bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design, EHR Integration and Evaluation of Clinical Decision Support Workflows Driven by a Mortality Prediction Model to Promote Goal Concordant Care*
Authors: Roberts Laura M. , Rossi Lorenzo A. , Zachariah Finly 
Published: February 2023

AbstractWe present a clinical decision support (CDS) framework to promote goal-concordant care for cancer patients nearing end of life, enabled by a 90-day mortality prediction model. Design, workflow, and deployment for four model driven CDS tools are described alongside utilization patterns and detailed performance analysis of the first of such tools integrated into clinical practice: an alert promoting advance directive completion. The alert achieved a precision of 44.1% (95% CI: 39.6 - 48.8%) and a recall of 34% (95% CI: 30.3 - 37.4%) with 9.8% 90-day mortality prevalence over a period of 8 months. Our analysis shows that both precision and recall of the alert were significantly impacted by the underlying clinical workflows. Based on feedback, clinicians have accepted model-driven CDS as a legitimate means to prioritize patients for advance care planning interventions.
Disease-causing Slack potassium channel mutations produce opposite effects on excitability of excitatory and inhibitory neurons
Authors: Wu Jing , Quraishi Imran H , Zhang Yalan , Bromwich Mark , Kaczmarek Leonard K 
Published: February 2023

SUMMARYKCNT1encodes the sodium-activated potassium channel Slack (KCNT1, KNa1.1), an important mediator of neuronal membrane excitability. Gain-of-function (GOF) mutations in humans lead cortical network hyperexcitability and seizures, as well as very severe intellectual disability. Using a mouse model of Slack GOF-associated epilepsy, we found that both excitatory and inhibitory neurons of the cerebral cortex have increased Na+-dependent K+(KNa) currents and voltage-dependent sodium (NaV) currents. The characteristics of the increased KNacurrents were, however, different in the two cell types such that the intrinsic excitability of excitatory neurons was enhanced but that of inhibitory neurons was suppressed. We further showed that the expression of NaVchannel subunits, particularly that of NaV1.6, is upregulated and that the length of the axon initial segment (AIS) and of axonal NaVimmunostaining is increased in both neuron types. We found that the proximity of the AIS to the soma is shorter in excitatory neurons than in inhibitory neurons of the mutant animals, potentially contributing to the different effects on membrane excitability. Our study on the coordinate regulation of KNacurrents and the expression of NaVchannels may provide a new avenue for understanding and treating epilepsies and other neurological disorders.In briefIn a genetic mouse model of Na+-activated K+potassium channel geneSlack-related childhood epilepsy, Wuet al. show that a disease-causing gain-of-function (GOF) mutationR455Hin Slack channel causes opposite effects on excitability of cortical excitatory and inhibitory neurons. In contrast to heterologous expression systems, they find that the increase in potassium current substantially alters the expression of sodium channel subunits, resulting in increased lengths of axonal initial segments.HighlightsGOF mutations in Slack potassium channel cause elevated outward K+currents and inward voltage-dependent Na+(NaV) currents in cortical neuronsSlack GOF does not alter the expression of Slack channel but upregulates the expression of NaVchannelSlack GOF enhances the excitability of excitatory neurons but suppresses the firing of inhibitory interneuronsSlack GOF alters the length of AIS in both excitatory and inhibitory neuronsProximity of AIS to the soma is different between excitatory neuron and inhibitory neuron
Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition
Authors: Kotov Vadim , Killer Maxime , Jungnickel Katharina E. J. , Lei Jian , Finocchio Giada , Steinke Josi , Bartels Kim , Strauss Jan , Dupeux Florine , Humm Anne-Sophie , Cornaciu Irina , Márquez José A. , Pardon Els , Steyaert Jan , Löw Christian 
Published: February 2023

SummaryProton-coupled oligopeptide transporters (POTs) are promiscuous transporters of the Major Facilitator Superfamily, that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several bacterial and mammalian POT homologs have been extensively studied on a structural and molecular level. However, the molecular basis of recognition and transport of the wide range of peptide substrates has remained elusive. Here we present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe if all natural 8400 di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides of a specific subset with compact hydrophobic residues are the best DtpB binders.
LPD-3 as a megaprotein brake for aging and insulin-mTOR signaling inC. elegans
Authors: Pandey Taruna , Wang Bingying , Wang Changnan , Zu Jenny , Deng Huichao , Shen Kang , Dias do Vale Goncalo , McDonald Jeffrey G. , Ma Dengke K. 
Published: February 2023

AbstractInsulin-mTOR signaling drives anabolic growth during organismal development, while its late-life dysregulation may detrimentally contribute to aging and limit lifespans. Age-related regulatory mechanisms and functional consequences of insulin-mTOR remain incompletely understood. Here we identify LPD-3 as a megaprotein that orchestrates the tempo of insulin-mTOR signaling duringC. elegansaging. We find that an agonist insulin INS-7 is drastically over-produced in early life and shortens lifespan inlpd-3mutants, aC. elegansmodel of human Alkuraya-Kučinskas syndrome. LPD-3 forms a bridge-like tunnel megaprotein to facilitate phospholipid trafficking to plasma membranes. Lipidomic profiling reveals increased abundance of hexaceramide species inlpd-3mutants, accompanied by up-regulation of hexaceramide biosynthetic enzymes, including HYL-1 (Homolog of Yeast Longevity). Reducing HYL-1 activity decreases INS-7 levels and rescues the lifespan oflpd-3mutants through insulin receptor/DAF-2 and mTOR/LET-363. LPD-3 antagonizes SINH-1, a key mTORC2 component, and decreases expression with age in wild type animals. We propose that LPD-3 acts as a megaprotein brake for aging and its age-dependent decline restricts lifespan through the sphingolipid-hexaceramide and insulin-mTOR pathways.
Exploring the ageing methylome in the model insect,Nasonia vitripennis
Authors: Brink K. , Thomas C.L. , Jones A. , Chan T.W. , Mallon E. B. 
Published: February 2023

AbstractBackgroundThe ageing process is a multifaceted phenomenon marked by the gradual deterioration of cellular and organismal functions, accompanied by an elevated susceptibility to diseases. The intricate interplay between genetic and environmental factors complicates research, particularly in complex mammalian models. In this context, simple invertebrate organisms have been pivotal, but the current models lack detectable DNA methylation limiting the exploration of this critical epigenetic ageing mechanism.This study introduces Nasonia vitripennis, the jewel wasp, as an innovative invertebrate model for investigating the epigenetics of ageing. Leveraging its advantages as a model organism and possessing a functional DNA methylation system, Nasonia emerges as a valuable addition to ageing research.ResultsWhole-genome bisulfite sequencing unveiled dynamic alterations in DNA methylation, with differentially methylated CpGs between distinct time points in both male and female wasps. These changes were associated with numerous genes, enriching for functions related to telomere maintenance, histone methylation, and mRNA catabolic processes. Additionally, other CpGs were found to be variably methylated at each timepoint. Sex-specific effects on epigenetic entropy were observed, indicating differential patterns in the loss of epigenetic stability over time. Constructing an epigenetic clock containing 19 CpGs revealed a robust correlation between epigenetic age and chronological age.ConclusionsNasonia vitripennis emerges as a promising model for investigating the epigenetics of ageing, shedding light on the intricate dynamics of DNA methylation and their implications for age-related processes. This research not only expands the repertoire of ageing models but also opens avenues for deeper exploration of epigenetic mechanisms in the context of ageing.
Organic cation transporter 2 contributes to SSRI antidepressant efficacy by controlling tryptophan availability in the brain
Authors: Orrico-Sanchez Alejandro , Guiard Bruno P. , Manta Stella , Callebert Jacques , Launay Jean-Marie , Louis Franck , Paccard Antoine , Gruszczynski Carole , Betancur Catalina , Vialou Vincent , Gautron Sophie 
Published: February 2023

ABSTRACTSelective serotonin reuptake inhibitors (SSRI) are common first-line treatments for major depression. However, a significant number of depressed patients do not respond adequately to these pharmacological treatments. In the present preclinical study, we demonstrate that organic cation transporter 2 (OCT2), an atypical monoamine transporter, contributes to the effects of SSRI by regulating the routing of the essential amino acid tryptophan to the brain. Contrarily to wild-type mice, OCT2-invalidated mice failed to respond to prolonged fluoxetine treatment in a chronic depression model induced by corticosterone exposure recapitulating core symptoms of depression,i.e., anhedonia, social withdrawal, anxiety, and memory impairment. After corticosterone and fluoxetine treatment, the levels of tryptophan and its metabolites serotonin and kynurenine were decreased in the brain ofOCT2mutant mice compared to wild-type mice and reciprocally tryptophan and kynurenine levels were increased in mutants’ plasma. OCT2 was detected by immunofluorescence in several structures at the blood-cerebrospinal fluid (CSF) or brain-CSF interface. Tryptophan supplementation during fluoxetine treatment increased brain concentrations of tryptophan in wild-type and OCT2 mutant mice, yet more efficiently in WT than in mutants, while discretely increasing 5-HT concentrations. Importantly, tryptophan supplementation improved the sensitivity to fluoxetine treatment ofOCT2mutant mice, impacting chiefly anhedonia and short-term memory. Western blot analysis showed that glycogen synthase kinase-3β (GSK3β) and mammalian/mechanistic target of rapamycin (mTOR) intracellular signaling was impaired inOCT2mutant mice brain after corticosterone and fluoxetine treatment and, conversely, tryptophan supplementation recruited selectively the mTOR protein complex 2. This study provides the first evidence of the physiological relevance of OCT2-mediated tryptophan transport, and its biological consequences on serotonin homeostasis in the brain and SSRI efficacy.
The Energetics and Ion Coupling of Cholesterol Transport Through Patched1
Authors: Ansell T. Bertie , Corey Robin A. , Viti Lucrezia Vittoria , Kinnebrew Maia , Rohatgi Rajat , Siebold Christian , Sansom Mark S. P. 
Published: February 2023

AbstractPatched1 (PTCH1) is the principal tumour suppressor protein of the mammalian Hedgehog (HH) signalling pathway, implicated in embryogenesis and tissue homeostasis. PTCH1 inhibits the Class F G protein-coupled receptor Smoothened (SMO) via a debated mechanism involving modulating accessible cholesterol levels within ciliary membranes. Using extensive molecular dynamics (MD) simulations and free energy calculations to evaluate cholesterol transport through PTCH1, we find an energetic barrier of ~15-20 kJ mol-1for cholesterol export. In simulations we identify cation binding sites within the PTCH1 transmembrane domain (TMD) which may provide the energetic impetus for cholesterol transport.In silicodata are coupled toin vivobiochemical assays of PTCH1 mutants to probe coupling between transmembrane motions and PTCH1 activity. Using complementary simulations of Dispatched1 (DISP1) we find that transition between ‘inward-open’ and solvent ‘occluded’ states is accompanied by Na+induced pinching of intracellular helical segments. Thus, our findings illuminate the energetics and ion-coupling stoichiometries of PTCH1 transport mechanisms, whereby 1-3 Na+or 2-3 K+couple to cholesterol export, and provide the first molecular description of transitions between distinct transport states.
GermanIxodes inopinatussamples may not actually represent this tick species
Authors: Rollins Robert E. , Margos Gabriele , Brachmann Andreas , Krebs Stefan , Mouchet Alexia , Dingemanse Niels J. , Laatamna AbdElkarim , Reghaissia Nassiba , Fingerle Volker , Metzler Dirk , Becker Noémie S. , Chitimia-Dobler Lidia 
Published: February 2023

AbstractTicks are important vectors of human and animal pathogens, but many questions remain unanswered regarding their taxonomy. Molecular sequencing methods have allowed research to start understanding the evolutionary history of even closely related tick species.Ixodes inopinatusis considered a sister species and highly similar toIxodes ricinus, an important vector of many tick-borne pathogens in Europe, but identification between these species remains ambiguous with disagreement on the geographic extent ofI. inopinatus. In 2018-2019, 1583 ticks were collected from breeding great tits (Parus major) in southern Germany, of which 45 were later morphologically identified asI. inopinatus. We aimed to confirm morphological identification using molecular tools. Utilizing two genetic markers (16S rRNA, TROSPA) (n=37) and whole genome sequencing of specific ticks (n=8), we were able to determine that German samples morphologically identified asI. inopinatus, genetically representI. ricinusregardless of previous morphological identification and most likely are notI. ricinus/I. inopinatushybrids. Further, our results showed that the entire mitochondrial genome, let alone singular mitochondrial genes (i.e., 16S), is unable to distinguish betweenI. ricinusandI. inopinatus. As most examples ofI. inopinatusin Germany were based on morphology and mitochondrial sequences, the results of the current study brings into question whetherI. inopinatuswas properly identified in previous research and if this species exists in Central Europe. Our results highlight the power of utilizing genomic data in answering questions regarding tick taxonomy even when closely related species are considered.HighlightsGermanIxodes inopinatussamples representI. ricinusbased on genomic dataThe mitochondrial genome is not sufficient for delineation ofI. inopinatusandI. ricinusGerman samples most likely do not representI. ricinus/I. inopinatushybrids
A single-cell map of antisense oligonucleotide activity in the brain
Authors: Mortberg Meredith A , Gentile Juliana E , Nadaf Naeem , Vanderburg Charles , Simmons Sean , Dubinsky Dan , Slamin Adam , Maldonado Salome , Petersen Caroline L , Jones Nichole , Kordasiewicz Holly B , Zhao Hien T , Vallabh Sonia M , Minikel Eric Vallabh 
Published: February 2023

ABSTRACTAntisense oligonucleotides (ASOs) dosed into cerebrospinal fluid (CSF) distribute broadly throughout the brain and hold the promise of treating myriad brain diseases by modulating RNA. CNS tissue is not routinely biopsied in living individuals, leading to reliance on CSF biomarkers to inform on drug target engagement. Animal models can link CSF biomarkers to brain parenchyma, but our understanding of how individual cells contribute to bulk tissue signal is limited. Here we employed single nucleus transcriptomics on tissue from mice treated with RNase H1 ASOs againstPrnpandMalat1and macaques treated with an ASO againstPRNP. Activity was observed in every cell type, though sometimes with substantial differences in magnitude. Single cell RNA count distributions implied target suppression in every single sequenced cell, rather than intense knockdown in only some cells. Duration of action up to 12 weeks post-dose differed across cell types, being shorter in microglia than in neurons. Suppression in neurons was generally similar to, or more robust than, the bulk tissue. In macaques, PrP in CSF was lowered 40% in conjunction withPRNPknockdown across all cell types including neurons, arguing that a CSF biomarker readout is likely to reflect disease-relevant cells in a neuronal disorder.
Development of the branchial musculature of the Siberian sturgeon (Acipenser baerii) reveals a heterochronic shift during the evolution of acipenseriform cranial muscles
Authors: Naumann Benjamin , Warth Peter , Hammel Jörg U. , Moosmann Julian , Konstantinidis Peter , Olsson Lennart 
Published: February 2023

AbstractHeterochronic shifts are regarded one of the major evolutionary changes acting on developmental modules and underlying the origin of morphological disparity. Conserved characters, rarely subject to heterochronic shifts during the curse of evolution, in contrast could indicate underlying developmental or functional constraints. Here we use the development of the cranial musculature Siberian sturgeon (Acipenser baerii) as a model to investigate the role of heterochrony during the evolution of the craniofacial system of Actinopterygii. Using histology, fluorescent antibody staining and fast propagation-based phase contrast imaging in combination with 3D-reconstruction we describe the development of the branchial and hypobranchial musculature. We show that the development of the first branchial arch is accelerated compared to other basal-branching actinopterygians leading to a more synchronous development with the hyoid arch. A pattern that could relate to the derived migratory behaviour of the neural crest cells in sturgeons. In contrast, the developmental timing of the more posterior branchial musculature, including thecucullarismuscle in the Siberian sturgeon, appears to be highly conserved compared to other Actinopterygii and even Osteognathostomata. This could indicate the presence of functional or developmental constraints underlying the evolution of the muscles at the head/trunk interface.
The composition of piRNA clusters inDrosophila melanogasterdeviates from expectations under the trap model
Authors: Wierzbicki Filip , Kofler Robert 
Published: February 2023

AbstractIt is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e. the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model. Therefore, we aim to test the trap model. We show with population genetic simulations that the composition of regions that act as transposon traps (i.e. possible piRNA clusters) ought to deviate from regions that have no effect on TE activity. Next, we investigated TEs in fiveD. melanogasterstrains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, we found that the distribution of the number of TE insertions in piRNA clusters is also much broader than expected, where some families have zero cluster insertions and others more than 14. One feasible explanation is that insertions in piRNA clusters have little effect on TE activity and that the trap model is therefore incorrect. Alternatively, dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may explain some of our observations.
A hyper-quiescent chromatin state formed during aging is reversed by regeneration
Authors: Yang Na , Occean James R. , Melters Daniël P. , Shi Changyou , Wang Lin , Stransky Stephanie , Doyle Maire E. , Cui Chang-Yi , Delannoy Michael , Fan Jinshui , Slama Eliza , Egan Josephine M. , De Supriyo , Cunningham Steven C. , de Cabo Rafael , Sidoli Simone , Dalal Yamini , Sen Payel 
Published: February 2023

SummaryEpigenetic alterations are a key hallmark of aging but have been limitedly explored in tissues. Here, using naturally aged murine liver as a model and extending to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach, and the first direct visualization of aged chromatin we find that globally, old cells show H3K27me3-driven broad heterochromatinization and transcription suppression. At the local level, site-specific loss of H3K27me3 over promoters of genes encoding developmental transcription factors leads to expression of otherwise non-hepatocyte markers. Interestingly, liver regeneration reverses H3K27me3 patterns and rejuvenates multiple molecular and physiological aspects of the aged liver.
High-throughput quantitative screening of glucose-stimulated insulin secretion and insulin content using automated MALDI-TOF mass spectrometry
Authors: Delannoy Clément Philippe , Heuson Egon , Herledan Adrien , Oger Frederik , Thiroux Bryan , Chevalier Mickaël , Gromada Xavier , Rolland Laure , Froguel Philippe , Deprez Benoit , Paul Sebastien , Annicotte Jean-Sébastien 
Published: February 2023

AbstractType 2 diabetes (T2D) is a metabolic disorder characterized by loss of pancreatic β- cell function, decreased insulin secretion and increased insulin resistance, that affects more than 400 million people worldwide. Although several treatments are proposed to patients suffering from T2D, long-term control of glycemia remains a challenge. Therefore, identifying new potential drugs and targets that positively affect β-cell function and insulin secretion remains crucial. Here, we developed an automated approach to allow the identification of new compounds or genes potentially involved in β-cell function in a 384-well plate format, using the murine β-cell model Min6. Using MALDI-TOF mass spectrometry, we have implemented a high-throughput screening (HTS) strategy based on the automation of a cellular assay allowing to detect insulin secretion in response to glucose, quantitative detection of insulin, in a miniaturized system. As a proof of concept, we screened siRNA targeting well-know β-cell genes and 1600 chemical compounds and identified several molecules as potential regulators of insulin secretion and/or synthesis, demonstrating that our approach allows HTS of insulin secretionin vitro.
Odor representations from the two nostrils are temporally segregated in human piriform cortex
Authors: Dikecligil Gülce Nazlı , Yang Andrew I. , Sanghani Nisha , Lucas Timothy , Chen H. Isaac , Davis Kathryn A. , Gottfried Jay A. 
Published: February 2023

SUMMARYThe human olfactory system has two discrete channels of sensory input, arising from olfactory epithelia housed in the left and right nostrils. Here, we asked whether primary olfactory cortex (piriform cortex, PC) encodes odor information arising from the two nostrils as integrated or distinct stimuli. We recorded intracranial EEG signals directly from PC while human subjects participated in an odor identification task where odors were delivered to the left, right, or both nostrils. We analyzed the time-course of odor-identity coding using machine learning approaches, and found that uni-nostril odor inputs to the ipsilateral nostril are encoded ∼480 ms faster than odor inputs to the contralateral nostril on average. During naturalistic bi-nostril odor sampling, odor information emerged in two temporally segregated epochs with the first epoch corresponding to the ipsilateral and the second epoch corresponding to the contralateral odor representations. These findings reveal that PC maintains distinct representations of odor input from each nostril through temporal segregation, highlighting an olfactory coding scheme at the cortical level that can parse odor information across nostrils within the course of a single inhalation.