bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial ecology and population dynamics of brown troutSalmo truttaL. in reservoirs and headwater tributaries
Authors: Dodd Jamie R. , Noble Richard A.A. , Nunn Andy D. , Owen Holly , Moccetti Paolo , Harvey Jonathan P. , Wallace Liam , Gillespie Ben , Joyce Domino A. , Bolland Jonathan D. 
Published: December 2023

ABSTRACTThis investigation compared the spatial ecology and population dynamics of brown troutSalmo trutta L. between reservoirs with (impact; Langsett Reservoir) and without (control; Grimwith Reservoir) barriers to fish movements into afferent headwater tributaries, including the effectiveness of a fish pass to remediate connectivity. Passive Integrated Transponder (PIT) telemetry revealed fish that emigrated from Langsett and Grimwith reservoirs were 1-3 and 0-2 years old, respectively, and predominantly did so in March-May and October-December in both. Weirs at Langsett Reservoir (emigration rate = 26%) appeared to thwart emigration relative to Grimwith Reservoir (emigration rate = 85%). Acoustic telemetry (2D positions) in the impact reservoir revealed the largest home range was in October – December (monthly K95 ± S.D. up to 26.9 ± 6.69 ha in November), activity was influenced by both month and time of day, and fish occupied shallow water depths (relative to reservoir depth), especially at night. Large proportions of brown trout tagged in Grimwith and Langsett reservoirs (42.9% and 64.1%, respectively) and fish that emigrated (37.2% and 27.7%, respectively) were detected moving upstream into tributaries. At both reservoirs, peak immigration for 3- and ≥4-year-old fish occurred in October-December, although upstream movements occurred throughout the year and by all age classes. Three brown trout passed upstream of each of the weirs on River Little Don (prior to fish pass construction; 3% of those that approached from downstream) and Thickwoods Brook (throughout the study; 2%). Overall fish pass solution passage efficiency was 14% but was higher for 2- and 3-year-old fish (32%), which was comparable to fish translocated from upstream (33%). Passage predominantly occurred at lower river levels than fish pass entrance / attraction, which was also lower than during approaches to the weir. A Before-After Control-Impact (BACI) design found that although juvenile (0+, but not >0+) brown trout densities were lower after fish pass construction, the reduction was significantly less than at control sites, i.e., the fish pass had a positive effect. Overall, this investigation significantly furthers our understanding of brown trout spatial ecology and population dynamics in reservoirs and headwater tributaries.
Biological characteristics and metabolic phenotypes of different anastomosis groups ofRhizoctonia solanistrains
Authors: Sun Meili , Wang Hancheng 
Published: December 2023

AbstractRhizoctonia solaniis an important plant pathogen worldwide, and causes serious target spot disease in tobacco in the last five years. This research studied the biological characteristics of four different anastomosis groups (R. solaniAG-3,R. solaniAG-5,R. solaniAG-6,R. solaniAG-1-IB) ofR. solanifrom tobacco, and analyzed the metabolic phenotype differences of these strains using metabolic phenotype technology. The results showed that the suitable temperature for mycelial growth of four anastomosis group strains were all from 20 to 30 °C, and for sclerotia formation were from 20 to 25 °C. Under different lighting conditions,R. solaniAG-6 strains produced the most sclerotium, followed byR. solaniAG-3,R. solaniAG-5 andR. solaniAG-1-IB. All strains had strong oligotrophic survivability, and can grow on water agar medium without any nitrutions. They exhibited three types of sclerotia distribution form, including dispersed type (R. solaniAG-5 andR. solaniAG-6), peripheral type (R. solaniAG-1-IB), and central type (R. solaniAG-3). They all presented different pathogenicities in tobacco leaves, with the most virulent was noted byR. solaniAG-6, followed byR. solaniAG-5 and AG-1-IB, finally wasR. solaniAG-3.R. solaniAG-1-IB strains firstly present symbtom about inoculation. Metabolic fingerprints of four anastomosis groups were different to each other.R. solaniAG-3, AG-6, AG-5 and AG-1-IB strains efficiently metabolized 88, 94, 71 and 92 carbon substrates, respectively. Nitrogen substrates of amino acids and peptides were the significant utilization patterns forR. solaniAG-3.R. solaniAG-3 and AG-6 showed a large range of adaptabilities and were still able to metabolize substrates in the presence of the osmolytes, including up to 8% sodium lactate. Four anastomosis groups all showed active metabolism in environments with pH values from 4 to 6 and exhibited decarboxylase activities.One-sentence summaryRhizoctonia solanistrains from different anastomosis groups have a different adaptability to habitats.
Apoplastic barrier establishment in roots and nodules of Lotus japonicus is essential for root-shoot signaling and N-fixation
Authors: Shen Defeng , Venado Rafael E. , Neumann Ulla , Dyballa-Rukes Nadine , Mahiwal Swati , Metzger Sabine , Nakano Ryohei Thomas , Marín Macarena , Andersen Tonni Grube 
Published: December 2023

AbstractThe molecular framework underlying apoplastic root barrier formation has been unveiled in the model speciesArabidopsis thalianawhere establishment of Casparian strips occurs at an early stage of root development. In legumes, this region overlaps with the area where nitrogen-fixing bacteria can induce nodule formation, termed the susceptible zone. Moreover, while nodules themselves also contain an endodermis spanning their vascular bundles, it is current unknown if Casparian strips serve as a filter for transport across this specialized organ. Here we establish barrier mutants in the symbiosis modelLotus japonicus.We find that the while genetic network controlling Casparian strip formation is conserved in this legume species, formation of functional barriers is crucial for establishment of N-fixing nodules. By probing this in detail, we establish a model where the Casparian strip, via its linked Schengen pathway, converge with long distance N signaling and systemic regulation of nodulation. Moreover, this also reveal that the genetic system for barrier establishment in the root endodermis is shared in nodule vascular endodermis and required for nodule function. Combined, our findings uncover a novel role of apoplastic root barriers and establishes a mutant collection suitable to probe the role of root barriers in symbiotic plant-microbe relationships.
Biases of Principal Component Analysis (PCA) in Physical Anthropology Studies Require a Reevaluation of Evolutionary Insights
Authors: Mohseni Nima , Elhaik Eran 
Published: December 2023

AbstractEvolutionary biologists, primarily palaeoanthropologists, anatomists and ontogenists, employ modern geometric morphometrics to quantitatively analyse physical forms (e.g., skull morphology) and explore relationships, variations, and differences between samples and taxa using landmark coordinates. The standard approach comprises two steps: Generalised Procrustes Analysis (GPA) followed by Principal Component Analysis (PCA). PCA projects the superimposed data produced by GPA onto a set of uncorrelated variables, which can be visualised on scatterplots and used to draw phenetic, evolutionary, and ontogenetic conclusions. Recently, the use of PCA in genetic studies has been challenged. Due to PCA’s central role in morphometrics, we sought to evaluate the standard approach and claims based on PCA outcomes. To test PCA’s accuracy, robustness, and reproducibility using benchmark data of the crania of five papionin genera, we developed MORPHIX, a Python package for processing superimposed landmark data with classifier and outlier detection methods, which can be further visualised using various plots. Throughout this manuscript, we address the recent and contentious use of PCA in physical anthropology and phylogenetic inference, such as the case ofHomo Nesher Ramla, an archaic hominin with a questionable taxonomy. We found that PCA outcomes are artefacts of the input data and are neither reliable, robust, nor reproducible as field members may assume. We also found that supervised machine learning classifiers are more accurate both for classification and detecting new taxa. Our findings raise concerns about PCA-based findings applied in 18,400 to 35,200 Physical anthropology studies. Our work can be used to evaluate prior and novel claims concerning the origins and relatedness of inter- and intra-species and improve phylogenetic and taxonomic reconstructions.
The Role of Attention in Multi Attribute Decision Making
Authors: Sampson Aaron , Yang You-Ping , Usher Marius , Levy Dino , Niebur Ernst , Stuphorn Veit 
Published: December 2023

AbstractReal-life decisions typically involve multiple options, each with multiple attributes affecting value. In such complex cases, sequential shifts of attention to specific options and attributes are thought to guide the decision process. We designed a task that allowed us to monitor attention in monkeys engaged in such multi-attribute decisions. We recorded pre-supplementary motor area neurons encoding action value signals reflecting the decision process. Attention guides this process through two mechanisms. First, attention enhances the activity of neurons representing the currently sampled option, independent of the attended option value. Second, attention up-regulates the gain of information integration towards the evolving value estimate for the attended option. In contrast, we found no evidence for a third suggested mechanism, in which only the attended option is represented. Instead, attention influences the ongoing information accumulation and competition between the options by modulating the strength of the value information that drives this circuit.
Time-dependent thermodynamic relationships for a Brownian particle that walks in a complex network
Authors: Taye Mesfin Asfaw 
Published: December 2023

The thermodynamics feature of systems that are driven out of equilibrium is explored forMBrownian ratchets that are arranged in a complex network. The exact time-dependent solution depicts that as the network size increases, the entropyS, entropy productionep(t), and entropy extractionhd(t) of the system step up which is feasible since these thermodynamic quantities exhibit an extensive property. In other words, as the number of lattice size increases, the entropyS, entropy productionep(t), and entropy extractionhd(t) step up revealing that these complex networks can not be reduced into the corresponding one-dimensional lattice. On the contrary, the rate for thermodynamic relations such as the velocity V, entropy production rateėp(t) and entropy extraction ratebecome independent of the network size in the long time limit. The exact analytic result also shows that the free energy decreases with the system size. The model system is further analyzed by including heat transfer via kinetic energy. Since the heat exchange via kinetic energy does not affect the energy extraction rate, the heat dumped to the cold reservoirs contributes only to the internal entropy production. As the result, such systems exhibit a higher degree of irreversibility. The thermodynamic features of a system that operates between hot and cold baths are also compared and contrasted with a system that operates in a heat bath where its temperature varies linearly along the reaction coordinate. Regardless of the network arrangements, the entropy, entropy production, and extraction rates are considerably larger for the linearly varying temperature case than a system that operates between hot and cold baths.PACS numbersValid PACS appear here
A two-step mechanism for creating stable, condensed chromatin by the Polycomb complex PRC1
Authors: Seif Elias , Francis Nicole J. 
Published: December 2023

ABSTRACTTheDrosophilaPRC1 complex regulates gene expression by modifying histone proteins and chromatin architecture. Two PRC1 subunits, PSC and Ph, are most implicated in chromatin architecture. In vitro, PRC1 compacts chromatin and inhibits transcription and nucleosome remodeling. The long disordered C-terminal region of PSC (PSC-CTR) is important for these activities, while Ph has little effect. In cells, Ph is important for condensate formation, long range chromatin interactions, and gene regulation, and its polymerizing Sterile alpha motif (SAM) is implicated in these activities. In vitro, truncated Ph containing the SAM and two other conserved domains (mini-Ph) undergoes phase separation with chromatin, suggesting a mechanism for SAM-dependent condensate formation in vivo. How the distinct activities of PSC and Ph on chromatin function together in PRC1 is not known. To address this question, we analyzed structures formed with large chromatin templates and PRC1 in vitro. PRC1 bridges chromatin into extensive fibrillar networks. Ph, its SAM, and SAM polymerization activity have little effect on these structures. Instead, the PSC-CTR controls their growth, and is sufficient for their formation. To understand how phase separation driven by Ph SAM intersects with the chromatin bridging activity of the PSC-CTR, we used mini-Ph to form condensates with chromatin and then challenged them with PRC1 lacking Ph (PRC1ΔPh). PRC1ΔPh converts mini-Ph chromatin condensates into clusters of small non-fusing condensates and bridged fibers. These condensates retain a high level of chromatin compaction and do not intermix. Thus, phase separation of chromatin by mini-Ph, followed by the action of the PSC-CTR creates a unique chromatin organization with regions of high nucleosome density and extraordinary stability. We discuss how this coordinated sequential activity of two proteins found in the same complex may occur and the possible implications of stable chromatin architectures in maintaining transcription states.
Stimulus selection influences prediction of individual phenotypes in naturalistic conditions
Authors: Li Xuan , Eickhoff Simon B. , Weis Susanne 
Published: December 2023

AbstractUnderstanding individual differences and brain-behaviour relationships is an essential goal of human neuroscience. Recent studies have shown the great potential of naturalistic stimuli, e.g., movie clips, in advancing this pursuit. While the use of naturalistic stimuli attracts increasing interest, the influence of stimulus selection remains largely unclear. In this study, we show that brain activity is generally sensitive to the choice of movie stimuli at both group and individual subject levels. Using sex classification as an example, we demonstrate that brain activity elicited by different stimuli can lead to distinct prediction performance and unique predictive features. The stimuli that yield better classification performance often elicit stronger synchrony of brain activity across all subjects and are mostly derived from Hollywood films with rich social content and cohesive narratives. Our results highlight the importance of stimulus selection and provide practical guidance for choosing appropriate stimuli, opening up new avenues for future studies on individual differences and brain-behaviour relationships.
Carbon usage in yellow-fleshedManihot esculentastorage roots shifts from starch biosynthesis to cell wall and raffinose biosynthesis via themyo-inositol pathway
Authors: Gutschker Sindy , Ruescher David , Rabbi Ismail Y. , Rosado-Souza Laise , Pommerrenig Benjamin , van Doorn Anna M. , Schlereth Armin , Neuhaus H. Ekkehard , Fernie Alisdair R. , Reinert Stephan , Sonnewald Uwe , Zierer Wolfgang 
Published: December 2023

AbstractCassava is a crucial staple crop for smallholder farmers in tropical Asia and Sub-Saharan Africa. Although high yield remains the top priority for farmers, the significance of nutritional values has increased in cassava breeding programs. A notable negative correlation between provitamin A and starch accumulation poses a significant challenge for breeding efforts. The negative correlation between starch and carotenoid levels in conventional and genetically modified cassava plants implies the absence of a direct genomic connection between the two traits. The competition among various carbon pathways seems to account for this relationship. In this study, we conducted a thorough analysis of 49 African cassava genotypes with varying levels of starch and provitamin A. Our goal was to identify factors contributing to differential starch accumulation. With the carotenoid levels of the varieties considered as a confounding effect on starch production, we found that yellow and white-fleshed storage roots did not differ significantly in most measured components of starch or de novo fatty acid biosynthesis. However, genes and metabolites associated with myo-inositol synthesis and cell wall component production were substantially enriched in high provitamin A genotypes. These results indicate that yellow-fleshed cultivars, in comparison to their white-fleshed counterparts, direct more carbon towards the synthesis of raffinose and cell wall components, a finding that is supported by a significant rise in the starch-free residue to total dry yield ratio in yellow storage roots versus white storage roots. Our findings enhance comprehension of the biosynthesis of starch and carotenoids in the storage roots of cassava.
Brain-wide topographic coordination of traveling spiral waves
Authors: Ye Zhiwen , Bull Matthew S. , Li Anna , Birman Daniel , Daigle Tanya L. , Tasic Bosiljka , Zeng Hongkui , Steinmetz Nicholas A. 
Published: December 2023

AbstractTraveling waves of activity are a prevalent phenomenon within neural networks of diverse brain regions and species1–4, and have been implicated in myriad brain functions including sensory perception5–8, memory9, spatial navigation10–12and motor control13,14. However, the anatomical basis for these waves, and whether they are locally confined versus distributed across the brain, remains unclear. Here we use cortex-wide imaging and large-scale electrophysiology in awake mice to reveal the organization of traveling waves across spatial scales. Traveling waves formed spiral patterns predominantly centered on somatosensory cortex. Strikingly, the local axonal architecture of neurons in sensory cortex exhibited a matching circular arrangement. At the cortex-wide scale, these spiral waves were mirrored between hemispheres and between sensory and motor cortex, reflecting topographic long-range axons. Finally, at the brain-wide scale, cortical spiral waves were coordinated with subcortical spiking patterns in the thalamus, striatum and midbrain. These results establish that traveling waves are structured by axonal pathways and globally impact neural activity across diverse brain systems.
DeconV: Probabilistic Cell Type Deconvolution from Bulk RNA-sequencing Data
Authors: Gynter Artur , Meistermann Dimitri , Lähdesmäki Harri , Kilpinen Helena 
Published: December 2023

AbstractBulk RNA-Seq remains a widely adopted technique to profile gene expression, primarily due to the persistent challenges associated with achieving single-cell resolution. However, a key challenge is accurately estimating the proportions of different cell types within these bulk samples. To address this issue, we introduce DeconV, a probabilistic framework for cell-type deconvolution that uses scRNA-Seq data as a reference. This approach aims to mitigate some of the limitations in existing methods by incorporating statistical frameworks developed for scRNA-Seq, thereby simplifying issues related to reference preprocessing such as normalization and marker gene selection. We benchmarked DeconV against established methods, including MuSiC, CIBERSORTx, and Scaden. Our results show that DeconV performs comparably in terms of accuracy to the best-performing method, Scaden, but provides additional interpretability by offering confidence intervals for its predictions. Furthermore, the modular design of DeconV allows for the investigation of discrepancies between bulk-sequenced samples and artificially generated pseudo-bulk samples.
The Exon Junction Complex component EIF4A3 plays a splicing-linked oncogenic role in Pancreatic Ductal Adenocarcinoma
Authors: Blázquez-Encinas Ricardo , Alors-Pérez Emilia , Moreno-Montilla María Trinidad , García-Vioque Víctor , Sánchez-Frías Marina Esther , Mafficini Andrea , López-Cánovas Juan L. , Bousquet Corinne , Gahete Manuel D. , Lawlor Rita T. , Luque Raúl M. , Scarpa Aldo , Arjona‐Sánchez Álvaro , Pedraza-Arevalo Sergio , Ibáñez-Costa Alejandro , Castaño Justo P. 
Published: December 2023

ABSTRACTPancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide and further research on its biology is needed to fully understand the disease. Dysregulation of alternative RNA splicing is a common hallmark in cancer, including PDAC, which provides an emerging source of knowledge and of novel biomarkers and therapeutic tools. Here, we examined the role of EIF4A3, a core component of the Exon Junction Complex intimately linked to RNA splicing, in pancreatic cancer biology. EIF4A3 is overexpressed in PDAC tissue and associated to clinical parameters of malignancy and poorer patient survival. Mechanistically, exploration of PDAC RNA-seq data unveiled the link of EIF4A3 to diverse malignancy processes, in line with its association to key molecular pathways. Accordingly, EIF4A3 targetingin vitrodecreased essential functional tumor features such as proliferation, migration, colony formation and sphere formation, while itsin vivotargeting reduced tumor growth.EIF4A3silencing in PDAC cell lines severely altered its transcriptional and spliceosomic landscapes, as shown by RNA-seq analyses, suggesting a role for EIF4A3 in maintaining RNA homeostasis. Our results indicate that EIF4A3 dysregulation in PDAC has a pleiotropic regulatory role on RNA biology, influencing key cellular functions. This paves the way to explore its potential as a novel biomarker and actionable target candidate for this lethal cancer.
Tracing the evolutionary emergence of the temperature sensing prion-like domain in EARLY FLOWERING 3 across the plant kingdom
Authors: Zhu Zihao , Trenner Jana , Quint Marcel 
Published: December 2023

AbstractPlants have evolved to anticipate and adjust their growth and development in response to environmental changes. To mitigate the negative influence of global climate change on crop production, understanding the key regulators of plant performance is imperative.EARLY FLOWERING 3(ELF3) is such a regulator involved in the circadian clock and thermomorphogenesis.Arabidopsis thalianaELF3 contains a prion-like domain (PrLD) that functions as a thermosensor, enabling its liquid-liquid phase separation at high ambient temperatures. To understand the conservation of this function across the plant kingdom, we traced the evolutionary emergence of ELF3 with a focus on PrLD existence. We observed that the presence of the domain within ELF3, mainly contributed by the length of polyglutamine (polyQ) repeats, is most prominentBrassicales. By analyzing 319 naturalArabidopsis thalianaaccessions, we detected a wide range of polyQ length variation in ELF3. However, it is only weakly associated with geographic origin, climate conditions and classic temperature-responsive phenotypes. Based on available prediction tools and limited experimental evidence, we conclude that although the emergence of PrLD is not likely to be a key driver of environmental adaptation, it adds an extra layer to ELF3’s role in thermomorphogenesis.