bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common and distinct BOLD correlates of Simon and flanker conflicts which can(not) be reduced to time-on-task effects
Authors: Wojciechowski Jakub , Jurewicz Katarzyna , Dzianok Patrycja , Antonova Ingrida , Paluch Katarzyna , Wolak Tomasz , Kublik Ewa 
Published: May 2023

AbstractThe ability to identify and resolve conflicts between standard, well trained behaviors, and behaviors required by the current context is an essential feature of cognitive control. To date, no consensus has been reached on the brain mechanisms involved in exerting such control: while some studies identified diverse patterns of activity across different conflicts, other studies reported common resources across conflict tasks or even across simple tasks devoid of conflict component. The latter reports attributed the entire activity observed in the presence of conflict to longer time spent on the task (i.e. to the so-called time-on-task effects). Here we used an extended Multi-Source Interference Task (MSIT) which combines Simon and flanker types of interference to determine shared and conflict-specific mechanisms of conflict resolution in fMRI, and their separability from the time-on-task effects. Large portions of the activity in the dorsal attention network and decreases of activity in the default mode network were shared across the tasks and scaled in parallel with increasing reaction times. Importantly, activity in the sensory and sensorimotor cortices, as well as in the posterior medial frontal cortex (pMFC)–a key region implicated in conflict processing–could not be exhaustively explained by the time-on-task effects.
Exercise modulates human hippocampal-cortical ripple dynamics
Authors: Cardenas Araceli R. , Ramirez-Villegas Juan F. , Kovach Christopher K. , Gander Phillip E. , Cole Rachel C. , Grossbach Andrew J. , Kawasaki Hiroto , Greenlee Jeremy D.W. , Howard Mathew A. , Nourski Kirill V. , Banks Matthew I. , Voss Michelle W. 
Published: May 2023

AbstractPhysical exercise acutely improves hippocampal-based learning and memory in rodents and humans. While animal studies have mainly offered cellular- and synaptic-level accounts of these effects, human neuroimaging studies show that exercise improves hippocampal-cortical connectivity at the macroscale level. However, the neurophysiological basis for exercise-induced effects on human hippocampal-cortical circuits remains unknown. A growing body of evidence supports the critical role of hippocampal sharp wave-ripples (SWRs) in learning and memory. Moreover, recent studies suggest that the coupling between ripples in the hippocampus and neocortex reflect acute modulations in inter-regional connectivity required by mnemonic processes. Here, we examine the hypothesis that exercise modulates hippocampal SWR events and their coupling with ripples in other cortical areas. We performed intracranial recordings in neurosurgery patients during awake resting state, before and after one session of aerobic exercise. Exercise elicited an increase in ripple rate and duration in mesio-temporal areas (hippocampus, amygdala and parahippocampal gyrus). These changes in ripple features were also observed in the limbic and the default mode (DMN) networks. Furthermore, after exercise, we observed an increase in coupling and phase synchrony between ripples in these two networks and hippocampal SWRs. Our results elucidate the potential mechanisms by which aerobic exercise elicits its reported short-term effects in cognition. Further investigations are needed to explore how these exercise-induced acute modulations contribute to long-term changes in neural plasticity.Significance StatementPhysical activity is a modifiable lifestyle factor that improves cognitive function and prevents age-related cognitive decline. Even one session of exercise can enhance hippocampal-based memory and learning. However, the neurophysiological mechanisms by which exercise acutely affects human cognition remain unknown. Using intracranial recordings in neurosurgical patients we show that the hippocampus and neocortex often synchronize their activities via high-frequency neural synchrony events known as ripples. After exercise, hippocampal and neocortical ripples were prolonged and emerged more frequently. Moreover, hippocampal and neocortical ripples exhibited increased coupling and phase synchrony. These effects were neocortical region-specific, favoring structures of the limbic and default mode networks. Ultimately, our results shed light on the mechanisms behind the preventive and therapeutic potential of exercise interventions.
The oscillation of mitotic kinase governs cell cycle latches in mammalian cells
Authors: Dragoi Calin-Mihai , Barr Alexis R. , Tyson John J. , Novák Béla 
Published: May 2023

SUMMARYThe mammalian cell cycle alternates between two phases: S-G2-M with high levels of A- and B-type cyclin-dependent kinases (CycA,B:CDK); and G1 with persistent degradation of CycA,B by Cdh1-activated APC/C (anaphase promoting complex/cyclosome). Because CDKs phosphorylate and inactivate Cdh1, these two phases are mutually exclusive. This ‘toggle switch’ is flipped from G1 to S by cyclin-E (CycE:CDK), which is not degraded by Cdh1:APC/C; and from M to G1 by Cdc20:APC/C, which is not inactivated by CycA,B:CDK. After flipping the switch, cyclin E is degraded and Cdc20:APC/C is inactivated. Combining mathematical modelling with single-cell timelapse imaging, we show that dysregulation of CycB:CDK disrupts strict alternation of the G1-S and M-G1 switches. Inhibition of CycB:CDK results in Cdc20-independent Cdh1 ‘endocycles’, and sustained activity of CycB:CDK drives Cdh1-independent Cdc20 endocycles. Our model provides one mechanistic explanation for how whole genome doubling can arise, a common event in tumorigenesis that can drive tumour evolution.
Spatio-relational inductive biases in spatial cell-type deconvolution
Authors: Viñas Ramon , Scherer Paul , Simidjievski Nikola , Jamnik Mateja , Liò Pietro 
Published: May 2023

AbstractSpatial transcriptomic technologies profile gene expressionin-situ, facilitating the spatial characterisation of molecular phenomena within tissues, yet often at multi-cellular resolution. Computational approaches have been developed to infer fine-grained cell-type compositions across locations, but they frequently treat neighbouring spots independently of each other. Here we present GNN-C2L, a flexible deconvolution approach that leverages proximal inductive biases to propagate information along adjacent spots. In performance comparison on simulated and semisimulated datasets, GNN-C2L achieves increased deconvolution performance over spatial-agnostic variants. We believe that accounting for spatial inductive biases can yield improved characterisation of cell-type heterogeneity in tissues.
Calorie Restriction Outperforms Bariatric Surgery in a Murine Model of Obesity and Triple-Negative Breast Cancer
Authors: Coleman Michael F , Camp Kristina K , McFarlane Tori L , Doerstling Steven S , Khatib Subreen A , Rezeli Erika T , Lewis Alfor G , Pfeil Alex J , Smith Laura A , Bowers Laura W , Fouladi Farnaz , Gong Weida , Glenny Elaine M , Parker Joel S , Milne Ginger L , Carroll Ian M , Fodor Anthony A , Seeley Randy J , Hursting Stephen D 
Published: May 2023

AbstractObesity promotes triple-negative breast cancer (TNBC), and effective interventions are urgently needed to break the obesity-TNBC link. Epidemiologic studies indicate that bariatric surgery reduces TNBC risk, while evidence is limited or conflicted for weight loss via low-fat diet (LFD) or calorie restriction (CR). Using a murine model of obesity- driven TNBC, we compared the antitumor effects of vertical sleeve gastrectomy (VSG) with LFD, chronic CR, and intermittent CR. Each intervention generated weight and fat loss and suppressed tumor growth relative to obese mice (greatest suppression with CR). VSG and CR regimens exerted both similar and unique effects, as assessed using multi-omic approaches, in reversing obesity-associated transcriptional, epigenetic, secretome, and microbiota changes and restoring antitumor immunity. Thus, in a murine model of TNBC, bariatric surgery and CR each reverse obesity-driven tumor growth via shared and distinct antitumor mechanisms, and CR is superior to VSG in reversing obesity’s procancer effects.
Changes in Cortical Directional Connectivity during Difficult Listening in Younger and Older Adults
Authors: Soleimani Behrad , Karunathilake I.M. Dushyanthi , Das Proloy , Kuchinsky Stefanie E. , Babadi Behtash , Simon Jonathan Z. 
Published: May 2023

SUMMARYOne way to investigate the mechanisms that underlie speech comprehension under difficult listening conditions is via cortical connectivity. The innovative Network Localized Granger Causality (NLGC) framework was applied to magnetoencephalography (MEG) data, obtained from older and younger subjects performing a speech listening task in noisy conditions, in delta and theta frequency bands. Directional connectivity between frontal, temporal, and parietal lobes was analyzed. Both aging- and condition-related changes were found, particularly in theta. In younger adults, as background noise increased, there was a transition from predominantly temporal-to-frontal (bottom-up) connections, to predominantly frontal-to-temporal (top-down). In contrast, older adults showed bidirectional information flow between frontal and temporal cortices even for speech in quiet, not changing substantially with increased noise. Additionally, younger listeners did not show changes in the nature of their cortical links for different listening conditions, whereas older listeners exhibited a switch from predominantly facilitative links to predominantly sharpening, when noise increased.Graphical AbstractHighlightsDifferent bands show strong differences in directional functional connectivity patternsDirectional functional connectivity patterns altered by listening task difficultyAging dramatically alters directional functional connectivity patterns in during listeningNature of functional connectivity, additive vs subtractive, depends on age and task
Recruitment status and host-fish-limitation threats to endangered freshwater pearl mussel (Margaritifera laevis) in eastern Hokkaido, northern Japan
Authors: Miura Kazuki , Ishiyama Nobuo , Negishi Junjiro N. , Kawajiri Keita , Izumi Hokuto , Ito Daisetsu , Nakamura Futoshi 
Published: May 2023

AbstractRecruitment failure is a major threat to freshwater mussel (Order Unionoida) populations worldwide. Assessments of the recruitment status and determining the bottleneck factors of mussel recruitment are crucial for preventing future declines in mussel populations. In this study, we investigated the recruitment status (i.e., size structure and the proportion of juveniles within a population) of the endangered freshwater pearl musselMargaritifera laevisin 22 rivers in eastern Hokkaido, northern Japan. We also quantified the density of the host fishOncorhynchus masou masouand examined the relationship between the proportion of juveniles and host-fish density to assess host-limitation threats toM. laevisrecruitment. Our assessments showed that 13 (59.1%) rivers had no signs of recent recruitment within 10 years, with a low mean proportion of juveniles (mean:0.02 [range:0.00–0.09] fraction), indicating that these populations are threatened by sustained recruitment failure. The proportion of juveniles was positively associated with host-fish density, suggesting that host-fish limitation could be a bottleneck factor forM. laevisrecruitment. These results highlight the urgent need for prompt conservation measures, including the enhancement of host-fish availability, to sustainM. laevispopulations in the study region.
Parsing the effect of co-culture with brain organoids on Diffuse Intrinsic Pontine Glioma (DIPG) using quantitative proteomics
Authors: Prior Victoria G , Maksour Simon , Miellet Sara , Hulme Amy J , Chen Yuyan , Mirzaei Mehdi , Wu Yunqi , Dottori Mirella , O’Neill Geraldine M 
Published: May 2023

ABSTRACTDiffuse Intrinsic Pontine Gliomas (DIPGs) are deadly brain cancers in children for which there is currently no effective treatment. This can partly be attributed to preclinical models that lack essential elements of thein vivotissue environment, resulting in treatments that appear promising preclinically, but fail to result in effective cures. Recently developed co-culture models combining stem cell-derived brain organoids with brain cancer cells provide tissue dimensionality and a human-relevant tissue-like microenvironment. As these models are technically challenging and time consuming it is imperative to establish whether interaction with the organoid influences DIPG biology and thus warrants their use. To address this question, we cultured DIPG cells with cortical organoids. We created “mosaic” co-cultures enriched for tumour cell-neuronal cell interactions versus “assembloid” co-cultures enriched for tumour cell-tumour cell interactions. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) was used to analyse the proteomes of DIPG fractions isolated by flow-assisted cell sorting. Control proteomes from DIPG spheroids were compared with DIPG cells isolated from mosaic and assembloid co-cultures. This revealed that tumour cell adhesion was reduced, and DNA synthesis and replication were increased, in DIPG cells under either co-culture condition. By contrast, the mosaic co-culture was associated with pathways implicated in dendrite growth. We propose that co-culture with brain organoids is a valuable tool to parse the contribution of the brain microenvironment to DIPG tumour biology.
Laboratory biomarkers associated with mortality in COVID-19 patients in Addis Ababa, Ethiopia
Authors: Sisay Abay , Woldesenbet Zerihun , Yalew Anteneh , Shamenna Aklilu Toma , Worku Asnake , Tesfaye Abraham , Getnet Fentabil , Tesfaye Latera , Hassen Mohammed B. , Geleso Mulugeta , Ngah Veranyuy D , Savieri Perseverence , Mirkuze Alemnesh H. , Sigwadhi Lovemore , Desta Adey Feleke , Nyasulu Peter S 
Published: May 2023

AbstractBackgroundLaboratory biomarkers are amongst the best imperative predictors of disease outcomes in hospital-admitted COVID-19 patients. Although data is available in this regard at a global level, there is a paucity of information in Ethiopia. Thus, this study aimed to assess the laboratory biomarkers association with death among COVID-19 patients in Ethiopia.MethodsA health facility-based longitudinal study was conducted from 2020 to 2022 among RT-PCR-confirmed COVID-19 patients admitted and on treatment follow-up at COVID-19 treatment hospitals in Addis Ababa. A robust Poisson regression model was fitted to assess the association between demographic, clinical, and laboratory factors and death. Significance was determined at p<0.05, and variables with p□<□ 0.15 in bivariate analyses were included in the final multivariable models. Incidence rate ratio (IRR) with a 95% confidence interval (CI) was used to describe associations.ResultsOf the 2357 COVID-19 patients, 248 (10.5%) died. The median age of participants was 59 (IQR= 45-70) years, and the majority (64.9%) of them were male. Lower median RBC was observed among those who died at 4.58 (4.06-5.07) as compared to those who survived at 4.69 (4.23-5.12) whereas high median (IQR) WBC was a predictor of mortality with 11.2 (7.7-15.9). After adjusting for confounders, death was associated with age >74 years having adjusted incidence rate ratio [aIRR (95%CI): 2.46 (1.40-4.34)], and critical clinical situations [aIRR (95% CI): 4.04 (2.18-7.52)].ConclusionOur results demonstrate that abnormal liver function tests, abnormal white blood cells, age of the patients, and clinical status of the patients during admission are associated with unfavorable outcomes of COVID-19. Hence, timely monitoring of these laboratory results at the earliest phase of the disease was highly commendable.
Evaluating the Association of Depressive Disorder Symptoms and Moral Injuries in Healthcare Workers during COVID-19 Pandemic
Authors: Behnampour Amirhossein , Ebrahimi Sedigheh , Bazrafshan Amir , Kamyab Amirhossein , Pakdin Majid , Ebrahimi Alireza 
Published: May 2023

AbstractBackgroundMoral injury occurs when negative distressing emotions appear and are suppressed. This could lead to several mental health problems such as depression and post-traumatic stress disorder, and result in long-lasting emotional, behavioral, and social problems. Moral injury, a term more commonly used in war contexts, has come into the spotlight during COVID-19 pandemic. We aimed to evaluate the rate of moral injury and its association with psychological injuries during this healthcare crisis.MethodsWe assessed the rates of depression, anxiety, stress, and their association with moral injury among 333 nurses, medical interns, and residents between December 2020 and January 2021. This study was done using validated versions of Depression Anxiety Stress Scales (DASS- and Moral Injury Symptom Scale-Healthcare Professionals (MISS-HP) scores.ResultsTotally 333 healthcare professionals participated in this study, mostly aged between 26 to 30 years old. Nearly half of the participants had a clinically significant moral injury. The average scores of anxiety and stress were significantly higher in women. The participants who were single showed higher rates of depression and moral injury than married ones. Moreover, anxiety, stress, depression, and moral injury were higher in nurses than other healthcare professionals. The scarcity of personal protective equipment at the workplace and giving care to patients with end-stage COVID-19 diagnosis were among the factors associated with a higher risk of developing mental health problems.ConclusionThe results of this study showed that anxiety, stress, depression, and moral injury were prevalent among healthcare professionals during COVID-19 pandemic. Also, the rates of anxiety, stress, and depression were associated with moral injuries.
WITHDRAWN: Reversing olorofim activity reveals multifactorial drug tolerance in Aspergillus fumigatus
Authors: Valero Clara , Mcmanus Myles , Ram Anna Durai Ashva , Tindale James , Gago Sara , Bromley Michael J 
Published: May 2023

Withdrawal StatementThe authors have withdrawn their manuscript owing to finding new evidence contradictory to the results and conclusions presented in this work. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Rapid classification vs. refined learning about harm intent: Roles of serotonin and racial bias
Authors: Moutoussis Michael , Barnby Joe , Durand Anais , Croal Megan , Dilley Laura , Rutledge Robb B. , Mason Liam 
Published: May 2023

AbstractAttributing motives to others is a crucial aspect of mentalizing, can be biased by prejudice, and also is affected by common psychiatric disorders. It is therefore important to understand in depth the mechanisms underpinning it. Toward improving models of mentalizing motives, we hypothesized that people quickly infer whether other’s motives are likely beneficial or detrimental, then refine their judgment (‘Classify-refine’). To test this, we used a modified Dictator game, a game theoretic task, where participants judged the likelihood of intent to harm vs. self-interest in economic decisions. Toward testing the role of serotonin in judgments of intent to harm, we delivered the task in a week-long, placebo vs. Citalopram study.Computational model comparison provided clear evidence for the superiority of Classify-refine models over traditional ones, strongly supporting the central hypothesis. Further, while Citalopram helped refine attributions about motives through learning, it did not induce more positive initial inferences about others’ motives. Finally, model comparison indicated a minimal role for racial bias within economic decisions for the large majority of our sample. Overall, these results support a proposal that classify-refine social cognition is adaptive, although relevant mechanisms of Serotonergic antidepressant action will need to be studied over longer time spans.
Optimized design andin vivoapplication of optogenetically functionalizedDrosophiladopamine receptors
Authors: Zhou Fangmin , Tichy Alexandra-Madelaine , Imambocus Bibi Nusreen , Rodriguez Jimenez Francisco J. , Martínez Marco González , Jahan Ishrat , Habib Margarita , Wilhelmy Nina , Bräuler Vanessa , Lömker Tatjana , Sauter Kathrin , Helfrich-Förster Charlotte , Pielage Jan , Grunwald Kadow Ilona C. , Janovjak Harald , Soba Peter 
Published: May 2023

AbstractNeuromodulatory signalingviaG protein-coupled receptor (GPCRs) plays a pivotal role in regulating neural network function and animal behavior. Recent efforts have led to the development of optogenetic tools to induce G protein-mediated signaling, with the promise of acute and cell type-specific manipulation of neuromodulatory signals. However, designing and deploying optogenetically functionalized GPCRs (optoXRs) with accurate specificity and activity to mimic endogenous signalingin vivoremains challenging. Here we optimized the design of optoXRs by considering evolutionary conserved GPCR-G protein interactions and demonstrate the feasibility of this approach using twoDrosophilaDopamine receptors (optoDopRs). We validated these optoDopRs showing that they exhibit high signaling specificity and light sensitivityin vitro.In vivowe detected receptor and cell type-specific effects of dopaminergic signaling in various behaviors including the ability of optoDopRs to rescue loss of the endogenous receptors. This work demonstrates that OptoXRs can enable optical control of neuromodulatory receptor specific signaling in functional and behavioral studies.
GlycoDraw: A Python Implementation for Generating High-Quality Glycan Figures
Authors: Lundstrøm Jon , Urban James , Thomès Luc , Bojar Daniel 
Published: May 2023

AbstractGlycans are essential to all scales of biology, with their intricate structures being crucial for their biological functions. The structural complexity of glycans is communicated through simplified and unified visual representations according to the Symbol Nomenclature for Glycans (SNFG) guidelines adopted by the community. Here, we introduce GlycoDraw, a Python-native implementation for high-throughput generation of high-quality, SNFG-compliant glycan figures with flexible display options. GlycoDraw is released as part of our glycan analysis ecosystem, glycowork, facilitating integration into existing workflows by enabling fully automated annotation of glycan-related figures and thus assisting the analysis of e.g., differential abundance data or glycomics mass spectra.