bluuebunny/crossref_metadata_2025 huggingface dataset:
Placental biomarkers in second trimester maternal serum are associated with postpartum hemorrhage: a secondary analysis of the NuMoM2b dataset
Authors: Rutherford Julienne N. , George Erin K. , Erickson Elise N.
Published: December 2024

Postpartum hemorrhage (PPH) is the leading cause of maternal mortality worldwide, which is often attributed to retained placenta (RP) after delivery. There are no biomarkers currently used to predict a risk of developing RP/PPH prior to labor. The objective of this study was to determine relationships between placental biomarkers measured in the first and second trimesters and proxy measures of postpartum blood loss relative to preeclampsia status in the Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-Be (nuMoM2b) dataset. 2,192 participants had placental analytes drawn during the first and second trimesters (9-13 and 16-22 weeks gestation, respectively); the outcome was a composite of retained placenta and/or PPH requiring blood transfusion (RP/PPH). Using Kruskal-Wallis tests, median differences in levels of soluble fms-like tyrosine kinase-1 (sFlt-1), placental growth factor (PlGF), sFlt-1/PlGF ratio, soluble endoglin (sEng), beta subunit of human chorionic gonadotropin (β-hCG), inhibin A (INHA), and pregnancy-associated protein-A (PAPP-A) were assessed between women with (n=67) and without (n=2125) RP/PPH overall and stratified by preeclampsia status. Women with RP/PPH had significantly higher median levels of sEng, β-hCG, INHA, PAPP-A in the second trimester and sFlt-1was higher in both first and second trimesters, which was observed again when stratifying by preeclampsia status. Our findings indicate that biomarkers associated with angiogenesis, particularly when measured in the second trimester, are important targets for further study of RP and/or PPH pathophysiology and potential risk screening development.
Gene-Burden Meta-Analysis of 748,879 Individuals Identifies LGI1-ADAM23 Protein Complex Association with Epilepsy
Authors: Lal Jessica Castrillon , Leu Costin , Boßelmann Christian M. , Ivaniuk Alina , Pérez-Palma Eduardo , Lal Dennis
Published: December 2024

Epilepsy affects over 50 million individuals globally and has a substantial genetic component that remains to be completely understood. Traditional studies have focused on severe, early-onset cases enrolled through clinical or research settings. Recent biobank-based approaches, leveraging large-scale population datasets, offer opportunities to explore genetic associations in broader epilepsy phenotypes, including milder, later-onset forms. We analyzed data from over 750,000 individuals across the UK Biobank, All of Us, and Massachusetts General Brigham Biobank, including 20,026 individuals with epilepsy. Rare coding variant burden testing revealed a significant association withLGI1, a known epilepsy gene. Other top-ranked genes, includingGABRG2, ATP1A3, andADAM23, demonstrated strong enrichment for epilepsy-associated variants. Notably,ADAM23, previously linked to epilepsy in dogs and strong brain expression in humans, emerged as a novel candidate, potentially contributing to human epilepsy through its direct interaction withLGI1. Phenome-wide analyses highlighted the pleiotropic effects of epilepsy genes, withLGI1andADAM23predominantly associated with epilepsy, while other genes such asKRIT1, TSC1, andTSC2exhibited broader systemic involvement. Our study shows the potential of population-scale genomic data and suggests that integrating these datasets with deep phenotyping will uncover more novel insights into epilepsy genetics in the future.
A nucleotide code governs Lis1’s ability to relieve dynein autoinhibition
Authors: Geohring Indigo C. , Chai Pengxin , Iyer Bharat R. , Ton William D. , Yang Jun , Ide Amy H. , George Sydney C. , Bagri Jaiveer S. , Baird Samuel V. , Zhang Kai , Markus Steven M.
Published: December 2024

Dynein-1 is a microtubule motor responsible for the transport of cytoplasmic cargoes. Activation of motility requires it first overcome an autoinhibited state prior to its assembly with dynactin and a cargo adaptor. Studies suggest that Lis1 may relieve dynein’s autoinhibited state. However, evidence for this mechanism is lacking. We first set out to determine the rules governing dynein-Lis1 binding, which reveals that their binding affinity is regulated by the nucleotide-bound states of each of three nucleotide-binding pockets within the dynein motor domain. We also find that distinct nucleotide ‘codes’ coordinate dynein-Lis1 binding stoichiometry by impacting binding affinity at two different sites within the dynein motor domain. Electron microscopy reveals that a 1 Lis1:1 dynein complex directly promotes an open, uninhibited conformational state of dynein, whereas a 2:1 complex resembles the autoinhibited state. Cryo-EM analysis reveals the structural basis for Lis1 opening dynein relies on interactions with the linker domain.
Sex-specific survival but not tissue wasting in the KPP mouse model of pancreatic cancer-induced cachexia
Authors: Weinzierl Natalia M. , Putri Jayarani , Spitler Kathryn M. , Talbert Erin E.
Published: December 2024

Cancer cachexia, a multifactorial condition resulting in muscle and adipose tissue wasting, reduces the quality of life of many people with cancer. Despite decades of research, therapeutic options for cancer cachexia remain limited. Cachexia is highly prevalent in people with pancreatic ductal adenocarcinoma (PDAC), and many animal models of pancreatic cancer are used to understand mechanisms underlying cachexia. One such model is theKrasLSL-G12D,Ptf1aCre-ER/+,Ptenflox/flox(KPP) model, which utilizes an inducible Cre recombinase to allow tumor development to be initiated at any age by tamoxifen administration. In our previous work, tumors were induced in KPP mice at 4 weeks of age. However, mice are still rapidly growing at this age, and a portion of the body weight differences seen between control and KPP mice is likely due to slowed growth of KPP mice. In our current study, pancreatic tumors were induced to develop with tamoxifen in KPP mice after rapid postnatal growth has slowed at 10 weeks of age (KPP10). Similar to our previous findings, KPP10 mice had lower body, muscle, and adipose tissue weights compared to non-tumor mice, and these differences were similar between male and female mice. However, male mice experienced greater relative weight loss. Unexpectedly, we identified that overall survival was significantly shorter in female KPP10 mice compared to KPP10 males. Greater body weight at tumor induction was associated with longer survival, suggesting that the sex difference in survival may be related to differences in body weight between male and female mice.

NEW & NOTEWORTHY

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Although male mice experience greater relative body weight losses, similar skeletal muscle and adipose tissue wasting occurs between male and female mice in theKrasLSL-G12D,Ptf1aCre-ER/+,Ptenflox/flox(KPP) model of pancreatic-cancer induced cachexia.

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Greater weight loss in males may be related to longer survival. However, differences in tamoxifen dose relative to body weight may have accelerated tumor formation in female mice and therefore may be a relevant consideration for inducible tumor models.
Predicting microbial transcriptome using genome sequence
Authors: Fu Guohao , Yan Yujing , Shao Bin
Published: December 2024

We present TXpredict, a transformer-based framework for predicting microbial transcriptomes using annotated genome sequences. By leveraging information learned from a large protein language model, TXpredict achieves an average Spearman correlation of 0.53 in predicting gene expression for new bacterial genomes. We further extend this framework to predict transcriptomes for 900 additional microbial genomes spanning 276 genera, 69% of which remain uncharacterized at the transcriptional level. Additionally, TXpredict enables the prediction of condition-specific gene expression, providing a powerful tool for understanding microbial adaptation and facilitating the rational design of gene regulatory sequences.
When do measured representational distances reflect the neural representational geometry?
Authors: Botero Veronica Bossio , Kriegeskorte Nikolaus
Published: December 2024

The representational geometry of a brain region can be characterized by the distances among neural activity patterns for a set of experimental conditions. Researchers routinely estimate representational distances from brain-activity measurements that either sparsely sample the underlying neural population (e.g. neural recordings) or pool across the activity of many neurons (e.g. fMRI voxels). Here we use theory and simulations to clarify under what circumstances representational distances estimated from brain-activity measurements reflect the representational geometry of the underlying neural population, and what distortions must be expected under other circumstances. We demonstrate that the estimated representational distances are undistorted if single neurons are sampled at random. For voxels that take non-negatively weighted linear combinations, the resulting geometry is linearly distorted, correctly reflecting the population-mean dimension, while downscaling all orthogonal dimensions, for which the averaging cancels a large portion of the signal. Surprisingly, removing the mean from voxel patterns recovers the underlying representational geometry exactly in expectation under idealized conditions. This explains why the correlation distance, the most popular measure of representational dissimilarity in neuroimaging studies, “works” so well, yielding geometries that can appear similar between fMRI and neural recordings. The Euclidean (or Mahalanobis) distance computed after removing the mean of each pattern (without normalizing its variance) is an attractive alternative to the correlation distance in that it corrects for the inflated relative contribution of the population-mean dimension, while avoiding the drawback of the correlation distance: it can be large for confusable low-norm patterns, failing to reflect decodability. Our results demonstrate that measured representational distances reflect the neural representational geometry when (1) single neurons are sampled at random or (2) the weights with which the measured responses sample the neurons are drawn i.i.d. and (2a) the weights are drawn from a zero-mean distribution or (2b) the population mean is the same for all conditions or (2c) the mean is removed from each estimated pattern. We discuss practical implications for analyses of neural representational geometries.
Transient glycan-shield reduction induces CD4-binding site broadly neutralizing antibodies in SHIV-infected macaques
Authors: Morris Daniel J. , Gorman Jason , Zhou Tongqing , Lora Jinery , Connell Andrew J. , Li Hui , Liu Weimin , Roark Ryan S. , Campion Mary S. , Carey John W. , Habib Rumi , Li Yingying , Martella Christian L. , Park Younghoon , Singh Ajay , Sowers Kirsten J. , Teng I-Ting , Wang Shuyi , Chohan Neha , Ding Wenge , Lauer Craig , Lewis Emily , Mason Rosemarie D. , Rando Juliette M. , Peyton Lowrey , Schramm Chaim A. , Wagh Kshitij , Korber Bette , Seaman Michael S. , Douek Daniel C. , Haynes Barton F. , Kulp Daniel W. , Roederer Mario , Hahn Beatrice H. , Kwong Peter D. , Shaw George M.
Published: December 2024

Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 CD4-binding site (CD4bs) occur infrequently in macaques and humans and have not been reproducibly elicited in any outbred animal model. To address this challenge, we first isolated RHA10, an infection-induced rhesus bNAb with 51% breadth. The cryo-EM structure of RHA10 with HIV-1 envelope (Env) resembled prototypic human CD4bs bNAbs with CDR-H3-dominated binding. Env-antibody co-evolution revealed transient elimination of two Env CD4bs-proximal glycans near the time of RHA10-lineage initiation, and these glycan-deficient Envs bound preferentially to early RHA10 intermediates, suggesting glycan deletions in infecting SHIVs could consistently induce CD4bs bNAbs. To test this, we constructed SHIV.CH505.D3 with CD4bs-proximal glycan deletions. Infection of 10 macaques resulted in accelerated CD4bs bNAb responses in 8, compared with 1 of 115 control macaques. Glycan hole-based immunofocusing coupled to Env-Ab co-evolution can consistently induce broad CD4bs responses in macaques and thus serve as a model for HIV vaccine design.

Highlights

Out of 115 wildtype HIV-1 Env bearing SHIV infected macaques, only one macaque (T681) developed CD4bs bNAbs

CD4bs bNAbs in macaque T681 recognized Env similarly to previously described CDR-H3 dominated human CD4bs bNAbs and exhibited comparable breadth and potency

Transient CD4bs-proximal glycan deletions in macaque T681 preceded bNAb induction

A novel SHIV with CD4bs-proximal glycan holes and enhanced CD4bs antigenicity immunofocused B cell responses to the CD4bs and elicited cross-clade neutralizing responses in 80% of macaques
Engineering Multiplexed Synthetic Breath Biomarkers as Diagnostic Probes
Authors: Wang Shih-Ting , Anahtar Melodi , Kim Daniel M. , Samad Tahoura S. , Zheng Claire M. , Patel Sahil , Ko Henry , Ngambenjawong Chayanon , Wang Cathy S. , Kirkpatrick Jesse D. , Kumar Vardhman , Fleming Heather E. , Bhatia Sangeeta N.
Published: December 2024

Breath biopsy is emerging as a rapid and non-invasive diagnostic tool that links exhaled chemical signatures with specific medical conditions. Despite its potential, clinical translation remains limited by the challenge of reliably detecting endogenous, disease-specific biomarkers in breath. Synthetic biomarkers represent an emerging paradigm for precision diagnostics such that they amplify activity-based biochemical signals associated with disease fingerprints. However, their adaptation to breath biopsy has been constrained by the limited availability of orthogonal volatile reporters that are detectable in exhaled breath. Here, we engineer multiplexed breath biomarkers that couple aberrant protease activities to exogenous volatile reporters. We designed novel intramolecular reactions that leverage protease-mediated aminolysis, enabling the sensing of a broad spectrum of proteases, and that each release a unique reporter in breath. This approach was validated in a mouse model of influenza to establish baseline sensitivity and specificity in a controlled inflammatory setting, and subsequently applied to diagnose lung cancer using an autochthonousAlk-mutant model. We show that combining multiplexed reporter signals with machine learning algorithms enables tumor progression tracking, treatment response monitoring, and detection of relapse after 30 minutes. Our multiplexed breath biopsy platform highlights a promising avenue for rapid, point-of-care diagnostics across diverse disease states.
A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense
Authors: Chang Renee B. , Toyoda Hunter C. , Hobbs Samuel J. , Richmond-Buccola Desmond , Wein Tanita , Burger Nils , Chouchani Edward T. , Sorek Rotem , Kranzusch Philip J.
Published: December 2024

Cyclic oligonucleotide-based antiviral signaling systems (CBASS) are bacterial anti-phage defense operons that use nucleotide signals to control immune activation. Here we biochemically screen 57 diverseE. coliandBacillusphages for the ability to disrupt CBASS immunity and discover anti-CBASS 4 (Acb4) from theBacillusphage SPO1 as the founding member of a large family of >1,300 immune evasion proteins. A 2.1 Å crystal structure of Acb4 in complex with 3′3′-cGAMP reveals a tetrameric assembly that functions as a sponge to sequester CBASS signals and inhibit immune activation. We demonstrate Acb4 alone is sufficient to disrupt CBASS activationin vitroand enable immune evasionin vivo. Analyzing phages that infect diverse bacteria, we explain how Acb4 selectively targets nucleotide signals in host defense and avoids disruption of cellular homeostasis. Together, our results reveal principles of immune evasion protein evolution and explain a major mechanism phages use to inhibit host immunity.
ProteoPlotter: an executable proteomics visualization tool compatible with Perseus
Authors: Olabisi-Adeniyi Esther , McAlister Jason A. , Ferretti Daniela , Cox Juergen , Geddes-McAlister Jennifer
Published: December 2024

Mass spectrometry-based proteomics experiments produce complex datasets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly-available proteomics data analysis platform, Perseus, is extensively used to perform such tasks, but opportunities to enhance visualization tools and promote accessibility of the data exist. In this study, we developed ProteoPlotter, a user-friendly, executable tool to complement Perseus for visualization of proteomics datasets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multi-dimensional proteomics data. ProteoPlotter provides mapping of one-dimensional enrichment analyses, enhanced adaptability of volcano plots through incorporation of Gene Ontology terminology, visualization of 95% confidence intervals in principal component analysis plots using data ellipses, and customizable features. ProteoPlotter is designed for intuitive use by biological and computational researchers alike, providing descriptive instructions (i.e., Help Guide) for preparing and uploading Perseus output files. Herein, we demonstrate the application of ProteoPlotter towards microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for improved biological characterization. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates a deeper understanding of proteomics data to drive new biological discoveries.
Cortical Changes Associated with Isha Kriya Meditation Revealed by Encephalography in Novice and Experienced Meditators – a Longitudinal Pilot Study
Authors: Vishnubhotla Ramana V. , Reed Preeti U. , Subramaniam Balachundhar
Published: December 2024

Abstract

Background

Isha Kriya (IK) is a widely available meditation practice that incorporates breathing regulation that has shown to improve self-reported symptoms of stress, anxiety, and depression. An increasing amount of research has been published on the effects of various meditative practices on scalp electroencephalography (EEG). However, the effects of IK on cortical activity have not been reported previously.

Methods

Healthy volunteers aged 18 years or older were invited to participate. Participants were categorized as novice or experienced in meditation. EEG spectral features, computed during the eyes-closed condition before and soon after each IK meditation practice, were evaluated both at the start and after 6 weeks of IK meditation training.

Results

This longitudinal study examined the effects of IK meditation on cortical state and trait patterns in a cohort of eight participants who practiced IK meditation over a period of 6 weeks. Across the two sessions, a simultaneous increase in global periodic alpha power was observed in multiple subjects (N=6) but this was not observed in all subjects/sessions. We observed an increase in periodic theta band power, particularly in the frontal regions, which emerged as a common state effect in all participants. Longitudinally, we observed an increased periodic gamma power in the resting state EEG in all the experienced meditators in the parietal occipital region. The changes in novices on the other hand was in the alpha and beta bands.

Conclusion

Overall, in this pilot study, we report the changes in the quantitative EEG of the practitioners of Isha Kriya meditation over a 6-week cycle and investigated the difference between the start and end of that period at an individual level. We recommend future studies with a larger sample size and over a longer duration.

Trial registration

This trial is registered with the US National Institutes of Health onClinicalTrials.govwith the trial identification numberNCT03459690on February 14, 2018.
Mapping Grip Force to Muscular Activity Towards Understanding Upper Limb Musculoskeletal Intent using a Novel Grip Strength Model
Authors: Lai Yujun , Abdel-Messih Elvera , Carmichael Marc G. , Member Gavin Paul
Published: December 2024

This study aims to evaluate a grip strength model designed to elucidate the relationship between measured grip force and muscular activity and assess its impact on an upper limb musculoskeletal model. This work aims to develop the grip strength model by utilizing a piecewise linear function based on the Woods and Bigland-Ritchie EMG-force model, which derives its parameters from 10 adult participants performing isometric and dynamic gripping tasks. Experimental results demonstrate the model’s efficacy in estimating surface electromyography (sEMG) readings from force measurements, with a mean root mean square error (RMSE) of 0.2035 and a standard deviation of 0.1207. Moreover, incorporating sEMG readings associated with grip force does not significantly affect the optimization of muscle activation in the upper arm, as evidenced by kinematic data analysis from dynamic tasks. This validation underscores the model’s potential to enhance musculoskeletal model-based motion analysis pipelines without distorting results. Consequently, this research emphasizes the prospect of integrating external models into existing human motion analysis frameworks, presenting promising implications for physical Human-Robot Interactions (pHRI).
Climate and performance-driven architectural floorplan optimization using deep graph networks
Authors: Yang Yang , Luo Hanzhong , Adibhesami Mohammad Anvar
Published: December 2024

Purpose

This study introduces a novel approach to generating and optimizing energy-efficient and climate-responsive architectural floorplans.

Design/methodology/approach

The DGraph-cGAN model utilizes advanced deep-learning techniques to produce diverse, realistic layouts that meet specific design constraints and functional requirements.

Findings

The results show significant energy savings (32.1% overall) across different building types and climate conditions, with reductions in energy use intensity, CO2 emissions and annual energy costs. Case studies demonstrate notable improvements in energy savings, CO2 emission reduction, daylight autonomy, thermal comfort and cost savings.

Practical implications

The DGraph-cGAN model has great potential for advancing architectural design optimization, with opportunities for further refinement and application in various contexts.

Originality/value

This study contributes to developing a novel approach to optimizing architectural floorplans using deep learning techniques. It provides a valuable tool for architects and designers to create energy-efficient, climate-responsive buildings.
Reshoring before and during the COVID-19 pandemic in an advanced economy
Authors: Olhager Jan , Harfeldt-Berg Magnus
Published: December 2024

Purpose

The purpose is to investigate how the coronavirus disease 2019 (COVID-19) pandemic changed relocation behavior in an advanced economy. We compare manufacturing relocations before and during the pandemic to identify differences and similarities over time and between offshoring and backshoring.

Design/methodology/approach

We use an exploratory longitudinal trend survey approach with data from two surveys, the first before the pandemic, 2010–2015, and the second during the pandemic, 2020–2022. Both rounds were targeted to the entire population of Swedish manufacturing plants with 50 or more employees. We captured the same set of data for offshoring and backshoring projects in both surveys.

Findings

The pandemic did not stop manufacturing relocations. The extent of offshoring decreased, but the extent of backshoring increased. Labor costs remained a key driver for offshoring, but a trade-off versus lead time, flexibility and risk were observed, suggesting a tension between labor cost and a strive for creating shorter supply chains for offshoring. Lead time, logistics costs, market proximity and risk formed a new backshoring construct, with an emphasis on short supply chains, and that increased significantly in importance. At the same time, the importance of quality decreased, creating a need to balance quality against the pursuit of short supply chains for backshoring. Thus, local supply chains seem to be a desired outcome for any manufacturing relocation, suggesting a move towards a multi-local supply chain setup for the global manufacturing footprint.

Originality/value

This is the first longitudinal survey study that captures offshoring as well as backshoring before and during the pandemic. The results offer unique insights into the COVID-19-induced impacts on manufacturing relocations as the same total population was sampled before and after the pandemic, and it provides empirical evidence that neither offshoring nor backshoring are “steady-state” concepts but changes over time.
Financial monitoring with humanitarian assistance: improving transparency and effectiveness in relief efforts
Authors: Maletova Olha , Utkina Maryna , Sukhonos Volodymyr V. , Ilchenko Oleksandr V.
Published: December 2024

Purpose

This study aims to critically analyse the current state of implementing financial monitoring of humanitarian aid in the context of the challenges of martial law and Ukraine’s European integration aspirations.

Design/methodology/approach

In this article, a comprehensive approach to research methodology is widely used when the methods complement each other, allowing one to consider the investigated processes and phenomena in their unity and diversity.

Findings

This article proves the necessity of applying the latest approaches and adapting the existing financial monitoring mechanisms to wartime challenges. Special attention is focused on digitalisation processes and transparency of financial monitoring of humanitarian aid provided to Ukraine from various sources.

Originality/value

This article critically analyses modern legislative changes, new tools for transparent and effective financial monitoring in martial law conditions and Ukraine’s European integration aspirations.
Theorizing knowledge worker productivity: utilizing a multi-theoretical approach
Authors: Kintu Gerald Joseph
Published: December 2024

Purpose

The global economy is experiencing an expansion in knowledge-based businesses, which has compelled organizations to search for mechanisms of raising knowledge worker productivity. This study utilizes multiple theories to explain lessons learned from a positive story on how to raise the productivity of knowledge workers.

Design/methodology/approach

The study used a qualitative methodology of storytelling, a form of narrative inquiry about a phenomenon. In-depth interviews were carried out with information and communication technology (ICT) workers in Uganda.

Findings

Findings reveal that knowledge workers who communicate and mutually support each other are inclined to share knowledge and best practices that promote cost-effective utilization of resources. Additionally, knowledge workers with a behavior oriented toward the continuous exploration of innovative ideas are proactive in creating knowledge on how to render quality services.

Research limitations/implications

The study was carried out in one country, which may limit generalization of results.

Practical implications

The study underscores the importance of continuously developing the human capital base and fostering a collaborative environment for knowledge workers. This nurtures the capacity and a shared responsibility to generate innovative ideas directed toward the effective utilization of resources. Moreover, the study advocates for the inclusion of social competencies, such as interpersonal skills, in the selection process of knowledge workers.

Originality/value

This study stands out from the existing literature since it uses a success story to document the real-life experiences of a knowledge worker who had to overcome numerous challenges to raise productivity in knowledge work.
Plant mycorrhizal status indicates partner selectivity in arbuscular mycorrhizal interaction networks
Authors: Koorem Kadri , Sepp Siim‐Kaarel , Bueno C. Guillermo , Davison John , Liu Siqiao , Meng Yiming , Semchenko Marina , Vasar Martti , Zobel Martin , Moora Mari
Published: December 2024

Mycorrhizal symbiosis, specifically arbuscular mycorrhiza, is one of Earth's oldest and most widespread symbiosis. Existing evidence suggests that plant species differ in their associations with mycorrhizal partners, with different species reported to be always (obligately mycorrhizal, OM), sometimes (facultatively mycorrhizal, FM) or never (non‐mycorrhizal, NM) associating with arbuscular mycorrhizal (AM) fungi and this plant reliance on AM fungi is called plant mycorrhizal status. However, very little is known about how host plant mycorrhizal status shapes the network topology of interacting AM fungi.

Here, we use a standardized sampling scheme to test whether plant species with different mycorrhizal statuses differ in mean AM fungal hyphal colonization and various indices of the AM fungal networks such as nestedness rank and resource range.

We collected the roots and rhizosphere soil of 19 plant species representing five families. Each plant species was sampled from three distinct habitats. We determined AM fungal colonization in the roots and AM fungal community composition in roots and rhizosphere soil using molecular methods.

We found that previously reported NM plant species had lower mean AM fungal colonization than FM plant species, but no differences were found between FM and OM plant species. Network analyses indicated that AM fungal communities in the roots of FM plant species had higher nestedness rank and resource range than networks associated with OM plant species, suggesting that OM plant species are more generalist regarding partner selection and interact with a wider range of fungal partners.

Our results suggest that plant mycorrhizal status conveys useful information about the characteristics of AM fungal interaction networks, revealing that plant species consistently associated with AM fungi are less selective towards their fungal partners.

Read the free Plain Language Summary for this article on the Journal blog.
STATE BUILDING IN CRISIS MANAGEMENT: Reflections on Statecraft from the Shanghai Lockdown
Authors: Wang Ying , Wu Fulong , Zhang Fangzhu
Published: December 2024

The exceptional measures to combat the Covid‐19 pandemic have brought great potential for reconfiguring urban governance. To examine such potential, this article presents how the pandemic crisis was managed in Chinese neighbourhoods. Following a statecraft approach and using Shanghai as a case, we show how a citywide lockdown played out on the ground as a joint product of state apparatus and citizens. Drawing on discourse analysis of interviews, policy documents, and news reports, we probe into Shanghai's contextualized neighbourhood pandemic responses, particularly by emerging neighbourhood voluntary practices in crisis management. We examine how these practices were tactically incorporated into the state's overall responses to the pandemic through co‐production, co‐option and mobilization. Instead of co‐governance, we argue that the grassroots state orchestrates and steers community participation and volunteerism to reinforce grassroots statecraft and consolidate its role in (post‐) pandemic neighbourhood governance. Through exceptional crisis management measures, the state penetrates everyday life. This process has facilitated local state‐building in urban neighbourhoods, thereby manifesting, perpetuating, and expanding state‐centred governance trends that were established well before the onset of Covid.
Effect of the First Laparoscopy in an Adolescent and Young Adult Female Population and Its Association With Chronic Pelvic Pain: A Randomised Controlled Trial
Authors: Nguyen Kimberly , Wu Joyce , Mallinder Hayley , Niranjan Madhulikaa Sarjapuram , Gerstl Brigitte , Abbott Jason A. , Deans Rebecca
Published: December 2024

Background

Chronic pelvic pain (CPP) is a common and debilitating presentation for adolescent and young adult females. Medical management is often utilised as first line therapy with surgical management considered if medical treatment has been unsuccessful. Laparoscopy in this young population remains controversial due to the high recurrence rate of pain, requirement for repeat surgeries and surgical risks. There is a need for prospective, longitudinal studies comparing medical and surgical management to guide management of young patients with CPP.

Aims

To determine the effect of the first laparoscopy in an adolescent and young adult female population and assess its association with CPP.

Materials and Methods

Patients aged 16–25 will be recruited from the gynaecological service at the study sites. Consented participants will be randomised to the surgical or non‐surgical arms. Those in the surgical arm will have a laparoscopy performed and those in the non‐surgical arm will be medically managed. At recruitment and at 6 weeks, 6 months, 12 months and 24 months follow‐up, patients will complete a number of validated questionnaires assessing pain and quality of life. An amendment was made to methodology to include patients who will choose their management pathway for CPP.

Results

An independent t‐test or Mann–Whitney U test will be used to compare the questionnaire scores between the surgical and non‐surgical groups. For questionnaire scores at baseline and follow‐up within the same arm, a paired t‐test or Wilcoxon signed‐rank test will be used. A p‐value of < 0.05 will be statistically significant.
CENP‐E haploinsufficiency causes chromosome misalignment and spindle assembly checkpoint activation in the spermatogonia
Authors: Chen Jie , He Jie‐Jie , Wu Shan , Deng Zhao‐Yang , Liu Yu‐Peng , Chen Jian‐Fan , Xu Yue , Fang Han‐Kai , Wei Ya‐Lan , She Zhen‐Yu
Published: December 2024

Background

The establishment of kinetochore–microtubule attachment is essential for error‐free chromosome alignment and segregation during cell division. Defects in chromosome alignment result in chromosome instability, birth defects, and infertility. Kinesin‐7 CENP‐E mediates kinetochore–microtubule capture, chromosome alignment, and spindle assembly checkpoint in somatic cells, however, mechanisms of CENP‐E in germ cells remain poorly understood.

Objectives

This study aimed to explore the functions of CENP‐E in the proliferation and self‐renewal of spermatogonia.

Materials and methods

A CENP‐E heterozygous knockout strain was established in C57BL/6J mice using the CRISPR/Cas9 and Cre/LoxP system. Hematoxylin–eosin staining was performed to study the histology. The inhibition of CENP‐E in the GC‐1 spg cells was performed using the specific inhibitor GSK923295. The expression and localization of spermatogonial marker proteins were determined by immunofluorescence using confocal microscopy in the control and CENP‐E+/− heterozygous mouse testes. The protein expression level was analyzed using Western blot. The cell‐cycle and apoptosis assay were measured using flow cytometry. In addition, karyotype analysis was performed using hypotonic preparation and chromosome spreading.

Results

Here, we reveal that CENP‐E haploinsufficiency results in chromosome misalignment, spindle disorganization, and metaphase arrest in spermatogonia, which leads to the loss of spermatogonia, chromosomal instability, and spermatogenic disorders. Notably, CENP‐E ablation leads to the activation of spindle assembly checkpoint and aneuploidy, which impairs the proliferation and self‐renewal of spermatogonia.

Discussion and conclusion

CENP‐E depletion disrupts the recruitment of key checkpoint proteins, including BubR1, Bub1, KIF2C, and Aurora B, indicating a causal relationship between chromosome misalignment and spindle assembly checkpoint activation in spermatogonia. Our findings demonstrate that CENP‐E regulates kinetochore–microtubule attachment, chromosome alignment, and spindle assembly checkpoint in spermatogonia.
Maternal postpartum infection risk following induction of labor: A Danish national cohort study
Authors: Hogh‐Poulsen Sidsel , Carlsen Sif Emilie , Bendix Jane M. , Clausen Tine D. , Lokkegaard Ellen C. L. , Axelsson Paul Vignir Bryde
Published: December 2024

Introduction

Induction of labor is a common procedure, and in Denmark, approximately one in four vaginal deliveries are induced. The association between induction and maternal postpartum infections such as endometritis, surgical site infection after cesarean section, urinary tract infection, and sepsis has been sparsely investigated. Our objective was to investigate the association between induction of labor and risk of maternal postpartum infection and to identify potential risk factors for infection.

Material and Methods

In a nationwide cohort study, all deliveries with live‐born singletons from January 1, 2007, to December 31, 2017 (n = 546 864) were included. Deliveries were grouped into categories of spontaneous onset of labor, induction of labor, and elective cesarean section. The primary outcome was any infection within 30 days postpartum based on discharge diagnosis codes and redeemed antibiotic prescriptions for endometritis, surgical site infection, urinary tract infection, and sepsis. Analyses were done using logistic regression.

Results

Infection within 30 days postpartum was found among 8.5% of the women undergoing induction of labor compared to 6.8% of the women with spontaneous onset of labor. In adjusted logistic regression analyses, the risk of postpartum infection was significantly increased after induction of labor compared to spontaneous onset of labor (adjusted ORs [aOR], 1.24; 95% confidence interval [CI], 1.21–1.27). Women with rupture of membranes were not at increased risk of postpartum infection (aOR 1.01; 95%CI 0.94–1.09). The risk of postpartum maternal sepsis was not significantly associated with induction of labor. Antibiotic treatment during pregnancy, pre‐eclampsia, and long education were all associated with increased risk of maternal postpartum infection, while either a low or high body mass index and previous deliveries were associated with decreased risk.

Conclusions

Induction of labor was associated with an increased risk of maternal postpartum infection. However, the absolute risk was 1.7% higher for the women with induced labor compared to spontaneous onset of labor, which we believe should not be a cause for concern. Unexpectedly, low and high body mass index was associated with decreased risk of infection, and rupture of membranes was not associated with increased risk after induction of labor, which might reflect actual clinical management.
Respiratory viruses were frequently detected in young children with cystic fibrosis but had limited clinical significance
Authors: Cömert Hatice N. , Sandvik Rikke M. , Ma Chih M. G. , Buchvald Frederik , Schønning Kristian , Skov Marianne , Schmidt Marika N. , Pressler Tacjana , Johansen Helle K. , Nielsen Kim G.
Published: December 2024

Aim

Knowledge about the clinical role that respiratory viruses play in infants and toddlers with cystic fibrosis (CF) remains limited. We determined the prevalence of respiratory viruses in routine respiratory secretion samples in children aged 0–3 years with CF. Associations with bacterial infections, respiratory tract symptoms and lung function were also explored.

Methods

This prospective, longitudinal, single‐centre study added viral polymerase chain reaction detection to the routine monitoring of CF lung disease at Copenhagen University Hospital, Denmark, from 1 July 2019 to 31 August 2020. The existing programme included monthly clinical assessments with endo‐laryngeal suction for bacterial culturing and quarterly lung function testing.

Results

We studied 19 children (11 males) with a median age of 1.8 (range 0.11–2.99) years. Viruses were detected in 86/193 (45%) samples. Rhinoviruses and enteroviruses were the most common (88%), followed by adenoviruses (9%), parainfluenza 1–3 (6%) and the respiratory syncytial virus (5%). A positive association was found between the annual incidence of viruses and bacteria, but there was no correlation with respiratory tract symptoms or lung function.

Conclusions

Respiratory viruses were commonly detected in routine respiratory secretion samples. However, the results from this small study did not justify specific conclusions.
Managing Hypoglycaemia in Patients With Insulinoma—A Tertiary Centre Experience and Review of the Literature
Authors: Howarth Sophie , Ho Tak‐Wai , Wimbury James , Casey Ruth
Published: December 2024

The management of hypoglycaemia is pivotal in the care of patients with insulinoma. Blood glucose monitoring and regulation needs careful attention pre‐ and peri‐operatively for patients undergoing surgical resection and as part of the long‐term management for patients with inoperable or metastatic disease. Hypoglycaemia symptoms are frequently pervasive and disabling, with many patients showing impaired hypoglycaemia awareness that can lead to life‐threatening severe hypoglycaemia. Herein, we review the literature and describe our tertiary centre experience in the mutli‐disciplinary management of hypoglycaemia for patients with proven insulinomas. We propose a stepwise algorithm for the management of hypoglycaemia, stratified by localised versus metastatic disease. We discuss our strategy for the nutritional management of hypoglycaemia, reviewing the evidence for the use of cornstarch products and artificial nutrition. We discuss pharmacological management including diazoxide, somatostatin receptor antagonists (SSAs), everolimus and glucocorticoids, in addition to other therapeutic interventions such as peptide receptor radionuclide therapy (PRRT) and endoscopic ablation.
Classification of direct threats to the conservation of ecosystems and species 4.0
Authors: Salafsky Nick , Relton Claire , Young Bruce E. , Lamarre Philippe , Böhm Monika , Chénier Maxime , Cochrane Erica , Dionne Mark , He Kevin K. , Hilton‐Taylor Craig , Latrémouille Charles , Morrison John , Raymond Calla V. , Seddon Mary , Suresh Varsha
Published: December 2024

Identifying and assessing the magnitude of direct threats to ecosystems and species are critical steps to prioritizing, planning, implementing, and assessing conservation actions. Just as medical clinicians and researchers need a standard way to talk about human diseases, conservation practitioners and scientists need a common and comprehensive language to talk about the threats they are facing to facilitate joint action, evaluation, and learning. To meet this need, in 2008 the IUCN Species Survival Commission and the Conservation Measures Partnership produced the first version of a common threats classification with the understanding that it would be periodically updated to take into account new information and learning. We present version 4.0 of this classification. For this latest update, we reviewed existing versions and derivatives of the original classification, over 1000 citations of the classification, threats data from over 2900 real‐world conservation projects, and comments from many users. Based on our findings, we made changes to the threats classification scheme, including addition of a level 0 threat class, refinement of levels 1 and 2 threat categories, and addition of the threat “Fencing & walls” to level 2. Also added were level 3 threat types and modifiers that provide a more detailed description of different types of direct threats and thus allow users to fine‐tune analyses and actions. The update also clarifies how to treat various stressors, including natural disaster events and climate change. As a result of these changes, we revised the formal definition of direct threats. They include human actions that are the direct cause of ecosystem or species‐population degradation and loss, such as agriculture, transport, natural resource use, and ecosystem management. They also include ultimate stressors in natural systems whose dynamics have been altered by the effects of current or historical human actions, such as invasive or problematic native species, pollution, natural disasters, and climate change.
Inheritance of Material Wealth in a Natural Population
Authors: Ålund Murielle , McFarlane S. Eryn , Husby Arild , Knape Jonas , Pärt Tomas , Sirkiä Päivi , Weissing Franz J. , Wheatcroft David , Zhu Yishu , Qvarnström Anna
Published: December 2024

Evolutionary adaptation occurs when individuals vary in access to fitness‐relevant resources and these differences in ‘material wealth’ are heritable. It is typically assumed that the inheritance of material wealth reflects heritable variation in the phenotypic abilities needed to acquire material wealth. We scrutinise this assumption by investigating additional mechanisms underlying the inheritance of material wealth in collared flycatchers. A genome‐wide association analysis reveals a high genomic heritability (h2 = 0.405 ± 0.08) of access to caterpillar larvae, a fitness‐relevant resource, in the birds' breeding territories. However, we find little evidence for heritable variation in phenotypic abilities needed to acquire this material wealth. Instead, combined evidence from simulations, experimental and long‐term monitoring data indicate that inheritance of material wealth is largely explained by philopatry causing a within‐population genetic structure across a heterogeneous landscape. Therefore, allelic variants associated with high material wealth may spread in the population without having causal connections to traits promoting local adaptation.
Multiple Long‐Term, Landscape‐Scale Data Sets Reveal Intraspecific Spatial Variation in Temporal Trends for Bird Species
Authors: Lindenmayer David , Scheele Ben C. , Bowd Elle , Evans Maldwyn John
Published: December 2024

Quantifying temporal changes in species occurrence has been a key part of ecology since its inception. We quantified multidecadal site occupancy trajectories for 18 bird species in four independent long‐term, large‐scale studies (571 sites, ~1000 km latitude) in Australia. We found evidence of a year × long‐term study interaction in the best‐fitting models for 14 of the 18 species analysed, with differences in the temporal trajectories of the same species in multiple studies consistent with non‐stationarity. Non‐stationarity patterns in occupancy were not related to the distance from a species niche centroid; species in locations further from their niche centroid did not demonstrate differing temporal trajectories to those closer to their niche centroid. Furthermore, temporal trajectories of species were not associated with climatic values for each study relative to their niche. Our findings demonstrate the need for multiple long‐term studies across a species range, especially when tailoring conservation decisions for populations.
Calibrated Ecosystem Models Cannot Predict the Consequences of Conservation Management Decisions
Authors: Lubiana Botelho Larissa , Jeynes‐Smith Cailan , Vollert Sarah A. , Bode Michael
Published: December 2024

Ecosystem models are often used to predict the consequences of management interventions in applied ecology and conservation. These models are often high‐dimensional and nonlinear, yet limited data are available to calibrate or validate them. Consequently, their utility as decision‐support tools is unclear. In this paper, we calibrate ecosystem models to time series data from 110 different experimental microcosm ecosystems, each containing three to five interacting species. Then, we assess their ability to predict the consequences of management interventions. Our results show that for each time series dataset, multiple divergent parameter sets offer equivalent, good fits. However, these models have poor predictive accuracy when forecasting future dynamics or when predicting how the ecosystem will respond to management intervention. Closer inspection reveals that the models fail because calibration cannot determine the nature of the interspecific interactions. Our findings question whether ecosystem models can support applied ecological decision‐making when calibrated against real‐world datasets.