bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forecasting parasite sharing under climate change
Authors: Morales-Castilla Ignacio , Pappalardo Paula , Farrell Maxwell J. , Aguirre A. Alonso , Huang Shan , Gehman Alyssa-Lois M. , Dallas Tad , Gravel Dominique , Davies T. Jonathan 
Published: September 2021

Species are shifting their distributions in response to climate change. This geographic reshuffling may result in novel co-occurrences among species, which could lead to unseen biotic interactions, including the exchange of parasites between previously isolated hosts. Identifying potential new host–parasite interactions would improve forecasting of disease emergence and inform proactive disease surveillance. However, accurate predictions of future cross-species disease transmission have been hampered by the lack of a generalized approach and data availability. Here, we propose a framework to predict novel host–parasite interactions based on a combination of niche modelling of future host distributions and parasite sharing models. Using the North American ungulates as a proof of concept, we show this approach has high cross-validation accuracy in over 85% of modelled parasites and find that more than 34% of the host–parasite associations forecasted by our models have already been recorded in the literature. We discuss potential sources of uncertainty and bias that may affect our results and similar forecasting approaches, and propose pathways to generate increasingly accurate predictions. Our results indicate that forecasting parasite sharing in response to shifts in host geographic distributions allow for the identification of regions and taxa most susceptible to emergent pathogens under climate change.
This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Identification of serotonin as a gut regulator of liver hepcidin expression
Authors: Coman Tereza , Falabrègue Marion , Rossignol Julien , Bonneau Pierre , Djebar Morgane , Bigorgne Amélie , Mathieu Jacques RR , Foretz Marc , Kautz Léon , Peoc’h’ Katel , Launay Jean-Marie , Maroteaux Luc , Peyssonnaux Carole , Hermine Olivier , Côté Francine 
Published: September 2021

AbstractIron is essential to key biological processes of all living organisms. Proper iron levels must be maintained to meet biological needs and prevent toxicity. Given the central role played by the hormone hepcidin in systemic iron homeostasis, extensive research has sought to identify regulators of its expression. Diverse evidence shows the gut to be an essential sensor and regulator of iron homeostasis, independently of other known hepcidin regulators, including bone marrow signals. Here we identify gut-derived serotonin as a key physiological factor in hepcidin regulation. In response to hypoxia, serotonin synthesized and secreted by enterochromaffin cells can act beyond the gut to repress hepcidin expression in the liver, through a 5-HT2Breceptor-dependent pathway. Bone marrow transplant experiments clearly indicate the gut is responsible for hepcidin repression. This regulatory system appears to be conserved in humans: a significant negative correlation exists between hepcidin and serotonin levels in the serum of healthy individuals. Our findings imply hepcidin regulation by serotonin is a physiological process, and modulation of the gut serotonergic system may have broad therapeutic implications.
Intergenerational effects of a paternal Western diet during adolescence on offspring gut microbiota, stress reactivity and social behavior
Authors: Bodden Carina , Pang Terence Y. , Feng Yingshi , Mridha Faria , Kong Geraldine , Li Shanshan , Watt Matthew J. , Reichelt Amy C. , Hannan Anthony J. 
Published: September 2021

AbstractThe global consumption of highly processed, calorie-dense foods has contributed to an epidemic of overweight and obesity, along with negative consequences for metabolic dysfunction and disease susceptibility. As it becomes apparent that overweight and obesity have ripple effects through generations, understanding of the processes involved is required, in both maternal and paternal epigenetic inheritance. We focused on the patrilineal effects of a Western-style high-fat (21%) and high-sugar (34%) diet (WD) compared to control diet (CD) during adolescence and investigated F0 and F1 mice for physiological and behavioral changes. F0 males (fathers) showed increased body weight, impaired glycemic control, and decreased attractiveness to females. Paternal WD caused significant phenotypic changes in F1 offspring, including higher body weights of pups, increased Actinobacteria abundance in the gut microbiota (ascertained using 16S microbiome profiling), a food preference for WD pellets, increased male dominance and attractiveness to females, as well as decreased behavioral despair. These results collectively demonstrate the long-term intergenerational effects of a Western-style diet during paternal adolescence. The behavioral and physiological alterations in F1 offspring provide evidence of adaptive paternal programming via epigenetic inheritance. These findings have important implications for understanding paternally mediated intergenerational inheritance, and its relevance to offspring health and disease susceptibility.
An ultra-low frequency spike timing dependent plasticity-based approach for treating alcohol use disorder
Authors: Asp Anders J. , Boschen Suelen Lucio , Lujan J. Luis 
Published: September 2021

AbstractAlcohol use disorder (AUD) is a chronic relapsing brain disorder characterized by an impaired ability to stop or control alcohol consumption despite adverse social, occupational, or health consequences. AUD affects nearly one-third of adults at some point during their lives, with an associated cost of approximately $249 billion annually in the U.S. alone. The effects of alcohol consumption are expected to increase significantly during the COVID-19 pandemic, with alcohol sales increased by approximately 54%, potentially exacerbating health concerns and risk-taking behaviors. Unfortunately, existing pharmacological and behavioral therapies for AUD have historically been associated with poor success rates, with approximately 40% of individuals relapsing within three years of treatment.Pre-clinical studies have shown that chronic alcohol consumption leads to significant changes in synaptic function within the dorsal medial striatum (DMS), one of the brain regions associated with AUD and responsible for mediating goal-directed behavior. Specifically, chronic alcohol consumption has been associated with hyperactivity of dopamine receptor 1 (D1) medium spiny neurons (MSN) and hypoactivity of dopamine receptor 2 (D1) MSNs within the DMS. Optogenetic, chemogenetic, and transgenic approaches have demonstrated that reducing the D1/D2 MSN signaling imbalance decreases alcohol self-administration in rodent models of AUD. However, these approaches cannot be studied clinically at this time.Here, we present an electrical stimulation alternative that uses ultra-low (<=1Hz) frequency (ULF) spike-timing dependent plasticity (STDP) to reduce DMS D1/D2 MSN signaling imbalances by stimulating D1-MSN afferents into the GPi and ACC glutamatergic projections to the DMS in a time-locked stimulation sequence. Our data suggest that GPi/ACC ULF-STDP selectively decreases DMS D1-MSN hyperactivity leading to reduced alcohol consumption without evoking undesired affective behaviors in a two-bottle choice mouse model of AUD.
Increased Activation in the Fusiform Face Area to Greebles is a Result of Expertise Training, Not by its Face-likeness
Authors: Liu Kuo , Chen Chiu-Yueh , Wang Le-Si , Kung Chun-Chia 
Published: September 2021

AbstractIn 2011, Brants, Wagemans, & Op de Beeck (JOCN 23:12, pp. 3949-3958) trained eight individuals to become Greeble experts, and found neuronal inversion effects [NIEs; i.e., higher Fusiform Face Area (FFA) activity for upright, rather than inverted Greebles]. These effects were also found for faces, both before and after training. By claiming to have replicated the seminal Greeble training study (i.e., Gauthier, Tarr, Anderson, Skudlarski, & Gore, 1999, Nat Neurosci, 2, 568-573), Brants et al. interpreted these results as participants viewing Greebles as faces throughout training, contrary to the original argument of subjects becoming Greeble experts only after training. However, such a claim presents two issues. First, the behavioral training results of Brants et al. did not replicate those of Gauthier et al (1999), raising concerns of whether the right training regime had been adopted. Second, both a literature review and meta-analysis of NIE in the FFA suggest its unreliability as an index of face(-like) processing. To empirically evaluate these issues, the present study compared two documented training paradigms (i.e., Gauthier & Tarr, 1997, Vision Res, 37, 1673-1682; and Gauthier, Williams, Tarr, & Tanaka, 1998, Vision Res, 38, 2401-2428) and explored their impact on the FFA. The results showed significant increases in the FFA for Greebles, and a clear neural “adaptation” (i.e., decreased activity for faces following Greebles, but not following non-face objects, in the FFA) both only in the Gauthier97 group, and only after training, reflecting clear modulation of expertise following “appropriate” training. In both groups, no clear NIE for faces nor Greebles were found. Collectively, these data invalidate the two assumptions behind the Brants et al. findings, and provide not only the updated support, but also the new evidence, for the perceptual expertise hypothesis of FFA.
A machine learning model that emulates experts’ decision making in vancomycin initial dose planning
Authors: Matsuzaki Tetsuo , Kato Yoshiaki , Mizoguchi Hiroyuki , Yamada Kiyofumi 
Published: September 2021

AbstractVancomycin is a glycopeptide antibiotic that has been used primarily in the treatment of methicillin-resistantStaphylococcus aureusinfections. To enhance its clinical effectiveness and prevent nephrotoxicity, therapeutic drug monitoring (TDM) of trough concentrations is recommended.Initial vancomycin dosing regimens are determined based on patient characteristics such as age, body weight, and renal function, and dosing strategies to achieve therapeutic concentration windows at initial TDM have been extensively studied. Although numerous dosing nomograms for specific populations have been developed, no comprehensive strategy exists for individually tailoring initial dosing regimens; therefore, decision making regarding initial dosing largely depends on each clinician’s experience and expertise.In this study, we applied a machine-learning (ML) approach to integrate clinician knowledge into a predictive model for initial vancomycin dosing. A dataset of vancomycin initial dose plans defined by pharmacists experienced in vancomycin TDM (i.e., experts) was used to build the ML model. The target trough concentration was attained at comparable rates with the model- and expert-recommended dosing regimens, suggesting that the ML model successfully incorporated the experts’ knowledge. The predictive model developed here will contribute to improved decision making for initial vancomycin dosing and early attainment of therapeutic windows.
Cerebellar stimulations prevent Levodopa-induced dyskinesia in mice and normalize brain activity
Authors: Coutant Bérénice , Frontera Jimena Laura , Perrin Elodie , Combes Adèle , Tarpin Thibault , Menardy Fabien , Mailhes-Hamon Caroline , Perez Sylvie , Degos Bertrand , Venance Laurent , Léna Clément , Popa Daniela 
Published: September 2021

SUMMARYChronic Levodopa therapy, the gold-standard treatment of Parkinson’s Disease (PD), leads to the emergence of involuntary movements, called levodopa-induced dyskinesia (LID). Cerebellar stimulations have been shown to decrease LID severity in PD patients. Here, in order to determine how cerebellar stimulations induce LID alleviation, we performed daily short trains of optogenetic stimulations of Purkinje cells (PC) in freely moving mice. We demonstrated that these stimulations are sufficient to suppress LID or even prevent their development. This symptomatic relief is accompanied by the normalization of aberrant neuronal discharge in the cerebellar nuclei, the motor cortex and the parafascicular thalamus. Inhibition of the cerebello-parafascicular pathway counteracted the beneficial effect of cerebellar stimulations. Moreover, cerebellar stimulations reversed plasticity in D1 striatal neurons and normalized the overexpression of FosB, a transcription factor causally linked to LID. These findings demonstrate LID alleviation and prevention by daily PC stimulations, which restore the function of a wide brain motor network, and may be valuable for LID treatment.
ProteoDisco: A flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies
Authors: van de Geer Wesley S. , van Riet Job , van de Werken Harmen J. G. 
Published: September 2021

AbstractSummaryWe present an R-based open-source software termed ProteoDisco that allows for flexible incorporation of genomic variants, fusion-genes and (aberrant) transcriptomic variants from standardized formats into protein variant sequences. ProteoDisco allows for a flexible step-by-step workflow allowing for in-depth customization to suit a myriad of research approaches in the field of proteogenomics, on all organisms for which a reference genome and transcript annotations are available.Availability and ImplementationProteoDisco (R package version ≥ 0.99) is available from https://github.com/ErasmusMC-CCBC/ProteoDisco/.Contacth.vandewerken@erasmusmc.nlSupplementary informationSupplementary table, figures and data files available.
Perception affects the brain’s metabolic response to sensory stimulation
Authors: DiNuzzo Mauro , Mangia Silvia , Moraschi Marta , Mascali Daniele , Hagberg Gisela E. , Giove Federico 
Published: September 2021

AbstractProcessing of incoming sensory stimulation triggers an increase of cerebral perfusion and blood oxygenation (neurovascular response) as well as an alteration of the metabolic neurochemical profile (neurometabolic response). Here we show that perceived and unperceived isoluminant chromatic flickering stimuli designed to have similar neurovascular responses as measured by blood oxygenation level dependent functional MRI (BOLD-fMRI) in primary visual cortex (V1) have markedly different neurometabolic responses as measured by functional MRS. In particular, a significant regional buildup of lactate, an index of aerobic glycolysis, and glutamate, an index of malate-aspartate shuttle, occurred in V1 only when the flickering is perceived, without any relation with behavioral or physiological variables. Wheras the BOLD-fMRI signal in V1, a proxy for input to V1, was insensitive to flickering perception by design, the BOLD-fMRI signal in secondary visual areas was larger during perceived than unperceived flickering indicating increased output from V1. These results indicate that the upregulation of energy metabolism induced by visual stimulation depends on the type of information processing taking place in V1, and that 1H-fMRS provides unique information about local input/output balance that is not measured by BOLD-fMRI.Significance statementVisual perception has a measurable metabolic effect in the primary visual cortex (V1). Here we show that the upregulation of energy metabolism induced by isoluminant chromatic flickering depends on subjective visual perception. Within V1, perceived and unperceived stimuli that are contrast-matched to elicit similar blood-oxygenation level-dependent fMRI response are associated with clearly distinct neurochemical profiles. Specifically, regional accumulations of lactate (an index of aerobic glycolysis) and glutamate (an index of malate-aspartate shuttle) only develop during perceived stimuli, together with a larger activation of secondary visual areas. Our results imply a dissociation between metabolic and functional response, and indicate that that the upregulation of energy metabolism induced by visual stimulation depends on the type of information processing taking place in V1.
Limitations of a proposed correction for slow drifts in decision criterion
Authors: Gupta Diksha , Brody Carlos D. 
Published: September 2021

AbstractTrial history biases in decision-making tasks are thought to reflect systematic updates of decision variables, therefore their precise nature informs conclusions about underlying heuristic strategies and learning processes. However, random drifts in decision variables can corrupt this inference by mimicking the signatures of systematic updates. Hence, identifying the trial-by-trial evolution of decision variables requires methods that can robustly account for such drifts. Recent studies (Lak’20, Mendonça‘20) have made important advances in this direction, by proposing a convenient method to correct for the influence of slow drifts in decision criterion, a key decision variable. Here we apply this correction to a variety of updating scenarios, and evaluate its performance. We show that the correction fails for a wide range of commonly assumed systematic updating strategies, distorting one’s inference away from the veridical strategies towards a narrow subset. To address these limitations, we propose a model-based approach for disambiguating systematic updates from random drifts, and demonstrate its success on real and synthetic datasets. We show that this approach accurately recovers the latent trajectory of drifts in decision criterion as well as the generative systematic updates from simulated data. Our results offer recommendations for methods to account for the interactions between history biases and slow drifts, and highlight the advantages of incorporating assumptions about the generative process directly into models of decision-making.
Self-healing of hyaluronic acid to improvein vivoretention and function
Authors: Gilpin Anna , Zeng Yuze , Hoque Jiaul , Ryu Ji Hyun , Yang Yong , Zauscher Stefan , Eward William , Varghese Shyni 
Published: September 2021

AbstractConvergent advances in the field of soft matter, macromolecular chemistry, and engineering have led to the development of biomaterials that possess autonomous, adaptive, and self-healing characteristics similar to living systems. These rationally designed biomaterials could surpass the capabilities of their parent material. Herein, we describe the modification of hyaluronic acid (HA) molecules to exhibit self-healing properties and studied its physical and biological function bothin vitroandin vivo. Ourin vitrofindings showed that self-healing HA designed to undergo autonomous repair improved lubrication, enhanced free radical scavenging, and resisted enzymatic degradation compared to unmodified HA. Longitudinal imaging following intra-articular injection of self-healing HA showed improvedin vivoretention despite the low molecular weight. Concomitant with these functions, intra-articular injection of self-healing HA mitigated anterior cruciate ligament injury-mediated cartilage degeneration in rodents. This proof-of-concept study shows how incorporation of functional properties like self-healing can be used to surpass the existing capabilities of biolubricants.
In vivointraoral waterflow quantification reveals hidden mechanisms of suction feeding in fish
Authors: Provini Pauline , Brunet Alexandre , Filippo Andréa , Van Wassenbergh Sam 
Published: September 2021

AbstractVirtually all fish rely on flows of water to transport food to the back of their pharynx. While external flows that draw food into the mouth are well described, how intra-oral water flows manage to deposit food at the esophagus entrance remains unknown. In theory, the posteriorly moving water must, at some point, curve laterally and/or ventrally to exit through the gill slits. Such flows would eventually carry food away from the esophagus instead of towards it. This apparent paradox calls for a filtration mechanism to deviate food from the suction-feeding streamlines. To study this gap in our fundamental understanding of how fish feed, we developed and applied a new technique to quantify three-dimensional patterns of intra-oral water flowsin vivo.We combined stereoscopic high-speed x-ray videos to quantify skeletal motion (XROMM) with 3D x-ray particle tracking (XPT) of approximately neutrally buoyant spheres of 1.4 mm in diameter. We showed, for carp (Cyprinus carpio) and tilapia (Oreochromis niloticus), that water tracers displayed higher curvatures than food tracers, indicating an inertia-driven filtration. In addition, tilapia also exhibited a ‘central jet’ flow pattern, which aids in quickly carrying food to the pharyngeal jaw region. When the food was trapped at the branchial basket, it was resuspended and carried more centrally by periodical bidirectional waterflows, synchronized with head-bone motions. By providing a complete picture of the suction-feeding process and revealing fundamental differences in food transport mechanisms among species, this new technique opens a new area of investigation to fully understand how most aquatic vertebrates feed.
Energy status-promoted growth and development of Arabidopsis require copper deficiency response transcriptional regulator SPL7
Authors: Schulten Anna , Pietzenuk Björn , Quintana Julia , Krause Marcus , Feil Regina , Romera-Branchat Maida , Wahl Vanessa , Severing Edouard , Coupland George , Krämer Ute 
Published: September 2021

AbstractCopper (Cu) is a cofactor of around 300 Arabidopsis proteins including photosynthetic and mitochondrial electron transfer chain enzymes critical for ATP production and carbon fixation. Plant acclimation to Cu deficiency requires the transcription factor SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 (SPL7). We report that in the wild type and in thespl7-1mutant, respiratory electron fluxviaCu-dependent cytochromecoxidase remained unaffected under both normal and low-Cu cultivation conditions. Contrary to the wild type, supplementing Cu-deficient media with exogenous sugar failed to stimulate growth ofspl7-1. Thespl7-1mutant accumulated carbohydrates including the signaling sugar trehalose 6-phosphate, as well as ATP and NADH, also under normal Cu supply and without sugar supplementation. Late flowering ofspl7-1was in agreement with its attenuated sugar responsiveness. Functional TOR and SnRK1 kinase signaling inspl7-1suggested against fundamental defects in these energy-signaling hubs. Sequencing of chromatin immunoprecipitates combined with transcriptomics identified direct targets of SPL7-mediated positive regulation, includingFE SUPEROXIDE DISMUTASE1(FSD1),COPPER-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR1(CITF1) and uncharacterizedbHLH23(CITF2), as well as an enriched upstream GTACTRC motif. In summary, transducing energy availability into growth and reproductive development requires the function of SPL7. Our results could help to increase crop yields, especially on Cu-deficient soils.