bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resource or slot model in visual working memory: Are they different?
Authors: Hojjati Fatemeh , Motahharynia Ali , Adibi Armin , Adibi Iman , Sanayei Mehdi 
Published: February 2024

AbstractWhen studying the working memory (WM), the ‘slot model’ and the ‘resource model’ are two main theories used to describe how information retention occurs. The slot model shows that WM capacity consists of a certain number of predefined slots available for information storage. This theory explains that there is a binary condition during information recall in which information is either wholly maintained within a slot or forgotten. The resource model gives a resolution-based approach defining a continuous resource able to be distributed among an unlimited number of items in the WM capacity. With newer hybrid models suggesting that WM may not strictly conform to one model, this study aimed to understand the relationship between the original models. By implementing correlational assessments of subjects’ performances in two different psychophysics tasks (analog recall paradigm with sequential bar presentation and delayed match-to-sample task (DMS) with checkerboard stimuli which are representative for resource and slot models, respectively), our study revealed significant correlations between WM performance (measured by DMS tasks) with recall error, precision, and sources of error (measured by sequential paradigm). Overall, the findings emphasize the importance of considering both models in understanding WM processes, shedding light on the debate between slot and resource models by demonstrating overlap in elements of both models.
Cryo-EM structure of a conjugative T4SS identifies a molecular switch regulating pilus biogenesis
Authors: Macé Kévin , Waksman Gabriel 
Published: February 2024

ABSTRACTConjugative Type IV Secretion Systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. Bacterial conjugation is the primary means by which antibiotic resistance genes spread among bacterial populations (Barlow, 2009; Virolleet al, 2020). Conjugative T4SSs elaborate a long extracellular filament, termed “pilus” to connect with the recipient cell. Previously, we solved the cryo-EM structure of a conjugative T4SS. In this article, based on additional data, we present a more complete T4SS cryo-EM structure than that published earlier. Novel structural features include details of the mismatch symmetry within the OMCC, the presence of a 4thVirB8 subunit in the asymmetric unit of both the Arches and the IMC, and a hydrophobic VirB5 tip in the distal end of the stalk. However, more significantly, we provide previously-undescribed structural insights into the protein VirB10 and identify a novel regulation mechanism of T4SS-mediated pilus biogenesis by this protein, that we believe is a key checkpoint for this process.
Ungulate substrate use in fauna passages
Authors: Helldin Jan Olof , Niemi Milla 
Published: February 2024

AbstractFauna passages are increasingly constructed at major roads and railways to mitigate the negative effects of infrastructure and traffic on wildlife. The function of such passages depends on design, including the construction materials, soil and vegetation. Providing “naturalness” in fauna passages may entail significant costs, yet its benefits are unclear. By using camera trap data, we examined ungulate substrate use in seven passages serving both fauna and local roads (overpasses) and fauna and watercourses (underpasses) in boreal Sweden and Finland. While all substrates were used, during snow-free periods, ungulates used smoother surfaces (fine-grained topsoil, grass, artificial fiber mat, and dirt road) more than expected based on their availability. Coarser surface (stony/rocky ground), shrub, and water were used less than expected. The results for road and water were, however, inconsistent between passages; in one overpass road was instead used less than expected, and in one underpass the water section was used particularly during winter but also by moose wading or swimming through in summer and autumn. General patterns of use largely remained when analysed byspecies, although sample sizes were limited. Despite limitations, our study offers valuable insights for planning and constructing fauna passages. To our knowledge, this study was the first of its kind describing how ungulates use different substrates in fauna passages. We suggest to conduct further research on this issue, for example by more detailed study of animal trajectories through passages and by experimental modification of substrates.
Heat Conduction Simulation of Chondrocyte-Embedded Agarose Gels Suggests Negligible Impact of Viscoelastic Dissipation on Temperature Change
Authors: Myers Erik , Piazza Molly , Owkes Mark , June Ronald K. 
Published: February 2024

AbstractAgarose is commonly used for 3D cell culture and to mimic the stiffness of the pericellular matrix of articular chondrocytes. Although it is known that both temperature and mechanical stimulation affect the metabolism of chondrocytes, little is known about the thermal properties of agarose hydrogels. Thermal properties of agarose are needed to analyze potential heat production by chondrocytes induced by various experimental stimuli (carbon source, cyclical compression, etc). Utilizing ASTM C177, a custom-built thermal conductivity measuring device was constructed and used to calculate the thermal conductivity of 4.5% low gelling temperature agarose hydrogels. Additionally, Differential Scanning Calorimetry was used to calculate the specific heat capacity of the agarose hydrogels. Testing of chondrocyte-embedded agarose hydrogels commonly occurs in Phosphate-Buffered Saline (PBS), and thermal analysis requires the free convection coefficient of PBS. This was calculated using a 2D heat conduction simulation within MATLAB in tandem with experimental data collected for known boundary and initial conditions. The specific heat capacity and thermal conductivity of 4.5% agarose hydrogels was calculated to be 2.85 J/g°C and 0.121 W/mK, respectively. The free convection coefficient of PBS was calculated to be 1000.1 W/m2K. The values of specific heat capacity and thermal conductivity for agarose are similar to the reported values for articular cartilage, which are 3.20 J/g°C and 0.21 W/mK (Moghadam, et al. 2014). This suggests that in addition to 4.5% agarose hydrogels mimicking the physiological stiffness of the cartilage PCM, they can also mimic the thermal properties of articular cartilage forin vitrostudies.
The Memorability of Voices is Predictable and Consistent across Listeners
Authors: Revsine Cambria , Goldberg Esther , Bainbridge Wilma A. 
Published: February 2024

AbstractMemorability, the likelihood that a stimulus is remembered, is an intrinsic stimulus property that is highly consistent across people—participants tend to remember and forget the same faces, objects, and more. However, these consistencies in memory have thus far only been observed for visual stimuli. We provide the first study of auditory memorability, collecting recognition memory scores from over 3000 participants listening to a sequence of different speakers saying the same sentence. We found significant consistency across participants in their memory for voice clips and for speakers across different utterances. Next, we tested regression models incorporating both low-level (e.g., fundamental frequency) and high-level (e.g., dialect) voice properties to predict their memorability. These models were significantly predictive, and cross-validated out-of-sample, supporting an inherent memorability of speakers’ voices. These results provide the first evidence that listeners are similar in the voices they remember, which can be reliably predicted by quantifiable voice features.
Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 21 species
Authors: Luo Xiaomei , Liu Yunke , Gong Xiao , Ye Meng , Xiao Qiangang , Zeng Zhen 
Published: February 2024

Abstract5S rDNA is essential component of all cell types. A survey was conducted to study the 5S rDNA site number, position, and origin of signal pattern diversity in 64 plants using fluorescencein situhybridization. The species used for this experiment were chosen due to the discovery of karyotype rearrangement, and for species checked in which 5S rDNA has not yet been explored. The chromosome number was 14–160, while the chromosome length was 0.63–6.88 μm, with 37 plants (58%) had small chromosome (<3 μm). The chromosome numbers of three species and 5S rDNA loci of 19 species have been reported for the first time. 5S rDNA was varied and abundant in signal site number (2–18), position (e.g., interstitial, distal, and proximal position, occasionally, outside chromosome), and even as intense (e.g., strong, weak, and slight). Our results exposed modifiability in the number and location of 5S rDNA in 33 plants and demonstrated an extensive stable number and location of 5S rDNA in 31 plants. The potential origin of signal pattern diversity was probably caused by chromosome rearrangement (e.g., deletion, duplication, inversion, translocation), polyploidization, self-incompatibility, and chromosome satellites. These data characterized the variability of 5S rDNA within the karyotypes of the 64 plants that exhibited massive chromosomal rearrangements and provided anchor points for genetic physical maps. These data prove the utility of the 5S rDNA oligonucleotide as a chromosome marker in identifying plant chromosomes. This method provides a basis for developing similar applications for cytogenetic analysis in other species.Article SummaryA survey was exploited to study 5S rDNA signal pattern diversity in 64 plants by FISH. The chromosome number of three species and 5S rDNA loci of 19 species have been reported by the first time. 5S rDNA was really rather various and abundant in signal site number (2–18), position (interstitial, distal, proximal position, occasionally, outside chromosome), even as the intense (strong, week, slight). These data prove the utility of 5S rDNA oligonucleotide as chromosome marker in identifying plant chromosomes.
Global neural encoding of model-free and inference-based strategies in mice
Authors: Wang Shuo , Gao Huayi , Ishizu Kotaro , Funamizu Akihiro 
Published: February 2024

AbstractWhen a simple model-free strategy does not provide sufficient outcomes, an inference-based strategy estimating a hidden task structure becomes essential for optimizing choices. However, the neural circuitry involved in inference-based strategies is still unclear. We developed a tone frequency discrimination task in head-fixed mice in which the tone category of the current trial depended on the category of the previous trial. When the tone category was repeated every trial, the mice continued to use the default model-free strategy, as well as when tone was randomly presented, to bias the choices. In contrast, the default strategy gradually shifted to an inference-based strategy when the tone category was alternated in each trial. Brain-wide electrophysiological recording during the overtrained phase suggested that the neural activity of the frontal and sensory cortices, hippocampus, and striatum was correlated with the reward expectation of both the model-free and inference-based strategies. These results suggest the global encoding of multiple strategies in the brain.
Single-molecule observations of human small heat shock proteins in complex with aggregation-prone client proteins
Authors: Rice Lauren , Marzano Nicholas , Cox Dezerae , van Oijen Antoine , Ecroyd Heath 
Published: February 2024

AbstractSmall heat shock proteins (sHsps) are molecular chaperones that act to prevent the aberrant aggregation of misfolded proteins. Whilst it is widely suggested that sHsps prevent aggregation by binding to misfolded client proteins, the dynamic and heterogeneous nature of sHsps has hindered attempts to establish the mechanistic details of how sHsp-client protein complexes form. Single-molecule approaches have emerged as a powerful tool to investigate dynamic and heterogeneous interactions such as those that can occur between sHsps and their client proteins. Here, we use total internal reflection fluorescence microscopy to observe and characterise the complexes formed between model aggregation-prone client proteins [firefly luciferase (FLUC), rhodanese, and chloride intracellular channel 1 protein (CLIC)], and the human sHsps αB-crystallin (αB-c; HSPB1) and Hsp27 (HSPB5). We show that small (monomeric or dimeric) forms of both αB-c and Hsp27 bind to misfolded or oligomeric forms of the client proteins at early stages of aggregation, resulting in the formation of soluble sHsp-client complexes. Stoichiometric analysis of these complexes revealed that additional αB-c subunits accumulate onto pre-existing sHsp-client complexes to form larger species - this does not occur to the same extent for Hsp27. Instead, Hsp27-client interactions tend to be more transient than those of αB-c. Elucidating these mechanisms of sHsp function is crucial to our understanding of how these molecular chaperones act to inhibit protein aggregation and maintain cellular proteostasis.
Self-assembled cell-scale containers made from DNA origami membranes
Authors: Karfusehr Christoph , Eder Markus , Simmel Friedrich C. 
Published: February 2024

AbstractDNA origami provides a methodology for the sequence-programmable generation of precisely defined molecular nanostructures with sizes of order 100 nm. A new frontier for the field is the generation of superstructures made from DNA origami subunits, which requires other self-assembly strategies than those used for DNA origami itself. Challenges faced by current approaches include the increasing complexity, cost and development time for the structures and off-target assembly. Here, we demonstrate how radially symmetric origami subunits that are inspired by the structure and interactions of lipids organize into giant DNA origami monolayer membranes that can be readily programmed to form vesicles or hollow tubes with diameters ranging from 100 nm to over 1 µm. DNA origami membranes are an unprecedented approach for compartmentalization that opens up new possibilities for bottom-up biology and cell-scale soft robotics.
Similar mechanisms of retron-mediated anti-phage defense for different families of tailed phages
Authors: García-Rodríguez Fernando Manuel , Martínez-Abarca Francisco , Wilkinson Max E. , Toro Nicolás 
Published: February 2024

SummaryBacterial retrons are tripartite systems consisting of a cognate non-coding RNA, reverse transcriptase, and additional (effector) protein with diverse predicted enzymatic functions. In this study, we investigated the role and mechanism of Retron-Eco11, a novel type III-A3 retron system associated with a phosphoribosyltransferase-like effector protein, in phage defense. Here, we show that the Retron-Eco11 tripartite system protects against phage infection and that UvsW and D10, two functional homolog helicases found in T4 and T5 phages, respectively, serve as specific triggers for the Retron-Eco11 defense system. Our findings confirmed that msDNA and both protein components of the intron complex are indispensable for its protective function. Once the retron system detects the activity of these helicase proteins, it activates the toxicity of the effector protein bound to the retron complex, leading to an abortive infection. These findings underscore the application of a comparable anti-phage defense strategy using Retron-Eco11 across diverse phage families. This should aid in deciphering the processes through which the Retron complex detects and identifies the invading phages.
Focused ultrasound increases gene delivery to deep brain structure following the administration of a recombinant adeno-associated virus in the cerebrospinal fluid
Authors: Kofoed Rikke Hahn , Noseworthy Kate , Wu Kathleen , Vecchio Laura Marie , Dibia Chinaza Lilian , Sivadas Shuruthisai , Wu Sheng-Kai , Mikloska Kristina , White Malik , Elmer Bradford , Ramachandran Shyam , Mueller Christian , Hynynen Kullervo , Aubert Isabelle 
Published: February 2024

AbstractGene delivery via adeno-associated viral vectors can provide lasting clinical benefits following a one-time treatment. Delivery throughout the brain is needed for the treatment of neurological disorders with widespread pathology, including Alzheimer and Parkinson diseases, and amyotrophic lateral sclerosis. Most gene vectors have poor diffusion in the brain tissue. Furthermore, it is only at high intravenous doses that gene vectors can overcome the blood-brain barrier. In contrast, relatively lower doses of gene vectors injected in the cerebrospinal fluid enable significant transduction of superficial brain regions. The remaining challenge and unmet need of gene therapy is to deliver gene vectors to deep brain structures using a minimally invasive strategy. Here, we demonstrate that non-invasive focused ultrasound blood-brain barrier modulation can increase the delivery of recombinant adeno-associated virus by 5-fold to deep brain structures following injection in the cisterna magna. Delivery of adeno-associated viral vectors to the central nervous system, via administration in the cerebrospinal fluid, is being evaluated in several clinical trials for treating beta-galactosidase-1 deficiency, Batten disease, Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis, and spinal muscular atrophy. Our findings suggest that the efficacy of gene therapies delivered in the cerebrospinal fluid can be enhanced by targeting brain areas of interest with focused ultrasound.Significance statementAdministration of viral vectors in the cerebrospinal fluid through the cisterna magna is being evaluated in patients with neurological disorders. Focused ultrasound combined with intravenous microbubbles safely increases the permeability of the blood-brain barrier in humans and enables delivery of intravenous adeno-associated virus in non-human primates. Here, we demonstrate that combining these two clinically relevant gene delivery methods, intracisterna magna administration and focused ultrasound with microbubbles, can facilitate gene delivery to superficial and deep brain structures. Our findings have the potential to increase the efficacy of gene therapies, particularly for disorders with brain regions that have remained difficult to reach.
Data-driven analyses of social complexity in bees reveal phenotypic diversification following a major evolutionary transition
Authors: Peled Ohad , Greenbaum Gili , Bloch Guy 
Published: February 2024

AbstractHow social complexity evolved is a long-standing enigma. In most animal groups, social complexity is typically classified into a few discrete classes. This approach is oversimplified and constrains our inference of social evolution to a narrow trajectory consisting of transitions between classes. This approach also limits quantitative studies on the molecular and environmental drivers of social complexity. However, the recent accumulation of relevant quantitative data has now set the stage to overcome these limitations. Here, we propose a data-driven approach for studying the full diversity of social phenotypes. We curated and analyzed a comprehensive dataset encompassing 17 social traits for 77 species and studied the evolution of social complexity in bees. We found that corbiculate bees — honey bees, stingless bees, and bumble bees — underwent a major evolutionary transition ∼70 mya, which is inconsistent with the stepwise progression of the social ladder conceptual framework. This major evolutionary transition was followed by a phase of substantial phenotypic diversification of social complexity. Non-corbiculate bee lineages display a continuum of social complexity, ranging from solitary to simple societies, but do not reach levels of social complexity comparable to those of corbiculate bees. Bee evolution provides a unique demonstration of a macroevolutionary process in which a major transition removed biological constraints and opened novel evolutionary opportunities, driving the exploration of the landscape of social phenotypes. Our approach can be extended to incorporate additional data types and readily applied to illuminate the evolution of social complexity in additional animal groups.
Low frequency stimulation for seizure suppression: identification of optimal targets in the entorhinal-hippocampal circuit
Authors: Kleis Piret , Paschen Enya , Häussler Ute , Haas Carola A. 
Published: February 2024

AbstractBackgroundMesial temporal lobe epilepsy (MTLE) with hippocampal sclerosis (HS) is a common form of drug-resistant focal epilepsy in adults. Treatment for pharmacoresistant patients remains a challenge, with deep brain stimulation (DBS) showing promise for alleviating intractable seizures. This study explores the efficacy of low-frequency stimulation (LFS) on specific neuronal targets within the entorhinal-hippocampal circuit in a mouse model of MTLE.Objective/HypothesisOur previous research demonstrated that LFS of the medial perforant path (MPP) fibers in the sclerotic hippocampus reduced seizures in epileptic mice. Here, we aimed to identify the critical neuronal population responsible for this antiepileptic effect by optogenetically stimulating presynaptic and postsynaptic compartments of the MPP-dentate granule cell (DGC) synapse at 1 Hz. We hypothesize that specific targets for LFS can differentially influence seizure activity depending on the cellular identity and location within or outside the seizure focus.MethodsWe utilized the intrahippocampal kainate (ihKA) mouse model of MTLE and targeted specific neural populations using Channelrhodopsin2 (ChR2) and stereotactic optic fiber implantation. We recorded intracranial neuronal activity from freely moving chronically epileptic mice with and without optogenetic LFS up to three hours.ResultsWe found that LFS of MPP fibers in the sclerotic hippocampus effectively suppressed epileptiform activity while stimulating principal cells in the MEC had no impact. Targeting DGCs in the sclerotic septal or non-sclerotic temporal hippocampus with LFS did not reduce seizure numbers but shortened the epileptiform bursts.ConclusionPresynaptic stimulation of the MPP-DGC synapse within the sclerotic hippocampus is critical for seizure suppression via LFS.
Identification of echinacoside as a tobramycin potentiator againstPseudomonas aeruginosaaggregates
Authors: Cai Yu-Ming , Crabbé Aurélie , Coenye Tom 
Published: February 2024

AbstractCyclic diguanylate (c-di-GMP) is a central biofilm regulator, where increased intracellular levels promote biofilm formation and antibiotic tolerance. Targeting the c-di-GMP network is a promising anti-biofilm approach. Most agents reported previously decreased c-di-GMP to eliminate surface-attached biofilms, which did not recapitulatein vivobiofilms well and may thus impede their clinical impact. Here, the expression profile of genes encoding proteins associated with c-di-GMP metabolism was analysed among 32Pseudomonas aeruginosastrains grown as suspended aggregates in synthetic sputum or planktonic cells. A diguanylate cyclase, SiaD, proved essential for auto-aggregation underin vivo-like conditions. Virtual screening against SiaD identified echinacoside as an inhibitor, which reduced intracellular c-di-GMP levels and aggregate sizes and potentiated the efficacy of tobramycin against aggregates established by >80% of tested strains. This synergistic effect was also observed forin vivo-like 3-D alveolar cells infected by cytotoxicP. aeruginosa, demonstrating its high potential as an adjunctive therapy for recalcitrantP. aeruginosainfections.