bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Cohort Study of Post-Acute Covid-19 Infection with a Nested, Randomized Controlled Trial of Ivabradine for Those With Postural Orthostatic Tachycardia Syndrome (The COVIVA Study)
Authors: Saunders David , Arnold Thomas B. , Lavender Jason M. , Bi Daoqin , Alcover Karl , Hellwig Lydia D. , Leazer Sahar T , Mohammed Roshila , Markos Bethelhem , Perera Kanchana , Shaw Dutchabong , Kobi Priscilla , Evans Martin , Mains Autumn , Tanofsky-Kraff Marian , Goguet Emilie , Mitre Edward , Pratt Kathleen P , Dalgard Clifton L , Haigney Mark C 
Published: April 2023

AbstractBackground:Significant clinical similarities have been observed between the recently Described ‘Long-Haul’ COVID-19 (LHC) syndrome, Postural Orthostatic Tachycardia Syndrome (POTS) and Inappropriate Sinus Tachycardia (IST). Shared symptoms include light-headedness, palpitations, tremulousness, generalized weakness, blurred vision, chest pain, dyspnea, “brain-fog”, and fatigue. Ivabradine is a selective sinoatrial node blocker FDA-approved for management of tachycardia associated with stable angina and heart failure not fully managed by beta blockers. In our study we aim to identify risk factors underlying LHC, as well as the effectiveness of ivabradine in controlling heart rate dysregulations and POTS/IST related symptoms.Methods/Design:A detailed prospective phenotypic evaluation combined with multi-omic analysis of 200 LHC volunteers will be conducted to identify risk factors for autonomic dysfunction. A comparator group of 50 volunteers with documented COVID-19 but without LHC will be enrolled to better understand the risk factors for LHC and autonomic dysfunction. Those in the cohort who meet diagnostic criteria for POTS or IST will be included in a nested prospective, randomized, placebo-controlled trial to assess the impact of ivabradine on symptoms and heart rate, assessed non-invasively based on physiologic response and ambulatory electrocardiogram. Additionally, studies on catecholamine production, mast cell and basophil degranulation, inflammatory biomarkers, and indicators of metabolic dysfunction will be measured to potentially provide molecular classification and mechanistic insights.Discussion:Optimal therapies for dysautonomia, particularly associated with LHC, have yet to be defined. In the present study, ivabradine, one of numerous proposed interventions, will be systematically evaluated for therapeutic potential in LHC-associated POTS and IST. Additionally, this study will further refine the characteristics of the LHC-associated POTS/IST phenotype, genotype and transcriptional profile, including immunologic and multi-omic analysis of persistent immune activation and dysregulation. The study will also explore and identify potential endotheliopathy and abnormalities of the clotting cascade.Trial registration:ClinicalTrials.gov, ID:NCT05481177Registered on 29 July 2022.
Genome structure and population genomics of the canine heartwormDirofilaria immitis
Authors: Gandasegui Javier , Power Rosemonde I. , Curry Emily , Lau Daisy Ching-Wai , O’Neill Connor M. , Wolstenholme Adrian , Prichard Roger , Šlapeta Jan , Doyle Stephen R. 
Published: April 2023

AbstractThe heartworm,Dirofilaria immitis, is a filarial parasitic nematode responsible for significant morbidity and mortality in wild and domesticated canids. Resistance to macrocyclic lactone drug prevention represents a significant threat to parasite control and has prompted investigations to understand the genetic determinants of resistance. This study aimed to improve the genomic resources ofD. immitisto enable a more precise understanding of how genetic variation is distributed within and between parasite populations worldwide, which will inform the likelihood and rate by which parasites, and in turn, resistant alleles, might spread. We have guided the scaffolding of a recently published genome assembly forD. immitis(ICBAS_JMDir_1.0) using the chromosomal-scale reference genomes ofBrugia malayiandOnchocerca volvulus, resulting in an 89.5 Mb assembly composed of four autosomal- and one X-linked chromosomal-scale scaffolds representing 99.7% of the genome. Publicly available and new whole-genome sequencing data from 32D. immitissamples from Australia, Italy and the USA were assessed using principal component analysis, nucleotide diversity (Pi) and absolute genetic divergence (Dxy) to characterise the global genetic structure and measure within- and between population diversity. These population genetic analyses revealed broad-scale genetic structure among globally diverse samples and differences in genetic diversity between populations; however, fine-scale subpopulation analysis was limited and biased by differences between sample types. Finally, we mapped SNPs previously associated with macrocyclic lactone resistance in the new genome assembly, revealing physical linkage of high-priority variants on chromosome 3, and determined their frequency in the studied populations. This new chromosomal assembly forD. immitisnow allows for a more precise investigation of selection on genome-wide genetic variation and will enhance our understanding of parasite transmission and the spread of genetic variants responsible for resistance to treatment.
Local Monomer Levels and Established Filaments Potentiate Non-Muscle Myosin 2 Assembly
Authors: Quintanilla Melissa A. , Patel Hiral , Wu Huini , Sochacki Kem A. , Akamatsu Matthew , Rotty Jeremy D. , Korobova Farida , Bear James E. , Taraska Justin W. , Oakes Patrick W. , Beach Jordan R. 
Published: April 2023

The ability to dynamically assemble contractile networks is required throughout cell physiology, yet the biophysical mechanisms regulating non-muscle myosin 2 filament assembly in living cells are lacking. Here we use a suite of dynamic, quantitative imaging approaches to identify deterministic factors that drive myosin filament appearance and amplification. We find that actin dynamics regulate myosin assembly, but that the actin architecture plays a minimal direct role. Instead, remodeling of actin networks modulates the local myosin monomer levels and facilitates assembly through myosin:myosin driven interactions. Using optogenetically controlled myosin, we demonstrate that locally concentrating myosin is sufficient to both form filaments and jump-start filament amplification and partitioning. By counting myosin monomers within filaments, we demonstrate a myosin-facilitated assembly process that establishes sub-resolution filament stacks prior to partitioning into clusters that feed higher-order networks.Together these findings establish the biophysical mechanisms regulating the assembly of non-muscle contractile structures that are ubiquitous throughout cell biology.
IPMK modulates FFA-induced insulin resistance in primary mouse hepatocytes
Authors: Jung Ik-Rak , Ahima Rexford S. , Kim Sangwon F. 
Published: April 2023

AbstractInsulin resistance is a critical mediator of the development of non-alcoholic fatty liver disease (NAFLD). An excess influx of fatty acids to the liver is thought to be a pathogenic cause of insulin resistance and the development of non-alcoholic fatty liver disease (NAFLD). Although elevated levels of free fatty acids (FFA) in plasma contribute to inducing insulin resistance and NAFLD, the molecular mechanism is not completely understood. This study aimed to determine whether inositol polyphosphate multikinase (IPMK), a regulator of insulin signaling, plays any role in FFA-induced insulin resistance in primary hepatocytes. Here, we show that excess FFA decreased IPMK expression, and blockade of IPMK decrease attenuated the FFA-induced suppression of Akt phosphorylation in primary mouse hepatocytes (PMH). Moreover, overexpression of IPMK prevented the FFA-induced suppression of Akt phosphorylation by insulin, while knockout of IPMK exacerbated insulin resistance in PMH. In addition, treatment with MG132, a proteasomal inhibitor, inhibits FFA-induced decrease in IPMK expression and Akt phosphorylation in PMH. Furthermore, treatment with the antioxidant N-Acetyl Cysteine (NAC) significantly attenuated the FFA-induced reduction of IPMK and restored FFA-induced insulin resistance in PMH. In conclusion, our findings suggest that excess FFA reduces IPMK expression and contributes to the FFA-induced decrease in Akt phosphorylation in PMH, leading to insulin resistance. Our study highlights IPMK as a potential therapeutic target for preventing insulin resistance and NAFLD.
Foxc1andFoxc2function in osteochondral progenitors for the progression through chondrocyte hypertrophy and mineralization of the primary ossification center
Authors: Almubarak Asra , Zhang Qiuwan , Zhang Cheng-Hai , Lassar Andrew B. , Kume Tsutomu , Berry Fred B 
Published: April 2023

AbstractThe forkhead box transcription factor genesFoxc1andFoxc2are expressed in the condensing mesenchyme of the developing skeleton prior to the onset of chondrocyte differentiation. To determine the roles of these transcription factors in limb development we deleted bothFoxc1andFoxc2in lateral plate mesoderm using the Prx1-cre mouse line. Resulting compound homozygous mice died shortly after birth with exencephaly, and malformations to this sternum and limb skeleton. Notably distal limb structures were preferentially affected, with the autopods displaying reduced or absent mineralization. The radius and tibia bowed and the ulna and fibula were reduced to an unmineralized rudimentary structure. Molecular analysis revealed reduced expression of Ihh leading to reduced proliferation and delayed chondrocyte hypertrophy at E14.5. At later ages, Prx1-cre;Foxc1Δ/Δ;Foxc2Δ/Δembryos exhibited restored Ihh expression and an expanded COLX-positive hypertrophic chondrocyte region, indicating a delayed exit and impaired remodeling of the hypertrophic chondrocytes. Osteoblast differentiation and mineralization were disrupted at the osteochondral junction and in the primary ossification center (POC). Levels of OSTEOPONTIN were elevated in the POC of compound homozygous mutants, while expression of Phex was reduced, indicating that impaired OPN processing by PHEX may underlie the mineralization defect we observe. Together our findings suggest that Foxc1 and Foxc2 act at different stages of endochondral ossification. Initially these genes act during the onset of chondrogenesis leading to the formation of hypertrophic chondrocytes. At later stages Foxc1 and Foxc2 are required for remodeling of HC and for Phex expression required for mineralization of the POC.
NextPolish2:a repeat-aware polishing tool for genomes assembled using HiFi long reads
Authors: Hu Jiang , Wang Zhuo , Liang Fan , Liu Shanlin , Ye Kai , Wang De-Peng 
Published: April 2023

AbstractThe high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies, but these assemblies still contain some base-level errors, particularly within the error-prone regions of HiFi long reads. However, existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here we describe an upgraded genome polishing tool - NextPolish2, which can fix base errors remaining in those “highly accurate” genomes assembled from HiFi long reads without introducing excess overcorrections and haplotype switch errors. We believe NextPolish2 has a great significance to further improve the accuracy of Telomere-to-Telomere (T2T) genomes. NextPolish2 is freely available athttps://github.com/Nextomics/NextPolish2.
A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads
Authors: Sugishita Hiroki , Hojo Kazunori , Hayashi Tetsutaro , Nikaido Itoshi , Gotoh Yukiko 
Published: April 2023

AbstractMagnetic microbeads are small iron oxide nanoparticles coated with a bioaffinity material that selectively binds to specific biomolecules of interest, enabling their capture and isolation from complex biological samples. Magnetic microbeads are widely used for purification of specific biomolecules in various experiments in molecular biology. However, current methods of manual pipetting to separate supernatants from magnetic microbeads are often inefficient- time-consuming, labor intensive and inaccurate. Furthermore, the use of pipetting robots and liquid handlers specifically designed for multi-well plates can be a cost-prohibitive approach due to the high cost of equipment and disposable supplies. Here, we developed a centrifugation-based method for high-throughput separation of supernatant from magnetic microbeads. To facilitate the centrifugal separation process, we used the 384 transfer plate™ (Watson, Japan) and a magnetic stand equipped with a 384-well magnetic stand, allowing easy handling of several hundred samples and rapid separation of supernatant from magnetic microbeads. The centrifugal force was used to drive the separation of target molecules from the magnetic microbeads, and sample were successfully separated with relatively high recovery rates. Thus, this technology provides a simple, rapid, and cost- and labor-effective biomolecule separation method with potential applications in various fields, including molecular biology, clinical diagnostics, and biotechnology, and is a valuable addition to the existing toolbox of biomolecule separation methods.
An unconventional gatekeeper mutation sensitizes inositol hexakisphosphate kinases to an allosteric inhibitor
Authors: Aguirre Tim , Dornan Gillian L. , Hostachy Sarah , Neuenschwander Martin , Seyffarth Carola , Haucke Volker , Schütz Anja , von Kries Jens P. , Fiedler Dorothea 
Published: April 2023

AbstractInositol hexakisphosphate kinases (IP6Ks) are emerging as relevant pharmacological targets because a multitude of disease-related phenotypes has been associated with their function. While the development of potent IP6K inhibitors is gaining momentum, a pharmacological tool to distinguish the mammalian isozymes is still lacking. Here, we implemented an analog-sensitive approach for IP6Ks and performed a high-throughput screen to identify suitable lead compounds. The most promising hit, FMP-201300, exhibited high potency and selectivity towards the unique valine gatekeeper mutants of IP6K1 and IP6K2, compared to the respective wild-type kinases. Biochemical validation experiments revealed an allosteric mechanism of action that was corroborated by HDX-MS measurements. The latter analysis suggested that displacement of theαC helix, caused by the gatekeeper mutation, facilitates the binding of FMP-201300 to an allosteric pocket adjacent to the ATP binding site. FMP-201300 therefore serves as a valuable springboard for the further development of compounds that can selectively target the three mammalian IP6Ks; either as analog-sensitive kinase inhibitors or as an allosteric lead compound for the wild-type kinases.
Shortwave infrared (SWIR) fluorescence imaging of peripheral organs in awake and freely moving mice
Authors: Arús Bernardo A. , Cosco Emily D. , Yiu Joycelyn , Balba Ilaria , Bischof Thomas S. , Sletten Ellen M. , Bruns Oliver T. 
Published: April 2023

AbstractExtracting biological information from awake and unrestrained mice is imperative to in vivo basic and pre-clinical research. Accordingly, imaging methods which preclude invasiveness, anesthesia, and/or physical restraint enable more physiologically relevant biological data extraction by eliminating these extrinsic confounders. In this article we discuss the recent development of shortwave infrared (SWIR) fluorescent imaging to visualize peripheral organs in freely-behaving mice, as well as propose potential applications of this imaging modality in the neurosciences.
Ketone Bodies in Right Ventricular Failure: A Unique Therapeutic Opportunity
Authors: Blake Madelyn , Puchalska Patrycja , Kazmirczak Felipe , Thenappan Thenappan , Crawford Peter A. , Prins Kurt W. 
Published: April 2023

Introductory ParagraphKetone bodies are pleotropic metabolites that play important roles in multiple biological processes ranging from bioenergetics to inflammation regulation via suppression of the NLRP3 inflammasome, and epigenetic modifications. Ketone bodies are elevated in left ventricular failure (LVF) and multiple approaches that increase ketone concentrations exert advantageous cardiac effects in rodents and humans. However, the relationships between ketone bodies and right ventricular failure (RVF) are relatively unexplored. Moreover, the cardioprotective properties of ketones in preclinical RVF are unknown. Here, we show a compensatory ketosis is absent in pulmonary arterial hypertension (PAH) patients with RVF. In the monocrotaline (MCT) rat model of PAH-mediated RVF, a dietary-induced ketosis improves RV function, suppresses NLRP3 inflammasome activation, and combats RV fibrosis. The summation of these data suggest ketogenic therapies may be particularly efficacious in RVF, and therefore future studies evaluating ketogenic interventions in human RVF are warranted.
TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets
Authors: Neugroschl Atara , Catrina Irina E. 
Published: April 2023

AbstractNucleic acid probes are valuable tools in biology and chemistry and are indispensable for PCR amplification of DNA, RNA quantification and visualization, and downregulation of gene expression. Recently, triplex forming oligonucleotides (TFO) have received increased attention due to their improved selectivity and sensitivity in recognizing purine-rich double-stranded RNA regions at physiological pH by incorporating backbone and base modifications. For example, triplex forming peptide nucleic acid (PNA) oligomers have been used for imaging structured RNA in cells and inhibiting influenza A replication. Although a handful of programs are available to identify triplex target sites (TTS) in DNA, none are available that find such regions in structured RNAs. Here, we describeTFOFinder, a Python program that facilitates the identification of intramolecular purine-only RNA duplexes that are amenable to forming parallel triple helices (pyrimidine/purine/pyrimidine). We performed genome- and transcriptome-wide analyses of TTS inDrosophila melanogasterand found that only 0.3% (123) of total unique transcripts (35,642) show the potential of forming 12-purine long triplex forming sites that contain at least one guanine. Using minimization algorithms, we predicted the secondary structure(s) of these transcripts, and usingTFOFinder, we found that 97 (79%) of the identified 123 transcripts are predicted to fold to form at least one TTS for parallel triple helix formation. The number of transcripts with potential purine TTS increases when the strict search conditions are relaxed by decreasing the length of the probes or by allowing up to two pyrimidine inversions or 1-nucleotide bulge in the target site. These results are encouraging for the use of modified triplex forming probes for live imaging of endogenous structured RNA targets, such as pre-miRNAs, and inhibition of target-specific translation and viral replication.
The dual role of a highly structured RNA (the S fragment) in the replication of foot-and-mouth disease virus
Authors: Ward Joseph C. , Lasecka-Dykes Lidia , Dobson Samuel J. , Gold Sarah , Kingston Natalie J. , Herod Morgan R. , King Donald P. , Tuthill Tobias J. , Rowlands David J. , Stonehouse Nicola J. 
Published: April 2023

AbstractSecondary and tertiary RNA structures play key roles in genome replication of single stranded positive sense RNA viruses. Complex, functional structures are particularly abundant in the untranslated regions of picornaviruses, where they are involved in initiation of translation, priming of new strand synthesis and genome circularisation. The 5′ UTR of foot-and-mouth disease virus (FMDV) is predicted to include ac.360 nucleotide-long stem-loop, termed the short (S) fragment. This structure is highly conserved and essential for viral replication, but the precise function(s) are unclear. Here, we used selective 2′ hydroxyl acetylation analysed by primer extension (SHAPE) to experimentally-determine aspects of the structure, alongside comparative genomic analyses to confirm structure conservation from a wide range of field isolates. To examine its role in virus replication, we introduced a series of deletions to the distal and proximal regions of the stem loop. These truncations affected genome replication in a size-dependent and, in some cases, host cell-dependent manner. Furthermore, during passage of viruses incorporating the largest tolerated deletion from the proximal region of the S fragment stem loop, an additional mutation was selected in the viral RNA-dependent RNA polymerase, 3Dpol.These data suggest that the S fragment and 3Dpolinteract in the formation of the FMDV replication complex.
Transcriptomic Analysis of the Ocular Posterior Segment Completes a Cell Atlas of the Human Eye
Authors: Monavarfeshani Aboozar , Yan Wenjun , Pappas Christian , Odenigbo Kenechukwu A. , He Zhigang , Segrè Ayellet V. , Zyl Tavé van , Hageman Gregory S. , Sanes Joshua R. 
Published: April 2023

ABSTRACTAlthough the visual system extends through the brain, most vision loss originates from defects in the eye. Its central element is the neural retina, which senses light, processes visual signals, and transmits them to the rest of the brain through the optic nerve (ON). Surrounding the retina are numerous other structures, conventionally divided into anterior and posterior segments. Here we used high-throughput single nucleus RNA sequencing (snRNA-seq) to classify and characterize cells in the extraretinal components of the posterior segment: ON, optic nerve head (ONH), peripheral sclera, peripapillary sclera (PPS), choroid, and retinal pigment epithelium (RPE). Defects in each of these tissues are associated with blinding diseases – for example, glaucoma (ONH and PPS), optic neuritis (ON), retinitis pigmentosa (RPE), and age-related macular degeneration (RPE and choroid). From ∼151,000 single nuclei, we identified 37 transcriptomically distinct cell types, including multiple types of astrocytes, oligodendrocytes, fibroblasts, and vascular endothelial cells. Our analyses revealed a differential distribution of many cell types among distinct structures. Together with our previous analyses of the anterior segment and retina, the new data complete a “Version 1” cell atlas of the human eye. We used this atlas to map the expression of >180 genes associated with the risk of developing glaucoma, which is known to involve ocular tissues in both anterior and posterior segments as well as neural retina. Similar methods can be used to investigate numerous additional ocular diseases, many of which are currently untreatable.