bluuebunny/crossref_metadata_2025 huggingface dataset:
The actin cytoskeleton regulates danger-associated molecular pattern signaling and PEP1 RECEPTOR1 internalization
Authors: Qian Hongping , Zuo Xinxiu , Man Yi , Xu Changwen , Luo Pengyun , Yao Lijuan , Geng Ruohan , Wang Binghe , Niu Shihui , Lin Jinxing , Cui Yaning
Published: January 2025

In plants, cytoskeletal proteins assemble into dynamic polymers that play numerous roles in diverse fundamental cellular processes, including endocytosis, vesicle trafficking, and the spatial distribution of organelles and protein complexes. Plant elicitor peptides (Peps) are damage/danger-associated molecular patterns (DAMPs) that are perceived by the receptor-like kinases PEP RECEPTOR 1 (PEPR1) and PEPR2 to enhance innate immunity and inhibit root growth in Arabidopsis (Arabidopsis thaliana). To date, however, there is little evidence that the actin cytoskeleton of the host cell participates in DAMP-induced innate immunity. Here, we demonstrated that the actin cytoskeleton alters the Pep1-triggered immune response. In addition, dual-color total internal reflection fluorescence–structured illumination microscopy (TIRF-SIM) showed that PEPR1 diffusion on the plasma membrane is closely related to the actin cytoskeleton. We performed single-particle tracking to quantify individual protein particles and found that the actin cytoskeleton notably regulates PEPR1 mobility and cluster size. More importantly, we demonstrated that actin filament reconfiguration is sufficient to inhibit Pep1-induced internalization, which alters the immune response. Taken together, these findings suggest that the actin cytoskeleton functions as an integration node for Pep1 signaling and PEPR1 endocytosis.
Measures to prevent esophageal stenosis are necessary after endoscopic submucosal dissection for early esophageal cancer lesions with a circumferential ratio of 75%–99%: a retrospective case analysis
Authors: Gao Yong , Zhu Jiao , Li Jianjun , Peng Xue , Nie Xubiao , Zhao Haiyan , Sheng Lifu , Fan Chaoqiang , Bai Jianying
Published: January 2025

Purpose

Endoscopic submucosal dissection (ESD) is currently one of the most curative treatments for early esophageal cancer. We conducted a retrospective case analysis to identify the characteristics of early esophageal cancer that indicate esophageal stenosis prevention measures. Our aim was to provide a reference for clinical decision-making.

Methods

Six hundred and fifty-four patients with early esophageal cancer treated with ESD were admitted to our hospital between January 2011 and December 2018.Clinical information such as patients’ demographic characteristics, lesion features, preventive measures if any, and complications of esophageal stenosis after ESD were collected from the hospital information system. The data were statistically analysed by SPSS software (version 23.0).

Results

1. Seventy-nine patients with early esophageal cancer suffered from esophageal stenosis after ESD. The median time from undergoing ESD to the first occurrence of stenosis was 27 (17–43) days. Specifically, among the 79 cases, 47 of them experienced stenosis within one month after ESD, and 23 cases experienced stenosis between 1 and 2 months after ESD, and 9 cases experienced stenosis more than 2 months after the operation.

2. Taking preventive measures significantly reduced overall esophageal stenosis incidence in patients with early esophageal cancer with lesion circumferential ratio of 75%–99% (P < 0.05).

3. Among patients with early esophageal cancer with 75%–99% circumferential proportion of lesions, the risk of esophageal stenosis within 2 months without prevention measures was 2.617(95% CI, 1.057–6.479) times higher than that with prevention measures.

Conclusion

It is necessary to take measures to prevent esophageal stenosis after ESD for early esophageal cancer lesions with a circumferential ratio of 75%–99%.
Anti-citrullinated protein antibody detection by hemagglutination
Authors: Kruis Ilmar , Kumari Jyoti , van der Heijden Annemarie , Weijn Amrah , Vree Egberts Wilma , Peeters Iris Rose , van Herwaarden Noortje , Salden Martin , Pruijn Ger J M
Published: January 2025

Objectives

ACPAs play an important role in the classification of RA and can be detected by serological tests. Several ACPA detection assays are available for clinical use, which are all based on ELISA(-like) tests with citrullinated peptides (CCP2) or alternative citrullinated proteins/peptides. We aimed to facilitate ACPA detection in low-volume laboratories and resource-poor environments by developing a rapid and easy-to-perform test.

Methods

We designed and generated an agglutination mediator by protein engineering. A single-chain antibody fragment that binds to glycophorin A, one of the major surface proteins of erythrocytes, was conjugated to a CCP2-like peptide. This agglutination mediator was used to assess ACPA in RA and PsA patients and in healthy individuals.

Results

The agglutination mediator bound to erythrocytes was reactive with ACPA and induced haemagglutination in an ACPA-dependent fashion, which can be detected by the naked eye. The applicability was assessed by the analysis of fresh blood samples from 204 RA patients, 77 PsA patients and 100 healthy individuals. Agglutination was observed in up to 61% of the RA samples, which correlated well with the results obtained with a standardized anti-CCP2 ELISA (63–67%). Depending on the minimal agglutination score, agglutination was observed in only 3–21% of the PsA samples and in 1% of the healthy controls.

Conclusion

We conclude that the agglutination mediator allows rapid and efficient detection of ACPA by haemagglutination in human blood samples and offers a low-threshold method for ACPA detection.
Maintained growth performance and reduced mortality of genetically resistant nursery pigs after an experimental virulent F18 enterotoxigenic Escherichia coli challenge
Authors: Welch Michael W , Cross Amanda J , Solar Diaz Iara D P , Johnson Danielle C , Parr Eric , Rathje Tom A , Borg Randy C , Boler Dustin D
Published: January 2025

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of postweaning diarrhea (PWD) and mortality of weaned pigs. The objective of this study was to evaluate genetic resistance of the polymorphism at nucleotide 307 (M307) in the FUT1 gene, to F18 E. coli infection considering different genotypes. A total of 179 pigs were used for this study. Pigs were genotyped for susceptibility to F18+ E. coli prior to the trial. Treatments included: genotype M307GA—heterozygous for E. coli susceptibility (A), genotype M307GG—homozygous E. coli susceptibility (B), or genotype M307AA—homozygous for E. coli resistance (C). Pigs were weighed, assigned to pens based on genotype, and allowed to acclimate for 3 d prior to the challenge. On days 4, 5, and 6, pigs were inoculated intraorally at the oropharynx with an F18+ E. coli isolate at a geometric mean concentration of 9.8 × 109. Growth rate (average daily gain [ADG]), feed intake (average daily feed intake), and gain-to-feed ratio (G:F) were calculated by pen. All pigs were humanely euthanized at the end of the trial. Two fixed sections of ileum and distal jejunum were collected from a subpopulation and tested by in situ hybridization (ISH) to evaluate F18+ E. coli adherence. Fresh ileum samples were used for enumeration of F18, total E. coli, and total bacteria by real-time polymerase chain reaction. Mortality rates during the trial were 26.7% for genotype A, 18.3% for genotype B, and 0.0% for genotype C (P < 0.01). Starting weights prior to inoculation were not different (P = 0.29) among genotypes. Overall, pigs from genotype C grew 223 g/d faster (P = 0.04) than genotype A. Pigs from genotype C tended to grow 185 g/d faster (P = 0.09) than genotype B. G:F for genotype C (0.74) was 23% greater (P < 0.01) than G:F for genotype A (0.60) and tended to be 12% greater (P = 0.07) than genotype B (0.66). There were no differences in ADG or G:F between genotypes A and B. F18-specifc Cq units were decreased by 7.74 and 6.47 in genotypes A and B compared with genotype C (P ≤ 0.03). Signal by ISH was increased by 14.0-fold in genotype A compared with genotype C (P = 0.02). Adherence was not different among genotypes (P = 0.40). Genotype A had greater mortality and poorer growth performance than genotype B or C. Genotype C had no mortalities during the trial, grew faster, was more feed efficient, and had less F18 E. coli in the ileal mucosa compared with genotype A. Resistant genotypes provide an opportunity to reduce PWD and mortality due to an F18+ E. coli infection.
Updates in nonhormonal therapy for perimenopausal and menopausal symptoms
Authors: Voedisch Amy J.
Published: January 2025

Purpose of review

Perimenopausal and menopausal symptoms are common and may significantly impact quality of life. Menopausal hormone therapy is the most effective treatment but may not be appropriate in all cases. Nonhormonal alternatives range from lifestyle changes and dietary supplements to medical interventions and prescription therapies. This review will summarize the newest advancements in nonhormonal therapies for bothersome perimenopausal and menopausal symptoms.

Recent findings

The Menopause Society recently updated their recommendations and guidelines for nonhormonal therapies. Previous recommendations, such as clonidine and pregabalin, are no longer recommended. A new class of medication, neurokinin B antagonists, are now available to target vasomotor symptoms and show promise in addressing sleep and mood issues.

Well tolerated, effective nonhormonal therapies are available to address perimenopausal and menopausal symptoms for those patients who are not candidates for or chose not to use menopausal hormone therapy.
Sleep disturbance and menopause
Authors: Carmona Nicole E. , Solomon Natalie L. , Adams Karen E.
Published: January 2025

Purpose of review

Sleep problems are among the most prevalent and bothersome symptoms of menopause. This review characterizes menopausal sleep disturbances, describes biopsychosocial predictors, and summarizes the evidence supporting pharmacological and nonpharmacological treatment options.

Recent findings

Recent studies found that sleep changes are early indicators of perimenopause and sought to disentangle the respective impacts of menopausal status, hot flashes (HFs), and changes in reproductive hormones on peri-/postmenopausal sleep problems. Both HFs and reproductive hormones predicted sleep problems, but neither solely accounted for the myriad changes in sleep, thus highlighting the contribution of additional biopsychosocial risk factors. Inconsistencies across studies were likely due to differences in study design and methodology, participants’ menopausal stage, and the presence of sleep complaints. Recent studies support the use of psychological (cognitive-behavioral therapy for insomnia) and pharmacological (e.g., neurokinin B antagonists) treatments in addition to hormone therapy.

Sleep problems are common and of critical import to women during the menopausal transition, significantly influencing treatment preferences and satisfaction. Thus, sleep problems should be routinely assessed from a biopsychosocial perspective and treated with evidence-based interventions throughout menopause. Treatment selection should be based on diagnosis and careful assessment.
Increased Incidence and Severity of Group A Streptococcal Infections in Children in Southeast Texas From June 2022 to May 2023
Authors: Hankins Julia D. , Johnson Coreen L. , Sanchez Belkys C. , Serrano Angela V. , Runge Jessica K. , Spinler Jennifer K. , Powell John W. , Luna Ruth Ann , Dunn James J. , Niles Denver T.
Published: January 2025

Background:

Group A Streptococcus (GAS) infections can cause a range of disease manifestations and severity, including invasive infections that can lead to death. In 2022–2023, there was an increased number of cases of invasive GAS in the United States following a decline in 2020–2022.

Methods:

We investigated this surge at a 3-hospital system of children’s hospitals in Southeast Texas. Cases of invasive GAS (n = 252) were retrospectively reviewed from peak periods of infection, beginning June 2019–May 2020 and continuing each successive year until May 2023. Cases were analyzed based on patient demographics, disease manifestations, coinfections, and hospital course. Isolates grown in culture were sequenced, and the emm types and genes associated with virulence were analyzed.

Results:

Compared with previous years, June 2022–May 2023 had the largest number of invasive GAS cases (n = 154, 2022–2023; 34, 2021–2022; 12, 2020–2021; 52, 2019–2020). Compared with the previous 3 years, patients from 2022 to 2023 were more likely to present with complicated pneumonia (23.4% vs. 7.1%; P = 0.0009), require respiratory support (34.4% vs. 14.3%; P < 0.001), be admitted to the intensive care unit (29.2% vs. 16.3; P = 0.0235), and be infected with emm type 12 isolates (40.6% vs. 10.3%; P = 0.0030).

Conclusions:

In June 2022–May 2023, there was a 5-fold surge of invasive GAS infection cases in children at Texas Children’s Hospital compared with the previous 3 years. These cases required greater intensive care unit hospitalization and respiratory support requirements due to higher rates of complicated pneumonia.
Feeding interruptions for extubation and other procedures
Authors: Landais Mickael , Ehrmann Stephan , Guitton Christophe
Published: January 2025

Purpose of review

The objective of this review is to examine the available evidence concerning feeding interruptions before extubation and other medical procedures in ICUs. We will analyze the physiological mechanisms involved, the potential risks associated with feeding interruptions, as well as the results of recent clinical studies. Additionally, we will explore current practices and recommendations from major professional societies, as well as recent innovations aimed at minimizing feeding interruptions.

Recent findings

Fasting before extubation is a common yet heterogeneous practice, varying across ICUs. Although dysphagia is a frequent complication after extubation, its prevalence decreases over time. However, physiologically, fasting before extubation appears ineffective in reducing gastric content or preventing aspiration. The Ambroisie study demonstrated that continuing enteral nutrition up to extubation is not inferior to a 6 h fasting strategy in terms of extubation failure at 7 days. The management of perioperative nutrition in intubated patients is debated. A retrospective study found no significant difference in postoperative respiratory events between patients fasting for at least 6 h and those fasting less or not at all but further prospective randomized studies are needed for definitive conclusions. For abdominal and digestive surgeries, fasting remains necessary to simplify procedures and reduce contamination risks. For invasive ICU procedures, such as catheter placement, the continuation of enteral nutrition appears reasonable. However, for percutaneous tracheotomy, limited evidence suggests no clear benefit from fasting, though the risk of large-volume aspiration during the procedure raises concerns. The approach to nutrition in this context requires further investigation.

Fasting before extubation in ICUs is a common practice inherited from anesthesia, aiming to reduce the risk of aspiration. The Ambroisie study demonstrates that continuing enteral nutrition until extubation is not inferior to a 6 h fasting strategy regarding extubation failure at 7 days.
Impact of COVID-19 on gut–lung microbiota a mini review
Authors: Emadi Reza , Yousefi Parastoo , Tabibzadeh Alireza
Published: January 2025

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19) affects the lungs and gastrointestinal tract. However, SARS-CoV-2 chiefly infects lungs through the binding of angiotensin-converting enzyme 2 (ACE2) receptors and type II transmembrane serine protease (TMPRSS2) expressed on the alveolar epithelial cells. Furthermore, the intestinal epithelial cells also express ACE2 receptors. Not only has the SARS-CoV-2 been detected in nasopharyngeal and mid-nasal samples, but also it seems SARS-CoV-2 RNA can be found in the feces of infectious patients. In fact, fecal samples of patients contain RNA of the virus. The intensity of COVID-19 has mainly been associated with aging and comorbidities. Older patients experience a decline in the alteration of the gut microbiome, and COVID-19 has proven to be most fatal in this age group, further emphasizing the potential critical role of gut microbiota in this disease. The lung was formerly believed to be a sterile area free from bacteria. However, the lung microbiome has received more attention due to its recent link to several respiratory illnesses and immunity. In this review article, data from COVID-19 research and gut–lung cross-talk in the prognosis of COVID-19 disease and explored the bidirectional impacts of it on the gut–lung axis microbiome were discussed.
Pessary Placement for Voiding Dysfunction Due to Prolapse Among Neurologically Intact Women
Authors: Ashmore Sarah , Mueller Margaret G. , Kenton Kimberly , Bretschneider C. Emi
Published: January 2025

Importance

Literature surrounding conservative management of voiding dysfunction (VD) due to pelvic organ prolapse (POP) is limited.

Objective

The objective of this study was to evaluate the effect of pessaries on VD in women with symptomatic POP.

Study Design

This was a retrospective case series of adult women who underwent a pessary fitting for POP and VD between January 2010 to December 2022 at 2 tertiary care centers. Voiding dysfunction was defined as a composite outcome of participant report of obstructive voiding symptoms and postvoid residual volume (PVR) ≥150 mL prior to pessary fitting. Obstructive voiding symptoms were determined by positive response on the Pelvic Floor Distress Inventory-20 to items 5, 6, 19, and/or 20.

Results

Sixty-one participants with POP and VD underwent successful pessary fitting at 2 large academic institutions. Median (range) age was 75 years (35–89) and body mass index of 26.5 (18.0–46.3). Participant reports of “difficult bladder emptying” and “sensation of incomplete bladder emptying” were the most reported symptoms of obstructive voiding. Advanced staged prolapse (prolapse ≥ stage 3) was documented for 84% of participants. Median point C, Ba, and genital hiatus were −2 cm, +3 cm, and 4 cm, respectively, on examination. Median PVR prior to pessary fitting was 263 mL (150–810). Voiding dysfunction resolved in 60 out of 61 participants (98%). Median repeat PVR after pessary placement was 50 mL (0–250).

Conclusion

Pessary placement resolved VD due to POP in 98% of participants. Clinicians can offer pessary placement as nonsurgical management for participants with VD due to POP.
SH2D2A is an indicator of favourable prognosis in bladder cancer and is enriched in activated Treg cells
Authors: Gilmour Brian C. , Visser Johan Georg , Köhn-Luque Alvaro , Borowicz Paweł , Lossius Andreas , Spurkland Anne
Published: January 2025

Given the expanding availability of RNA-seq and other such high dimensional data it is now possible to consider a complementary approach working in the opposite directioni.e., from transcriptomics up towards protein function. This approach may prove fruitful in producing information on the function of cytosolic-bound proteins such as adapter proteins. To test the validity of this method, we made use of several public datasets to interrogate the cancer-specific role of the adapter protein SH2D2A: a protein enriched in T and NK cells and a known interactor of the kinase LCK, whose function remains uncertain. We found that SH2D2A is a favourable marker for prognosis in urothelial bladder cancer (BLCA). Digging further, we identified a population of SH2D2A+FOXP3+IL2RAhiactivated Tregs as the main expressors of SH2D2A in BLCA. This suggests that the expression of SH2D2A in these Tregs contributes to a beneficial prognostic effect. Further comprehension of SH2D2A’s function in these cells holds the potential for advancing treatment in BLCA and diversifying possible targets for immunotherapies.
Benchmarking of automated cancer cell annotation methods for scRNA-seq data reveals Consensus annotation as the preferred method
Authors: Abdelaal Tamim , Klijn Christiaan , Hancock Matt
Published: January 2025

Targeted cancer therapies have shown therapeutic advantages due to tumor-specific drug activity. Single-cell RNA-sequencing has been widely used in cancer studies to define different cellular identities. However, accurate identification of tumor vs other normal cells is essential to define novel tumor-specific targets. Recent methods have been developed to perform the task of tumor cell annotation, which can be divided into two categories: CNV-based methods, which use transcriptome measurements to infer copy number variations and identify cells with alterations as tumor, and Reference-based methods which train a classifier using previously annotated tumor data and use it to annotate new datasets. We benchmarked the state-of-the-art method of each category, SCEVAN and scATOMIC, respectively, together with Consensus annotation method where a cell is considered tumor if both methods agree on that. Across 20 cancer datasets spanning 9 cancer types with a total of 379 samples, the Consensus annotation outperformed other methods in terms of precision score. SCEVAN works well when clear CNVs are detected, otherwise cells are randomly split between normal and tumor producing many false positives. While scATOMIC efficiently detects all normal cells except normal epithelial cells, where all epithelial cells (normal and malignant) are considered cancerous. The Consensus annotation method overcomes the limitations of both methods, being able to detect normal epithelial cells together with other normal cell types as non-tumor, also annotating malignant epithelial cells as tumor even with weak CNVs. This produces overall higher precision with the least number of false positives, leading to confident tumor-specific potential therapeutic targets. Implementation is available in the MACE R package through GitLab (https://gitlab.com/genmab-public/mace/).
Targeting anemia-induced CD71+reticulocytes protects mice fromPlasmodiuminfection
Authors: Zeydabadinejad Sareh , Kim Jong Sung Anthony , Zheng Anna , Kandalgaonkar Mrunmayee Rajendra , Ababio Prince Boakye , Vijay-Kumar Matam , Yeoh Beng San , Saha Piu
Published: January 2025

Malaria, caused byPlasmodiumspp., is a global health concern linked to anemia and increased mortality. Compensatory erythropoiesis seen during acute anemia results in an increased circulating reticulocyte count (i.e., immature RBC) a key factor in understanding the relationship between pre-existing anemia andPlasmodiumburden. Reticulocytes in mice are marked by transferrin receptor (CD71+) and glycophorin A-associated protein (Ter119+). To model acute anemia with increased reticulocytes, C57BL/6 mice were either bled (i.e.phlebotomized) or administered phenylhydrazine, before being infected withPlasmodium yoelii(P. yoelii), a mouse-specific strain with a preference for reticulocytes. InP. yoelii-infected anemic mice, we observed heightened parasitemia and significant body weight loss compared with non-anemicP. yoelii-infected mice. Additionally, serum inflammatory cytokines, erythropoietin, and liver injury markers, along with hemozoin deposition significantly increased in anemicP. yoelii-infected mice. RBC transfusion from healthy normal donors toP. yoelii-infected anemic recipient mice ameliorated anemia by reducing overall reticulocyte count and increasing mature RBC count. RBC transfusion rescued body weight loss, decreased parasitemia, and reduced serum erythropoietin levels. Finally, to confirm the role of reticulocytes inP. yoeliiinfection, reticulocytes were depleted using anti-CD71 monoclonal antibody inP. yoelii-infected mice. We observed improvement in hematologic parameters and stark reduction in parasitemia in both pre-existing anemic and non-anemicP. yoelii-infected mice. Collectively, our results suggest that pre-existing anemia may increase the risk ofPlasmodiuminfection due to the greater reticulocytes population. Anti-CD71 treatment inPlasmodiuminfection may offer a novel therapeutic strategy to combatPlasmodiuminfection and malaria.

Grant support

This work was supported by grants from the Crohn’s and Colitis Foundation (CCF) and American Heart Association (AHA) Career Development Award (854385 and 855256 respectively) to Piu Saha; grant from the National Institutes of Health (NIH) to Matam Vijay-Kumar (DK134053) and Liver Scholar Award from American liver Foundation to Beng San Yeoh.
SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data
Authors: Saldanha Oliver Lester , Goepp Vivien , Pfeiffer Kevin , Kim Hyojin , Zhu Jie Fu , Kramann Rafael , Hayat Sikander , Kather Jakob Nikolas
Published: January 2025

Rapid technological advancements have made it possible to generate single-cell data at a large scale. Several laboratories around the world can now generate single-cell transcriptomic data from different tissues. Unsupervised clustering, followed by annotation of the cell type of the identified clusters, is a crucial step in single-cell analyses. However, there is no consensus on the marker genes to use for annotation, and celltype annotation is currently mostly done by manual inspection of marker genes, which is irreproducible, and poorly scalable. Additionally, patient-privacy is also a critical issue with human datasets. There is a critical need to standardize and automate celltype annotation across datasets in a privacy-preserving manner. Here, we developed SwarmMAP that uses Swarm Learning to train machine learning models for cell-type classification based on single-cell sequencing data in a decentralized way. SwarmMAP does not require any exchange of raw data between data centers. SwarmMAP has a F1-score of 0.93, 0.98, and 0.88 for cell type classification in human heart, lung, and breast datasets, respectively. Swarm Learning-based models yield an average performance of0.907which is on par with the performance achieved by models trained on centralized data (p-val=0.937, Mann-WhitneyUTest). We also find that increasing the number of datasets increases cell-type prediction accuracy and enables handling higher cell-type diversity. Together, these findings demonstrate that Swarm Learning is a viable approach to automate cell-type annotation. SwarmMAP is available athttps://github.com/hayatlab/SwarmMAP.
Plant domestication does not reduce diversity in root microbiomes
Authors: Hernández-Terán Alejandra , Escalante Ana E. , Rebolleda-Gómez Maria
Published: January 2025

Domestication has profoundly shaped human civilization and the genetic makeup of numerous plant and animal species. While the effects of plant domestication at the genetic and phenotypic levels are well-documented, its impact on plant microbiome remains less understood. Root microbiomes play crucial roles in nutrient acquisition, pathogen defense, and biotic stress tolerance, yet the influence of domestication on their diversity and assembly is still debated. Two primary hypotheses have been proposed: 1) the reduction in microbial diversity resulting from the domestication process, and 2) the diminished ability of host plants to control their microbiomes. To evaluate these hypotheses, we conducted a meta-analysis of multiple crops, comparing the root microbiomes of domesticated plants and their wild relatives. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased microbial diversity and more structured communities, while others show no significant change. Overall, this study provides evidence that plant domestication does not lead to a uniform reduction in microbial diversity or a consistently diminished ability of plants to influence their microbiomes. Based on these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation in such experiments, analyzing not only diversity but also microbiome function, and considering how root morphology might affect microbiome recruitment. Finally, we highlight the need for research on the potential adaptive or maladaptive consequences that introgression between wild and domesticated plants could have from a microbiome perspective.

SIGNIFICANCE STATEMENT

Plant domestication has had profound impacts on plant traits and their genetic makeup. These traits are likely to influence microbial interactions with the plants, but the overall effect of domestication on plant microbiomes is still subject to debate. In this work, we challenge two primary hypotheses regarding the effects of domestication on root microbiomes; we compared published microbiomes of wild and domesticated plants and found that domestication does not reduce microbial diversity or the plant’s contribution to their associated microbial communities. Instead, these effects vary between plant species and environmental conditions. This work provides insights into how domestication shapes plant-microbe relationships and discusses new approaches that are critical for advancing this area of research.
Engaging Private Pharmacies in Referring Tuberculosis Suspects in Pakistan: Findings and Implications
Authors: Saleem Zikria , Kiani Ayyaz
Published: January 2025

Background

World Health Organization (WHO) considers local pharmacies as an underused source that can contribute more effectively to the health care programs of the community. This study was aimed to evaluate the impact of involving private pharmacies for timely referral to facilitate TB case detection in Pakistan.

Methods

In this study, 398 pharmacies in five major districts of Pakistan were contacted. Patients having apparent TB symptoms or chronic cough for more than two weeks were referred for TB case detection to the nearby center of National TB Control Program (NTP). The patients were monitored and followed up to analyze the results of the diagnostic tests by involving pharmacy students.

Results

Out of 398 enrolled pharmacies, only 224 pharmacies (56.28%) were producing referrals. A total of 994 TB suspects were referred for tests out of which 839 (84.4%) actually appeared for the TB examination tests while 155 (15.5%) were missing. Of total 839 tested suspects, 189 (22.5%) were diagnosed with smear positive TB.

Conclusion

Community pharmacies under the thematic model of public private partnership can be the key players in tracing, preventing and early diagnosis of TB. This project can be extended and implemented in all provinces of Pakistan with more technical and financial inputs in the existing system in order to completely eradicate TB.
Reproducibility and associated regression dilution bias of accelerometer-derived physical activity and sleep in the UK Biobank
Authors: Zisou Charilaos , Taylor Hannah , Lacey Ben , Hammami Imen , Walmsley Rosemary , Strain Tessa , Wijndaele Katrien , Smith-Byrne Karl , Bennett Derrick , Lewington Sarah , Hopewell Jemma C , Doherty Aiden
Published: January 2025

Background: Previous studies on the reproducibility of 7-day accelerometer measurements have been limited by small sample sizes and short follow-up periods. We aimed to assess the long-term reproducibility of accelerometer-derived physical activity and sleep, and to illustrate the impact of regression dilution bias on the association between daily step count and coronary heart disease (CHD) in UK Biobank (UKB). Methods: We analysed data from 3138 UKB participants in the main accelerometry sub-study with up to four repeat accelerometer measurements after 3-4 years. Nine physical activity and sleep phenotypes were extracted to capture different movement behaviours. Reproducibility was assessed using intraclass correlation coefficients (ICCs). The impact on disease associations was illustrated by considering daily step count and incident CHD using Cox regression (87 180 participants; 3899 CHD events), before and after correction for regression dilution. Results: Among the 3138 participants, 51% were women and the mean (SD) age was 63.1 (9.4) years. Reproducibility of phenotypes was moderate to good, with the ICC (95% CI) for overall activity at 0.75 (0.74-0.76), and individual phenotypes ranging from 0.58 (0.56-0.59) for sleep efficiency to 0.69 (0.68-0.70) for sedentary behaviour. In our example, the inverse association between daily step count and CHD showed a 20% lower risk of CHD per 4000 usual steps after correcting for regression dilution, compared to 13% before correction. Conclusions: Accelerometer measurements are moderately reproducible and comparable to measures like blood pressure. Correcting for regression dilution bias is crucial to quantify associations of usual physical activity and sleep with disease risk.
Multilayer regulation underlies the functional precision and evolvability of the olfactory system
Authors: Mermet Jérôme , Cruchet Steeve , Borbora Asfa Sabrin , Lee Daehan , Chai Phing Chian , Jang Andre , Menuz Karen , Benton Richard
Published: January 2025

Sensory neurons must be reproducibly specified to permit accurate neural representation of external signals but also able to change during evolution. We studied this paradox in theDrosophilaolfactory system by establishing a single-cell transcriptomic atlas of all developing antennal sensory lineages, including latent neural populations that normally undergo programmed cell death (PCD). This atlas reveals that transcriptional control is robust, but imperfect, in defining selective sensory receptor expression. A second layer of precision is afforded by the intersection of expression of functionally-interacting receptor subunits. A third layer is defined by stereotyped PCD patterning, which masks promiscuous receptor expression in neurons fated to die and removes “empty” neurons lacking receptors. Like receptor choice, PCD is under lineage-specific transcriptional control; promiscuity in this regulation leads to previously-unappreciated heterogeneity in neuronal numbers. Thus functional precision in the mature olfactory system belies developmental noise that might facilitate the evolution of sensory pathways.
Evidence of dengue virus transmission and a diverseAedesmosquito virome on the Democratic Republic of Congo-Angola border
Authors: He Wenqiao , Bobanga Thierry , Piantadosi Anne , Popkin-Hall Zachary R. , Vulu Fabien , Collins Matthew H. , Kashamuka Melchior M. , Tshefu Antoinette K. , Juliano Jonathan J. , Parr Jonathan B.
Published: January 2025

Aedesmosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collectedAedesmosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools of 115 mosquitoes confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.
The mismatch repair factor Mlh1-Pms1 uses ATP to compact and remodel DNA
Authors: Collingwood Bryce W. , Bhalkar Amruta N. , Manhart Carol M.
Published: January 2025

In eukaryotes, mismatch repair begins withMutS homolog (MSH) complexes, which scan newly replicated DNA for mismatches. Upon mismatch detection, MSH complexes recruit the PCNA- stimulated endonuclease Mlh1-Pms1/PMS2 (yeast/human), which nicks the DNA to allow downstream proteins to remove the mismatch. Past work has shown that although Mlh1-Pms1 is an ATPase and this activity is importantin vivo, ATP is not required to nick DNA. Our data, using yeast as a model, suggests that Mlh1-Pms1 forms oligomeric complexes that drive DNA conformational rearrangements using the protein’s ATPase activity. Experiments with non-B-form DNA structures, common in microsatellite regions, show that these structures inhibit Mlh1-Pms1’s activities, likely through impeding Mlh1-Pms1-dependent DNA conformational changes. This could explain an additional mode for instability in these regions of the genome. These findings highlight the importance of DNA compaction and topological rearrangements in Mlh1-Pms1’s function and provide insight into how mismatch repair relies on DNA structure to coordinate events.

GRAPHICAL ABSTRACT
Environmental, Developmental, and Genetic Conditions Shaping Monarch Butterfly Migration Behavior
Authors: Tsai Hsiang-Yu , Molina Cristian , Pleasants John , Kronforst Marcus R.
Published: January 2025

Monarch butterflies in North America migrate south each autumn, but the mechanisms that initiate their migratory flight remain incompletely understood. We investigated environmental, developmental, and genetic factors that contribute to directional flight by testing summer and autumn-generation monarchs in three flight simulators: two at ground level (with and without wind blockage) and a novel balloon-based system that raised butterflies 30 meters into the air. Monarchs reared under autumn-like conditions in a growth chamber during the summer were also tested to explore the influence of developmental cues. Autumn generation monarchs demonstrated significant southwestern flight orientation, observed exclusively in the balloon simulator, underscoring the importance of high-altitude flight for migratory behavior. Summer generation monarchs reared under autumn-like conditions displayed southward orientation, larger wing sizes, and partial reproductive diapause, indicating specific seasonal environmental cues that are sufficient to induce migratory traits. In contrast, a lab line of monarchs reared in captivity since 2016 exhibited diminished wing size and reduced orientation ability, even when raised outdoors in the autumn, consistent with a loss of migratory traits in the absence of migration. Surprisingly, butterflies in the balloon simulator tended to orient upwind, which suggests that wind may also serves as a directional cue during migration. These findings highlight the critical roles of altitude, wind, and environmental cues in monarch migration and validate the balloon flight simulator as a powerful tool for studying migratory behavior. This research advances our understanding of the initiation of monarch migration and informs strategies for conservation efforts amidst environmental change.
An extended thermal pressure equation of state for sodium fluoride
Authors: Clough Lewis A. , Funnell Nicholas P. , Ridley Christopher J. , Daisenberger Dominik , Hriljac Joseph A. , Lozinšek Matic , Angel Ross J. , Parsons Simon
Published: January 2025

The effect of pressure and temperature on the unit-cell volume of NaF has been measured by X-ray powder diffraction at ambient pressure between 12 and 300 K and neutron powder diffraction up to 5 GPa between 140 and 350 K. These data have been combined with high-pressure volume data at 300 and 950 K to 25 GPa and adiabatic bulk modulus data to 650 K to define an equation of state for NaF relating molar volume to both temperature and pressure. The model combines a fourth-order Birch–Murnaghan equation of state at 295 K with a Mie–Grüneisen–Debye model for thermal pressure. The parameters of the model set at 295 K and ambient pressure are as follows: reference unit-cell volume V
0 = 14.9724 (5) cm3 mol−1, isothermal bulk modulus K
0T
 = 46.79 (14) GPa, first derivative of the bulk modulus K′0T
 = 5.72 (12), second derivative of the bulk modulus K′′0T
 = −0.43 (4) GPa−1, Debye temperature T
MGD = 459 (3) K, and Anderson Grüneisen parameters γ0 = 1.547 (11) and q = 0.94 (18).
Novel starting points for fragment-based drug design against human heat-shock protein 90 identified using crystallographic fragment screening
Authors: Huang Liqing , Wang Weiwei , Zhu Zhimin , Li Qianhui , Li Minjun , Zhou Huan , Xu Qin , Wen Wen , Wang Qisheng , Yu Feng
Published: January 2025

Heat-shock protein 90 (HSP90) is a highly active molecular chaperone that plays a crucial role in cellular function. It facilitates the folding, assembly and stability of various oncogenic proteins, particularly kinases and transcription factors involved in regulating tumor growth and maintenance signaling pathways. Consequently, HSP90 inhibitors are being explored as drugs for cancer therapy. Crystallographic fragment screening is a novel screening method that has been developed in recent years for fragment-based drug discovery and is known for its high hit rate and its ability to provide direct insights into the complex structures of proteins and compounds. In this paper, high-diffraction-resolution crystals of the N-terminal domain of human HSP90α were employed in crystallographic fragment screening to discover binding fragments and binding sites. A diverse library of 800 structurally distinct fragments was screened, yielding 91 starting points for the fragment-based drug design of new HSP90α N-terminal inhibitors. Nearly a thousand crystals were measured, with 738 being processed and phased using a highly automated data-processing pipeline including data reduction and phasing, refinement and hit identification via PanDDA multi-data-set analysis. The 91 identified compounds bind to eight distinct regions of the HSP90α N-terminus, with 63 fragments located in the ATP-binding pocket and its surroundings, thus demonstrating the potential for the development of HSP90α- and ATP-binding inhibitors. This study emphasizes crystallographic fragment screening as a powerful method that can effectively identify fragment molecules and inhibitors that bind to HSP90α, contributing to ongoing efforts in cancer drug discovery.
An analysis of literacy differences related to the identification and dissemination of misinformation in Japan
Authors: Yamaguchi Shinichi , Oshima Hidetaka , Watanabe Tomoaki , Osaka Yukiko , Tanihara Tsukasa , Inoue Eri , Tanabe Shinnosuke
Published: January 2025

Purpose

This study aims to examine the relationship between various types of literacy on one hand and identification of misinformation and dissemination of such information on the other, in search for better countermeasures against misinformation.

Design/methodology/approach

Based on data from a large-scale survey, models are constructed and analyzed to assess the relationships of literacy with both the identification of inaccuracies and dissemination behavior.

Findings

Regarding the identification of misinformation, individuals with high critical thinking attitudes (subjective literacy) are less likely to recognize misinformation, while other objective literacies do not have a significant relationship. Regarding dissemination behavior, individuals with high information literacy, media literacy and critical thinking scores tend not to disseminate misinformation, whereas those with high critical thinking attitudes are more likely to disseminate such information.

Originality/value

First, it quantitatively elucidates the relationships various literacies have with the accuracy judgment and dissemination behavior of misinformation. This highlights the effectiveness of objective indicators of literacies and the need for caution regarding subjective literacy – i.e. self-confidence in their own literacy. Second, it provides a cross-disciplinary analysis of the relationships, covering not only oft-studied politics and health care but also various other fields, thereby identifying comprehensive literacy strategies against misinformation. Third, it addresses differences in dissemination methods and offers insights into more practical countermeasures.
Contemporary value of historical business culture: the role of merchant guild culture in firm internationalization
Authors: Huang Jianbo , Su Hengyi , Wu Hanqi
Published: January 2025

Purpose

Merchant guild culture derives from business practices associated with medieval and early modern merchant guilds. This study aims to investigate the nexus between merchant guild culture and firm internationalization as well as the factors that moderate this nexus.

Design/methodology/approach

Based on the distribution of the ten merchant guilds in China and data on Chinese listed companies, this study uses the geographical proximity-based method to measure the intensity of merchant guild culture, which is the nearest distance between the ten merchant guilds’ origins and each firm’s registered address.

Findings

This study provides robust evidence that merchant guild culture positively relates to the degree of firm internationalization. It also documents that this nexus is stronger for firms with overseas background executives and those situated in highly marketized regions.

Practical implications

The findings of this study have valuable implications for both governments and firms. Governments can leverage local cultures to promote the internationalization of domestic firms, particularly in emerging economies with rich cultural heritage. Firms can further enhance their internationalization efforts by hiring more executives with overseas backgrounds.

Originality/value

This study advances the imprinting literature, provides a novel perspective on the antecedents of firm internationalization and expands research on the contemporary value of historical business culture.
Karma-related influences on moral obligation and empathy: an ethical perspective
Authors: Duong Cong Doanh , Pham Dan Khanh , Ngo Thi Viet Nga , Tran Nhat Minh , Dao Van Thanh
Published: January 2025

Purpose

This study aims to explore how the three dimensions of karma – karmic duty orientation, indifference to rewards and equanimity – influence empathy and moral obligation, with implications for social economics.

Design/methodology/approach

The research was conducted on a valid sample of 401 university students in Vietnam, using hierarchical regression to test formulated hypotheses.

Findings

The analysis reveals that karmic duty orientation and indifference to rewards significantly enhance empathy and moral obligation, indicating that individuals with a strong sense of moral duty and intrinsic motivation are more likely to engage in ethical and pro-social behaviors. Equanimity was not found to impact empathy or moral obligation significantly.

Practical implications

Organizations and policymakers should focus on cultivating moral duties, intrinsic motivations and resilience in ethical behavior to promote social responsibility and sustainability and ensure long-term social and economic stability.

Originality/value

This study contributes to social economics by integrating ethical dimensions of karma into the analysis of moral behavior, offering a fresh perspective that challenges traditional economic models centered on self-interest. The research provides a comprehensive framework for understanding how moral principles influence economic decisions and social outcomes.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-07-2023-0571