bluuebunny/crossref_metadata_2025_split huggingface dataset:
(1→3)-β-D-glucan derivatives with unique structural properties differentially affect murine lung inflammation and histology
Authors: Metwali N. , Stapleton E.M. , Hadina S. , Thorne P.S. 
Published: October 2023

ABSTRACTBackgroundβ-D-glucan (BDG) compounds are proinflammatory fungal cell wall polysaccharides known to cause respiratory pathology. However, the specific immunological effect of unique BDG structures on pulmonary inflammation is understudied. We sought to characterize the effect of four unique fungal BDGs with unique branching patterns, solubility, molecular weights and higher order structure in murine airways.MethodsScleroglucan (1→3) (1→6)-highly branched BDG, laminarin (1→3) (1→6)-branched BDG, curdlan (1→3)-linear BDG, and pustulan (1→6)-linear BDG were assessed by nuclear magnetic resonance spectroscopy (NMR). Glucan compounds were confirmed negative for endotoxin by kinetic chromogenic Limulus amebocyte lysate assay. Each BDG was tested using an inhalation model with C3HeB/FeJ mice and compared to control mice exposed to saline and unexposed sentinels (all, n=3-19). Inhalation studies were performed using all BDGs ±heat-inactivation (1-hr. autoclave) given BDG solubility increases after heat-inactivation. Outcomes included bronchoalveolar lavage (BAL), differential cell counts (macrophages, neutrophils, lymphocytes, and eosinophils), BALF cytokine and serum IgE and IgG2a expression (by multiplex immunoassay and ELISA). Lastly,ex vivocultured left lung cells were BDG stimulated, and cytokines (multiplex) compared to unstimulated cells. Right lung histology was performed.ResultsWhile each BDG affected lung inflammatory outcomes, pustulan exposure led to the most pro-inflammatory profile of all BDGs tested, including increased inflammatory infiltrate into BAL, increased serum IgE and IgG2a and increased cytokine production. Secondary stimulation of sensitized lung cells by lipopolysaccharide (LPS) significantly increased cytokine expression. Lung histology revealed significant fibrosis in lungs exposed to soluble BDGs pustulan and scleroglucan.ConclusionInhalation of BDGs with distinct branching patterns exhibited varying inflammatory potency and immunogenicity, which lichen-derived pustulan having the greatest effect. Glucan source and solubility should be considered in exposure and toxicological studies.
A neural modeling approach to study mechanisms underlying the heterogeneity of visual spatial frequency sensitivity in schizophrenia
Authors: Dugan Caroline , Zikopoulos Basilis , Yazdanbakhsh Arash 
Published: October 2023

AbstractPatients with schizophrenia exhibit abnormalities in spatial frequency sensitivity, and it is believed that these abnormalities indicate more widespread dysfunction and dysregulation of bottom-up processing. The early visual system, including the first-order Lateral Geniculate Nucleus of the thalamus (LGN) and the primary visual cortex (V1), are key contributors to spatial frequency sensitivity. Medicated and unmedicated patients with schizophrenia exhibit contrasting changes in spatial frequency sensitivity, thus making it a useful probe for examining potential effects of the disorder and antipsychotic medications in neural processing. We constructed a parameterized, rate-based neural model of on-center/off-surround neurons in the early visual system to investigate the impacts of changes to the excitatory and inhibitory receptive field subfields. By incorporating changes in both the excitatory and inhibitory subfields that are associated with pathophysiological findings in schizophrenia, the model successfully replicated perceptual data from behavioral/functional studies involving medicated and unmedicated patients. Among several plausible mechanisms, our results highlight the dampening of excitation and/or increase in the spread and strength of the inhibitory subfield in medicated patients and the contrasting decreased spread and strength of inhibition in unmedicated patients. Given that the model was successful at replicating results from perceptual data under a variety of conditions, these elements of the receptive field may be useful markers for the imbalances seen in patients with schizophrenia.
Phylogenomics, biogeography, and trait evolution of the Boletaceae (Boletales, Agaricomycetes, Basidiomycota)
Authors: Tremble Keaton , Henkel Terry , Bradshaw Alexander , Domnauer Colin , Brown Lyda , Thám Lê Xuân , Furci Guliana , Aime Cathie , Moncalvo Jean-Marc , Dentinger Bryn 
Published: October 2023

ABSTRACTThe species-rich porcini mushroom family Boletaceae is a widespread and well-known group of ectomycorrhizal (ECM) mushroom-forming fungi that has eluded intrafamilial phylogenetic resolution despite many attempts using morphological traits and multi-locus molecular datasets. In this study, we present a genome-wide molecular dataset of 1764 single-copy gene families from a global sampling of 418 Boletaceae specimens. The resulting phylogenetic analysis has strong statistical support for most branches of the tree, including the first statistically robust backbone. The enigmaticPhylloboletellus chloephorusfrom non-ECM Argentinian subtropical forests was recovered as an early diverging lineage within the Boletaceae. Time-calibrated branch lengths estimate that the family first arose in the early- to mid-Cretaceous and underwent a rapid radiation in the Eocene, possibly when the ECM nutritional mode arose with the emergence and diversification of ECM angiosperms. Biogeographic reconstructions reveal a complex history of vicariance and episodic long-distance dispersal correlated with historical geologic events, including Gondwanan origins and cladogenesis patterns that parallel its fragmentation. Ancestral state reconstruction of sporocarp morphological traits predicts that the ancestor of the Boletaceae was lamellate with ornamented basidiospores, contrary to most contemporary “bolete” morphologies. Transition rates indicated that the lamellate hymenophore and sequestrate sporocarp are reversible traits. Together, this study represents the most comprehensively sampled, data-rich molecular phylogeny of the Boletaceae to date, enabling robust inferences of trait evolution and biogeography in the group.
WITHDRAWN: Impaired Mitochondrial Calcium Homeostasis Induces Failed Remodeling of the Spiral Artery in Preeclampsia
Authors: Lu Xiyuan , Wang Yifan , Zou Zhiguo , Wang Chuan , Feng Xueqing , Geng Na , Wang Yuehong , Xu Zhice , Pu Jun 
Published: October 2023

Withdrawal StatementThe authors have withdrawn their manuscript owing to further revisions and additional experiments are needed to ensure the accuracy and completeness of the research findings. As a result, we believe it is in the best interest of the scientific community and the integrity of the manuscript to withdraw it at this time. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.
Bioinfo-Bench: A Simple Benchmark Framework for LLM Bioinformatics Skills Evaluation
Authors: Chen Qiyuan , Deng Cheng 
Published: October 2023

AbstractLarge Language Models (LLMs) have garnered significant recognition in the life sciences for their capacity to comprehend and utilize knowledge. The contemporary expectation in diverse industries extends beyond employing LLMs merely as chatbots; instead, there is a growing emphasis on harnessing their potential as adept analysts proficient in dissecting intricate issues within these sectors. The realm of bioinformatics is no exception to this trend. In this paper, we introduce Bioinfo-Bench, a novel yet straightforward benchmark framework suite crafted to assess the academic knowledge and data mining capabilities of foundational models in bioinformatics. Bioinfo-Benchsystematically gathered data from three distinct perspectives: knowledge acquisition, knowledge analysis, and knowledge application, facilitating a comprehensive examination of LLMs. Our evaluation encompassed prominent models ChatGPT, Llama, and Galactica. The findings revealed that these LLMs excel in knowledge acquisition, drawing heavily upon their training data for retention. However, their proficiency in addressing practical professional queries and conducting nuanced knowledge inference remains constrained. Given these insights, we are poised to delve deeper into this domain, engaging in further extensive research and discourse. It is pertinent to note that project Bioinfo-Benchis currently in progress, and all associated materials will be made publicly accessible.1
Characterization of the cryptic interspecific hybridLemna × mediterraneaby an integrated approach provides new insights into duckweed diversity
Authors: Braglia Luca , Ceschin Simona , Iannelli M. Adelaide , Bog Manuela , Fabriani Marco , Frugis Giovanna , Gavazzi Floriana , Gianì Silvia , Mariani Flaminia , Muzzi Maurizio , Pelella Emanuele , Morello Laura 
Published: October 2023

ABSTRACTLemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms, reduced to a single leaf-like structure called frond, without or with one to few roots. Although molecular taxonomy has helped clarify the phylogenetic history of this family, inconsistency between morphological data and nuclear and plastid markers still poses challenging questions in some cases, leading to frequent misclassifications in the genusLemna. Recently, the finding thatLemna japonicais an interspecific hybrid betweenLemna minorandLemna turionifera, provided a clear explanation to one of such taxonomic questions. Here we demonstrated thatL. minoris also capable to hybridize withLemna gibba, generating a cryptic, previously unrecognized, but widespread taxon in the Mediterranean area. The nothotaxonLemna×mediterraneais described through the detailed investigation of seven hybrid clones from a living germplasm collection and compared with clones of the putative parental speciesL. minorandL. gibba. Genetic analysis revealed that two different cytotypes, diploid and triploid, originated by at least two independent hybridization events. Despite high overall similarity, morphometrical, physiological and biochemical analyses showed an intermediate position ofL.×mediterraneabetween its parental species in most qualitative and quantitative characters, and also separation of the two hybrid cytotypes by some criteria. These data provide evidence that hybridization and polyploidization, driving forces of terrestrial plant evolution, contribute to the duckweed genetic diversity and may have also shaped the phylogenetic history of these mainly asexual, aquatic plants. Further elucidation of hybridization mechanisms and flowering regulation will provide perspectives for future breeding strategies.
ClusterV-Web: A User-Friendly Tool for Profiling HIV Quasispecies and Generating Drug Resistance Reports from Nanopore Long-Read Data
Authors: Su Junhao , Li Shumin , Zheng Zhenxian , Lam Tak-Wah , Luo Ruibang 
Published: October 2023

AbstractSummaryThird-generation long-read sequencing is an increasingly utilized technique for profiling HIV quasispecies and detecting drug resistance mutations due to its ability to cover the entire viral genome in individual reads. Recently, the ClusterV tool has demonstrated accurate detection of HIV quasispecies from Nanopore long-read sequencing data. However, the need for scripting skills and a computational environment may act as a barrier for many potential users. To address this issue, we have introduced ClusterV-Web, a user-friendly web-based application that enables easy configuration and execution of ClusterV, both remotely and locally. Our tool provides interactive tables and data visualizations to aid in the interpretation of results. This development is expected to democratize access to long-read sequencing data analysis, enabling a wider range of researchers and clinicians to efficiently profile HIV quasispecies and detect drug resistance mutations.Availability and implementationClusterV-Web is freely available and open source, with detailed documentation accessible athttp://www.bio8.cs.hku.hk/ClusterVW/. The standalone Docker image and source code are also available athttps://github.com/HKU-BAL/ClusterV-Web.Contactrbluo@cs.hku.hk, Department of Computer Science, The University of Hong Kong, Hong Kong, China;jhsu@cs.hku.hk, Department of Computer Science, The University of Hong Kong, Hong Kong, ChinaSupplementary informationNone
Role of transcription and translation during the early development of the brown algaEctocarpus
Authors: Liesner Daniel , Luthringer Rémy , Colin Sébastien , Morales Julia , Cock J. Mark , Coelho Susana M. 
Published: October 2023

AbstractBackground and aimsParthenogenesis, the embryonal development of an unfused gamete, is a widespread trait within the brown algae (Phaeophyceae). We hypothesized that the parthenogenetic development of male gametes of the model brown algaEctocarpusspecies 7 would rapidly be dependent onde novotranscription and translation because of the small size of the gamete cell.MethodsWe followed the development of maleEctocarpusgametes to parthenosporophytes in the presence of either the transcription inhibitor thiolutin or the translation inhibitor emetine. Responses in morphology and growth were compared to development in inhibitor-free control conditions at three time points over 12 days. Potentially persistent inhibitor effects were then investigated by growing parthenosporophytes in an inhibitor-free post-culture for 14 days.Key resultsThiolutin did not affect gamete germination, but growth of parthenosporophytes was significantly delayed. While almost all control parthenosporophytes had grown larger than 10 cells over 12 days, thiolutin inhibited growth beyond a size of 5-10 cells. The effects of thiolutin were reversible in the post-culture. Consequences of the emetine treatment were more severe, germination was already strongly inhibited by day 5, and on average only 27.5% of emetine-treated gametes had completed the first cell division on day 12. Emetine fully inhibited development beyond the 5-cell stage during the treatment, and induced morphological abnormalities (i.e., round cell shape and abnormal cell division planes) which persisted throughout the post-culture.ConclusionsThese results imply thatEctocarpusgametes contain sufficient proteins to germinate, and that the first cell cycles of parthenogenetic gamete development presumably utilize mRNA already present in the gametes. We discuss that storing mRNA and proteins in the developing gametes before release may be an adaptive trait inEctocarpusto ensure quick development after fertilization, or alternatively the vegetative completion of the life cycle in the absence of mates.
C9ORF72 deficiency results in degeneration of the zebrafish retinain vivo
Authors: Jaroszynska Natalia , Salzinger Andrea , Tsarouchas Themistoklis M. , Becker Catherina G. , Becker Thomas , Lyons David A. , MacDonald Ryan B. , Keatinge Marcus 
Published: October 2023

AbstractG4C2 Hexanucleotide repeat expansions within the geneC9ORF72are the most common cause of the neurodegenerative diseases Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD). This disease-causing expansion leads to a reduction in C9ORF72 expression levels in patients, suggesting haploinsufficiency could contribute to disease. To further understand the consequences of C9ORF72 deficiencyin vivo, we generated ac9orf72mutant zebrafish line. Analysis of the spinal cord revealed no appreciable neurodegenerative pathology such as loss of motor neurons, or increased levels of neuroinflammation. However, detailed examination ofc9orf72-/-retinas showed prominent neurodegenerative features, including a decrease in retinal thickness, gliosis, and an overall reduction in neurons of all subtypes. Structurally, analysis of rod and cone cells within the photoreceptor layer showed a disturbance in the outer cells of the retina and rhodopsin mis-localisation from rod outer segments to their cell bodies and synaptic endings. Thus, C9ORF72 may play a previously unappreciated role in retinal homeostasis and suggests C9ORF72 deficiency can induce tissue specific neuronal loss.
A matter of life and death – Hunting tactics of Southern elephant seals(Mirounga leonina)and anti-predatory behaviours of their prey
Authors: Chevallay Mathilde , Guinet Christophe , Goulet Pauline , du Dot Tiphaine Jeanniard 
Published: October 2023

AbstractFor air-breathing marine predators that must save energy during dives, the ability to adopt hunting tactics that minimise the risk of triggering an escape reaction from the prey is crucial for an efficient foraging. Female Southern elephant seals(Mirounga leonina,SES hereafter) forage on small mesopelagic prey that they must hunt almost continuously to meet their high-energy requirements. Here we aimed at understanding how these large time-limited deep-divers can efficiently exploit their small sized prey. To do so, we used data recorded by a new biologger, the sonar tag, deployed on SES during their post-breeding foraging trips. This tag combines an active acoustic sensor with ultra-high-resolution movement and bioluminescence sensors, offering a unique opportunity to simultaneously describe SES’ hunting tactics to capture their prey and defence mechanisms employed by prey. We analysed more than 5,800 prey capture events in nine SES and show that they adopt a “stalking” hunting behaviour allowing them to get as close as possible to their prey before attacking. The ability of SES to adopt stealth approach tactics, minimising the risk of initiating a flight reaction from their prey, might be a key factor in the success of this far-ranging generalist predator.
The Unexpected Functional Diversity of Photoexcited NAD
Authors: Kufner Corinna L. , Janicki Mikołaj J. , Lozano Gabriella G. , Sasselov Dimitar D. 
Published: October 2023

AbstractDespite the vital role of nicotinamide adenine dinucleotide (NAD) as a cofactor in all living organisms, the diversity of its functions is poorly understood. Particularly in interaction with ultraviolet (UV) light, a variety of photorelaxation channels can be accessed, which current models lack to explain. In this work, for the first time, we used picosecond UV pump, mid-infrared (mIR) probe spectroscopy and accurate quantum-chemical calculations to elucidate the ultrafast photodynamics of NAD+and NADH to unify contradictory mechanisms from the past decades in the big picture. We found direct evidence for a long-lived (∼900 ps) charge-separated state in NADH, which has been unobserved previously and results in the parallel population of a fluorescent state. The photochemical pathways demonstrated here open up functions of NAD in chemistry and molecular biology, such as an electron donor, as a FRET agent or as a redox pair switch, which have not been considered previously.TOC GRAPHICS
Cross-species imputation and comparison of single-cell transcriptomic profiles
Authors: Zhang Ran , Yang Mu , Schreiber Jacob , O’Day Diana R. , Turner James M. A. , Shendure Jay , Disteche Christine M. , Deng Xinxian , Noble William Stafford 
Published: October 2023

AbstractCross-species comparison and prediction of gene expression profiles are important to understand regulatory changes during evolution and to transfer knowledge learned from model organisms to humans. Single-cell RNA-seq (scRNA-seq) profiles enable us to capture gene expression profiles with respect to variations among individual cells; however, cross-species comparison of scRNA-seq profiles is challenging because of data sparsity, batch effects, and the lack of one-to-one cell matching across species. Moreover, single-cell profiles are challenging to obtain in certain biological contexts, limiting the scope of hypothesis generation. Here we developed Icebear, a neural network framework that decomposes single-cell measurements into factors representing cell identity, species, and batch factors. Icebear enables accurate prediction of single-cell gene expression profiles across species, thereby providing high-resolution cell type and disease profiles in under-characterized contexts. Icebear also facilitates direct cross-species comparison of single-cell expression profiles for conserved genes that are located on the X chromosome in eutherian mammals but on autosomes in chicken. This comparison, for the first time, revealed evolutionary and diverse adaptations of X-chromosome upregulation in mammals.
Assessing climate change risks associated with precipitation at unfavorable times in winter wheat using an improved crop calendar model incorporating vernalization and winter survival
Authors: Murakami Keach , Iizumi Toshichika , Shimoda Seiji 
Published: October 2023

AbstractCrop phenology calendars are necessary for designing breeding goals and for developing effective management practices. Winter wheat is a representative biennial, the cultivation schedule of which is constrained by winter climate conditions, particularly the processes of vernalization and winter survival. Here, we present improvements to a rule-based crop phenology model by incorporating these factors so that it can be used to accurately estimate the phenological events of winter wheat from daily meteorological data. We tested the improved model in Hokkaido, the northernmost Japanese island, which is characterized by seasonal snow cover and a wet summer. The results confirmed that implementing these factors contributed to accurate estimates of peak occurrence dates of winter wheat phenological events. Furthermore, we applied the improved model to simulate wheat phenology under 2 K and 4 K warmer scenarios. The results showed a delayed sowing period up to approximately one month and slight advancements in both flowering and harvesting, leading to a shorter growth period. While this shortened period may be largely compensated by a decrease in the snow-covered period, the shifts in the vegetative and reproductive phases may have a significant influence on sink-source balance of wheat. We also assessed the risks of pollination failure and preharvest sprouting, both of which are associated with the timing of precipitation, based on the number of rainy days around flowering, and the incidence of precipitation over two consecutive days around the time of harvesting. Our simulations suggested increased risk of pollination failure and reduced risk of preharvest sprouting, leading to an increase in the probability of crop failure. These findings underscore the importance of implementing adaptive measures to mitigate precipitation-related risk under future climate scenarios. Further, the findings provide valuable insights for winter wheat breeders and agronomists, thereby facilitating crop production adaptation strategies.