bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatomical Abnormalities Suggest a Compensatory Role of the Cerebellum in Early Parkinson’s Disease
Authors: Yun Juyoung Jenna , Gailly de Taurines Anastasia , Tai Yen F , Haar Shlomi 
Published: August 2024

AbstractBrain atrophy is detected in early Parkinson’s disease (PD) and accelerates over the first few years post-diagnosis. This was captured by multiple cross-sectional studies and a few longitudinal studies in early PD. Yet only a longitudinal study with a control group can capture accelerated atrophy in early PD and differentiate it from healthy ageing. Accordingly, we performed a multicohort longitudinal analysis between PD and healthy ageing, examining subcortical regions implicated in PD pathology, including the basal ganglia, thalamus, corpus callosum (CC), and cerebellum. Longitudinal volumetric analysis was performed on 56 early PD patients and 53 matched controls, with scans collected 2-3 years apart. At baseline, the PD group showed a greater volume in the pallidum, thalamus, and cerebellar white matter (WM), suggesting potential compensatory mechanisms in prodromal and early PD. After 2-3 years, accelerated atrophy in PD was observed in the putamen and cerebellar WM. Interestingly, healthy controls – but not PD patients – demonstrated a significant decline in Total Intracranial Volume (TIV), and atrophy in the thalamus and mid-CC. Between-group analysis revealed more severe atrophy in the right striatum and cerebellar WM in PD, and in the mid-posterior CC in controls. Using CEREbellum Segmentation (CERES) for lobule segmentation on the longitudinal PD cohort, we found a significant decline in the WM of non-motor regions in the cerebellum, specifically Crus I and lobule IX. Our results highlight an initial increase in cerebellar WM volume during prodromal PD, followed by significant degeneration over the first few years post-diagnosis.
Multimodal brain imaging of insomnia, depression and anxiety symptoms: transdiagnostic commonalities and differences
Authors: de Lange Siemon C. , Tissink Elleke , Bresser Tom , Savage Jeanne E. , Posthuma Danielle , van den Heuvel Martijn P. , van Someren Eus J.W. 
Published: August 2024

AbstractInsomnia disorder, major depressive disorder and anxiety disorders are the most common mental health conditions, with high comorbidity and genetic overlap suggesting shared brain mechanisms. Studies on brain correlates of these disorders have not fully addressed this overlap. Aiming to distinguish shared from specific brain structural and functional properties associated with symptoms of these disorders, this study analyzed multimodal brain imaging data from over 40,000 UK Biobank participants. Functional enrichment analyses were conducted to understand the cognitive-emotional and neurotransmission implications of the identified brain regions and connections. Results showed that smaller cortical surfaces, smaller thalamic volumes, and weaker functional connectivity were linked to more severe symptoms across all symptom types. Several symptom-specific associations were revealed, most commonly in different parts of the amygdala-hippocampal-medial prefrontal circuit. These findings revealed both transdiagnostically shared and unique brain properties that could lead to more directed treatment targets for insomnia, depression, and anxiety.
Distinct metabolite profiles in tissues and exudates of a monocot and dicot shaped by the environment
Authors: Siffert Alexandra , McLaughlin Sarah , Sasse Joëlle 
Published: August 2024

AbstractPlants exhibit remarkable plasticity in response to environmental changes. Understanding how plants adapt to diverse environmental conditions through changes in their metabolite profiles can provide insights into their adaptive strategies under suboptimal climate conditions. For this, metabolite profiles of tissues and root-derived, exuded compounds in various environmental conditions need to be characterized. Here, we compare the shoot, root, and root exudate metabolite profiles of the monocotBrachypodium distachyonand the dicotArabidopsis thalianagrown in sterile, non-sterile, and sucrose-supplied basal salt medium or soil extract to represent natural and various standard laboratory conditions. We report unique metabolite fingerprints in shoots and roots for each species and environmental condition. Exuded compounds of Arabidopsis displayed higher sensitivity to soil extract conditions, whereas Brachypodium showed significant changes in response to non-sterile conditions. Organic acids, lipids, organic oxygen compounds, and phenylpropanoids were major contributors to the observed differences. Our results highlight the importance of considering environmental aspects when investigating plant metabolism and point towards crucial chemical classes involved in plant-microbe-environment interactions.
Human deep sleep facilitates faster cerebrospinal fluid dynamics linked to brain oscillations for sleep homeostasis and memory
Authors: Uji Makoto , Li Xuemei , Saotome An , Katsumata Ryosuke , Waggoner R. Allen , Suzuki Chisato , Ueno Kenichi , Aritake Sayaka , Tamaki Masako 
Published: August 2024

AbstractWhile cerebrospinal fluid (CSF) dynamics during sleep have been implicated in metabolic waste reduction in animals, how CSF dynamics are driven in the human brain remains elusive. Here, by leveraging a simultaneous sparse-fMRI and polysomnography method designed specifically for acquiring deep stable sleep data, we present the first evidence of deep sleep-specific faster CSF dynamics in healthy young human participants. Slow waves and sleep spindles during slow-wave sleep and rapid eye movements and sawtooth waves during rapid eye movement (REM) sleep induce frequent low-amplitude CSF fluctuations, contributing to faster CSF dynamics during deep sleep. In contrast, arousal-related brain activities during light sleep produced infrequent large CSF changes. Furthermore, these brain oscillations during light and deep sleep recruited essentially different brain networks, with deep sleep emphasizing memory and homeostatic circuits. Thus, human deep sleep has a unique way of enabling faster CSF dynamics that are distinctive from arousal mechanisms.
Plasma membrane H+-ATPase activation increases global transcript levels and promotes the shoot growth of light-grown Arabidopsis seedlings
Authors: Kinoshita Satoru Naganawa , Taki Kyomi , Okamoto Fumika , Nomoto Mika , Takahashi Koji , Hayashi Yuki , Ohkanda Junko , Tada Yasuomi , Finkemeier Iris , Kinoshita Toshinori 
Published: August 2024

Summary(1)Plant cell growth require the elongation of cells mediated by cell wall remodelling and turgor pressure changes. The plasma membrane (PM) H+-ATPase facilitates both cell wall remodelling and turgor pressure changes, by acidifying the apoplast of cells, referred to as acid growth. The acid growth theory is mostly established on the auxin-induced activation of PM H+-ATPase in non-photosynthetic tissues. However, how PM H+-ATPase affect the growth in photosynthetic tissues of Arabidopsis remains unclear.(2)Here, a combination of transcriptomics and cis-regulatory element analysis was conducted to identify the impact of PM H+-ATPase on global transcript levels and the molecular mechanism downstream of the PM H+-ATPase.(3)The PM H+-ATPase activation increased transcript levels globally, especially cell wall modification-related genes. The transcript level changes were in PM H+-ATPase-dependent manner. Involvement of Ca2+was suggested as CAMTA motif was enriched in the promoter of PM H+-ATPase-induced genes and cytosolic Ca2+elevated upon PM H+-ATPase activation.(4)PM H+-ATPase activation in photosynthetic tissues promote the expression of cell wall modification enzymes and shoot growth, adding a novel perspective of photosynthesis-dependent PM H+-ATPase activation in photosynthetic tissues to the acid growth theory that has primarily based on findings from non-photosynthetic tissues.
Antimicrobial nanolayers of thymol and carvacrol on titanium surfaces: the crucial role of interfacial properties in thymol’s superior osteogenic response
Authors: Gonzalez Ariel , Miñán Alejandro , Prieto Eduardo , Schilardi Patricia , Fagali Natalia S. , Fernández Lorenzo de Mele Mónica 
Published: August 2024

ABSTRACT“Green’’ nanotechnologies have emerged as environmentally friendly alternatives against microbial multidrug-resistant biofilms. In this study, bactericidal “green” nanolayers (NL) were developed on Ti surfaces using two isomeric phytocompounds, carvacrol (Carv-Ti-NL) and thymol (TOH-Ti-NL). These NLs were fabricated using a one-step immersion treatment method based on a simple and spontaneous self-assembly process. Both NLs revealed strong antimicrobial activity, displaying anti-biofilm and biocidal effects. Notably, TOH-Ti-NL exhibited superior osteogenic performance compared to Carv-Ti-NL, as evidenced by enhanced pre-osteoblast cell attachment and growth, and the production of ALP, collagen type I and Ca2+deposition. In contrast, fibroblastic cells exhibited reduced attachment on TOH-Ti-NL and enhanced proliferation on Carv-Ti-NL. Considering the biological differential effects, the physicochemical properties of these conformational isomers’ NLs were studied to elucidate potential differences that could impact on cell response. Although the ATR-FTIR spectra of the NLs were similar and indicated the spontaneous oxidation of Carv and TOH leading to ketonic structures, distinct contributions were observed after the electrooxidation of each NL. Slight differences in hydrophilicity were found for both nanostructures, but higher roughness was found for TOH-Ti-NL. Furthermore, the release curves of Carv and TOH from the NLs revealed distinct profiles over time. Overall, Carv and TOH formed self-assembled layers on Ti able to eradicateStaphylococcus aureusbiofilms. Their different physical and chemical characteristics induced distinct responses from eukaryotic cells attached to the NLs. Given these characteristics one might envisage the use of either Carv-Ti-NL or TOH-Ti-NL in order to fine-tune specific chemical physical properties of Ti-based implants.Graphical abstract
Novel iGluSnFR3 variants with improved kinetics and dynamic range for tracking high frequency firing at glutamatergic synapses
Authors: Tran Oanh , Bertelli Sara , Hughes Holly J. , Lozo Luka , Plested Andrew , Török Katalin 
Published: August 2024

AbstractThe first genetically encoded single fluorescent protein-based glutamate sensor, iGluSnFR opened a new era of imaging neuronal activity at the level of circuits as well as at synapses. With slowoff-kinetics, iGluSnFR could only resolve low frequency glutamate release. A binding site variant of iGluSnFR, iGluuwith significantly fasteroff-kinetics, enabled the resolution of high (100 Hz) frequency glutamate release in hippocampal slices at individual CA3-CA1 synapses. Moreover, iGluurevealed impairment of glutamate retrieval in HD mice models pointing to defective glutamate transport. Recently, the iGluSnFR3 generation (SF-Venus-iGluSnFR. v857) has been developed with increased dynamic range and rapidon-kinetics, making it attractive forin vivoimaging. However, similarly to iGluSnFR, glutamateoff-kinetics of iGluSnFR3 were predicted to limit it to resolving low frequency release only. We undertook to improve the kinetic properties of iGluSnFR3 for resolving high (100 Hz) frequency glutamate release. We generated and characterized iGlu3fast, an ultrafast decay variant of iGluSnFR3. For iGlu3Fast we obtained a decay rate constant of 340 ± 48 s-1, ∼5-fold faster than iGluSnFR3 at 71 ± 3 s-1, at 20°C. Furthermore, iGlu3Fast superseded iGluSnFR3 with a 42-fold glutamate-induced fluorescence increase compared to 26 for iGluSnFR3. Thus, with rapidoff-kinetics comparable to that of iGluuas well as significantly increased fluorescence dynamic range and preserved rapidon-kinetics, iGlu3fast represents an excellent novel sensor for imaging high frequency glutamate release at all levels of organisation. Two novel variants with superslowoff-kinetics are also reported, expanding the range of applications in neurobiology.
Chromatin Remodelling in Damaged Intestinal Crypts Orchestrates Redundant TGFβ and Hippo Signalling to Drive Regeneration
Authors: Fink Mardi , Njah Kizito , Patel Shyam J. , Cook David P. , Man Vanessa , Ruso Francesco , Rajan Arsheen , Narimatsu Masahiro , Obersterescu Andreea , Pye Melanie J. , Trcka Daniel , Chan Kin , Ayyaz Arshad , Wrana Jeffrey L. 
Published: August 2024

SummaryCell state dynamics underlying regeneration are under-characterized. Intestinal damage prompts reprogramming into revival stem cells (revSCs) that reconstitute Lgr5+ intestinal stem cells (ISCs). Single nuclei multiomics of chromatin accessibility and transcriptomes during regeneration from irradition showed revSCs display epigenetic profiles shared with ISCs and differentiated lineages. Furthermore, while revSC genes are accessible throughout homeostatic epithelia, damage-induced global alterations in crypt and revSC chromatin converge on TGFβ, as well as Hippo pathways. We show TGFβ directly induces functional revSCs and demonstrate individual revSCs form organoids with reconstituted Lgr5+ ISCs. Despite this, loss of TGFβ signalling yielded mild regenerative defects. In contrast, interference in both Hippo and TGFβ abolished revSCs, precluded generation of new ISCs and led to rapid intestinal collapse. Thus, the epithelium is poised to engage the revSC regenerative program that relies on crypt-localized, transient morphogen cues that function in a compensatory manner to support intestinal regeneration.
Starshipgiant transposable elements cluster by host taxonomy using kmer-based phylogenetics
Authors: Hill Rowena , Smith Daniel , Canning Gail , Grey Michelle , Hammond-Kosack Kim E. , McMullan Mark 
Published: August 2024

ABSTRACTStarshipsare a recently established superfamily of giant cargo-mobilising transposable elements in the fungal subphylumPezizomyotina(phylumAscomycota). To date,Starshipelements have been identified up to ∼700 Kbp in length and carrying hundreds of accessory genes, which can confer both beneficial and deleterious traits to the host genome. Classification ofStarshipelements has been centred on the tyrosine recombinase gene that mobilises the element, termed the captain. We contribute a new perspective toStarshipclassification by using an alignment-free kmer-based phylogenetic tree building method, which can infer relationships between elements in their entirety, including both active and degraded elements and irrespective of high variability in element length and cargo content. In doing so we found that relationships between entireStarshipsdiffered from those inferred from captain genes and revealed patterns of element relatedness corresponding to host taxonomy. UsingStarshipsfromGaeumannomycesspecies as a case study, we found that kmer-based relationships correspond with similarity of cargo gene content. Our results suggest thatStarship-mediated horizontal transfer events are frequent between species within the same genus but are less prevalent across larger host evolutionary distances. This novel application of a kmer-based phylogenetics approach overcomes the issue of how to represent and compare highly variableStarshipselements as a whole, and in effect shifts the perspective from a captain to a cargo-centred concept ofStarshipidentity.SUMMARYWe applied a kmer-based phylogenetic classification approach to giantStarshipcargo-mobilising elements from species across thePezizomycotina(Ascomycota,Fungi). We foundStarshipelements to frequently cluster according to host taxonomy, suggesting horizontal transfer of elements is less common across larger evolutionary distances. Kmer-based phylogenetics approaches show promise for both element classification and to inform our understanding of the evolution ofStarshipsand other giant cargo-mobilising elements.
Innovating the bank-firm relationship: a spherical fuzzy approach to SME funding
Authors: Palmieri Egidio , Ferilli Greta Benedetta 
Published: August 2024

PurposeInnovation in financing processes, enabled by the advent of new technologies, has supported the development of alternative finance funding tools. In this context, the study analyses the growing importance of alternative finance instruments (such as equity crowdfunding, peer-to-peer (P2P) lending, venture capital, and others) in addressing the small and medioum enterprises' (SMEs) financing needs beyond traditional bank and market-based funding channels. By providing more flexible terms and faster approval times, these instruments are gradually reshaping the traditional bank-firm relationship.Design/methodology/approachTo comprehensively understand this innovation shift in funding processes, the study employs a novel approach that merges three MCDA methods: Spherical Fuzzy Entropy, ARAS and TOPSIS. These methodologies allow for handling ambiguity and subjectivity in financial decision-making processes, examining the effects of multiple criteria, including interest rate, flexibility, accessibility, support, riskiness, and approval time, on the appeal of various financial alternatives.FindingsThe study’s results have significant theoretical and practical implications, supporting SMEs in carefully evaluate financing alternatives and enables banks to better identify the main “competitors” according to the “financial need” of the firm. Moreover, the rise of alternative finance, notably P2P lending, indicates a shift towards more efficient capital access, suggesting banks must innovate their funding channels to remain competitive, especially in offering flexible solutions for restructuring and high-risk scenarios.Practical implicationsThe study advises top management that SMEs prefer traditional loans for their reliability and accessibility, necessitating banks to enhance transparency, innovate, and adopt digital solutions to meet evolving financing needs and improve customer satisfaction.Originality/valueThe study introduces a novel integration of Spherical Fuzzy TOPSIS, Entropy, and ARAS methodologies to face the complexities of financial decision-making for SME financing, addressing ambiguity and multiple criteria like interest rates, flexibility, and riskiness. It emphasizes the importance of traditional loans, the rising significance of alternative financing such as P2P lending, and the necessity for banks to innovate, thereby enriching the literature on bank-firm relationships and SME funding strategies.
Policy discounting across and beyond the lifespan
Authors: BARNFIELD MATTHEW 
Published: August 2024

AbstractLegislators face a challenge when implementing long‐termist policies that prioritise sustainability and the well‐being of future generations: citizens prefer policies that pay off sooner rather than later. In this research note, I assess the hypothesis that the lifespan structures this temporal discounting effect. Do people show a particular preference for policies that pay off within, rather than beyond, their own lifetime? In a pre‐registered conjoint analysis with age‐group blocking (N = 2405), I find little evidence in support of this explanation. Although they significantly prefer nearer‐term policy benefits, citizens show no sign of especially preferring policies whose benefits will materialise within their own lifetimes. This pattern holds across a range of personal, political and philosophical differences. The temporal discounting effect is also substantially smaller than other policy features, such as how large the payoff of that policy is expected to be. Additionally, people are clearly willing in principle to trade off the timing of benefits for the scale of benefits, preferring larger later payoffs to sooner smaller ones. Across and beyond the lifespan, the sooner a policy pays off, the better. But, whenever they materialise, the bigger the societal benefits of that policy, the better. These findings strongly suggest that temporal policy discounting is not driven by selfish concerns, while also reinforcing that any such effect does not overwhelm citizens’ evaluations of policy proposals in principle.
The effect of listening to the sound of running water on pain and anxiety experienced during cannulation by hemodialysis patients: A randomized, controlled, open‐label study
Authors: Sayilan Samet , Aydin Sayilan Aylin , Temiz Zeynep , Kandemir Didem 
Published: August 2024

AbstractIntroductionThis study was conducted to determine the effect of the sound of running water, which we had not previously encountered being used in dialysis patients, on invasive pain and anxiety experienced during cannulation.MethodsThe research was conducted as a randomized, controlled study. A descriptive form, a VAS pain scale, and state–trait anxiety scales were used as a data collection form. The data were analyzed on SPSS version 22.00 for Windows software. The independent groups t‐test was applied to compare descriptive statistics such as mean, standard deviation, number, and percentage in independent groups, while categorical data were compared using the chi‐square test. The effect of an independent variable on a dependent variable was tested using linear regression analysis. p values < 0.05 were considered statistically significant.ResultsThe study was completed with 32 experimental and 33 control group patients. There was no significant difference in pre‐intervention pain and anxiety between the groups. The pain levels of the patients after the first and 12th cannulations were significantly lower in the experimental group (p < 0.05). State and trait anxiety levels were also significantly lower in the experimental group at the 12th session (p < 0.05).ConclusionWe conclude that the sound of running water has a significant positive effect on pain and anxiety experienced during cannulation by dialysis patients. We recommend that clinicians apply such a simple method as listening to the sound of running water for reducing pain and anxiety during invasive procedures.
Improving the odds: Artificial intelligence and the great plate count anomaly
Authors: Sipkema Detmer 
Published: August 2024

AbstractNext‐generation DNA sequencing has shown that the great plate count anomaly, that is, the difference between bacteria present in the environment and those that can be obtained in culture from that environment, is even greater and more persisting than initially thought. This hampers fundamental understanding of bacterial physiology and biotechnological application of the unculture majority. With big sequence data as foundation, artificial intelligence (AI) may be a game changer in bacterial isolation efforts and provide directions for the cultivation media and conditions that are most promising and as such be used to canalize limited human and financial resources. This opinion paper discusses how AI is or can be used to improve the success of bacterial isolation.