bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and directional tuning of serial dependence for tracking eye movements
Authors: Goettker Alexander , Stewart Emma E.M. 
Published: June 2024

AbstractAn attractive influence of past sensory experience on current behaviour has been observed in many domains, such as for perceptual decisions and motor responses. However, it is unclear what sort of information is integrated across trials, and the limits of this integration, especially for oculomotor behavior. Here we provide a detailed and systematic investigation of the spatial and directional tuning of serial dependence for oculomotor tracking. In a series of experiments, we measured oculomotor responses to sequences of movements: the first movement (the prior) could move at different velocities (5 or 15 deg/s), and could additionally vary in its spatial location or direction relative to the following movement. The second movement (the probe) always moved at the same velocity (10 deg/s) and was constant across all experiments. We observed that eye velocity for the probe movement was faster when following the fast prior compared to following the slow prior, replicating attractive serial dependence. Importantly, this effect stayed consistent for distances of up to 30 deg between probe and prior, strongly suggesting a retinotopic coordinate frame. When we manipulated the direction of the prior, we observed that the strength of the serial dependence on eye velocity as well as eye direction was modulated by the relative angle between prior and probe. We observed stronger serial dependence for prior directions more similar to the probe direction. The strength of the effect on eye velocity and eye direction was correlated, suggesting a shared mechanism controlling these effects. Across all experiments, we observed that even when the prior moved in the opposite direction to the probe, there was a residual attractive effect. This suggests that serial dependence for oculomotor tracking consists of two components, one retinotopic, direction-tuned component and one more general component that is not direction-specific.
Three’s a crowd: The relationship among endoparasites, an epibiont and theirDaphniahost
Authors: Hirshberg Ofir , Ben-Ami Frida 
Published: June 2024

AbstractIn freshwater communities, organisms interact in a variety of ways, including predation, competition and parasitism. Parasites are ubiquitous, playing an important role in shaping freshwater communities. Endoparasites live within internal organs of their host, while ectoparasites, also known as epibionts, are confined to the external part of the host’s body. We conducted a series of experiments to examine the relationship between endoparasites and epibionts using the crustaceanDaphnia magnaas host, the rotiferBrachionus rubensas epibiont and three species of endoparasites. First, we tested host preference of the epibiont betweenDaphniainfected by endoparasites and uninfectedDaphnia. Epibiont were found to attach more to uninfectedDaphniathan toDaphniainfected by the yeastMetschnikowia bicuspidata.On the other hand, epibionts attached more toDaphniainfected by the microsporidiumHamiltosporidium tvaerminnensisthan to uninfectedDaphnia. Second, we examined the effect of epibionts on the infection ofDaphniaby endoparasites. Infection prevalence tended to be higher, though not significantly, in the presence of epibionts. For two of the endoparasites,M. bicuspidataandH. tvaerminnensis, infection intensity (i.e., parasite spore production) was higher in the presence of epibionts. The infection intensity ofM. bicuspidataand the bacteriumPasteuria ramosawas affected by the time of death of theDaphnia(i.e., virulence). Finally, we examined the effects of endoparasites and epibionts on the survival and offspring production of theDaphnia. Both host survival and offspring production were negatively affected by the endoparasites, while epibionts did not seem to affect the fitness of their host.
Prediction of phase separation propensities of disordered proteins from sequence
Authors: von Bülow Sören , Tesei Giulio , Lindorff-Larsen Kresten 
Published: June 2024

AbstractPhase separation is thought to be one possible mechanism governing the selective cellular enrichment of biomolecular constituents for processes such as transcriptional activation, mRNA regulation, and immune signaling. Phase separation is mediated by multivalent interactions of biological macromolecules including intrinsically disordered proteins and regions (IDRs). Despite considerable advances in experiments, theory and simulations, the prediction of the thermodynamics of IDR phase behaviour remains challenging. We combined coarse-grained molecular dynamics simulations and active learning to develop a fast and accurate machine learning model to predict the free energy and saturation concentration for phase separation directly from sequence. We validate the model using both experimental and computational data. We apply our model to all 27,663 IDRs of chain length up to 800 residues in the human proteome and find that 1,420 of these (5%) are predicted to undergo homotypic phase separation with transfer free energies<−2kBT. We use our model to understand the relationship between single-chain compaction and phase separation, and find that changes from charge-to hydrophobicity-mediated interactions can break the symmetry between intra-and inter-molecular interactions. We also analyse the structural preferences at condensate interfaces and find substantial heterogeneity that is determined by the same sequence properties as phase separation. Our work refines the established rules governing the relationships between sequence features and phase separation propensities, and our prediction models will be useful for interpreting and designing cellular experiments on the role of phase separation, and for the design of IDRs with specific phase separation propensities.
Leveraging epigenetic signatures to determine the cell-type of origin from long read sequencing data
Authors: Hannon Eilis , Mill Jonathan 
Published: June 2024

AbstractDNA methylation differs across tissue- and cell-types with important implications for the analysis of disease-associated differences in tissues such as blood. To uncover the biological processes affected by epigenetic dysregulation, it is essential for epigenetic studies to generate data from the appropriate cell-types. Here we propose a framework to do this computationally from long-read sequencing data, bypassing the need to isolate subtypes of cells experimentally. Using reference data for six common blood cell-types, we evaluate the potential of this approach for attributing reads to specific cells using sequencing data generated from whole blood. Our analyses show that cell-type can be accurately classified using small regions of the genome comparable in size to those generated by long-read sequencing platforms, although the accuracy of classification varies across different regions of the genome and between cell-types. We found that for approximately one third of the genome it is possible to accurately discriminate reads originating from lymphocytes and myeloid cells with the prediction of more specialised subtypes of blood cell-types also encouraging. Our approach provides an alternative computational method for generating cell-specific DNA methylation profiles for epigenetic epidemiology, accelerating our ability to reveal critical insights of the role of the epigenome in health and disease.
Live-cell imaging of circular and long non-coding RNAs associated to FUS pathological aggregates by Pepper fluorescent RNA
Authors: Vitiello Erika , Castagnetti Francesco , Stufera Mecarelli Lorenzo , D’Ambra Eleonora , Tollis Paolo , Ruocco Giancarlo , Laneve Pietro , Caffarelli Elisa , Mariani Davide , Bozzoni Irene 
Published: June 2024

ABSTRACTLately, important advancements in visualizing RNAs in fixed and live cells have been achieved. While mRNA imaging techniques are well-established, the development of effective methods for studying non-coding RNAs (ncRNAs) in living cells are still challenging but necessary, as they cover a variety of function and of intracellular localization, including highly dynamic processes like phase-transition, still poorly studiedin vivo. Addressing this issue, we tagged two exemplary ncRNAs with the innovative fluorescent RNA (fRNA) Pepper. Specifically, we show circ-HDGFRP3 interaction with p-bodies, we recapitulate its recruitment in pathological FUS aggregates in a dynamic fashion and we super-resolve its distribution in such aggregates via Structured Illumination Microscopy. Moreover, we tracked the long non-coding RNA (lncRNA) nHOTAIRM1, a motor neurons-specific constituent of stress granules (SG), monitoring its behavior throughout the oxidative-stress response in physiological and pathological conditions. Overall, as fRNAs development advances, our work shows a successful use of Pepper for the monitoring of complex processes, as phase-transition, of paradigmatic molecules like circular RNAs (circRNAs) and lncRNAs with super-resolution potential in living mammalian cells.
Mosaic midbrain organoids: a new tool to study Progressive Supranuclear Palsy and advancing clinical neurology research
Authors: Parrotta Elvira Immacolata , Lucchino Valeria , Zannino Clara , Valente Desirèe , Scalise Stefania , Benedetto Giorgia Lucia , Iazzetta Maria Roberta , Talarico Mariagrazia , Conforti Francesco , Di Agostino Silvia , Fiorenzano Alessandro , Quattrone Aldo , Cuda Giovanni , Quattrone Andrea 
Published: June 2024

AbstractProgressive supranuclear palsy (PSP) is a severe neurodegenerative disease pathologically characterized by intracellular tangles of hyperphosphorylated tau protein, widely distributed across the neocortex, basal ganglia, and midbrain. Developing effective drugs for PSP presents challenges due to its complex underpinning mechanism and the absence of robust human models that accurately recapitulate biochemical and pathological features of the disease phenotype. Brain organoids have recently emerged as a three-dimensional tissue culture platform to study brain development and pathology. Here, we present a novel induced pluripotent stem cell (iPSC)-derived mosaic midbrain organoid (mMOs) system from four patients with progressive supranuclear palsy-Richardson syndrome (PSP-RS), aimed at reproducing key molecular disease features while reducing variability across organoids derived from different iPSC donors. The PSP-RS 3D model exhibited accumulation of hyperphosphorylated tau protein, predominance of 4R-tau, increased GFAP-positive cells, and PSP-associated histological alterations compared to organoids derived from healthy donors. Pathologically, diseased mMOs showed typical neurofibrillary tangles and tufted-shaped astrocytes, and poorly branched processes of Tyrosine Hydroxylase-immunoreactive cells with thin terminal branches. Our results suggest that mMOs represent a valuable experimental model for PSP research and hold great promise for future identification of new therapeutic targets for progressive supranuclear palsy.
Medial amygdalar tau is associated with anxiety symptoms in preclinical Alzheimer’s disease
Authors: Li Joyce S , Tun Samantha M , Ficek-Tani Bronte , Xu Wanwan , Wang Selena , Horien Corey L , Toyonaga Takuya , Nuli Shreya S , Zeiss Caroline J , Powers Albert R , Zhao Yize , Mormino Elizabeth C , Fredericks Carolyn A 
Published: June 2024

ABSTRACTBACKGROUNDWhile the amygdala receives early tau deposition in Alzheimer’s disease (AD) and is involved in social and emotional processing, the relationship between amygdalar tau and early neuropsychiatric symptoms in AD is unknown. We sought to determine whether focal tau binding in the amygdala and abnormal amygdalar connectivity were detectable in a preclinical AD cohort and identify relationships between these and self-reported mood symptoms.METHODSWe examined n=598 individuals (n=347 amyloid-positive (58% female), n=251 amyloid-negative (62% female); subset into tau PET and fMRI cohorts) from the A4 Study. In our tau PET cohort, we used amygdalar segmentations to examine representative nuclei from three functional divisions of the amygdala. We analyzed between-group differences in division-specific tau binding in the amygdala in preclinical AD. We conducted seed-based functional connectivity analyses from each division in the fMRI cohort. Finally, we conducted exploratory post-hoc correlation analyses between neuroimaging biomarkers of interest and anxiety and depression scores.RESULTSAmyloid-positive individuals demonstrated increased tau binding in medial and lateral amygdala (F(4, 442)=14.61,p=0.00045;F(4, 442)=5.83,p=0.024, respectively). Across amygdalar divisions, amyloid-positive individuals had relatively increased regional connectivity from amygdala to other temporal regions, insula, and orbitofrontal cortex. There was an interaction by amyloid group between tau binding in the medial and lateral amygdala and anxiety. Medial amygdala to retrosplenial connectivity negatively correlated with anxiety symptoms (rs=-0.103,p=0.015).CONCLUSIONSOur findings suggest that preclinical tau deposition in the amygdala may result in meaningful changes in functional connectivity which may predispose patients to mood symptoms.
Variation in relaxation of non-photochemical quenching between the founder genotypes of the soybean (Glycine max) nested association mapping population
Authors: Gotarkar Dhananjay , Digrado Anthony , Wang Yu , Doran Lynn , Blakey Bethany , Diers Brian W. , Eck Daniel J. , Burgess Steven J. 
Published: June 2024

SummaryImproving the efficiency of crop photosynthesis has the potential to increase yields. Genetic manipulation showed photosynthesis can be improved by speeding up relaxation of photoprotective mechanisms during sun to shade transitions. However, it is unclear if natural variation in relaxation of non-photochemical quenching (NPQ) can be exploited in crop breeding programs. To address this issue, we measured six NPQ parameters in the 40 founder lines and common parent of a Soybean Nested Association Mapping (SoyNAM) panel over two field seasons in Illinois. NPQ parameters did not show consistently variable trends throughout development, and variation between sampling days suggests environmental impacts on NPQ which last more than 24 hours. 17 genotypes were found to show small but consistent differences in NPQ relaxation kinetics relative to a reference line providing a basis for future mapping studies. Finally, a soybean canopy model predicted available phenotypic variation could result in a 1.6% difference in carbon assimilation when comparing fastest and slowest relaxing NPQ values.Significance StatementEvidence suggests increasing the rate of relaxation of photoprotection can lead to improved biomass and yield. We compare photoprotection relaxation rates in 41 diverse soybean genotypes grown in the field, identifying lines with faster rates of relaxation, and predict a potential 1.6% difference in daily carbon assimilation which could contribute to improving soybean performance.
Excitability and synaptic transmission after vitrification of mouse corticohippocampal slices
Authors: German Alexander , Akdaş Enes Yağız 
Published: June 2024

ABSTRACTCryopreservation of adult neural tissue is of considerable practical and theoretical interest. Utilizing 61% w/v ethylene glycol, we vitrified and rewarmed acute mouse corticohippocampal slices to evaluate field excitatory postsynaptic potentials (fEPSP) in the stratum radiatum of the CA1 region of the hippocampus. Our results demonstrate successfully recovered synaptic transmission, and high-frequency stimulation (HFS)-induced potentiation. However, we failed to induce a stable potentiation following HFS stimulation. Structural analysis post-vitrification revealed cellular alterations such as swelling and vacuolization, which likely contributed to the unstable potentiation. Despite high variability in results, this study highlights the potential of vitrification to partially preserve brain function.
Searching for weakly interacting sub-eV particles with a fiber interferometer in a strong magnetic field
Authors: Batllori Josep Maria , Gu Yikun , Horns Dieter , Maroudas Marios , Ulrichs Johannes 
Published: June 2024

A novel table-top experiment is introduced to detect photon-axion conversion: WISP searches on a fiber interferometer (WISPFI). The setup consists of a Mach-Zehnder-type interferometer with a fiber placed inside an external magnetic field, where mixing occurs which is detected by measuring changes in amplitude. Hollow-core photonic crystal fibers (HC-PCF) will be used to achieve resonant mixing that is tuneable by regulating the gas pressure in the fiber. An unexplored axion mass-range (28 meV–100 meV) can be probed reaching the two-photon coupling expected for the QCD axion.

Published by the American Physical Society
2024
Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples
Authors: Parkhurst James M. , Varslot Trond , Dumoux Maud , Siebert C. Alistair , Darrow Michele , Basham Mark , Kirkland Angus , Grange Michael , Evans Gwyndaf , Naismith James H. 
Published: June 2024

For cryo-electron tomography (cryo-ET) of beam-sensitive biological specimens, a planar sample geometry is typically used. As the sample is tilted, the effective thickness of the sample along the direction of the electron beam increases and the signal-to-noise ratio concomitantly decreases, limiting the transfer of information at high tilt angles. In addition, the tilt range where data can be collected is limited by a combination of various sample-environment constraints, including the limited space in the objective lens pole piece and the possible use of fixed conductive braids to cool the specimen. Consequently, most tilt series are limited to a maximum of ±70°, leading to the presence of a missing wedge in Fourier space. The acquisition of cryo-ET data without a missing wedge, for example using a cylindrical sample geometry, is hence attractive for volumetric analysis of low-symmetry structures such as organelles or vesicles, lysis events, pore formation or filaments for which the missing information cannot be compensated by averaging techniques. Irrespective of the geometry, electron-beam damage to the specimen is an issue and the first images acquired will transfer more high-resolution information than those acquired last. There is also an inherent trade-off between higher sampling in Fourier space and avoiding beam damage to the sample. Finally, the necessity of using a sufficient electron fluence to align the tilt images means that this fluence needs to be fractionated across a small number of images; therefore, the order of data acquisition is also a factor to consider. Here, an n-helix tilt scheme is described and simulated which uses overlapping and interleaved tilt series to maximize the use of a pillar geometry, allowing the entire pillar volume to be reconstructed as a single unit. Three related tilt schemes are also evaluated that extend the continuous and classic dose-symmetric tilt schemes for cryo-ET to pillar samples to enable the collection of isotropic information across all spatial frequencies. A fourfold dose-symmetric scheme is proposed which provides a practical compromise between uniform information transfer and complexity of data acquisition.
Exploring consumers’ perception of stingless bee honey using projective techniques
Authors: de Souza Andressa Pedroso Carlotto , Leães Fernanda Leal , Danieli Gabriele , Ruaro Eduarda Letícia , Righi Eléia , Meirelles Rafael Narciso , Sant’Anna Voltaire 
Published: June 2024

PurposeThe objective of this study was to evaluate Brazilian consumers’ perceptions of stingless bee honey and the drivers involved in this product choice.Design/methodology/approachThree projective techniques were applied to 480 consumers who answered a rating task about liking, health, sustainability, quality taste, and utilization as ingredients, fulfilled completion sentences, and performed a hard laddering task.FindingsThe results showed a significant increase in the expected liking and flavor, and consumers perceived stingless bee honey as more sustainable, of higher quality, and more beneficial to health. Health, sustainability, and taste are the main drivers of purchasing this type of honey, and consumers are aware that it costs a premium price. In the value chain involved in choosing stingless bee honey, the appreciation of native bees, flavor, nutritional value, medicinal properties, producer appreciation, and curiosity were strong aspects for choosing the product. These aspects lead consumers to feel good, have peace of mind, feel like protecting nature and planets, and longevity.Originality/valueHoney is popular worldwide, but stingless bee honey has little information on how consumers perceive it and on the purchasing decision chain. The results of the present study provide important information to enhance the consumption of this product with social and environmental importance and the growing demand for natural products that replace refined sugars.
Exploring business and SDG discourse on X: topics, users and engagement
Authors: Ascencio Christine , Eramudugoda Randika 
Published: June 2024

PurposeThis paper examines thematic discourses concerning business and the Sustainable Development Goals (SDGs) on X (formerly Twitter), aiming to uncover active user groups and evaluate engagement levels across various topics. The study also explores the engagement patterns among different user categories, ultimately seeking deeper insights into platform discourse regarding business and the SDGs.Design/methodology/approachUtilizing unsupervised machine learning technique Latent Dirichlet Allocation (LDA), we perform exploratory topic modeling on X data referencing business and the SDGs, generating 16 thematic clusters. Subsequently, we analyze user descriptions to categorize users involved in these discussions. Finally, we employ binomial logit models to assess the relationship between topics and engagement and chi-squared test to evaluate the relationship between users and topics.FindingsThe exploratory research identifies 16 business and SDG topics, while the analysis of users reveals 6 stakeholder groups contributing to these discussions. Business groups emerge as the most frequent contributors, posting on topics related to partnership, action advocacy, and economic outcomes. Topics about updates on progress and transformative initiatives garnered strongest support for engagement.Originality/valueThis research not only sheds light on the current state of business and SDG discourse on X, but also underscores the significance of engaging external stakeholders in driving positive social change globally.
A novel higher-order sliding mode control for DC-DC boost converter system in PMDC motor exploring mismatched disturbances
Authors: R Dhanasekar , Srinivasan Ganesh Kumar , Rivera Marco 
Published: June 2024

Purpose
The purpose of this study is to stabilize the rotating speed of the permanent magnet direct current (PMDC) motor driven by a DC-DC boost converter under mismatched disturbances (i.e.) under varying load circumstances like constant, frictional, fan type, propeller and undefined torques.

Design/methodology/approach
This manuscript proposes a higher order sliding mode control to elevate the dynamic behavior of the speed controller and the robustness of the PMDC motor. A second order classical sliding surface and proportional-integral-derivative sliding surface (PIDSS) are designed and compared.

Findings
For the boost converter with PMDC motor, both simulation and experimentation are exploited. The prototype is built for an 18 W PMDC motor with field programmable gate arrays. The suggested sliding mode with second order improves the robustness of the arrangement under disturbances with a wide range of control. Both the simulation and experimental setup shows satisfactory results.

Originality/value
According to software-generated mathematical design and experimental findings, PIDSS exhibits excellent performance with respect to settling speed, steady-state error and peak overshoot.