bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical Method Development for Evaluation of Pharmacokinetics and Tissue Distribution of Thiourea-Based Antivirals through nLC/MS-MS
Authors: Kumar Jitendra , Tyagi Purnima , Yadav Manisha , Sharma Deepti , Maras Jaswinder Singh , Kumar Vijay 
Published: July 2023

AbstractThiourea-based antivirals are organosulfur chemical compounds. Due to their various medicinal uses, including antiviral, antioxidant, and anticancer properties, they are becoming more popular. In this study, pharmacokinetics, Metabolism, bioavailability, and distribution of thiourea derivatives to organs of rats. Thiourea derivatives, namely DSA-00, DSA-02, and DSA-09, exhibit characteristics similar to those of conventional drugs when evaluated in terms of pharmacokinetics, drug-likeness, and medicinal chemistry throughin-silico analysis. Then a simple and sensitive analytical method was developed for quantified DSA-00, DSA-02, and DSA-09, using prednisolone as an internal standard (IS) and nano liquid chromatography tandem mass spectrometry (nLC-MS/MS). The plasma and tissue samples were preprocessing with acetonitrile before chromatographic separation by C18 column with isocratic elution using a mobile phase of water-methanol (30:70, v/v) at a flow rate of 0.6 mL/min. A triplequadrupole tandem mass spectrometer in multiple-reaction monitoring (MRM) scanning via an electrospray ionization (ESI) source functioning in negative and positive mode detection. For DSA-00, DSA-02, DSA-09 and, internal standard the optimized mass transition ion-pairs (m/z) for quantification were 297.2, 311.2, 309.09, and 361.19 respectively. Each analytic run required only 15 minutes between injections. The calibration curve for thiourea derivatives showed good linear regression coefficient (R2>.99) over a range of 1.00-10000 pg/mL except DSA-09. The lower limit of quantification (LLOQ) was 1.00 ng/mL. The intra- and inter-day precisions were no more than 10.8%, and relative errors (RE) ranged from 0.5 to 5.98%. The validated method was effectively used to explore the pharmacokinetics of orally administrative thiourea derivatives in rats.
Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power
Authors: LaPierre Nathan , Pimentel Harold 
Published: July 2023

AbstractA core problem in genetics is eQTL mapping, in which genetic variants associated with changes in expression of genes are identified. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual isoforms from the same gene and then performing linear regression between SNPs and this aggregated gene expression level. However, SNPs may regulate isoforms from the same gene in different directions due to alternative splicing, or only regulate the expression level of one isoform, causing this approach to lose power. In this study, we provide a systematic evaluation of methods for accounting for individual isoform expression levels based on generative isoform expression heritability models and real data. Over a range of conditions, we show that these approaches substantially increase the power to map eQTLs in both simulations and commonly analyzed large data sets. We identify settings in which different approaches yield an inflated number of false discoveries or lose power. In particular, we show that calling an eGene if there is a significant association between a SNP and any isoform fails to control False Discovery Rate, even when applying standard False Discovery Rate correction. We show that similar trends are observed in real data from the GEUVADIS and GTEx studies, suggesting the possibility that similar effects are present in these consortia.
Using Drosophila to model a variant of unknown significance in the human cardiogenic geneNkx2.5
Authors: Lovato TyAnna L. , Blotz Brenna , Bileckyj Cayleen , Johnston Christopher A. , Cripps Richard M. 
Published: July 2023

AbstractSequencing of human genome samples has unearthed genetic variants for which functional testing is necessary to validate their clinical significance. We used the Drosophila system to analyze a variant of unknown significance in the human congenital heart disease gene,Nkx2.5. We generated an R321N allele of theNkx2.5orthologtinman(tin) to model a human K158N variant and tested its function in vitro and in vivo. The R321N Tin isoform bound poorly to DNA in vitro and was deficient in activating a Tin-dependent enhancer in tissue culture. Mutant Tin also showed a significantly reduced interaction with a Drosophila Tbox cardiac factor named Dorsocross1. We generated atinR321Nallele using CRISPR/Cas9, for which homozygotes were viable and had normal heart specification, but showed defects in the differentiation of the adult heart that were exacerbated by further loss oftinfunction. We conclude that the human K158N mutation is likely pathogenic through causing both a deficiency in DNA binding and a reduced ability to interact with a cardiac cofactor, and that cardiac defects might arise later in development or adult life.
Reprogramming human B cells with custom heavy chain antibodies
Authors: Rogers Geoffrey L. , Huang Chun , Mathur Atishay , Huang Xiaoli , Chen Hsu-Yu , Stanten Kalya , Morales Heidy , Chang Chan-Hua , Kezirian Eric J. , Cannon Paula M. 
Published: July 2023

AbstractWe describe a genome editing strategy to reprogram the immunoglobulin heavy chain (IgH) locus of human B cells to express custom molecules that respond to immunization. These heavy chain antibodies (HCAbs) comprise a custom antigen-recognition domain linked to an Fc domain derived from the IgH locus and can be differentially spliced to express either B cell receptor (BCR) or secreted antibody isoforms. The HCAb editing platform is highly flexible, supporting antigen-binding domains based on both antibody and non-antibody components, and also allowing alterations in the Fc domain. Using HIV Env protein as a model antigen, we show that B cells edited to express anti-Env HCAbs support the regulated expression of both BCRs and antibodies, and respond to Env antigen in a tonsil organoid model of immunization. In this way, human B cells can be reprogrammed to produce customized therapeutic molecules with the potential forin vivoamplification.
Applying high-resolution spatial transcriptomics to characterize the amyloid plaque cell niche in Alzheimer’s Disease
Authors: Mallach Anna , Zielonka Magdalena , van Lieshout Veerle , An Yanru , Khoo Jia Hui , Vanheusden Marisa , Chen Wei-Ting , Moechars Daan , Arancibia-Carcamo I. Lorena , Fiers Mark , De Strooper Bart 
Published: July 2023

AbstractThe amyloid plaque cell niche is a pivotal hallmark of Alzheimer’s disease (AD). Where early spatial transcriptomics (ST) technologies have provided valuable information on transcriptomic alterations in the small tissue domains overlaying with amyloid plaques, they lacked cellular resolution. Here we compare two novel high-resolution ST platforms, CosMx and Stereo-seq, in their ability to characterize the cellular response in the amyloid plaque niche in an AD mouse model. Combining the results from both techniques empowered us to survey the highly variable microglial-astrocytic response across the amyloid plaque micro-environment and provided a first insight into how these responses could relate to neuronal transcriptomic alterations. This pilot study demonstrates the great potential of high-resolution ST, while simultaneously highlighting limitations that, when addressed, will unleash the full power of these techniques to map the progression of molecular and cellular changes in the brains of AD patients.
Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome
Authors: Wang Wenliang , Hariharan Manoj , Ding Wubin , Bartlett Anna , Barragan Cesar , Castanon Rosa , Rothenberg Vince , Song Haili , Nery Joseph , Aldridge Andrew , Altshul Jordan , Kenworthy Mia , Liu Hanqing , Tian Wei , Zhou Jingtian , Zeng Qiurui , Chen Huaming , Wei Bei , Gündüz Irem B. , Norell Todd , Broderick Timothy J , McClain Micah T. , Satterwhite Lisa L. , Burke Thomas W. , Petzold Elizabeth A. , Shen Xiling , Woods Christopher W. , Fowler Vance G. , Ruffin Felicia , Panuwet Parinya , Barr Dana B. , Beare Jennifer L. , Smith Anthony K. , Spurbeck Rachel R. , Vangeti Sindhu , Ramos Irene , Nudelman German , Sealfon Stuart C. , Castellino Flora , Walley Anna Maria , Evans Thomas , Müller Fabian , Greenleaf William J. , Ecker Joseph R. 
Published: July 2023

AbstractThe epigenomic landscape of human immune cells is dynamically shaped by both genetic factors and environmental exposures. However, the relative contributions of these elements are still not fully understood. In this study, we employed single-nucleus methylation sequencing and ATAC-seq to systematically explore how pathogen and chemical exposures, along with genetic variation, influence the immune cell epigenome. We identified distinct exposure-associated differentially methylated regions (eDMRs) corresponding to each exposure, revealing how environmental factors remodel the methylome, alter immune cell states, and affect transcription factor binding. Furthermore, we observed a significant correlation between changes in DNA methylation and chromatin accessibility, underscoring the coordinated response of the epigenome. We also uncovered genotype-associated DMRs (gDMRs), demonstrating that while eDMRs are enriched in regulatory regions, gDMRs are preferentially located in gene body marks, suggesting that exposures and genetic factors exert differential regulatory control. Notably, disease-associated SNPs were frequently colocalized with meQTLs, providing new cell-type-specific insights into the genetic basis of disease. Our findings underscore the intricate interplay between genetic and environmental factors in sculpting the immune cell epigenome, offering a deeper understanding of how immune cell function is regulated in health and disease.
Laminin γ1-dependent basement membranes are instrumental to ensure proper olfactory placode shape, position and boundary with the brain, as well as olfactory axon development
Authors: Tignard P , Pottin K , Geeverding A , Doulazmi M , Cabrera M , Fouquet C , Liffran M , Fouchard J , Rosello M , Albadri S , Del Bene F , Trembleau A , Breau MA 
Published: July 2023

AbstractDespite recent progress, the complex roles played by the extracellular matrix in development and disease are still far from being fully understood. Here, we took advantage of the zebrafishslymutation which affects Laminin γ1, a major component of basement membranes, to explore its role in the development of the olfactory system. Following a detailed characterisation of Laminin distribution in the developing olfactory circuit, we analysed basement membrane integrity, olfactory placode and brain morphogenesis, and olfactory axon development inslymutants, using a combination of immunochemistry, electron microscopy and quantitative live imaging of cell movements and axon behaviours. Our results point to an original and dual contribution of Laminin γ1-dependent basement membranes in organising the border between the olfactory placode and the adjacent brain: they maintain placode shape and position in the face of major brain morphogenetic movements, they establish a robust physical barrier between the two tissues while at the same time allowing the local entry of the sensory axons into the brain and their navigation towards the olfactory bulb. This work thus identifies key roles of Laminin γ1-dependent basement membranes in neuronal tissue morphogenesis and axon developmentin vivo.
The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins
Authors: Nixon Charlotte , Lim Shion A. , Sternke Matt , Barrick Doug , Harms Mike , Marqusee Susan 
Published: July 2023

AbstractA protein sequence encodes its energy landscape - all the accessible conformations, energetics, and dynamics. The evolutionary relationship between sequence and landscape can be probed phylogenetically by compiling a multiple sequence alignment of homologous sequences and generating common ancestors via Ancestral Sequence Reconstruction or a consensus protein containing the most common amino acid at each position. Both ancestral and consensus proteins are often more stable than their extant homologs - questioning the differences and suggesting that both approaches serve as general methods to engineer thermostability. We used the Ribonuclease H family to compare these approaches and evaluate how the evolutionary relationship of the input sequences affects the properties of the resulting consensus protein. While the overall consensus protein is structured and active, it neither shows properties of a well-folded protein nor has enhanced stability. In contrast, the consensus protein derived from a phylogenetically-restricted region is significantly more stable and cooperatively folded, suggesting that cooperativity may be encoded by different mechanisms in separate clades and lost when too many diverse clades are combined to generate a consensus protein. To explore this, we compared pairwise covariance scores using a Potts formalism as well as higher-order couplings using singular value decomposition (SVD). We find the SVD coordinates of a stable consensus sequence are close to coordinates of the analogous ancestor sequence and its descendants, whereas the unstable consensus sequences are outliers in SVD space.
Uncovering the Vital Role of Lipid Droplets in Coronavirus Replication: A Novel Insight Arising from the Biological Activity of 2-Bromopalmitate
Authors: Liu Dongxiao , Cruz-cosme Ruth , Leibowitz Julian , Wu Yong , Tang Qiyi 
Published: July 2023

ABSTRACTThe emergence of viral infections with global impact highlights the urgent need for broad-spectrum antivirals. In this study, we evaluated the effect of palmitoylation inhibitors [2-bromopalmitate (2-BP), cerulenin, and 2-fluoro palmitic acid (2-FPA)] and the enhancer palmostatin B on the replication of human coronaviruses (hCoV-229E, hCoV-Oc43) and murine hepatitis virus (MHV-A59) at non-cytotoxic concentrations. The results demonstrated that 2-BP strongly suppressed MHV-A59 replication, while cerulenin and 2-FPA only moderately inhibited viral replication. Palmostatin B significantly enhanced viral replication. Notably, 2-BP exhibited superior efficacy. Interestingly, palmostatin B failed to rescue the inhibitory effects of 2-BP but effectively rescued cerulenin and 2-FPA, suggesting additional biological activities of 2-BP beyond palmitoylation inhibition. Furthermore, we discovered that 2-BP specifically disrupted lipid droplets (LDs), and this LD disruption was correlated with viral replication inhibition. Based on our findings, we conclude that the inhibitory effects of 2-BP on viral replication primarily stem from LD disruption rather than palmitoylation inhibition. Therefore, we revealed the crucial role of LDs in the viral replication. Our study provides insights into the development of wide-spectrum antiviral strategies.
Meta-analysis of macrophage nanoparticle targeting across blood and solid tumors using an eLDA Topic modeling Machine Learning approach
Authors: Brown Chloe , Bilynsky Colette , Gainey Melanie , Young Sarah , Kitchin John , Wayne Elizabeth 
Published: July 2023

AbstractThe role of macrophages in regulating the tumor microenvironment has spurned the exponential generation of nanoparticle targeting technologies. With the large amount of literature and the speed at which it is generated it is difficult to remain current with the most up-to-date literature. In this study we performed a topic modeling analysis of the most common usages of nanoparticle targeting of macrophages in solid tumors. The data spans 20 years of literature, providing an extensive meta-analysis of the nanoparticle strategies. Our topic model found 6 distinct topics: Immune and TAMs, Nanoparticles, Imaging, Gene Delivery and Exosomes, Vaccines, and Multi-modal Therapies. We also found distinct nanoparticle usage, tumor types, and therapeutic trends across these topics. Moreover, we established that the topic model could be used to assign new papers into the existing topics, thereby creating a Living Review. This type of meta-analysis provides a useful assessment tool for aggregating data about a large field.
Validating Dynamic Body Acceleration metrics as a measure of energy expenditure in a Neotropical primate
Authors: Rezende Gabriela C. , Cruz-Neto Ariovaldo P. , Börger Luca , Redcliffe James , Hambly Catherine , Speakman John R. , Garbino Guilherme S. T. , Pissinatti Alcides , Moreira Silvia Bahadian , Wilson Rory , Culot Laurence 
Published: July 2023

2AbstractQuantifying energy expenditure in free-living primates is fundamentally important yet challenging. Acceleration-based metrics such as Dynamic Body Acceleration (DBA), obtained from accelerometers, are potential proxies for energy expenditure, yet have not been previously validated in primates. Here, we validated DBA in black lion tamarins (Leontopithecus chrysopygus) by comparison to doubly labelled water (DLW) in 10 captive tamarins housed at the Rio de Janeiro Primate Centre. Individuals were equipped over 48 hours with a backpack with a tri-axial accelerometer and received an intra-peritoneal DLW injection at the beginning of the experiment, with blood samples taken 1 and 48h later. Daily Energy Expenditure by DLW was 326 (SD=66) kJ/day, close to expected values for primates of their size. The accelerometers recorded at 40 Hz, collecting >6.9 million records per axis for each individual. Individual DBA metrics were calculated and regressed against DLW daily energy measures. From this regression, we found a consistent and significant linear relationship (R2= 0.46) between DLW and DBA, which could be improved by the incorporation of activity and resting time information (R2= 0.52). Our results provide the first estimates of total daily energy expenditure for black lion tamarins and a validation of the method for estimating energy expenditure through accelerometers. Given the similar levels of total energy expenditure of captive and wild primates, this method can now be used in the field to estimate the energy cost of black lion tamarin movements in its natural environment.1 Summary statementDynamic body acceleration was validated against doubly labelled water in black lion tamarins, showing it is a useful tool for measuring free-living energy demands.
Fork in the road: how self-confidence about terrain influences gaze behaviour and path choice
Authors: Eira Silva Vinicius da , Marigold Daniel S. 
Published: July 2023

ABSTRACTDecisions about where to move occur throughout the day and are essential to life. Different movements may present different challenges and affect the likelihood of achieving a goal. Certain choices may have unintended consequences, some of which may cause harm and bias the decision. Movement decisions rely on a person gathering necessary visual information via shifts in gaze. Here we sought to understand what influences this information-seeking gaze behaviour. We had participants choose between walking across one of two paths that consisted of images of terrain commonly found in either hiking or urban environments. We manipulated the number and type of terrain of each path. We recorded gaze behaviour during the approach to the two paths and had participants rate their self-confidence about walking across each type of terrain as though it was real. Participants did not direct gaze to the path with greater visual information, regardless of how we quantified information. Rather, we show that a person’s self-confidence about their motor abilities predicts how they visually explore the environment with their eyes as well as their choice of action. The greater the self-confidence about walking across one path, the more they directed gaze to it, and the more likely they chose to walk across it. Overall, our results reveal a key role of a cognitive factor (self-confidence) in decision-making during a natural, movement-related behaviour.
A frame and a hotspot in cochlear mechanics
Authors: Strimbu C. Elliott , Chiriboga Lauren A. , Frost Brian L. , Olson Elizabeth S. 
Published: July 2023

AbstractAuditory sensation is based in nanoscale vibration of the sensory tissue of the cochlea, the organ of Corti complex (OCC). Motion within the OCC is now observable due to optical coherence tomography. In the cochlear base, in response to sound stimulation, the region that includes the electro-motile outer hair cells (OHC) was observed to move with larger amplitude than the basilar membrane (BM) and surrounding regions. The intense motion is based in active cell mechanics, and the region was termed the “hotspot” (Cooper et al., 2018, Nature comm). In addition to this quantitative distinction, the hotspot moved qualitatively differently than the BM, in that its motion scaled nonlinearly with stimulus level at all frequencies, evincing sub-BF activity. Sub-BF activity enhances non-BF motion; thus the frequency tuning of the hotspot was reduced relative to the BM. Regions that did not exhibit sub-BF activity are here defined as the OCC “frame”. By this definition the frame includes the BM, the medial and lateral OCC, and most significantly, the reticular lamina (RL). The frame concept groups the majority OCC as a structure that is largely shielded from sub-BF activity. This shielding, and how it is achieved, are key to the active frequency tuning of the cochlea. The observation that the RL does not move actively sub-BF indicates that hair cell stereocilia are not exposed to sub-BF activity. A complex difference analysis reveals the motion of the hotspot relative to the frame.
Deep Divergences Among Inconspicuously Colored Clades ofEpipedobatesPoison Frogs
Authors: López-Hervas Karem , Santos Juan C. , Ron Santiago R. , Betancourth-Cundar Mileidy , Cannatella David C. , Tarvin Rebecca D. 
Published: July 2023

AbstractPoison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic.Epipedobatesis among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species ofEpipedobatesbut relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified asE. boulengeriandE. espinosai, which reveals two putative new species, one in west-central Colombia (E.sp. 1) and the other in north-central Ecuador (E.aff.espinosai). We conclude thatE. darwinwallaceiis a junior subjective synonym ofE. espinosai. We also clarify the geographic distributions of inconspicuousEpipedobatesspecies including the widespreadE. boulengeri.We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude thatEpipedobatescontains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor ofEpipedobatesis ∼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation this text is available in the supplementary materials on the publisher’s website (biorxiv does not allow posting in non-English languages).