bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair
Authors: Perez-Bermejo Juan A. , Efagene Oghene , Matern William M. , Holden Jeffrey K. , Kabir Shaheen , Chew Glen M. , Andreoletti Gaia , Catton Eniola , Ennis Craig L. , Garcia Angelica , Gerstenberg Trevor L. , Hill Kaisle A. , Jain Aayami , Krassovsky Kristina , Lalisan Cassandra D. , Lord Daniel , Quejarro B. Joy , Sales-Lee Jade , Shah Meet , Silva Brian J. , Skowronski Jason , Strukov Yuri G. , Thomas Joshua , Veraz Michael , Vijay Twaritha , Wallace Kirby A. , Yuan Yue , Grogan Jane L. , Wienert Beeke , Lahiri Premanjali , Treusch Sebastian , Dever Daniel P. , Soros Vanessa B. , Partridge James R. , Seim Kristen L. 
Published: November 2023

AbstractHomology Directed Repair (HDR) enables precise genome editing and holds great promise in the gene therapy field. However, the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we demonstrate the development of a functional, pooled screening platform utilizing an HDR-based readout to identify protein-based reagents that improve HDR outcomes in human hematopoietic stem and progenitor cells (HSPCs), a clinically relevant cell type for gene therapy. We leveraged this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, and we identified optimized i53 variants that enable new intermolecular bonds and robustly increase HDR. These variants specifically reduce insertion-deletion outcomes and also synergize with a DNAPK inhibitor to increase HDR rates. When applied at manufacturing scale, the incorporation of improved variants results in a significant increase in cells with at least one repaired allele and improved HDR in long-term HSPCs subpopulations, while not increasing off-target editing or gross chromosomal rearrangements. We anticipate the pooled screening platform will enable discovery of future gene editing reagents that improve HDR outcomes, such as the i53 variants reported here.
Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges
Authors: Arias J. Salvador 
Published: November 2023

ABSTRACTMost popular methods of phylogenetic biogeography discard the spatial component of geographic distributions, dividing Earth into a handful of predefined areas. Other methods use explicit geographic ranges, but unfortunately, these methods assume a static Earth, ignoring the effects of plate tectonics and the changes in the landscape. To address this limitation, I propose a method that uses explicit geographic ranges and incorporates a plate motion model and a paleolandscape model directly derived from the models used by geologists in their tectonic and paleogeographic reconstructions. The underlying geographic model is a high-resolution pixelation of a spherical Earth. Biogeographic inference is based on diffusion, approximates the effects of the landscape, uses a time-stratified model to take into account the geographic changes, and directly integrates over all probable histories. By using a simplified stochastic mapping algorithm, it is possible to infer the ancestral locations as well as the distance and speed traveled by the ancestral lineages. For illustration, I applied the method to an empirical phylogeny of the Sapindaceae plants. This example shows that methods based on explicit geographic data, coupled with high-resolution paleogeographic models, can provide detailed reconstructions of the ancestral areas but also include inferences about the probable dispersal paths and traveling speed across the taxon history that are not possible with current methods based on predefined areas.
Krisp: A python package for designing CRISPR and amplification-based diagnostic assays from whole genome data
Authors: Foster Zachary S. L. , Tupper Andrew S. , Press Caroline M. , Grünwald Niklaus J. 
Published: November 2023

AbstractRecent pandemics such as COVID-19 have highlighted the importance of rapidly developing diagnostics to detect and monitor evolving pathogens. CRISPR-Cas technology, combined with isothermal DNA amplification methods, has recently been used to develop diagnostic assays for sequence-specific recognition of DNA or RNA. These assays have similar sensitivity to the gold standard qPCR but can be deployed as easy to use and inexpensive test strips. However, the discovery of diagnostic regions of a genome flanked by conserved regions where primers can be designed requires extensive bioinformatic analyses of genome sequences. We developed the python packagekrispto find primers and diagnostic sequences that differentiate groups of samples from each other at any taxonomic scale, using either unaligned genome sequences or a variant call format (VCF) file as input.Krisphas been optimized to handle large datasets by using efficient algorithms that run in near linear time, use minimal RAM, and leverage parallel processing when available. The validity ofkrispresults has been demonstrated in the laboratory with the successful design of SHERLOCK assays to distinguish the sudden oak death pathogenPhytophthora ramorumfrom closely relatedPhytophthoraspecies.Krispis released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays.Author summaryPathogens continue to emerge at accelerated rates affecting animals, plants, and ecosystems. Rapid development of novel diagnostic tools is needed to monitor novel pathogen variants or groups. We developed the computational toolkrispto identify genetic regions suitable for development of CRISPR diagnostics and traditional amplification-based diagnostics such as PCR.Krispscans whole genome sequence data for target and non-target groups to identify diagnostic regions based on DNA or RNA sequences. This computational tool has been validated using genome data for the sudden oak death pathogenPhytophthora ramorum.Krispis released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays and other amplification-based assays.
SMAD4 promotes formation of terminally differentiated CTLs that localize in the microvasculature of the lungs but are excluded from the lumen of the airways
Authors: Suarez-Ramirez Jenny , Chandiran Karthik , Cauley Linda S 
Published: November 2023

AbstractCytotoxic T lymphocytes (CTLs) circulate around the body searching for infected and transformed cells, that undergo apoptosis when lytic granules are delivered into the cytoplasm. To find pathogens that propagate in different tissues, naïve CD8 T cells differentiate into heterogeneous populations of effector (TEFF) and memory CD8 T cells with different migratory properties. Several subsets can be identified using antibodies that recognize surface receptors that are expressed at specific stages during CD8 T cell differentiation. Although flow cytometry is a powerful method for tracking antigen specific CTLs during a dynamic immune response, the data provide little information about the distribution of cells in specific anatomical compartments. In this study, confocal imaging was used to explore how signaling via SMAD4 influenced the tissue-tropism of antigen specific CTLs during respiratory infection. During microbial infection, wildtype CTLs gave rise to terminally differentiated TEFFcells that expressed KLRG1 and CX3CR1 at high levels and localized in the microvasculature of the lungs. However, both markers were expressed at reduced levels on SMAD4-deficient CTLs, which preferentially entered the lumen of the airways. These disparate homing properties emphasize the important contributions of SMAD signaling pathways to cell-mediated immunity.
Modeling spatial evolution of multi-drug resistance under drug environmental gradients
Authors: Freire Tomas , Hu Zhijian , Wood Kevin B. , Gjini Erida 
Published: November 2023

AbstractMulti-drug combinations to treat bacterial populations are at the forefront of approaches for infection control and prevention of antibiotic resistance. Although the evolution of antibiotic resistance has been theoretically studied with mathematical population dynamics models, extensions to spatial dynamics remain rare in the literature, including in particular spatial evolution of multi-drug resistance. In this study, we propose a reaction-diffusion system that describes the multi-drug evolution of bacteria, based on a rescaling approach (Gjini and Wood, 2021). We show how the resistance to drugs in space, and the consequent adaptation of growth rate is governed by a Price equation with diffusion. The covariance terms in this equation integrate features of drug interactions and collateral resistances or sensitivities to the drugs. We study spatial versions of the model where the distribution of drugs is homogeneous across space, and where the drugs vary environmentally in a piecewise-constant, linear and nonlinear manner. Applying concepts from perturbation theory and reaction-diffusion equations, we propose an analytical characterization ofaverage mutant fitnessin the spatial system based on the principal eigenvalue of our linear problem. This enables an accurate translation from drug spatial gradients and mutant antibiotic susceptibility traits, to the relative advantage of each mutant across the environment. Such a mathematical understanding allows to predict the precise outcomes of selection over space, ultimately from the fundamental balance between growth and movement traits, and their diversity in a population.
Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery
Authors: Warren Wesley C. , Rice Edward S. , Maggs X , Roback Emma , Keene Alex , Martin Fergal , Ogeh Denye , Haggerty Leanne , Carroll Rachel A. , McGaugh Suzanne , Rohner Nicolas 
Published: November 2023

AbstractThe ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra,Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique toA. mexicanus.When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
Vascularized Liver Tissue Embedded Bioprinting Utilizing GelMA/Nanoclay-based Composite hydrogels
Authors: Rezaei Nima Tabatabaei , Dixit Kartikeya , Kumar Hitendra , John Jacob , Natale Giovanniantonio , Park Simon S. , Kim Keekyoung 
Published: November 2023

AbstractAs the aging population grows, the need to regenerate non-self-repairing tissues becomes increasingly crucial for enhancing our quality of life. Tissue engineering offers a promising solution, particularly in recreating the intricate networks of blood vessels crucial for tissue vitality. These tissues rely on effective nutrient and oxygen circulation, with an optimal oxygen diffusion range of 100–200 µm. Yet, crafting vascularized in vitro tissues remains a significant challenge. This study addresses the challenge by using GelMA-based hydrogels as a photocrosslinkable support bath, a biocompatible and versatile choice for biological applications. To enhance the rheological properties for in vitro tissue engineering, Laponite (LPN) is introduced as a rheology modifier. The study optimizes the GelMA-LPN nanocomposite hydrogel composition, ensuring the desired physical, mechanical, and rheological properties, including recovery. The research also explores the biological implications, encapsulating liver cells within the nanocomposite hydrogel, and studying their behavior under perfusion conditions. This research presents a promising avenue for creating vascularized in vitro tissues, potentially advancing tissue engineering and regenerative medicine.
Unveiling the Burden of Drug-Induced Impulsivity: A Network Analysis of the FDA Adverse Event Reporting System
Authors: Fusaroli Michele , Polizzi Stefano , Menestrina Luca , Giunchi Valentina , Pellegrini Luca , Raschi Emanuel , Weintraub Daniel , Recanatini Maurizio , Castellani Gastone , De Ponti Fabrizio , Poluzzi Elisabetta 
Published: November 2023

AbstractIntroductionImpulsivity induced by dopaminergic agents, like pramipexole and aripiprazole, can lead to behavioral addictions impacting social functioning and quality of life of patients and families (e.g., resulting in unemployment, marital problems, anxiety). These secondary effects, interconnected in networks of signs and symptoms, are usually overlooked by clinical trials, not reported in package inserts, and neglected in clinical practice.ObjectiveThis study explores the syndromic burden of impulsivity induced by pramipexole and aripiprazole, pinpointing key symptoms for targeted mitigation.MethodsAn event-event Information Component (IC) on the FDA Adverse Event Reporting System (January 2004 – March 2022) identified the syndrome of events disproportionally co-reported with impulsivity, separately for pramipexole and aripiprazole. A greedy-modularity clustering on composite network analyses (PPMI, Ising, Φ) identified subsyndromes. Bayesian network modeling highlighted possible precipitating events.ResultsSuspected drug-induced impulsivity was documented in 7.49% pramipexole and 4.50% aripiprazole recipients. The highest IC concerned obsessive-compulsive disorder (reporting rate = 26.77%; IC median = 3.47, 95%CI = 3.33-3.57) and emotional distress (21.35%; 3.42, 3.26-3.54) for pramipexole, bankruptcy (10.58%; 4.43, 4.26-4.55) and divorce (7.59%; 4.38, 4.19-4.53) for aripiprazole. The network analysis identified delusional jealousy and dopamine dysregulation subsyndromes for pramipexole, obesity-hypoventilation and social issues for aripiprazole. The Bayesian network highlighted anxiety and economic problems as potentially precipitating events.ConclusionThe under-explored consequences of drug-induced impulsivity significantly burden patients and families. Network analyses, exploring syndromic reactions and potential precipitating events, complement traditional techniques and clinical judgment. Characterizing the secondary impact of reactions will support informed patient-centered decision-making.HighlightsDrug-induced impulsivity significantly impacts patients’ lives. Network analyses help characterize reactions as syndromes.We explore the impulsivity syndrome and subsyndromes resulting from pramipexole and aripiprazole.The manifestation of drug-induced impulsivity was different for the two drugs. Anxiety and economic problems bridge between other symptoms and could be important therapeutical targets.
Estimating Demand for Potential Disease modifying Therapies for Alzheimer’s Disease in the UK
Authors: Laurell Axel AS , Venkataraman Ashwin V , Schmidt Tatjana , Montagnese Marcella , Mueller Christoph , Stewart Robert , Lewis Jonathan , Mundell Clare , Isaacs Jeremy D , Krishnan Mani S , Barber Robert , Rittman Timothy , Underwood Benjamin R 
Published: November 2023

AbstractBackgroundPhase three trials of the monoclonal antibodies lecanemab and donanemab, which target brain amyloid, have reported statistically significant differences in clinical endpoints in early Alzheimer’s disease. These drugs are already in use in some countries and are going through the regulatory approval process for use in the UK. Concerns have been raised about the ability of healthcare systems, including those in the UK, to deliver these treatments considering the resources required for their administration and monitoring.AimTo estimate the scale of real-world demand for monoclonal antibodies for AD in the United Kingdom.MethodWe used anonymised patient record databases from two National Health Service trusts for the year 2019 to collect clinical, demographic, cognitive and neuroimaging data for these cohorts. Eligibility for treatment was assessed using the inclusion criteria from the clinical trials of donanemab and lecanemab with consideration given to diagnosis, cognitive performance, cerebrovascular disease, and willingness to receive treatment.ResultsWe examined the records of 82,386 people referred to services covering some 2.2 million people. After applying the trial criteria, we estimate that a maximum of 906 people per year would start treatment with monoclonal antibodies in the two services, equating to 30,200 people if extrapolated nationally.ConclusionsMonoclonal antibody treatments for AD are likely to present a significant challenge for healthcare services to deliver in terms of the neuroimaging and treatment delivery. The data provided here allows health services to understand the potential demand and plan accordingly.
Distinct Functions for Beta and Alpha Bursts in Gating of Human Working Memory
Authors: Liljefors Johan , Almeida Rita , Rane Gustaf , Lundström Johan N. , Herman Pawel , Lundqvist Mikael 
Published: November 2023

ABSTRACTMultiple neural mechanisms underlying gating to and from working memory (WM) have been proposed, with divergent results obtained in human and animal studies. Previous results from non-human primate studies suggest information encoding and retrieval is regulated by high-power bursts in the beta frequency range, whereas human studies suggest that alpha power in sensory regions filters out unwanted stimuli from entering WM. Discrepancies between studies, whether due to differences in analysis, species, or cortical regions, remain unexplained. We addressed this by performing similar single-trial burst analysis we earlier deployed on non-human primates on human whole-brain electrophysiological activity. Participants performed a sequential working memory task that allowed us to track the distinct electrophysiological activity patterns associated with neural processing of targets and distractors. Intriguingly, our results reconcile earlier findings by demonstrating that both alpha and beta bursts are involved in the filtering and control of WM items, but with region and task-specific differences between the two rhythms. Occipital beta burst patterns regulate the transition from sensory processing to WM retention whereas prefrontal and parietal beta bursts track sequence order and proactively suppress retained information prior to upcoming target encoding. Occipital alpha bursts instead suppress unwanted sensory stimuli during their presentation. These results suggest that human working memory is regulated by multiple neural mechanisms that operate in different cortical regions and serve distinct computational roles.
Pneumococcal competence, a populational health sensor driving multilevel heterogeneity in response to antibiotics
Authors: Prudhomme Marc , Johnston Calum H. G. , Soulet Anne-Lise , De Lemos David , Campo Nathalie , Polard Patrice 
Published: November 2023

AbstractCompetence for natural transformation is a central driver of genetic diversity in bacteria. In the human pathogenStreptococcus pneumoniae, competence exhibits a populational character mediated by the stress-induced ComABCDE quorum-sensing (QS) system. Here, we explore how this cell-to-cell communication mechanism proceeds and the functional properties acquired by competent cells grown under lethal stress. We show that populational competence development depends on self-induced cells stochastically emerging in response to stresses, including antibiotics. Competence is demonstrated to propagate through the population from a low threshold density of self-induced cells, defining a biphasic Self-Induction and Propagation (SI&P) QS mechanism. We also reveal that a competent population displays either increased sensitivity or improved tolerance to lethal doses of antibiotics, dependent in the latter case on the competence-induced ComM division inhibitor. Remarkably, these surviving competent cells also display an altered transformation potential. Thus, the unveiled SI&P QS mechanism shapes pneumococcal competence as a health sensor of the clonal population, promoting a bet-hedging strategy that both responds to and drives cells towards heterogeneity.
Cardiac recovery from pressure overload is not altered by thyroid hormone status in old mice
Authors: Kerp Helena , Gassen Janina , Grund Susanne Camilla , Hönes Georg Sebastian , Dörr Stefanie , Mittag Jens , Härting Nina , Kaiser Frank , Moeller Lars Christian , Lorenz Kristina , Führer Dagmar 
Published: November 2023

1AbstractThyroid hormones (TH) are known to have various effects on the cardiovascular system. However, the impact of TH levels on preexisting cardiac diseases are still unclear. Pressure overload due to arterial hypertension or aortic stenosis and aging are major risk factors for the development of structural and functional abnormalities and subsequent heart failure.Here, we assessed the sensitivity to altered TH levels in aged mice with maladaptive cardiac hypertrophy and cardiac dysfunction induced by transverse aortic constriction (TAC). Mice at the age of 12 months underwent TAC and after induction of left ventricular pressure overload, received T4 or anti-thyroid medication in the drinking water over the course of 4 weeks.T4 excess or deprivation in older mice had no or only very little impact on cardiac function (fractional shortening), cardiac remodeling (cardiac wall thickness, heart weight, cardiomyocyte size, apoptosis and interstitial fibrosis) and mortality. This is surprising, because T4 excess or deprivation had significantly changed the outcome after TAC in young 8-week-old mice.In summary, our study shows that low and high TH availability have little impact on cardiac function and remodeling in older mice with preexisting pressure induced cardiac damage. This suggests that even though cardiovascular risk is increasing with age, the response to TH stress may be dampened in certain conditions.