bluuebunny/crossref_metadata_2025 huggingface dataset:
Endophytic and ectomycorrhizal, an overlooked dual ecological niche? Insights from natural environments andRussulaspecies
Authors: Laurent-Webb Liam , Rech Philippe , Bourceret Amélia , Chaumeton Chloé , Deveau Aurélie , Genola Laurent , Januario Mélanie , Petrolli Rémi , Selosse Marc-André
Published: January 2024

Ectomycorrhizal (EcM) fungi play key roles in ecosystem functioning, in particular temperate ones. Recent findings suggest that they can endophytically colonize the roots of non-EcM plants. Here we aim at (i) providing new evidence of colonization of non-EcM hosts by EcM fungi, (ii) exploring factors driving such colonization (plant identity, site, root filter), and (iii) providing direct microscopical evidence for endophytism.

Using amplicon sequencing (ITS2), we described the root fungal communities of 42 plant species collected at nine locations in France. In two of those sites, we also compared rhizosphere and root fungal communities to identify a potential root filter. Finally, we investigated endophytism inRussulaspp. at twoRussula-rich sites using fluorescencein situhybridization (FISH) paired with confocal microscopy.

We find a large but variable share of EcM sequences in roots of non-EcM plant species, in particular nearby EcM hosts, suggesting that endophytism is a secondary ecological niche. Though EcM fungi were more abundant in the rhizosphere compared to roots, their composition was similar to that of roots, suggesting a poor root filter. We observed metabolically active hyphae ofRussulaspp. endophytically colonizing the apoplast of two non-EcM plant species.

As shown for other EcM fungi (e.g.,Tuberspp., Ascomycota) we demonstrate the dual EcM/endophyte niche forRussula(Basidiomycota). The ecological consequences of this duality still need to be addressed. The ability to colonize two ecological niches may be a trait kept by EcM fungi which evolved from endophytic fungi, as stipulated by the “waiting room hypothesis”.
High-resolution Inference of Multiplexed Anti-HIV Gene Editing using Single-Cell Targeted DNA Sequencing
Authors: Bouzidi Mohamed , Dossani Zain , Di Benedetto Carolina , Raymond Kyle , Desai Shivani , Chavez Leonard , Betancur Paola , Pillai Satish K.
Published: January 2024

Gene therapy-based HIV cure strategies typically aim to excise the HIV provirus directly, or target host dependency factors (HDFs) that support viral persistence. Cure approaches will likely require simultaneous co-targeting of multiple sites within the HIV genome to prevent evolution of resistance, and/or co-targeting of multiple HDFs to fully render host cells refractory to HIV infection. Bulk cell-based methods do not enable inference of co-editing within individual viral or target cell genomes, and do not discriminate between monoallelic and biallelic gene disruption. Here, we describe a targeted single-cell DNA sequencing (scDNA-seq) platform characterizing the near full-length HIV genome and 50 established HDF genes, designed to evaluate anti-HIV gene therapy strategies. We implemented the platform to investigate the capacity of multiplexed CRISPR-Cas9 ribonucleoprotein complexes (Cas9-RNPs) to simultaneously 1) inactivate the HIV provirus, and 2) knockout the CCR5 and CXCR4 HDF (entry co-receptor) genes in microglia and primary monocyte-derived macrophages (MDMs). Our scDNA-seq pipeline revealed that antiviral gene editing is rarely observed at multiple loci (or both alleles of a locus) within an individual cell, and editing probabilities across sites are linked. Our results demonstrate that single-cell sequencing is critical to evaluate the true efficacy and therapeutic potential of HIV gene therapy.
High interleukin-3 concentrations prime murine myeloid progenitor cells towards granulocytic differentiation
Authors: Hakobyan Mariam , Rohdjeß Hannah , Lipka Daniel B.
Published: January 2024

Impaired differentiation a key feature of many hematopoietic malignancies. To decipher the molecular processes underlying malignant transformation, it is important to understand the mechanisms regulating hematopoietic differentiation. Cell lines derived from transformed hematopoietic progenitors or from leukemia patients have proven to be valuable model systems for mechanistic investigations of hematopoiesis. In the present work, we investigated the cell-intrinsic differentiation capacity of the interleukin 3 (IL-3) dependent murine myeloid progenitor cell line 32D. We demonstrated that 32D cells have a cell-intrinsic granulocytic differentiation potential which requires the presence of high IL-3 concentrations in order to induce granulocytic priming. We also show that 32D cells still proliferate at comparable rates but lack granulocytic priming in the presence of intermediate IL-3 concentrations. This phenotypic plasticity is fully reversible and entirely depends on the IL-3 concentrations present in the culture media. RNA-seq analysis revealed that, among other myeloid genes, the expression ofCsf3ris strongly induced exclusively in the presence of high IL-3 concentrations, likely explaining the granulocytic differentiation in response to G-CSF treatment. Together, our work provides detailed cellular and molecular insights into the phenotypic plasticity of 32D cells driven by different IL-3 concentrations and suggest culture conditions for different experimental set ups.

Key points

32D cells represent a murine myeloid cell line with endogenous granulocytic differentiation potential.

32D cells present molecular and functional plasticity depending on their culture conditions.

High IL-3 culture conditions prime 32D cells towards the granulocytic lineage.

Low IL-3 culture conditions lead to a reversible loss of the granulocytic differentiation potential of 32D cells while fully maintaining their proliferative activity.
ImprintedGrb10, encoding growth factor receptor bound protein 10, regulates fetal growth independently of the insulin-like growth factor type 1 receptor (Igf1r) and insulin receptor (Insr) genes
Authors: Moorwood Kim , Smith Florentia M. , Garfield Alastair S. , Ward Andrew
Published: January 2024

Background

Optimal size at birth dictates perinatal survival and long-term risk of developing common disorders such as obesity, type 2 diabetes and cardiovascular disease. The imprintedGrb10gene encodes a signalling adaptor protein capable of inhibiting receptor tyrosine kinases, including the insulin receptor (Insr) and insulin-like growth factor type 1 receptor (Igf1r).Grb10restricts fetal growth such thatGrb10knockout (KO) mice are at birth some 25-35% larger than wild type. Using a mouse genetic approach, we test the widely held assumption that Grb10 influences growth through interaction with Igf1r, which has a highly conserved growth promoting role.

Results

Should Grb10 interact with Igf1r to regulate growthGrb10:Igf1rdouble mutant mice should be indistinguishable fromIgf1rKO single mutants, which are around half normal size at birth. Instead,Grb10:Igf1rdouble mutants were intermediate in size betweenGrb10KO andIgf1rKO single mutants, indicating additive effects of the two signalling proteins having opposite actions in separate pathways. Some organs examined followed a similar pattern, thoughGrb10KO neonates exhibited sparing of the brain and kidneys, whereas the influence ofIgf1rextended to all organs. An interaction between Grb10 and Insr was similarly investigated. While there was no general evidence for a major interaction for fetal growth regulation, the liver was an exception. The liver inGrb10KO mutants was disproportionately overgrown with evidence of excess lipid storage in hepatocytes, whereasGrb10:Insrdouble mutants were indistinguishable fromInsrsingle mutants or wild types.

Conclusions

Grb10 acts largely independently of Igf1r or Insr to control fetal growth and has a more variable influence on individual organs. Only the disproportionate overgrowth and excess lipid storage seen in theGrb10KO neonatal liver can be explained through an interaction between Grb10 and the Insr. Our findings are important for understanding how positive and negative influences on fetal growth dictate size and tissue proportions at birth.
Nr4a2 blocks oAβ-mediated synaptic plasticity dysfunction and ameliorates spatial memory deficits in the APPSw,Indmouse
Authors: Català-Solsona Judit , Lutzu Stefano , Lituma Pablo J. , Fábregas-Ordoñez Cristina , Siedlecki Dolores , Giménez-Llort Lydia , Miñano-Molina Alfredo J. , Saura Carlos A. , Castillo Pablo E. , Rodriguez-Álvarez José
Published: January 2024

Alzheimer’s disease AD is associated with disruptions in neuronal communication, especially in brain regions crucial for learning and memory, such as the hippocampus. The amyloid hypothesis suggests that the accumulation of amyloid-beta oligomers (oAβ) contributes to synaptic dysfunction by internalisation of synaptic AMPA receptors. Recently, it has been reported that Nr4a2, a member of the Nr4a family of orphan nuclear receptors, plays a role in hippocampal synaptic plasticity by regulating BDNF and synaptic AMPA receptors. Here, we demonstrate that oAβ inhibits activity-dependent Nr4a2 activation in hippocampal neurons, indicating a potential link between oAβ and Nr4a2 down-regulation. Furthermore, we have observed a reduction in Nr4a2 protein levels in postmortem hippocampal tissue samples from early AD stages. Pharmacological activation of Nr4a2 proves effective in preventing oAβ-mediated synaptic depression in the hippocampus. Notably, Nr4a2 overexpression in the hippocampus of AD mouse models ameliorates spatial learning and memory deficits. In conclusion, the findings suggest that oAβ may contribute to early cognitive impairment in AD by blocking Nr4a2 activation, leading to synaptic dysfunction. Thus, our results further support that Nr4a2 activation is a potential therapeutic target to mitigate oAβ-induced synaptic and cognitive impairments in the early stages of Alzheimer’s disease.
Ising model formulation for highly accurate topological color codes decoding
Authors: Takada Yugo , Takeuchi Yusaku , Fujii Keisuke
Published: January 2024

Quantum error correction is an essential ingredient for reliable quantum computation for theoretically provable quantum speedup. Topological color codes, one of the quantum error correction codes, have an advantage against the surface codes in that all Clifford gates can be implemented transversally. However, the hardness of decoding makes the color codes not suitable as the best candidate for experimentally feasible implementation of quantum error correction. Here we propose an Ising model formulation that enables highly accurate decoding of the color codes. In this formulation, we map stabilizer operators to classical spin variables to represent an error satisfying the syndrome. Then we construct an Ising Hamiltonian that counts the number of errors and formulate the decoding problem as an energy minimization problem of an Ising Hamiltonian, which is solved by simulated annealing. In numerical simulations on the (4.8.8) lattice, we find an error threshold of 10.36(5)% for bit-flip noise model, 18.47(5)% for depolarizing noise model, and 2.90(4)% for phenomenological noise model (bit-flip error is located on each of data and measurement qubits), all of which are higher than the thresholds of existing efficient decoding algorithms. Furthermore, we verify that the achieved logical error rates are almost optimal in the sense that they are almost the same as those obtained by exact optimizations by CPLEX with smaller decoding time in many cases. Since the decoding process has been a bottleneck for performance analysis, the proposed decoding method is useful for further exploration of the possibility of the topological color codes.

Published by the American Physical Society
2024
High-Sensitivity ac-Charge Detection with a MHz-Frequency Fluxonium Qubit
Authors: Najera-Santos B.-L. , Rousseau R. , Gerashchenko K. , Patange H. , Riva A. , Villiers M. , Briant T. , Cohadon P.-F. , Heidmann A. , Palomo J. , Rosticher M. , le Sueur H. , Sarlette A. , Smith W. C. , Leghtas Z. , Flurin E. , Jacqmin T. , Deléglise S.
Published: January 2024

Owing to their strong dipole moment and long coherence times, superconducting qubits have demonstrated remarkable success in hybrid quantum circuits. However, most qubit architectures are limited to the GHz frequency range, severely constraining the class of systems they can interact with. The fluxonium qubit, on the other hand, can be biased to very low frequency while being manipulated and read out with standard microwave techniques. Here, we design and operate a heavy fluxonium with an unprecedentedly low transition frequency of 1.8 MHz. We demonstrate resolved sideband cooling of the “hot” qubit transition with a final ground state population of 97.7%, corresponding to an effective temperature of 23  μK. We further demonstrate coherent manipulation with coherence times T1=34  μs, T2*=39  μs, and single-shot readout of the qubit state. Importantly, by directly addressing the qubit transition with a capacitively coupled waveguide, we showcase its high sensitivity to a radio-frequency field. Through cyclic qubit preparation and interrogation, we transform this low-frequency fluxonium qubit into a frequency-resolved charge sensor. This method results in a charge sensitivity of 33  μe/Hz, or an energy sensitivity (in joules per hertz) of 2.8ℏ. This method rivals state-of-the-art transport-based devices, while maintaining inherent insensitivity to dc-charge noise. The high charge sensitivity combined with large capacitive shunt unlocks new avenues for exploring quantum phenomena in the 1–10 MHz range, such as the strong-coupling regime with a resonant macroscopic mechanical resonator.

Published by the American Physical Society
2024
A web-based dashboard for RELION metadata visualization
Authors: González-Rodríguez Nayim , Areán-Ulloa Emma , Fernández-Leiro Rafael
Published: January 2024

Cryo-electron microscopy (cryo-EM) has witnessed radical progress in the past decade, driven by developments in hardware and software. While current software packages include processing pipelines that simplify the image-processing workflow, they do not prioritize the in-depth analysis of crucial metadata, limiting troubleshooting for challenging data sets. The widely used RELION software package lacks a graphical native representation of the underlying metadata. Here, two web-based tools are introduced: relion_live.py, which offers real-time feedback on data collection, aiding swift decision-making during data acquisition, and relion_analyse.py, a graphical interface to represent RELION projects by plotting essential metadata including interactive data filtration and analysis. A useful script for estimating ice thickness and data quality during movie pre-processing is also presented. These tools empower researchers to analyse data efficiently and allow informed decisions during data collection and processing.
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons
Authors: Caramello Nicolas , Royant Antoine
Published: January 2024

Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump–probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.
The retail environment design (RED) scale: conceptualization and measurement
Authors: Steen Julie , Rutherford Brian N. , Babin Barry J. , Hair, Jr. Joseph F.
Published: January 2024

Purpose

Design is an important construct in the retail environment literature. Yet, the measures used for design have not followed appropriate scale development procedures. The purpose of this study is to provide a conceptual definition and then develop a scale for retail environment design (RED).

Design/methodology/approach

Interviews with both consumers and marketing researchers are used to generate a potential list of items. Using four different studies, these items are refined, and the RED scale is offered.

Findings

This study develops and validates the four-dimensional RED scale to measure the design of retail environments. The dimensions are functional, aesthetic, lighting and signage.

Research limitations/implications

The newly developed RED scale will allow retailing researchers to measure lighting and signage qualities as part of retail design, measure design of retail environments more accurately and allow different studies to be compared.

Practical implications

The newly developed RED scale will allow retailers to better understand customers’ perceptions of the four dimensions of design. Retailers spend significant time and money designing and redesigning retail environments. The RED scale will enable managers to ensure these significant investments create competitive advantages and an appropriate return on investment.

Originality/value

A scale to measure retail environment design is developed. The scale includes two dimensions (lighting and signage) that are not typically investigated.
Nexus between formal institutions and inward FDI in India: a nonlinear autoregressive distributive lag approach
Authors: Patel Richa , Mohapatra Dipti Ranjan , Yadav Sunil Kumar
Published: January 2024

Purpose

This study presents time-series data estimations on the association between the indicators of institutional environment and inward foreign direct investment (FDI) in India utilizing a comprehensive data set from 1996 to 2021.

Design/methodology/approach

The study employs the nonlinear autoregressive distributive lag (NARDL) model. The asymmetric ARDL framework evaluates the existence of cointegration among the factors under study and highlights the underlying nonlinear effects that may exist in the long and short run.

Findings

The significance of coefficients of negative shock to “control of corruption” and positive shock to “rule of law” is greater when compared to “government effectiveness, regulatory quality, political stability/absence of violence.” The empirical outcomes suggest the positive influence of rule of law, political stability and government effectiveness on FDI inflows. A high “regulatory quality” is observed to deter foreign investment. The “voice and accountability” index and negative shocks to the “rule of law” are exhibited to have no substantial impact on the amount of FDI that the country receives.

Originality/value

This study empirically examines the institutional determinants of FDI in India for a comprehensive period of 1996–2021. The study's findings imply that quality of the institutional environment has a significant bearing on India's inward FDI.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-05-2023-0375
DoS attack detection using Aquila deer hunting optimization enabled deep belief network
Authors: Thomas Merly , B.B. Meshram
Published: January 2024

Purpose

Denial-of-service (DoS) attacks develop unauthorized entry to various network services and user information by building traffic that creates multiple requests simultaneously making the system unavailable to users. Protection of internet services requires effective DoS attack detection to keep an eye on traffic passing across protected networks, freeing the protected internet servers from surveillance threats and ensuring they can focus on offering high-quality services with the fewest response times possible.

Design/methodology/approach

This paper aims to develop a hybrid optimization-based deep learning model to precisely detect DoS attacks.

Findings

The designed Aquila deer hunting optimization-enabled deep belief network technique achieved improved performance with an accuracy of 92.8%, a true positive rate of 92.8% and a true negative rate of 93.6.

Originality/value

The introduced detection approach effectively detects DoS attacks available on the internet.
Striking gold: navigating the education massification maze for work readiness
Authors: Enstroem Rickard , Schmaltz Rodney
Published: January 2024

Purpose

This study investigates the impact of large-scale teaching in higher education on students’ preparedness for the workforce within the context of evolving labour market demands, the expansion of higher education and the application of high-impact teaching strategies. It synthesizes perspectives on employer work readiness, the challenges and opportunities of large-scale teaching and strategies for fostering a dynamic academia-industry feedback loop. This multifaceted approach ensures the relevance of curricula and graduates’ preparedness while addressing the skills gap through practical recommendations for aligning teaching methodologies with employer expectations.

Design/methodology/approach

The research methodically examines the multifaceted challenges and opportunities inherent in large-scale teaching. It focuses on sustaining student engagement, maintaining educational quality, personalizing learning experiences and cultivating essential soft skills in extensive student cohorts.

Findings

This study highlights the critical role of transversal skills in work readiness. It also uncovers that despite its challenges, large-scale teaching presents unique opportunities. The diversity of large student groups mirrors modern workplace complexities, and technological tools aid in personalizing learning experiences. Approaches like peer networking, innovative teaching methods, real-world simulations and collaborative resource utilization enrich education. The importance of experiential learning for augmenting large-scale teaching in honing soft skills is emphasized.

Originality/value

This manuscript contributes to the discourse on large-scale teaching, aligning it with employer expectations and the dynamic requirements of the job market. It offers a nuanced perspective on the challenges and opportunities this educational approach presents, providing insights for crafting engaging and effective learning experiences in large cohorts. The study uniquely integrates experiential learning, co-creation in education and industry-academia feedback loops, underscoring their importance in enhancing student work readiness in large-scale teaching.
Seed dispersal by frugivores without seed swallowing: Evaluating the contributions of stomatochoric seed dispersers
Authors: McConkey Kim R. , Sushma H. S. , Sengupta Asmita
Published: January 2024

The process of seed dispersal that underpins ecosystem maintenance is performed by diverse arrays of fruit‐eating animals. However, seed dispersal studies are primarily focused on a subset of these animal communities that disperse seeds by endozoochory. Stomatochory (seed dispersal in which seeds are carried externally and are not swallowed) is rarely considered to be effective, despite an increasing number of taxa‐focused studies that indicate otherwise.

We collated the available information on stomatochory to provide a quantitative overview of the dispersal mechanism, including plant types and fruit traits dispersed, dispersal distances and germination potential for all available taxa. We compared seed sizes dispersed, dispersal distances and germination potential with corresponding data on endozoochory for bats and primates. We also identified the main taxa dispersing seeds by stomatochory and assessed what factors influenced the distances that they carried seeds to.

Stomatochoric dispersers can displace large quantities of seeds, including large seeds and those of large fruits, and over short to long distances (>1 km). Compared with similar‐sized endozoochoric dispersers, they can disperse larger seeds, but over shorter distances, on average. Similar to endozoochory, seed handling by stomatochory also improves the germination potential of dispersed seeds. Dispersal distances achieved by stomatochory were influenced by body mass, daily path length, seed width, fruit type and seed handling techniques.

Five main taxonomic groups of stomatochoric dispersers were identified: bats, parrots, squirrels, corvids and Old World monkeys (cercopithecines). Parrots perform dispersal services for the largest fruits and over the longest distances. However, given the lack of research on stomatochory, it is likely other taxa are also important stomatochoric dispersers but have not been identified yet.

More research attention must be directed towards seed dispersal services that are not provided by endozoochory. Many stomatochoric dispersers are common animals within communities and could be playing dominant seed dispersal roles, even without swallowing seeds. Community‐wide studies should incorporate all seed dispersal interactions, rather than focusing solely on endozoochory. This will ensure a more robust understanding of community‐wide patterns.

Read the free Plain Language Summary for this article on the Journal blog.
The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet
Authors: Doting Eva L. , Jensen Marie B. , Peter Elisa K. , Ellegaard‐Jensen Lea , Tranter Martyn , Benning Liane G. , Hansen Martin , Anesio Alexandre M.
Published: January 2024

Microbial blooms colonize the Greenland Ice Sheet bare ice surface during the ablation season and significantly reduce its albedo. On the ice surface, microbes are exposed to high levels of irradiance, freeze–thaw cycles, and low nutrient concentrations. It is well known that microorganisms secrete metabolites to maintain homeostasis, communicate with other microorganisms, and defend themselves. Yet, the exometabolome of supraglacial microbial blooms, dominated by the pigmented glacier ice algae Ancylonema alaskanum and Ancylonema nordenskiöldii, remains thus far unstudied. Here, we use a high‐resolution mass spectrometry‐based untargeted metabolomics workflow to identify metabolites in the exometabolome of microbial blooms on the surface of the southern tip of the Greenland Ice Sheet. Samples were collected every 6 h across two diurnal cycles at 5 replicate sampling sites with high similarity in community composition, in terms of orders and phyla present. Time of sampling explained 46% (permutational multivariate analysis of variance [PERMANOVA], pseudo‐F = 3.7771, p = 0.001) and 27% (PERMANOVA, pseudo‐F = 1.8705, p = 0.001) of variance in the exometabolome across the two diurnal cycles. Annotated metabolites included riboflavin, lumichrome, tryptophan, and azelaic acid, all of which have demonstrated roles in microbe–microbe interactions in other ecosystems and should be tested for potential roles in the development of microbial blooms on bare ice surfaces.
Willingness to pay for improved public education and public healthcare systems: the role of income mobility prospects
Authors: Wiese Rasmus , Eriksen Steffen
Published: January 2024

Income mobility prospects affect individuals’ willingness to pay higher taxes, or give part of their income, to improve the public healthcare and public education systems. In line with the prospects of the upward mobility hypothesis, risk‐willing individuals who expect to move far up the socio‐economic ladder are less willing to pay compared with individuals who expect no upward transition. Consistent with a social insurance effect, risk‐averse individuals who hold modest upward prospects are more willing to pay compared with individuals without upward prospects. These findings are based on more than 19,000 observations from the third round of the Life in Transition Survey.
Multi‐attribute temporal descriptive methods in sensory analysis applied in food science: A systematic scoping review
Authors: Visalli Michel , Galmarini Mara Virginia
Published: January 2024

Among descriptive sensory evaluation methods, temporal methods have a wide audience in food science because they make it possible to follow perception as close as possible to the moment when sensations are perceived. The aim of this work was to describe 30 years of research involving temporal methods by mapping the scientific literature using a systematic scoping review. Thus, 363 research articles found from a search in Scopus and Web of Science from 1991 to 2022 were included. The extracted data included information on the implementation of studies referring to the use of temporal methods (details related to subjects, products, descriptors, research design, data analysis, etc.), reasons why they were used and the conclusions they allowed to be drawn. Metadata analysis and critical appraisal were also carried out. A quantitative and qualitative synthesis of the results allowed the identification of trends in the way in which the methods were developed, refined, and disseminated. Overall, a large heterogeneity was noted in the way in which the temporal measurements were carried out and the results presented. Some critical research gaps in establishing the validity and reliability of temporal methods have also been identified. They were mostly related to the details of implementation of the methods (e.g., almost no justification for the number of consumers included in the studies, absence of report on panel repeatability) and data analysis (e.g., prevalence of use of exploratory data analysis, only 20% of studies using confirmatory analyses considering the dynamic nature of the data). These results suggest the need for general guidelines on how to implement the method, analyze and interpret data, and report the results. Thus, a template and checklist for reporting data and results were proposed to help increase the quality of future research.
Assessment of oral methotrexate intolerance in Japanese adult patients with rheumatoid arthritis
Authors: Kanda Masatoshi , Sato Mayumi , Nagahata Ken , Naishiro Yasuyoshi , Murakami Rieko , Honda Saho , Suzuki Chisako
Published: January 2024

Aim

The objective of this study was to assess the gastrointestinal side (GI) effects of oral methotrexate (MTX) in Japanese adult patients with rheumatoid arthritis (RA).

Methods

In this single‐center retrospective study, 112 Japanese adult patients (over 18 years old) with RA were examined by Methotrexate Intolerance and Severity assessment in Adults (MISA) questionnaire.

Results

Forty‐five (40.2%) of patients were MTX intolerant (MISA score ≥1). Twelve patients (11.2%) were moderate‐to‐severe MTX intolerant (MISA cross‐product score ≥4). The most common GI side effects of MTX were gastric discomfort (26.8%), followed by loss of appetite or dysgeusia (14.3%), fatigue and lethargy (12.5%), and nausea (10.7%).

Conclusions

Japanese adult patients with RA showed a high prevalence of MTX intolerance even in low‐dose oral MTX. The MISA questionnaire was practical for finding patients with MTX intolerance.
AllergoOncology: Biomarkers and refined classification for research in the allergy and glioma nexus—A joint EAACI‐EANO position paper
Authors: Turner Michelle C. , Radzikowska Urszula , Ferastraoaru Denisa E. , Pascal Mariona , Wesseling Pieter , McCraw Alexandra , Backes Claudine , Bax Heather J. , Bergmann Christoph , Bianchini Rodolfo , Cari Luigi , de las Vecillas Leticia , Izquierdo Elena , Lind‐Holm Mogensen Frida , Michelucci Alessandro , Nazarov Petr V. , Niclou Simone P. , Nocentini Giuseppe , Ollert Markus , Preusser Matthias , Rohr‐Udilova Nataliya , Scafidi Andrea , Toth Reka , Van Hemelrijck Mieke , Weller Michael , Jappe Uta , Escribese Maria M. , Jensen‐Jarolim Erika , Karagiannis Sophia N. , Poli Aurélie
Published: January 2024

Epidemiological studies have explored the relationship between allergic diseases and cancer risk or prognosis in AllergoOncology. Some studies suggest an inverse association, but uncertainties remain, including in IgE‐mediated diseases and glioma. Allergic disease stems from a Th2‐biased immune response to allergens in predisposed atopic individuals. Allergic disorders vary in phenotype, genotype and endotype, affecting their pathophysiology. Beyond clinical manifestation and commonly used clinical markers, there is ongoing research to identify novel biomarkers for allergy diagnosis, monitoring, severity assessment and treatment. Gliomas, the most common and diverse brain tumours, have in parallel undergone changes in classification over time, with specific molecular biomarkers defining glioma subtypes. Gliomas exhibit a complex tumour‐immune interphase and distinct immune microenvironment features. Immunotherapy and targeted therapy hold promise for primary brain tumour treatment, but require more specific and effective approaches. Animal studies indicate allergic airway inflammation may delay glioma progression. This collaborative European Academy of Allergy and Clinical Immunology (EAACI) and European Association of Neuro‐Oncology (EANO) Position Paper summarizes recent advances and emerging biomarkers for refined allergy and adult‐type diffuse glioma classification to inform future epidemiological and clinical studies. Future research is needed to enhance our understanding of immune–glioma interactions to ultimately improve patient prognosis and survival.
Impact of climate change on atopic dermatitis: A review by the International Eczema Council
Authors: Wang Sheng‐Pei , Stefanovic Nicholas , Orfali Raquel L. , Aoki Valeria , Brown Sara J. , Dhar Sandipan , Eichenfield Lawrence F. , Flohr Carsten , Ha Alex , Mora Camilo , Murase Jenny E. , Rosenbach Misha , Srinivas Sahana M. , Thyssen Jacob P. , Wei Maria L. , Irvine Alan D. , Abuabara Katrina
Published: January 2024

Atopic dermatitis (AD), the most burdensome skin condition worldwide, is influenced by climatic factors and air pollution; however, the impact of increasing climatic hazards on AD remains poorly characterized. Leveraging an existing framework for 10 climatic hazards related to greenhouse gas emissions, we identified 18 studies with evidence for an impact on AD through a systematic search. Most climatic hazards had evidence for aggravation of AD the impact ranged from direct effects like particulate matter‐induced AD exacerbations from wildfires to the potential for indirect effects like drought‐induced food insecurity and migration. We then created maps comparing the past, present, and future projected burden of climatic hazards to global AD prevalence data. Data are lacking, especially from those regions most likely to experience more climatic hazards. We highlight gaps important for future research: understanding the synergistic impacts of climatic hazards on AD, long‐term disease activity, the differential impact on vulnerable populations, and how basic mechanisms explain population‐level trends.
Maternal singing reduced pain indexes in 2‐month‐old infants and increased proximity during vaccinations
Authors: Monaci Maria Grazia , Caruzzo Chiara Maria , Raso Romina , Spagnuolo Carmen , Benedetti Maria Clorinda , Grandjean Didier , Filippa Manuela
Published: January 2024

Aim

Immunisation is a global health priority, but methods of non‐pharmacological pain relief are not widely used in routine clinical practice. In this study, we set out to investigate the effects of maternal singing during the routine vaccination of infants.

Methods

We recruited 67 mother–infant pairs at Health Centres in the Aosta Region of Italy. Infants aged 2–4 months were randomly allocated to a singing intervention group or to a control group whose injections were administered following standard practice. Pre‐ and post‐immunisation pain was blindly assessed using the Modified Behavioural Pain Scale, and mother–infant proximity indexes were assigned based on muted video‐tracks.

Results

When assessed for pain, the infants in the maternal singing group were assigned significantly lower movement indexes (p = 0.032) and marginally significantly lower cry indexes (p = 0.076). A higher frequency of mother‐to‐infant gaze (p < 0.005) was observed in the singing group dyads. Finally, the intervention group mothers' self‐perceived ease in singing was correlated with their previous singing experience and with lower anxiety following the vaccination procedure (p < 0.05).

Conclusion

Maternal singing during immunisation procedures benefits both mothers and babies. The practice of singing is a biologically rooted and adaptive form of intuitive parental communication that should be encouraged, especially in at‐risk populations.
Identification and analysis of gemstone binding materials on imperial rank belts excavated from the tomb of Murongzhi
Authors: Liang Yun , Chen Guoke , Liu Bingbing , Yu Chun , Xian Yiheng
Published: January 2024

This paper analyzes and identifies the binders used in the jewel settings of the Baodian and Diexie belts excavated from the tomb of Murongzhi in Wuwei, Gansu, China. Fourier transform infrared spectroscopy (FTIR) indicated the presence of protein in the binder samples. The result of gas chromatography–mass spectrometry (GC‐MS) shows that samples from both contained hydroxyproline, a characteristic amino acid for animal glue. Principal component analysis was performed on one of the samples, and it was concluded that the binder was a mixture of hide glue and egg glue. Further analysis using scanning electron microscopy with energy‐dispersive X‐ray (SEM‐EDX) and laser Raman spectroscopy (Raman) found that a red particulate matter visually identified in the binder was cinnabar, which was apparently added to binder in order to modify the color of the jewels. This study provides a basis for the conservation and restoration of future finds of elite jewelry. It also shows how imperial jewelry was made during the Tang Dynasty. Finally, the analysis of these heraldic belts provides a key insight the life and role of an exiled prince in the Tang court.
Immune thrombocytopenia (ITP) in pregnancy
Authors: Bussel James B. , Knightly Katherine A.
Published: January 2024

Immune thrombocytopenia (ITP) in pregnancy is challenging for both mother and fetus. Understanding the pathophysiology, treatments, and risks to the mother and fetus leads to proper management resulting in successful pregnancy and delivery in almost all cases.1 ITP in a pregnant woman has many similarities to ITP not in pregnancy although gestational thrombocytopenia can be confused with ITP. However, recognizing differences is instrumental in avoiding bleeding complications and toxicities of treatment. This Nutshell review focuses on the natural history of ITP in pregnancy, its treatment, and dilemmas.
Identifiability and estimability of Bayesian linear and nonlinear crossed random effects models
Authors: Rohloff Corissa T. , Kohli Nidhi , Lock Eric F.
Published: January 2024

Crossed random effects models (CREMs) are particularly useful in longitudinal data applications because they allow researchers to account for the impact of dynamic group membership on individual outcomes. However, no research has determined what data conditions need to be met to sufficiently identify these models, especially the group effects, in a longitudinal context. This is a significant gap in the current literature as future applications to real data may need to consider these conditions to yield accurate and precise model parameter estimates, specifically for the group effects on individual outcomes. Furthermore, there are no existing CREMs that can model intrinsically nonlinear growth. The goals of this study are to develop a Bayesian piecewise CREM to model intrinsically nonlinear growth and evaluate what data conditions are necessary to empirically identify both intrinsically linear and nonlinear longitudinal CREMs. This study includes an applied example that utilizes the piecewise CREM with real data and three simulation studies to assess the data conditions necessary to estimate linear, quadratic, and piecewise CREMs. Results show that the number of repeated measurements collected on groups impacts the ability to recover the group effects. Additionally, functional form complexity impacted data collection requirements for estimating longitudinal CREMs.
Japanese Society of Medical Oncology clinical guidelines: Molecular testing for colorectal cancer treatment, 5th edition
Authors: Bando Hideaki , Yamaguchi Kyoko , Mitani Seiichiro , Sawada Kentaro , Mishima Saori , Komine Keigo , Okugawa Yoshinaga , Hosoda Waki , Ebi Hiromichi
Published: January 2024

Molecular testing to determine optimal therapies is essential for managing patients with colorectal cancer (CRC). In October 2022, the Japanese Society of Medical Oncology published the 5th edition of the Molecular Testing Guideline for Colorectal Cancer Treatment. In this guideline, in patients with unresectable CRC, RAS/BRAF V600E mutational and mismatch repair tests are strongly recommended prior to first‐line chemotherapy to select optimal first‐ and second‐line therapies. In addition, HER2 testing is strongly recommended because the pertuzumab plus trastuzumab combination is insured after fluoropyrimidine, oxaliplatin, and irinotecan in Japan. Circulating tumor DNA (ctDNA)‐based RAS testing is also strongly recommended to assess the indications for the readministration of anti‐EGFR antibodies. Both tissue‐ and ctDNA‐based comprehensive genomic profiling tests are strongly recommended to assess the indications for targeted molecular drugs, although they are currently insured in patients with disease progression after receiving standard chemotherapy (or in whom disease progression is expected in the near future). Mutational and mismatch repair testing is strongly recommended for patients with resectable CRC, and RAS/BRAF V600E mutation testing is recommended to estimate the risk of recurrence. Mutational and mismatch repair and BRAF testing are also strongly recommended for screening for Lynch syndrome. Circulating tumor DNA‐based minimal residual disease (MRD) testing is strongly recommended for estimating the risk of recurrence based on clinical evidence, although MRD testing was not approved in Japan at the time of the publication of this guideline.
The colon does not reach! A technical note with tricks to avoid colorectal anastomoses under tension
Authors: Dalmau Mar , Marti‐Gallostra Marc , Pellino Gianluca , Espin‐Basany Eloy , Armengol Manuel
Published: January 2024

Aim

We describe two options for colorectal anastomosis suitable in cases when the colon would reach the pelvis under tension.

Method

Deloyers procedure and the retro‐ileal colorectal anastomosis are presented, focusing on practical tips and tricks to perform them. Insights on patients who underwent the procedures are provided to demonstrate the advantages and feasibility of the techniques.

Results

Each step of both techniques is detailed. Ten patients underwent Deloyers procedure and nine underwent retro‐ileal anastomosis at our unit. A minimally invasive approach was attempted in 13 patients, of whom five required conversion to open surgery due to the technical complexity of the abdominal procedure. Colorectal anastomosis was successfully performed in all patients. There were no major intra‐operative complications, although five patients had postoperative complications requiring further treatment.

Conclusions

Both techniques are effective in patients at risk of receiving a colorectal anastomosis under tension, and a minimally invasive approach can be used. However, owing to the complexity of surgery in this group of patients, the perioperative morbidity is not negligible. Careful postoperative management is advisable, and patients should be informed of the risks. In expert hands, the outcomes are acceptable, avoiding an ileorectal anastomosis and its constraints.
The influence of socioeconomic deprivation on outcomes in transplant patients infected with SARS‐CoV‐2 in Wales
Authors: Koimtzis Georgios , Geropoulos Georgios , Chalklin Christopher , Karniadakis Ioannis , Szabo Laszlo , Ilham Mohammed Adel , Stephens Michael , Asderakis Argiris , Khalid Usman
Published: January 2024

Introduction

SARS‐CoV‐2 infection has had a significant impact on vulnerable individuals including transplant patients. Socioeconomic deprivation negatively affects outcomes of many health conditions. The aim of this study was to evaluate the effect of socioeconomic deprivation on the incidence and severity of SARS‐CoV‐2 infection among Welsh transplant patients.

Methods

This study is a retrospective, cross‐sectional study on the transplant population of Wales. The Welsh Index of Multiple Deprivation (WIMD) was used to assess the influence of socioeconomic deprivation on outcomes of Welsh transplant patients who developed SARS‐CoV‐2 infection. Outcome measures were the incidence of SARS‐CoV‐2 infection, rates of hospital and ICU admission, development of acute kidney injury (AKI) and mortality. A logistic binomial regression analysis was used to correlate the various risk factors with the incidence of SARS‐CoV‐2 infection.

Results

Two hundred and sixty‐six (25%) of regular follow up patients had SARS‐CoV‐2 infection; of these 55 (20.7%) were admitted, 15 (5.6%) to ICU, 37 (13.9%) developed AKI, and 23 (8.6%) died. In a regression analysis, patients of younger age were associated with more (p = .001) and those with SPK (simultaneous pancreas kidney) transplant less chance of infection (p = .038), whereas social deprivation was not associated with the chance of infection (p = .14). In regression analysis increased social deprivation was associated with higher chance of AKI post SARS‐CoV‐2 (p = .049).

Conclusions

Socioeconomic deprivation did not affect the rates or severity of SARS‐CoV‐2 infection apart from the degree of AKI in Welsh Transplant patients. Adherence to the preventive measures for this high‐risk population must continue to remain a priority.
Risk factors for cerebral palsy in children in Taiwan
Authors: Chen Yuping , Huang Jing‐Yang , Wei James Cheng‐Chung , Lee Shih‐Yu , Huang Ya‐Fang
Published: January 2024

Aim

To determine the significant risk factors of cerebral palsy (CP) in Taiwanese children and the associations between infant‐related and parent‐related factors.

Method

Data from 1 459 093 infants and their parents in Taiwan's national databases collected between 2009 and 2016 were used. The cohort with CP included children diagnosed with CP between birth and age 3 years; a total of 3254 children with CP were included in the final analysis. Hierarchical logistic regression models were used to estimate the odds ratio for the risk factors of CP.

Results

The hierarchical logistic regression models indicated that significant risk factors associated with CP are suburban location, low income, maternal and paternal diabetes mellitus, paternal substance abuse, paternal seizure disorder, male sex, birth by Cesarean section, singleton birth, low birthweight, being born extremely and very preterm, intraventricular hemorrhage, and periventricular leukomalacia, as well as tube feeding, ventilator use, and dopamine administration within 6 months of age.

Interpretation

In addition to common maternal and infant risk factors, we identified significant paternal risk factors associated with CP, including diabetes mellitus, seizure disorder, and substance abuse. The combination of maternal, paternal, and infant risk factors in CP holds great promise for early identification and intervention.