bluuebunny/crossref_metadata_2025 huggingface dataset:
Preoperative dexamethasone administration in hepatectomy of 25-minute intermittent Pringle’s maneuver for hepatocellular carcinoma: a randomized controlled trial
Authors: Huang Yang , Xu Liangliang , Wang Ning , Wei Yonggang , Wang Wentao , Xu Mingqing , Jiang Li
Published: August 2023

Background:

A previous randomized controlled trial (RCT) demonstrated that intermittent Pringle’s maneuver (IPM) with a 25-minute ischemic interval can be applied safely and efficiently in hepatectomy for patients with hepatocellular carcinoma (HCC). But prolonging the hepatic inflow clamping time will inevitably aggravate the ischemia-reperfusion injury (IRI). Therefore, we aimed to evaluate the effect of prophylactic dexamethasone on alleviating the surgical stress for HCC patients with a 25-minute ischemic interval.

Methods:

From December 2022 to April 2023, patients met the inclusion criteria were randomly assigned to dexamethasone group or control group. Perioperative data and short-term survival outcomes between the two groups were recorded and compared, and subgroup analysis was performed.

Results:

Two hundred and seventy patients were allocated to the dexamethasone group (n=135) and control group (n=135). Patients in dexamethasone group had lower area under the curve of serial alanine aminotransferase (AUCALT) (P=0.043) and aspartate aminotransferase (AUCAST) (P=0.009), total bilirubin (TB) (P=0.018), procalcitonin (PCT) (P=0.012), interleukin-6 (IL-6) (P=0.006), incidence of major complication (P=0.031) and shorter postoperative hospital stay (P=0.046) than those in control group. Subgroup analysis showed that the dexamethasone group experienced milder hepatocellular injury than the control group for patients with cirrhosis, and for patients without cirrhosis, the dexamethasone group experienced milder inflammatory response. Moreover, the dexamethasone group preserved better liver function and experienced milder inflammatory response for patients undergoing major hepatectomy, although hepatocellular injury was not significantly improved.

Conclusion:

Preoperative dexamethasone administration can help improve perioperative outcomes for HCC patients when applying IPM with a 25-minute ischemic interval in hepatectomy.
Preoperative low muscle mass and early postoperative outcomes in children undergoing living donor liver transplantation: A retrospective study
Authors: Jeong Daun , Lee Sang-Wook , Jang Hwa-Young , Kwon Hye-Mee , Shin Won-Jung , Song In-Kyung
Published: August 2023

Low skeletal muscle mass may develop in children with end-stage liver disease, affecting postoperative outcomes. We retrospectively investigated whether preoperative low muscle mass was associated with early postoperative outcomes in pediatric patients undergoing living donor liver transplantation (LDLT). Electronic medical records of children (age below 12 y) who underwent LDLT between February 1, 2007, and January 31, 2018, were reviewed. The cross-sectional areas of psoas, quadratus lumborum, and erector spinae muscles at the level of fourth-fifth lumbar intervertebral disks were measured using abdominal CT images, divided by the square of the height and were added to obtain the total skeletal muscle index (TSMI). The patients were divided into two groups according to the median TSMI in the second quintile (1859.1 mm2/m2). Complications in the early postoperative period (within 30 d after surgery) classified as Clavien-Dindo grade 3 or higher were considered major complications. Logistic regression analyses were performed to determine the association between preoperative low muscle mass and early postoperative outcomes. In the study population of 123 patients (median age, 14 mo; range, 8–38 mo) who underwent LDLT, 29% and 71% were classified in the low (mean TSMI, 1642.5 ± 187.0 mm2/m2) and high (mean TSMI 2188.1 ± 273.5 mm2/m2) muscle mass groups, respectively. The rates of major complications, mechanical ventilation >96 hours, intensive care unit stay >14 days, hospital stay >30 days, and in-hospital mortality were not significantly different between the 2 groups. Additionally, adverse outcomes according to pediatric end-stage liver disease scores and sex were not significantly different between the 2 groups. In conclusion, preoperative low muscle mass defined by TSMI was not associated with early postoperative outcomes in pediatric patients undergoing LDLT.
Binucleated Myocytes and Heart Weight
Authors: Gadsby Zeena , Garland Jack , Thompson Melissa , Ondruschka Benjamin , Da Broi Ugo , Tse Rexson
Published: August 2023

Hypertrophy of the heart is assessed by heart weight (and dimensions) and myocyte hypertrophy. Establishing an association between the two may be useful in assessing hypertrophy in cases where there are limitations in assessing the heart weight. This preliminary study explored the association between the number of binucleated myocytes (a feature of myocyte hypertrophy) in a randomly chosen single high-power field of the left ventricular free wall and heart weight in an adult White population. It also compared the number of binucleated myocytes between cases with increased heart weight (>400 g in female and >500 g in male) and cases with normal heart weight. Heart weight and number of binucleated myocytes correlated significantly in male only. Increased heart weight had a significantly higher number of binucleated myocytes, with 8.5 binucleated myocytes being able to segregate cases with increased heart weight (74% sensitivity and 79% specificity). The results of this study showed the number of binucleated myocytes may have a complementary role in assessing hypertrophy of the heart.
Entanglement and indistinguishability: facing some challenges from a new perspective
Authors: Lombardi Olimpia
Published: July 2023

While entanglement in the case of distinguishable particles is clearly understood, in the case of indistinguishable particles, there is still a wide debate regarding basic conceptual issues. Here, I will address two such issues. First, the debate almost always rests on a differentiated treatment of the cases of distinguishability and indistinguishability, even with respect to the definition of the concept of entanglement. Second, the fact that symmetrized and antisymmetrized states of indistinguishable particles are non-factorizable leads to certain perplexities about the very nature of entanglement. In the present work, both issues will be addressed from the perspective of an ontology of properties, which finds its natural expression in the algebraic formalism of quantum mechanics. The final goal will be to show that the proposed ontology allows a unified treatment of entanglement in the distinguishability and indistinguishability cases and offers a straightforward way out to perplexities.

This article is part of the theme issue 'Identity, individuality and indistinguishability in physics and mathematics'.
Entanglement and discernibility of identical particles
Authors: Bigaj Tomasz
Published: July 2023

This article follows an unorthodox approach to the individuation of quantum particles of the same type. According to this approach, individuation of the components of a composite system of identical particles is done not with the help of unphysical labels (indices) but physically meaningful projection operators. This unorthodox conception requires a modification of the standard notion of entanglement, in order to exclude states whose non-factorizability arises merely from the (anti)symmetrization of a product state. I will report several facts regarding the connections of the modified concept of entanglement with the issue of discernibility. I will also discuss recent experiments involving measurement-induced entanglement, and I will point out that they do not threaten the cogency of the new concept of entanglement. The statistical correlations observed in these experiments are explainable not by the entanglement of the initial state but by the creation of a new, genuinely entangled state by means of a pre-measurement selection. Finally, I will identify and discuss a genuine difference between non-entangled but non-factorizable states of identical particles and ordinary product states, which is that the former but not the latter admits an infinity of alternative and incompatible individuations by single-particle properties. This phenomenon can be accounted for using the concept of emergent particles proposed by Dennis Dieks.

This article is part of the theme issue 'Identity, individuality and indistinguishability in physics and mathematics'.
Quantum Haecceity
Authors: Kastner Ruth E.
Published: July 2023

There is an extensive philosophical literature on the interrelated issues of identity, individuality and distinguishability in quantum systems. A key consideration is whether quantum systems are subject to a strong form of individuality termed ‘haecceity’ (from the Latin for ‘this-ness’). I argue that the traditional, strong form of haecceity does not apply at the quantum level, but that in order to properly account for the need for symmetrization in quantum systems, a weaker kind of haecceity must be involved, which I call
quantum haecceity
. In the process, I also question some generally accepted tenets of the current debate, such as the idea that symmetrization of states for identical quanta must be postulated and reflects permutation invariance. Instead, I note that a perturbative Hamiltonian is required for exchange effects, which suggests that the need for symmetrization arises from specific physical conditions.

This article is part of the theme issue ‘Identity, individuality and indistinguishability in physics and mathematics’.
Emergence and identity of quantum particles
Authors: Dieks Dennis
Published: July 2023

According to classical physics,particlesare basic constituents of the physical world. Quantum theory is much less friendly to particles; in particular, relativistic quantum field theory (RQFT) creates serious obstacles for the idea that particles are fundamental. Apparently, when moving from the domain of RQFT to that of classical mechanics (CM), particles have toemergeat some stage. It is standard to assume that this emergence has been completed at the level of quantum mechanics, halfway between RQFT and CM, even though particles of the same kind in many-particle quantum mechanics have the curious feature of being ‘entities without identity’. Against this ‘Received View’ about the nature of quantum particles we outline and defend anAlternative View(AV), in which the emergent character of particles is emphasized. According to this AV, the step to a particle theory has not yet been made in quantum mechanics: conditions have still to be satisfied in order to make the particle concept applicable. If these conditions are met, the quantum particles that emerge aredistinguishableindividuals possessing physically defined identities, in stark contrast to what the Received View asserts. We will compare and contrast the two Views, both from a physical and a logical/conceptual point of view.

This article is part of the theme issue ‘Identity, individuality and indistinguishability in physics and mathematics’.
Indistinguishable entangled fermions: basics and future challenges
Authors: Majtey Ana P. , Valdés-Hernández Andrea , Cuestas Eloisa
Published: July 2023

The study of entanglement in systems composed of identical particles raises interesting challenges with far-reaching implications in both, our fundamental understanding of the physics of composite quantum systems, and our capability of exploiting quantum indistinguishability as a resource in quantum information theory. Impressive theoretical and experimental advances have been made in the last decades that bring us closer to a deeper comprehension and to a better control of entanglement. Yet, when it involves composites of indistinguishable quantum systems, the very meaning of entanglement, and hence its characterization, still finds controversy and lacks a widely accepted definition. The aim of the present paper is to introduce, within an accessible and self-contained exposition, the basic ideas behind one of the approaches advanced towards the construction of a coherent definition of entanglement in systems of indistinguishable particles, with focus on fermionic systems. We also inquire whether the corresponding tools developed for studying entanglement in identical-fermion systems can be exploited when analysing correlations in distinguishable-party systems, in which the complete information of the individual parts is not available. Further, we open the discussion on the broader problem of constructing a suitable framework that accommodates entanglement in the presence of generalized statistics.

This article is part of the theme issue ‘Identity, individuality and indistinguishability in physics and mathematics’.
Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens
Authors: Gharani N. , Calendo G. , Kusic D. , Madzo J. , Scheinfeldt L.
Published: July 2023

Here we describe a new public pharmacogenetic (PGx) annotation database of a large (n=3202) and diverse biospecimen collection of 1000 Genomes Project cell lines and DNAs. The database is searchable with a user friendly, web-based tool (www.coriell.org/StarAllele/Search). This resource leverages existing whole genome sequencing data and PharmVar annotations to characterize *alleles for each biospecimen in the collection. This new tool is designed to facilitate in vitro functional characterization of *allele haplotypes and diplotypes as well as support clinical PGx assay development, validation, and implementation.
Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples
Authors: Domanskyi Sergii , Srivastava Anuj , Kaster Jessica , Li Haiyin , Herlyn Meenhard , Rubinstein Jill C. , Chuang Jeffrey H.
Published: July 2023

Highlights

We have developed an automated data processing pipeline to quantify mouse and human data from patient-derived xenograft samples assayed by Visium spatial transcriptomics with matched hematoxylin and eosin (H&E) stained image. We enable deconvolution of reads with Xenome, quantification of spatial gene expression from host and graft species with Space Ranger, extraction of B-allele frequencies, and splicing quantification with Velocyto. In the H&E image processing sub-workflow, we generate morphometric and deep learning-derived feature quantifications complementary to the Visium spots, enabling multi-modal H&E/expression comparisons. We have wrapped the pipeline into Nextflow DSL2 in a scalable, portable, and easy-to-use framework.

We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genomes input and stand-alone image analysis. We showed the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of imaging features of H&E data reveal similar patterns arising from the two data modalities.
Sustained Effects of Developmental Exposure to Inorganic Arsenic on Hepatic Gene Expression and Mating Success in Zebrafish
Authors: Koomson Abigail Ama , Delaney Patrice , Sadler Kirsten C.
Published: July 2023

The impacts of exposure to the pervasive environmental toxicant, inorganic arsenic (iAs), on human and fish health are well characterized and several lines of evidence suggest that some impacts can manifest years after exposure cessation. Using a developmental exposure protocol whereby zebrafish embryos were exposed to 0.5 and 1.5 mM iAs from 4-120 hours post fertilization (hpf) and then was removed, we investigated the sustained effects of iAs on gene expression in the liver, survival, reproductive success, and susceptibility to iAs toxicity in the subsequent generation. Developmental exposure to iAs has massive effects on the hepatic transcriptome, with 23% of genes differentially expressed at the end of exposure at 120 hpf, and some of these genes remain deregulated in the liver 9 months after iAs was removed. Developmental exposure to 1.5 mM iAs, but not 0.5 mM, increased mortality through 3 months by over 50%. Adults that were developmentally exposed to 0.5 mM iAs had reduced mating success, but their offspring had no differences in observable aspects of development or their susceptibility to iAs toxicity. This demonstrates that developmental exposure of zebrafish to iAs reduces long-term survival, reproductive success and causes sustained changes to gene expression in the liver.

SUMMARY STATEMENT

This work investigates the long-term effects of developmental exposure to inorganic arsenic (iAs) using zebrafish. Months after iAs-exposure was terminated, we found increased mortality, changes in gene expression in the liver and decreased mating success.
A multiplex, prime editing framework for identifying drug resistance variants at scale
Authors: Chardon Florence M. , Suiter Chase C. , Daza Riza M. , Smith Nahum T. , Parrish Phoebe , McDiarmid Troy , Lalanne Jean-Benoît , Martin Beth , Calderon Diego , Ellison Amira , Berger Alice H. , Shendure Jay , Starita Lea M.
Published: July 2023

CRISPR-based genome editing has revolutionized functional genomics, enabling screens in which thousands of perturbations of either gene expression or primary genome sequence can be competitively assayed in single experiments. However, for libraries of specific mutations, a challenge of CRISPR-based screening methods such as saturation genome editing is that only one region (e.g.one exon) can be studied per experiment. Here we describe prime-SGE (“prime saturation genome editing”), a new framework based on prime editing, in which libraries of specific mutations can be installed into genes throughout the genome and functionally assessed in a single, multiplex experiment. Prime-SGE is based on quantifying the abundance of prime editing guide RNAs (pegRNAs) in the context of a functional selection, rather than quantifying the mutations themselves. We apply prime-SGE to assay thousands of single nucleotide changes in eight oncogenes for their ability to confer drug resistance to three EGFR tyrosine kinase inhibitors. Although currently restricted to positive selection screens by the limited efficiency of prime editing, our strategy opens the door to the possibility of functionally assaying vast numbers of precise mutations at locations throughout the genome.
The molecular mechanism of positive allosteric modulation at the dopamine D1 receptor
Authors: Goldberg Alexander , Xie Bing , Shi Lei
Published: July 2023

The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na+binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207’s allosteric action at the D1R pave the way for the rational design of more potent and effective allosteric modulators.
A prospective observational cohort study to investigate the effect of frailty on mortality of adults following lower limb amputation
Authors: Welsh S , Gale J , Carter B , Hussey K , Orr D , Quinn T , Braude P
Published: July 2023

Introduction

Frailty is common in patients with atherosclerotic disease and is associated with substantially increased morbidity, mortality and significant economic and resource implications. Major limb amputation (MLA) secondary to critical limb threatening ischaemia (CLTI) is also associated with high mortality rates. This study aims to examine the association between frailty, as defined by the Rockwood Clinical Frailty Scale (CFS), on mortality rates in patients undergoing MLA for CLTI.

Methods

This multi-centre, prospective observational cohort study will collect data on MLA performed for CLTI between November 2017 to December 2021 (North Bristol Trust) and January 2016 to October 2021 (NHS Greater Glasgow & Clyde). All patients undergoing MLA for CLTI will be included. Exclusion criteria are MLA for other aetiology, insufficient data to generate CFS score and minor lower limb amputations. Data collected includes age, sex, deprivation index and Charlson Comorbidity Index variables. A consultant/registrar with specialist-interest in frailty will allocate CFS scores based on pre-operative functional status. Three categories will be used: robust (CFS 1-3), mildly frail (CFS 4-5) and frail (CFS 6-8). CFS 9, ‘terminally ill’, will be presented separately. Primary outcome is all-cause mortality following MLA. Secondary outcome is length of stay. Sample size calculation assumed a mortality of 30% in robust and 40% in frail patients (HR=0.7) in a 1:2 ratio (robust:frail), calculating 1000 patients required, using a 0.05 significance level and 90% power. Outcome data will be analysed by multivariable Cox proportional baseline hazards regression controlling for demographic and operative variables (e.g., sex, age, deprivation index, comorbidity index, urgency of operation).

Discussion

It is expected the study results will inform clinical decision-making and contribute toward an evidence pool which will inform service planning.

KEY STUDY CONTACTS

STUDY SUMMARY

FUNDING AND SUPPORT IN KIND

PROTOCOL CONTRIBUTORS

Study contributors

NBT vascular department – proving data on all patients that have undergone LLA in the last 5 years.

NHSGGC vascular department – proving data on all patients that have undergone LLA in the last 5 years.
Community Support for Injured Patients: A Scoping Review and Narrative Synthesis
Authors: Jhunjhunwala Rashi , Jayaram Anusha , Mita Carol , Davies Justine , Chu Kathryn
Published: July 2023

BACKGROUND

Community-based support groups have been effective in facilitating access to and retention in the healthcare system for patients with HIV/AIDS, cancer, diabetes, and other communicable and non-communicable diseases. Given the high incidence of morbidity that results from traumatic injuries, and the barriers to reaching and accessing care for injured patients, community-based support groups may prove to be similarly effective in this population.

OBJECTIVES

The objective of this review is to identify the extent and impact of community and peer support groups for injured patients.

ELIGIBILITY

We included primary research on studies that evaluated community support groups that were solely based in the community. Hospital-based or healthcare-professional led groups were excluded.

EVIDENCE

Sources were identified from a systematic search of Medline / PubMed, CINAHL, and Web of Science Core Collection.

CHARTING METHODS

We utilized a narrative synthesis approach to data analysis.

RESULTS

4,989 references were retrieved from database search; 25 were included in final data extraction. There was a variety of methodologies represented, and the groups represented patients with spinal cord injury (N=2), traumatic brain or head injury (N=7), burns (N=4), intimate partner violence (IPV) (N=5), mixed injuries (N=5), torture (N=1), and brachial plexus injury (N=1). Multiple benefits were reported by support group participants; categorized as social, emotional, logistical, or educational benefits.

CONCLUSIONS

community-based peer support groups can provide education, community, and may have implications for retention in care for injured patients.
Ploidy-specific transcriptomes shed light on the heterogeneous identity and metabolism of developing pericarp cells
Authors: Tourdot Edouard , Maza Elie , Djari Anis , Martin Pascal GP , Gévaudant Frédéric , Chevalier Christian , Pirrello Julien , Gonzalez Nathalie
Published: July 2023

Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programs that are characteristic to each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types and especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of genes differentially expressed when comparing ploidy levels at a specific developmental stage. We found that non-endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome-based predictions were validated by quantifying ploidy levels within the pericarp tissue. Thisin situploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation, and gene expression patterns in the tomato pericarp.

Significance statement

The progression of endoreduplication is very dynamic during early fruit development and displays cell layer specific patterns. The integration of ploidy distribution maps with ploidy-specific transcriptome data revealed that gene expression in the pericarp is controlled in a ploidy-specific manner during the early stages of tomato fruit development, resulting in the spatialization of transcriptional programs.
Developmental noise and phenotypic plasticity are correlated inDrosophila simulans
Authors: Saito Keita , Tsuboi Masahito , Takahashi Yuma
Published: July 2023

Non-genetic variation is the phenotypic variation induced by the differential expression of a genotype in response to varying environmental cues and is broadly categorized into two types: phenotypic plasticity and developmental noise. These variation aspects have been suggested to play an important role in adaptive evolution; however, the mechanisms by which these two types of non-genetic variations influence the evolutionary process are currently poorly understood. Using a machine-learning based phenotyping tool, we independently quantified the phenotypic plasticity and developmental noise in the wing morphological traits of a fruit flyDrosophila simulans.Utilizing a rearing experiment, we demonstrated plastic responses in both wing size and shape as well as non-zero heritability of both phenotypic plasticity and developmental noise, which suggests that adaptive phenotypic plasticity can evolve via genetic accommodation in the wing morphology ofD. simulans. We found a positive correlation between phenotypic plasticity and developmental noise, while the correlation between the plastic response to three kinds of environmental factors that were examined (nutrient condition, temperature, and light–dark cycle) were poor. These results suggest that phenotypic plasticity and developmental noise contribute to evolvability in a similar manner, however, the mechanisms that underlie the correspondence between these two variation types remains to be elucidated.

Lay Summary

Non-genetic variations consist of phenotypic plasticity and developmental noise, and these variations have been suggested to influence the direction and the rate of evolution. However, the role of phenotypic plasticity and developmental noise in evolutionary process is still poorly understood. Using a rearing experiment, we examined the heritability of plasticity and developmental noise, the correlation of the strength of plastic response to three kinds of environmental factors, and the relationship between plasticity and developmental noise in wing size and wing shape inDrosophila simulans. We found that the degree of phenotypic plasticity and developmental noise were heritable, and positively correlated with each other. Our results suggest that there two non-genetic variations dependently affect the direction and the rate of evolution together.
napari-threedee: a toolkit for human-in-the-loop 3D image analysis in napari
Authors: Yamauchi Kevin A. , Burt Alister
Published: July 2023

With recent advances in three-dimensional bioimaging acquisition and analysis methods, imaging data are an important tool for unveiling the complex architecture of biological organisms. However, extracting insights from these complex datasets requires interactive exploration as well as annotation for training supervised analytical methods. Here we present napari-threedee, a library of composable components and napari plugins for interactively exploring and annotating image data in 3D. We demonstrate how napari-threedee can be used for human-in-the-loop 3D image analysis in diverse image data including fluorescence microscopy and cryoelectron tomography.
Analysis of human BBS protein homologues in insects support alternative non-ciliary functions
Authors: Ewerling Alexander , Graebling Isa , Wierczeiko Anna , Kotzurek Elisa , Foitzik Susanne , Gerber Susanne , Colgan Thomas J. , May-Simera Helen
Published: July 2023

Cilia and flagella were one of the characteristic traits of the last eukaryotic common ancestor and as such, are highly conserved among eukaryotes. Their proteomic makeup is consequently remarkably similar throughout all eukaryotic lineages. Recently, one subgroup of ciliary transport proteins in mammalian cells, the Bardet-Biedl Syndrome (BBS) proteins, was shown to have the ability to traverse the nuclear envelope, and to engage in protein-protein-interactions that modulate gene expression, signalling cascades, and cell homeostasis. Insects have been critically understudied in cilia biology because of their highly specialised cilia being localised on only a small subset of cell types. In this study, we present evidence that the BBSome, a hetero-octameric ciliary transport complex of BBS proteins, is largely conserved in multiple insect lineages. Using the honeybeeApis melliferaas a study system to explore BBS-associated gene expression, our analyses suggest that not all BBSome-associated genes are expressed equally, indicating possible non-ciliary functions. We also demonstrate that the expression of individual BBS proteins varies significantly between the tissues of queens and males inA. mellifera, especially in neuronal tissue. This result raises the question of what role BBS proteins play in these tissues and whether they are involved in gene regulation in insects. The potential gene regulatory function of BBS proteins should be explored in other eukaryotes due to their high degree of conservation.
Multi-omic study of genome-edited human colonoid models of colorectal cancer reveal genotype-specific patterns of microRNA regulation
Authors: Villanueva Jonathan W. , Pan Fong Cheng , Rice Edward J. , Hung Yu-Han , Winnicki Mary , Chen Shuibing , Danko Charles G. , Sethupathy Praveen
Published: July 2023

Combinations of oncogenic mutations drive inter-tumor heterogeneity in colorectal cancer (CRC), which promotes distinct phenotypes and affects therapeutic efficacy. We recently demonstrated that combinations of mutations in mouse small intestinal organoids lead to unique changes in microRNA (miRNA) expression profiles. However, it remains unknown how different mutational backgrounds shape miRNA profiles in the human colon. We leveraged human colonic organoid models, termed colonoids, with gene edits targeting genes commonly mutated in CRC to profile genotype-specific changes in miRNA expression. By small RNA-sequencing we characterized genotype-specific miRNA profiles. We identified one group of miRNAs, including mir-34a-5p and mir-10a-5p, that is strongly downregulated inAPC/KRAS/TP53mutant (AKP-mutant) colonoids. Using chromatin run-on sequencing, we showed that most miRNA alterations in AKP-mutant colonoids are concordant with transcriptional changes. Transcription factor (TF) motif enrichment analysis using transcriptional regulatory elements with increased activity in AKP-mutant colonoids revealed an enrichment of binding sites for multiple oncogenic TFs. Several of these harbor predicted binding sites for mir-10a-5p and/or mir-34a-5p, suggesting these miRNAs may play a role in regulating transcriptional programs in AKP-mutant contexts. Ultimately, our study offers a glimpse into regulatory mechanisms that drive inter-tumor heterogeneity, and we highlight candidate therapeutic targets for the advancement of precision medicine.
A seven-year record of fluctuating core body temperatures of nesting leatherback and hawksbill sea turtles
Authors: Kennedy Malcolm W.
Published: July 2023

Sea turtles experience changes in water temperatures during migrations and seasonal movements that will influence their body temperatures. Nothing is known of how sea turtles’ core body temperatures vary from season to season at nesting sites. Over seven consecutive seasons we measured the surface temperatures of freshly laid eggs as proxies of core temperatures of sea turtles using non-contact infrared thermometers. We measured egg temperatures of two species that have contrasting lifestyles - leatherbacks, the largest, which are adapted to migrate between tropical breeding sites to cold temperate waters, and the smaller hawksbills that are confined to the tropics and sub-tropics. We found considerable year-to-year variations in temperatures in both species (year means 30.4 °C to 31.5 °C in leatherbacks), hawksbills the more so (28.1 °C to 30.3 °C). These differences will likely be modified by both natural seasonal variations and anthropogenic changes in global ocean temperatures and resulting changes in currents and water temperatures local to nesting beaches. These previously unrecognised diversities in body temperatures of nesting turtles are pertinent to predicting environmental tolerances, reproductive success, and nest site selection by sea turtles, and could contribute to predicting which rookeries may remain viable or not during future ocean warming.
Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics
Authors: Kumler William , Hazelton Bryna J. , Ingalls Anitra E.
Published: July 2023

Background

Chromatographic peakpicking continues to represent a significant bottleneck in automated LC-MS workflows. Uncontrolled false discovery rates and the lack of manually-calibrated quality metrics require researchers to visually evaluate individual peaks, requiring large amounts of time and breaking replicability. This problem is exacerbated in noisy environmental datasets and for novel separation methods such as hydrophilic interaction columns in metabolomics, creating a demand for a simple, intuitive, and robust metric of peak quality.

Results

Here, we manually labeled four HILIC oceanographic particulate metabolite datasets to assess the performance of individual peak quality metrics. We used these datasets to construct a predictive model calibrated to the likelihood that visual inspection by an MS expert would include a given mass feature in the downstream analysis. We implemented two novel peak quality metrics, a custom signal-to-noise metric and a test of similarity to a bell curve, both calculated from the raw data in the extracted ion chromatogram and found that these outperformed existing measurements of peak quality. A simple logistic regression model built on two metrics reduced the fraction of false positives in the analysis from 70-80% down to 1-5% and showed minimal overfitting when applied to novel datasets. We then explored the implications of this quality thresholding on the conclusions obtained by the downstream analysis and found that while only 10% of the variance in the dataset could be explained by depth in the default output from the peakpicker, approximately 40% of the variance was explained when restricted to high-quality peaks alone.

Conclusions

We conclude that the poor performance of peakpicking algorithms significantly reduces the power of both univariate and multivariate statistical analyses to detect environmental differences. We demonstrate that simple models built on intuitive metrics and derived from the raw data are more robust and can outperform more complex models when applied to new data. Finally, we show that in properly curated datasets, depth is a major driver of variability in the marine microbial metabolome and identify several interesting metabolite trends for future investigation.
Virus-derived circular RNAs populate hepatitis C virus-infected cells
Authors: Cao Qian , Boonchuen Pakpoom , Chen Tzu-Chun , Lei Shaohua , Somboonwiwat Kunlaya , Sarnow Peter
Published: July 2023

It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a back- splicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into novel proteins that displayed pro-viral functions. Furthermore, a highly abundant, non-translated vcircRNA was shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus.

Significance Statement

Processing of an RNA viral genome into hundreds of circular RNAs provides novel pro-viral functions and can promote translation of novel viral peptides.
Surface crosslinking of virus-like particles increases resistance to proteases, low pH, and mechanical stress for mucosal applications
Authors: Ali Ahmed , Ganguillet Suwannee , Turgay Yagmur , Keys Tim , Causa Erika , Fradique Ricardo , Lutz-Bueno Viviane , Chesnov Serge , Lin Chia-wei , Lentsch Verena , Kotar Jurij , Cicuta Pietro , Mezzenga Raffaele , Slack Emma , Radiom Milad
Published: July 2023

Abstract

Virus-like particles (VLPs) are emerging as nano-scaffolds in a variety of biomedical applications including the delivery of vaccine antigens to mucosal surfaces. These soft, colloidal, and proteinaceous structures (capsids) are nevertheless susceptible to mucosal environmental factors which limit their usefulness. We addressed this issue by crosslinking multiple capsid surface reactive residues using polyethylene glycol tethers. Surface crosslinking enhanced the colloidal stability and mechanical strength of VLPs against low pH, proteases, and mechanical agitation, while it did not interfere with function as vaccine. Chemical crosslinking thus offers a viable means to enhance the resilience of VLPs in mucosal applications.
AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein
Authors: Guo Hao-Bo , Huntington Baxter , Perminov Alexander , Smith Kenya , Hastings Nicholas , Dennis Patrick , Kelley-Loughnane Nancy , Berry Rajiv
Published: July 2023

We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP),Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures ofNvjp-1when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions inNvjp-1are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.

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Effect of a topically applied gel containing antibodies from bovine milk on the relative abundance of Staphylococci in the canine skin microbiome
Authors: Klaassens Eline S. , Auxilia Silvia , Baak Mirna L. , Bongoni Radhika , van Damme Catharina M.M. , Bijker Sannah , Dietz Nardy , Winter Esther , Broere Femke , Foerster Beatrix
Published: July 2023

Canine pyoderma is characterised by a predominant colonisation of the skin withStaphylococcus pseudintermediusand inflammatory symptoms associated with it. Immunoglobulins isolated from cow’ ss milk are neutralizing virulence factors and toxins ofS. pseudintermedius. In a pilot study with four dogs with pyoderma we were able to show that the application of immunoglobulin gel leads to a decrease in the staphylococcal population and an increase in the diversity of the skin microbiome.

Due to the limited number of animals, the measurable effect is not statistically significant. Therefore, we are planning a follow-up study that includes more animals.
Machine learning assisted health viability assay for mouse embryos with artificial confocal microscopy (ACM)
Authors: Goswami Neha , Winston Nicola , Choi Wonho , Lai Nastasia Z. E. , Arcanjo Rachel B. , Chen Xi , Sobh Nahil , Nowak Romana A. , Anastasio Mark A. , Popescu Gabriel
Published: July 2023

The combination of a good quality embryo and proper maternal health factors promise higher chances of a successful in vitro fertilization (IVF) procedure leading to clinical pregnancy and live birth. Of these two factors, selection of a good embryo is a controllable aspect. The current gold standard in clinical practice is visual assessment of an embryo based on its morphological appearance by trained embryologists. More recently, machine learning has been incorporated into embryo selection “packages”. Here, we report a machine-learning assisted embryo health assessment tool utilizing a quantitative phase imaging technique called artificial confocal microscopy (ACM). We present a label-free nucleus detection method with novel quantitative embryo health biomarkers. Two viability assessment models are presented for grading embryos into two classes: healthy/intermediate (H/I) or sick (S) class. The models achieve a weighted F1 score of 1.0 and 0.99 respectively on the in-distribution test set of 72 fixed embryos and a weighted F1 score of 0.9 and 0.95 respectively on the out-of-distribution test dataset of 19 time-instances from 8 live embryos.
Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase dependent mechanism
Authors: Gilsbach Bernd K. , Ho Franz Y. , Riebenbauer Benjamin , Zhang Xiaojuan , Guaitoli Giambattista , Kortholt Arjan , Gloeckner Christian Johannes
Published: August 2023

The Parkinson’s Disease (PD)-linked protein Leucine Rich Repeat Kinase 2 (LRRK2) consists of seven domains, including a kinase and a Roc G domain. Despite the availability of several high-resolution structures, the dynamic regulation of its unique intramolecular domain stack is nevertheless still not well understood. By in-depth biochemical analysis, assessing the Michaelis-Menten kinetics of the Roc G domain, we have confirmed that LRRK2 has, similar to other Roco protein family members, a KMvalue of LRRK2 that lays within the range of the physiological GTP concentrations within the cell. Furthermore, the R1441G PD variant located within a mutational hotspot in the Roc domain showed an increased catalytic efficiency. In contrast, the most common PD variant G2019S, located in the kinase domain, showed an increased KMand reduced catalytic efficiency, suggesting a negative feedback mechanism from the kinase domain to the G domain. Autophosphorylation of the G1+2 residue (T1343) in the Roc P-loop motif is critical for this phosphoregulation of both the KMas well as the kcatvalues of the Roc-catalyzed GTP hydrolysis, most likely by changing the monomer-dimer equilibrium. The LRRK2 T1343A variant has a similar increased kinase activity in cells compared to G2019S and the double mutant T1343A/G2019S has no further increased activity suggesting that T1343 is crucial for the negative feedback in the LRRK2 signaling cascade. Together our data reveal a novel intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase dependent mechanism. Interestingly, PD mutants differently change the kinetics of the GTPase cycle, which might in part explain the difference in penetrance of these mutations in PD patients.