bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating batch correction methods for image-based cell profiling
Authors: Arevalo John , Su Ellen , van Dijk Robert , Carpenter Anne E. , Singh Shantanu 
Published: September 2023

SummaryHigh-throughput image-based profiling platforms are powerful technologies capable of collecting data from billions of cells exposed to thousands of perturbations in a time- and cost-effective manner. Therefore, image-based profiling data has been increasingly used for diverse biological applications, such as predicting drug mechanism of action or gene function. However, batch effects pose severe limitations to community-wide efforts to integrate and interpret image-based profiling data collected across different laboratories and equipment. To address this problem, we benchmarked seven high-performing scRNA-seq batch correction techniques, representing diverse approaches, using a newly released Cell Painting dataset, the largest publicly accessible image-based dataset. We focused on five different scenarios with varying complexity, and we found that Harmony, a mixture-model based method, consistently outperformed the other tested methods. Our proposed framework, benchmark, and metrics can additionally be used to assess new batch correction methods in the future. Overall, this work paves the way for improvements that allow the community to make best use of public Cell Painting data for scientific discovery.
Ontogeny of Projections from the Motor Cortex Governing Whisker and Neck Movements to the Striatum in the Rat
Authors: Gu Albert T , Han Victor Z , Jiang Yanfen 
Published: September 2023

SummaryCorticostrial or cortico-basal ganglia circuitry plays an important role in integrating sensory and motor information, developing appropriate goal-directed behavior, promoting the maturation of GABAergic interneurons in the striatum, and regulating the nigrostriatal pathways. Dysfunction of this circuitry has been seen in some movement disorders. However, the dynamic changes of this circuitry in early life are not fully elucidated. Previous studies demonstrated that projections from motor cortices of caudal forelimb and jaw-lip-tongue areas to the striatum developed postnatally with terminal-like fibers evident at postnatal day 7. Here we report the development of the projections from the motor cortex governing whisker and neck movements to the striatum. Corticostriatal projections from this area were mainly ipsilateral and also underwent a progressive, postnatal development. The pyramidal tract and its collaterals to the dorsal striatum appeared on the day of birth (postanatal day 0 (P0)), peaked on P6 in density, and continued to be tuned until P36. The intertelencephalic projections in the dorsolateral striatum were established between P6 and P12 and continued to be refined between P20 and P36. Neurons in this motor cortex sent their axons to the contralateral motor cortex via the corpus callosum at the age between P6 and P12. Our results suggest that the time window between P6 and P12 is critical for the development of the projections from the motor cortex governing whisker and neck movement to the striatum in the rat. The overall process of the development of this circuitry appears to correspond to the functional development of whisker movement and locomotor activities.
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation
Authors: Duncan Andrew G , Mitchell Jennifer A , Moses Alan M 
Published: September 2023

Structured abstractMotivationSupervised deep learning is used to model the complex relationship between genomic sequence and regulatory function. Understanding how these models make predictions can provide biological insight into regulatory functions. Given the complexity of the sequence to regulatory function mapping (the cis-regulatory code), it has been suggested that the genome contains insufficient sequence variation to train models with suitable complexity. Data augmentation is a widely used approach to increase the data variation available for model training, however current data augmentation methods for genomic sequence data are limited.ResultsInspired by the success of comparative genomics, we show that augmenting genomic sequences with evolutionarily related sequences from other species, which we term phylogenetic augmentation, improves the performance of deep learning models trained on regulatory genomic sequences to predict high-throughput functional assay measurements. Additionally, we show that phylogenetic augmentation can rescue model performance when the training set is down-sampled and permits deep learning on a real-world small dataset, demonstrating that this approach improves experimental data efficiency. Overall, this data augmentation method represents a solution for improving model performance that is applicable to many supervised deep learning problems in genomics.Availability and implementationThe open-source GitHub repository agduncan94/phylogenetic_augmentation_paper includes the code for rerunning the analyses here and recreating the figures.Contactalan.moses@utoronto.ca
A robust knock-in approach using a minimal promoter and a minicircle
Authors: Keating Margaret , Hagle Ryan , Osorio-Mendez Daniel , Rodriguez-Parks Anjelica , Almutawa Sarah I , Kang Junsu 
Published: September 2023

AbstractKnock-in reporter (KI) animals are essential tools in biomedical research to study gene expression impacting diverse biological events. While CRISPR/Cas9-mediated genome editing allows for the successful generation of KI animals, several factors should be considered, such as low expression of the target gene, prevention of bacterial DNA integration, and in-frame editing. To circumvent these challenges, we developed a new strategy that utilizes minicircle technology and introduces a minimal promoter. We demonstrated that minicircles serve as an efficient donor DNA in zebrafish, significantly enhancing KI events compared to plasmids containing bacterial backbones. In an attempt to generate a KI reporter forscn8ab,we precisely integrated a fluorescence gene at the start codon. However, the seamlessly integrated reporter was unable to direct expression that recapitulates endogenousscn8abexpression. To overcome this obstacle, we introduced thehsp70minimal promoter to provide an ectopic transcription initiation site and succeeded in establishing stable KI transgenic reporters forscn8ab. This strategy also created afgf20bKI reporter line with a high success rate. Furthermore, our data revealed that an unexpectedly edited genome can inappropriately influence the integrated reporter gene expression, highlighting the importance of selecting a proper KI line. Overall, our approach utilizing a minicircle and an ectopic promoter establishes a robust and efficient strategy for KI generation, expanding our capacity to create KI animals.
Development of an undergraduate cell biology laboratory to assess pigmentation and cell size in a zebrafish model of uveal melanoma
Authors: Henle Andrea M. 
Published: September 2023

AbstractThis study outlines a two-week laboratory module for an authentic cell biology undergraduate research experience that uses zebrafish (Danio rerio), a popular model organism for research. Previous research has indicated that course-based undergraduate research experiences such as this one increase student confidence, active learning, and retention. During this research experience, students investigate variations in pigmentation in the caudal fins of wild type and transgenic fish (Tg(mitfa:GNAQQ209L)). The transgenic fish express a hyperactive Gα protein, GNAQQ209L, under the melanocyte-specific mitfa promoter, offering insights into uveal melanoma, a common eye cancer. Students specifically analyze the black pigmented cells, melanophores, within the caudal fin. We determined that the transgenic zebrafish have increased pigmentation in their caudal fins but smaller melanophores. These results suggest there are more melanophores in theTg(mitfa:GNAQQ209L)fish compared to the wild type. Future undergraduate research could investigate these cellular differences. This research experience imparts microscopy and image analysis skills and instills the ability to grapple with large datasets, statistical tests, and data interpretation in alignment with biology education principles. Post-lab surveys reveal students attain confidence in the above skills and in handling animals, along with a deeper appreciation for model organism research and its relevance to cancer cell biology.
Comprehensive Metabolomic Analysis of Human Heart Tissue Enabled by Parallel Metabolite Extraction and High-Resolution Mass Spectrometry
Authors: Wancewicz Benjamin , Pergande Melissa R. , Zhu Yanlong , Gao Zhan , Shi Zhuoxin , Plouff Kylie , Ge Ying 
Published: September 2023

AbstractThe heart contracts incessantly and requires a constant supply of energy, utilizing numerous metabolic substrates such as fatty acids, carbohydrates, lipids, and amino acids to supply its high energy demands. Therefore, a comprehensive analysis of various metabolites is urgently needed for understanding cardiac metabolism; however, complete metabolome analyses remain challenging due to the broad range of metabolite polarities which makes extraction and detection difficult. Herein, we implemented parallel metabolite extractions and high-resolution mass spectrometry (MS)-based methods to obtain a comprehensive analysis of the human heart metabolome. To capture the diverse range of metabolite polarities, we first performed six parallel liquid-liquid extractions (three monophasic, two biphasic, and one triphasic extractions) of healthy human donor heart tissue. Next, we utilized two complementary MS platforms for metabolite detection - direct-infusion ultrahigh-resolution Fourier-transform ion cyclotron resonance (DI-FTICR) and high-resolution liquid chromatography quadrupole time-of-flight tandem MS (LC-Q-TOF MS/MS). Using DI-FTICR MS, 9,521 metabolic features were detected where 7,699 were assigned a chemical formula and 1,756 were assigned an annotated by accurate mass assignment. Using LC-Q-TOF MS/MS, 21,428 metabolic features were detected where 626 metabolites were identified based on fragmentation matching against publicly available libraries. Collectively, 2276 heart metabolites were identified in this study which span a wide range of polarities including polar (benzenoids, alkaloids and derivatives and nucleosides) as well as non-polar (phosphatidylcholines, acylcarnitines, and fatty acids) compounds. The results of this study will provide critical knowledge regarding the selection of appropriate extraction and MS detection methods for the analysis of the diverse classes of human heart metabolites.Table of Contents Graphical Abstract
Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription
Authors: Mahat Dig B. , Tippens Nathaniel D. , Martin-Rufino Jorge D. , Waterton Sean K. , Fu Jiayu , Blatt Sarah E. , Sharp Phillip A. 
Published: September 2023

AbstractTranscription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1–5. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations6–9. However, fundamental questions in the temporal regulation of transcription and enhancer-gene synchrony remain unanswered primarily due to the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq - a novel single-cell nascent RNA sequencing assay using click-chemistry - and unveil the coordinated transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription, and estimates burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells. It reveals the co-transcription of functionally related genes and leverages the replication-dependent non-polyadenylated histone genes transcription to elucidate cell-cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq identifies networks of enhancers and genes and indicates that the bursting of transcription at super-enhancers precedes the burst from associated genes. By imparting insights into the dynamic nature of transcription and the origin and propagation of transcription signals, scGRO-seq demonstrates its unique ability to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.
Computational Insights on Xenobiotic Nuclear Receptor-Air Pollutant Interactions Through Molecular Docking and Dynamics Simulations
Authors: Ullah Samee , Khan Nasir Ali 
Published: September 2023

AbstractAir pollution is a major global health risk, contributing to millions of deaths each year. Exposure to air pollutants can lead to a variety of adverse health effects, including oxidative stress, inflammation, and DNA damage. The nuclear receptor pregnane X receptor (PXR) is a xenobiotic sensor that plays a key role in the detoxification of environmental chemicals and air pollutants can activate these receptors, leading to the expression of genes involved in drug metabolism and detoxification. Elucidating the structural interactions of air pollutants with PXR provides insights into the mechanisms by which these pollutants exert their toxic effects. Using computational techniques, we screened 124 air pollutants toxic compounds from (APDB) against PXR and identified priority compounds for molecular dynamics simulation that revealed the dynamic binding mechanisms and structural conformations involved in PXR activation. Furthermore, the root mean square deviation (RMSD) and root mean square fluctuation (RMSF) analyses characterized the stability and flexibility of PXR-pollutant complexes. Together, these computational approaches provide unprecedented insights into the molecular basis of PXR activation by air pollutants. By enabling high-throughput screening and multi-faceted biophysical characterization of PXR interactions, this work elucidates the structural mechanisms linking air pollution to impaired xenobiotic metabolism. Integration of virtual screening, molecular dynamics, and rigorous biophysical analyses represents a powerful computational systems pharmacology pipeline for assessing health risks posed by ubiquitous environmental toxicants.
Tailpiece Heating device for effective prevention of biofilm growth in sink plumbing
Authors: Kotay Shireen M , Guilford William , Pettygrove Brian A , Komisarcik Alan J , Hughes Samantha A. , Mathers Amy J 
Published: September 2023

ABSTRACTIn recent years, numerous hospitals have linked patient infections toKlebsiella pneumoniaeproducing Enterobacterales (KPCE) and other resistant bacterial species in their wastewater systems and handwashing sinks. Wastewater plumbing provides a reservoir for bacteria, making them incredibly difficult to eliminate through traditional disinfection methods. Data suggests that patients become infected when bacteria grow or migrate up the proximal wastewater plumbing and into the sink basin, and are subsequently dispersed onto surrounding surfaces. Therefore, a novel electronic device was developed that acts at the highest risk area, just below the sink drain, to heat and dry out the biofilm and creating a biofilm barrier and prevent upward growth from the sink trap. The efficacy of the first prototype of a tailpiece heater (TPH) in preventing drain colonization was tested using GFP-expressingEscherichia coli(GFP-E. coli) as the challenge organism. In control sinks without the TPH, GFP-E. colibiofilm grew from the p-trap upwards to colonize the drain within 7 days. Sinks with a TPH set to 75°C were found to prevent sink drain colonization. In contrast, 65°C was not adequate to prevent drain colonization. Using KPCE the TPH was more effective than no heat control in preventing drain colonization in sinks over time. Lastly, when challenged with seeding from above, the TPH also effectively prevented KPCE colonization at the drain level. Heating of the tailpiece may offer a safe, effective, and economically attractive approach to preventing the spread of resistant bacterial species from contaminated drain biofilm to patients.
Evidence for individual vocal recognition in a pair bonding poison frog? Insights from no-choice and two-choice paradigms
Authors: Podraza Molly E. , Moss Jeanette B. , Fischer Eva K. 
Published: September 2023

ABSTRACTIndividually distinctive vocalizations are widespread in nature, although the ability of receivers to discriminate these signals has only been studied through limited taxonomic and social lenses. Here we ask whether anuran advertisement calls, typically studied for their role in territory defense and mate attraction, facilitate recognition and preferential association with partners in a pair bonding poison frog. Combining no- and two-stimulus choice playback experiments, we evaluated behavioral and physiological responses of females to male acoustic stimuli. Virgin females oriented to and approached speakers broadcasting male calls independent of caller identity, implying that females are generally attracted to male acoustic stimuli outside the context of a pair bond. When pair bonded females were presented with calls of a mate and a stranger, they showed a slight preference for calls of their mate. Moreover, behavioral responses varied with breeding status: females with eggs were faster to approach stimuli and spent more time in the mate arm than females that were pair bonded but did not currently have eggs. Our study suggests a potential role for individual vocal recognition in the formation and maintenance of pair bonds in a poison frog and raises new questions about how acoustic signals are perceived in the context of monogamy and biparental care.
Dietary Availability Acutely Governs Puberty Onset via Hypothalamic Neural Circuit
Authors: Goto Teppei , Hagihara Mitsue , Irie Satsuki , Abe Takaya , Kiyonari Hiroshi , Miyamichi Kazunari 
Published: September 2023

SummaryReproduction poses a substantial burden, especially for mammalian females. Puberty onset serves as a vital checkpoint, regulated based on the body’s energy state, to prevent inappropriate reproductive activity under malnutrition. However, the neural basis of this puberty checkpoint remains poorly understood. Here, we demonstrate that peripubertal malnutrition in female mice reduces the synchronous activity episodes of arcuate kisspeptin neurons (SEskiss), which are critical regulators of the gonadotropin axis. Improved dietary availability boosts SEskissfrequency, facilitating puberty onset. Using a viral-genetic approach, we show that the activating agouti-related protein neurons in the arcuate nucleus (ARCAgrpneurons), a hunger center, suppresses SEskiss, even with enough food. Conversely, loss-of-function of ARCAgrpneurons enhances SEskissduring malnutrition, partly promoting irregular sexual maturation. Collectively, a neural circuit connecting feeding to reproductive centers is responsible for disinhibiting SEskissfrequency based on dietary availability, which sheds light on the neural basis of puberty checkpoint.HighlightsThe pulsatile activity of arcuate kisspeptin neurons emerges and grows before vaginal opening.Pubertal impairment resulting from malnutrition is associated with a reduction in the pulsatile activity of kisspeptin neurons.Pubertal recovery by food availability follows the elevated pulsatile activity of kisspeptin neurons during catch-up growth.The arcuate Agrp neurons suppress the frequency of pulsatile activity of kisspeptin neurons under negative energy balance.
bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis
Authors: Huang Yizhou Peter , Harmon Lauren , Deering-Gardner Eve , Ma Xiaotu , Harsh Josiah , Xue Zhaoyu , Wen Hong , Ramos Marcel , Davis Sean , Triche Timothy J. 
Published: September 2023

AbstractThe NCI Genomic Data Commons (GDC) provides controlled access to sequencing data from thousands of subjects, enabling large-scale study of impactful genetic alterations such as simple and complex germline and structural variants. However, efficient analysis requires significant computational resources and expertise, especially when recalling variants from raw sequence reads. We thus developedbamSliceR, an R/Bioconductor package that builds upon theGenomicDataCommonspackage to extract aligned sequence reads from cross-GDC meta-cohorts, followed by targeted analysis of variants and effects (including transcript-aware variant annotation from transcriptome-aligned GDC RNA data). Here we demonstrate population-scale genomic & transcriptomic analyses with minimal compute burden viabamSliceR, identifying recurrent, clinically relevant sequence and structural variants in the TARGET AML and BEAT-AML cohorts. We then validate results in the (non-GDC) Leucegene cohort, demonstrating how thebamSliceRpipeline can be seamlessly applied to replicate findings in non-GDC cohorts. These variants directly yield clinically impactful and biologically testable hypotheses for mechanistic investigation.bamSliceRhas been submitted to the Bioconductor project, where it is presently under review, and is available on GitHub athttps://github.com/trichelab/bamSliceR.
Carvedilol suppresses ryanodine receptor-dependent Ca2+bursts in human neurons bearingPSEN1variants found in early onset Alzheimer’s disease
Authors: Hori Atsushi , Ai Tomohiko , Hato Takashi , Inaba Haruka , Tanaka Kimie , Sato Shoichi , Okamoto Mizuho , Horiuchi Yuna , Paran Faith Jessica , Tabe Yoko , Rosales Corina , Akamatsu Wado , Murayama Takashi , Kurebayashi Nagomi , Sakurai Takashi , Miida Takashi 
Published: September 2023

AbstractSeizures are increasingly being recognized as the hallmark of Alzheimer’s disease (AD). Neuronal hyperactivity can be a consequence of neuronal damage caused by abnormal amyloid β (Aß) depositions. However, it can also be a cell-autonomous phenomenon causing AD by Aß-independent mechanisms. Indeed, various studies using animal models showed that Ca2+releases from the endoplasmic reticulum (ER) via type 1 inositol triphosphate receptors (InsP3R1s) and ryanodine receptors (RyRs). To investigate which is the main pathophysiological mechanism in human neurons, we measured Ca2+signaling in neural cells derived from three early-onset AD patients harboring variants of Presenilin-1 (PSEN1p.A246E, p.L286V, and p.M146L). Of these, it has been reported that PSEN1 p.A246E and p.L286V did not produce a significant amount of abnormal Aß. We found that allPSEN1-mutant neurons, but not wild-type, caused abnormal Ca2+-bursts in a manner dependent on the calcium channel, Ryanodine Receptor 2 (RyR2). Indeed, carvedilol, anRyR2 inhibitor, and VK-II-86, an analog of carvedilol without the β-blocking effects, sufficiently eliminated the abnormal Ca2+bursts. In contrast, Dantrolene, a RyR1 inhibitor, and Xestospongin c, an IP3R inhibitor, did not attenuate the Ca2+-bursts. The RNA-Seq data revealed that ER-stress responsive genes were increased, and mitochondrial Ca2+-transporter genes were decreased in PSEN1A246Ecells compared to the WT neurons. Thus, we propose that aberrant Ca2+signaling is a key link between human pathogenicPSEN1variants and cell-intrinsic hyperactivity prior to deposition of abnormal Aß, offering prospects for the development of targeted prevention strategies for at-risk individuals.One Sentence SummaryAberrant Ca2+-signaling causesPSEN1-related early onset Alzheimer’s disease.