bluuebunny/crossref_metadata_2025_split huggingface dataset:
With a little help from my friends: the roles of microbial symbionts in insect populations and communities
Authors: Łukasik Piotr , Kolasa Michał R. 
Published: May 2024

To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales.
This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.
PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes
Authors: Li Roy , Ratnasingham Sujeevan , Zarubiieva Iuliia , Somervuo Panu , Taylor Graham W. 
Published: May 2024

DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX’s key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics.This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.
Extensive data engineering to the rescue: building a multi-species katydid detector from unbalanced, atypical training datasets
Authors: Madhusudhana Shyam , Klinck Holger , Symes Laurel B. 
Published: May 2024

Passive acoustic monitoring (PAM) is a powerful tool for studying ecosystems. However, its effective application in tropical environments, particularly for insects, poses distinct challenges. Neotropical katydids produce complex species-specific calls, spanning mere milliseconds to seconds and spread across broad audible and ultrasonic frequencies. However, subtle differences in inter-pulse intervals or central frequencies are often the only discriminatory traits. These extremities, coupled with low source levels and susceptibility to masking by ambient noise, challenge species identification in PAM recordings. This study aimed to develop a deep learning-based solution to automate the recognition of 31 katydid species of interest in a biodiverse Panamanian forest with over 80 katydid species. Besides the innate challenges, our efforts were also encumbered by a limited and imbalanced initial training dataset comprising domain-mismatched recordings. To overcome these, we applied rigorous data engineering, improving input variance through controlled playback re-recordings and by employing physics-based data augmentation techniques, and tuning signal-processing, model and training parameters to produce a custom well-fit solution. Methods developed here are incorporated into Koogu, an open-source Python-based toolbox for developing deep learning-based bioacoustic analysis solutions. The parametric implementations offer a valuable resource, enhancing the capabilities of PAM for studying insects in tropical ecosystems.
This article is part of the theme issue ‘Towards a toolkit for global insect biodiversity monitoring’.
Genotypic and phenotypic consequences of domestication in dogs
Authors: Sweetalana  , Nataneli Shirin , Huang Shengmiao , Mooney Jazlyn A , Szpiech Zachary A 
Published: May 2024

AbstractRuns of homozygosity (ROH) are genomic regions that arise when two copies of identical haplotypes are inherited from a shared common ancestor. In this study, we leverage ROH to identify associations between genetic diversity and non-disease phenotypes inCanis lupus familiaris(dogs). We find significant association between the ROH inbreeding coefficient (FROH) and several phenotypic traits. These traits include height, weight, lifespan, muscled, white coloring of the head and chest, furnishings, and fur length. After correcting for population structure, we identified more than 45 genes across the examined quantitative traits that exceed the threshold for suggestive significance. We observe distinct distributions of inbreeding and elevated levels of long ROH in modern breed dogs compared to more ancient breeds, which aligns with breeding practices during Victorian era breed establishment. Our results highlight the impact of non-additive variation and of polygenicity on complex quantitative phenotypes in dogs due to domestication and the breed formation bottleneck.
Study demands and health status among medical students in two German universities
Authors: Voss Amanda , Dettmer Susanne , Tschorn Mira , Zoellick Jan C. 
Published: May 2024

AbstractBackground and objectivesMedical students regularly report high study demands and low mental health. We thus studied medical students in two different curricula in Germany investigating their study demands, study and life satisfaction, and overall and mental health with emphasis on contrasting beginners and advanced students.Design and methodsWe used online surveys with convenience samples through university mailing lists and student union channels. Uni1 participants (N=357; 70% female,M=24.83 years) were older than Uni2 participants (N=126; 79% female;M=23.39 years), but the cohorts did not differ further regarding sociodemographic variables. For analyses, we usedt-tests for comparisons and correlations for associations.ResultsStudents of both universities reported good mental and overall health as well as high satisfaction with their studies and lives, yet sleep difficulties were prevalent. Study demands were low to medium with the highest demands being learning activities (M=5.31;SD=2.19, scale 0-10), self-structuring (M=4.61;SD=2.01), and performance pressure (M=4.45;SD=2.27). The students in the reformed degree programme reported fewer issues with integrating theory and practice compared to those in the regular degree programme (MUni1=3.38;SDUni1=2.05;MUni2=4.17;SDUni2=2.06;t(430)=-3.53,p<.001).Discussion and conclusionsOur sample was rather resilient regarding mental health and coping with study demands. The two universities showed little to no differences. With relative increased demands regarding learning activities, self-structuring, and performance pressure we suggest to focus on learning strategies for beginners and strategies for stress reduction to address, among other things, the reported sleep difficulties.
Using explainable artificial intelligence to identify linguistic biomarkers of amyloid pathology in primary progressive aphasia
Authors: Robertson Cole , Rezaii Neguine , Hochberg Daisy , Quimby Megan , Wolff Phillip , Dickerson Bradford C. 
Published: May 2024

AbstractIntroductionRecent success has been achieved in Alzheimer’s disease (AD) clinical trials targeting amyloid beta (β), demonstrating a reduction in the rate of cognitive decline. However, testing methods for amyloid-β positivity are currently costly or invasive, motivating the development of accessible screening approaches to steer patients toward appropriate diagnostic tests. Here, we employ a pre-trained language model (Distil-RoBERTa) to identify amyloid-β positivity from a short, connected speech sample. We further use explainable AI (XAI) methods to extract interpretable linguistic features that can be employed in clinical practice.MethodsWe obtained language samples from 74 patients with primary progressive aphasia (PPA) across its three variants. Amyloid-β positivity was established through the analysis of cerebrospinal fluid, amyloid PET, or autopsy. 51% of the sample was amyloid-positive. We trained Distil-RoBERTa for 16 epochs with a batch size of 6 and a learning rate of 5e−5, and used the LIME algorithm to train interpretation models to interpret the trained classifier’s inference conditions.ResultsOver ten runs of 10-fold cross-validation, the classifier achieved a mean accuracy of 92%, SD = 0.01. Interpretation models were able to capture the classifier’s behavior well, achieving an accuracy of 97% against classifier predictions, and uncovering several novel speech patterns that may characterize amyloid-β positivity.DiscussionOur work improves previous research which indicates connected speech is a useful diagnostic input for prediction of the presence of amyloid-β in patients with PPA. Further, we leverage XAI techniques to reveal novel linguistic features that can be tested in clinical practice in the appropriate subspecialty setting. Computational linguistic analysis of connected speech shows great promise as a novel assessment method in patients with AD and related disorders.
Time-course analysis of the transcriptome ofArabidopsis thalianaleaves under high-concentration ammonium sulfate treatment
Authors: Iwanaga Hiroko , Arai Yuki , Nezuo Maiko , Doi Akiko , Takei Takahito , Fujiwara Masayuki , Hachiya Takushi , Hamada Takahiro 
Published: May 2024

AbstractNitrogen is essential for plant growth and is sourced primarily from nitrate and ammonium in the soil. Even though plants can take ammonium up for nutrition, it often results in toxic effects such as growth suppression and chlorosis. To elucidate the mechanism of ammonium toxicity, a time-course analysis of the transcriptome was performed onA. thalianaleaves treated with high concentrations of ammonium sulfate in the presence of sufficient nitrate. The expression of nitrate-inducible genes tended to be downregulated by the treatment. The expression of genes relating to abscisic acid, jasmonic acid (JA), salicylic acid (SA), and membrane trafficking was upregulated, whereas that of photosynthesis-, auxin-, and cytokinin-related genes involved in growth and development was downregulated. The induction of many osmotic stress-responsive genes suggests the involvement of osmotic stress in ammonium toxicity. Furthermore, the upregulation of nitric oxide (NO)-inducible genes and the simultaneous upregulation of genes involved in JA biosynthesis, glutathione metabolism, and SA response suggested the involvement of endogenous NO and protein S-nitrosylation in response to high concentrations of ammonium sulfate. This study provides a novel and comprehensive overview of transcriptional changes occurring in response to high ammonium sulfate concentrations and proposes possible mechanisms of ammonium toxicity that can be explored in future research.
Modification of xylan in secondary walls alters cell wall biosynthesis and wood formation programs
Authors: Sivan Pramod , Urbancsok János , Donev Evgeniy N. , Derba-Maceluch Marta , Barbut Félix R. , Yassin Zakiya , Gandla Madhavi L. , Mitra Madhusree , Heinonen Saara E. , Šimura Jan , Cermanová Kateřina , Karady Michal , Scheepers Gerhard , Jönsson Leif J. , Master Emma R. , Vilaplana Francisco , Mellerowicz Ewa J. 
Published: May 2024

AbstractWood of broad-leaf tree species is a valued source of renewable biomass for biorefinery and a target for genetic improvement efforts to reduce its recalcitrance. Glucuronoxylan (GX) plays a key role in recalcitrance through its interactions with cellulose and lignin. To reduce recalcitrance, we modified wood GX by expressing GH10 and GH11 endoxylanases fromAspergillus nidulansin hybrid aspen (Populus tremulaL. xtremuloidesMichx.) and targeting the enzymes to cell wall. The xylanases reduced tree height, modified cambial activity by increasing phloem and reducing xylem production, and reduced secondary wall deposition. Xylan molecular weight was decreased, and the spacing between acetyl and MeGlcA side chains was reduced in transgenic lines. The transgenic trees produced hypolignified xylem having thin secondary walls and deformed vessels. Glucose yields of enzymatic saccharification without pretreatment almost doubled indicating decreased recalcitrance. The transcriptomics, hormonomics and metabolomics data provided evidence for activation of cytokinin and ethylene signaling pathways, decrease in ABA levels, transcriptional suppression of lignification and a subset of secondary wall biosynthetic program, including xylan glucuronidation and acetylation machinery. Several candidate genes for perception of impairment in xylan integrity were detected. These candidates could provide a new target for uncoupling negative growth effects from reduced recalcitrance. In conclusion, our study supports the hypothesis that xylan modification generates intrinsic signals and evokes novel pathways regulating tree growth and secondary wall biosynthesis.
Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination
Authors: Roze Ludmila V. , Antoniak Anna , Sarkar Daipayan , Liepman Aaron H. , Tejera-Nieves Mauricio , Vermaas Josh V. , Walker Berkley J. 
Published: May 2024

AbstractAs global temperatures rise, maintaining and improving crop yields will require enhancing the thermotolerance of crops. One approach for improving thermotolerance is using bioengineering to increase the thermostability of enzymes catalyzing essential biological processes. Photorespiration is an essential recycling process in plants that is integral to photosynthesis and crop growth. The enzymes of photorespiration are targets for enhancing plant thermotolerance as this pathway limits carbon fixation at elevated temperatures. Exploring inter-specific variation of the key photorespiratory enzyme glycerate kinase (GLYK) from various photosynthetic organisms, we found that the homolog from the thermophilic algaCyanidioschyzon merolaewas more thermotolerant than those from mesophilic plants, includingArabidopsis thaliana. To understand factors influencing thermotolerance ofC. merolaeGLYK (CmGLYK), we performed molecular dynamics simulations using AlphaFold-predicted structures, which revealed greater movement of loop regions of mesophilic plant GLYKs at higher temperatures compared to CmGLYK. Based on these simulations, a series of hybrid proteins were produced and analyzed. These hybrid enzymes contained selected loop regions from CmGLYK replacing the most highly mobile corresponding loops of AtGLYK. Two of these hybrid enzymes had enhanced thermostability, with melting temperatures increased by 6 °C. One hybrid with three grafted loops maintained higher activity at elevated temperatures. While this hybrid enzyme exhibited enhanced thermostability and a similar Kmfor ATP compared to AtGLYK, its Kmfor glycerate increased threefold. This study demonstrates that molecular dynamics simulation-guided structure-based recombination offers a promising strategy for enhancing thermostability of other plant enzymes.
Multiomic analysis of genes related to oil traits in legumes provide insights into lipid metabolism and oil richness in soybean
Authors: Turquetti-Moraes Dayana K. , Cardoso-Silva Cláudio Benício , Almeida-Silva Fabricio , Venancio Thiago M. 
Published: May 2024

AbstractSoybean (Glycine max) and common bean (Phaseolus vulgaris) diverged approximately 19 million years ago. While these species share a whole-genome duplication (WGD), theGlycinelineage experienced a second, independent WGD. Despite the significance of these WGDs, their impact on gene families related to oil-traits remains poorly understood. Here, we report an in-depth investigation of oil-related gene families in soybean, common bean, and twenty-eight other legume species. We adopted a systematic approach that included transcriptome and co-expression analysis, identification of orthologous groups, gene duplication modes and evolutionary rates, and family expansions and contractions. We curated a list of oil candidate genes and found that 91.5% of the families containing these genes expanded in soybean in comparison to common bean. Notably, we observed an expansion of triacylglycerol (TAG) biosynthesis (∼3:1) and an erosion of TAG degradation (∼1.4:1) families in soybean in comparison to common bean. In addition, TAG degradation genes were two-fold more expressed in common bean than in soybean, suggesting that oil degradation is also important for the sharply contrasting seed oil contents in these species. We found 17 transcription factor hub genes that are likely regulators of lipid metabolism. Finally, we inferred expanded and contracted families and correlated these patterns with oil content found in different legume species. In summary, our results do not only shed light on the evolution of oil metabolism genes in soybean, but also present multifactorial evidence supporting the prioritization of candidates for crop improvement.
Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo
Authors: Chang Caleb , Zhou Grace , Gao Yang 
Published: May 2024

AbstractMetal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysisin crystallowith His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
Protocol for assessing the impact of the 6thNational Audit Project recommendations on practice
Authors: Clark Sigrún Eyrúnardóttir , Moppett Iain , Moonesinghe S. Ramani , Vindrola-Padros Cecilia 
Published: May 2024

1.AbstractPatient safety has been a growing area of concern, especially within perioperative care where risks of major complications during surgery exist. Anaphylaxis in the operating theatre is a life-threatening drug reaction that happens suddenly, without warning and can affect anyone. The 6th National Audit Project (NAP6) of the Royal College of Anaesthetists (RCoA): Perioperative Anaphylaxis was the largest ever prospective study of anaphylaxis related to anaesthesia and surgery. The findings from the audit were collated into a report and included recommendations for improved patient care. The purpose of this study is to understand the perceptions of the NAP6 recommendations and their impact on practice. This study will use ethnographic qualitative methods in the form of observations, interviews and a documentary analysis. The sessions targeted for observations will include departmental or hospital meetings, and educational or training sessions, related to perioperative anaphylaxis. The target sample size of 78 healthcare professionals across six hospitals within England, will include individuals with roles specific to anaesthesia, surgery, immunology, allergy and governance. Additionally, six stakeholders will be interviewed who can provide insights into the NAP6 recommendations at the national level. Across the six sites, local collaborators will share any relevant documents related to perioperative anaphylaxis or the NAP-6 recommendations. The study has received regulatory approvals from the Health Research Authority and has been funded by the National Institute for Health and Care Research.