largest family of ubiquitin E3 ligases. CRL activity is tightly regulated by cullin neddylation, which has been associated with various diseases. Although inhibitors of CRLs neddylation have been reported, there is a lack of small molecules that can selectively target individual cullins. Here, we identified a natural product, liquidambaric acid (LDA), with relatively selective inhibition properties against cullin (Cul) 2 neddylation, and found that its target, Tumor Necrosis Factor receptor‐associated factor 2 (TRAF2) was required for the activity. TRAF2 associates with the Cul2 neddylation complex and regulates the machinery assembly, especially that of E2 (UBC12) and E3 (RBX1) enzymes. In addition, we demonstrated that by intervention of the associations between TRAF2 and the neddylation machinery, LDA disturbed NEDD8 transfer from E1 to E2, therefore blocking Cul2 neddylation. Taken together, we show that TRAF2 plays a positive role in neddylation cascades, and we have identified a small molecule capable of selective modulation of cullin neddylation.