bluuebunny/crossref_metadata_2025 huggingface dataset:
Unfolding of 239Pu–Be and 252Cf neutron energy spectra using passive multi-layer neutron spectrometer
Authors: Maciak Maciej , Domański Szymon , Tulik Piotr , Tymińska Katarzyna , Gryziński Michał A
Published: October 2023

In the study, the passive multi-layer neutron spectrometer, based on thermoluminescence detectors, was tested in a calibration laboratory with 239Pu–Be and 252Cf isotopic sources. MCNP code was used for the calculation of the response functions for the neutron energy range from 1 meV to 100 MeV. It was also utilised for initial guess spectra calculations. Deconvolution was performed with MAXED and GRAVEL deconvolution codes resulting in the neutron spectra defined at the measuring point in the calibration laboratory.
Mechanisms by which the cystic fibrosis transmembrane conductance regulator may influence SARS‐CoV‐2 infection and COVID‐19 disease severity
Authors: Tedbury Philip R. , Manfredi Candela , Degenhardt Frauke , Conway Joseph , Horwath Michael C. , McCracken Courtney , Sorscher Adam J. , Moreau Sandy , Wright Christine , Edwards Carolina , Brewer Jo , Guarner Jeannette , de Wit Emmie , Williamson Brandi N. , Suthar Mehul S. , Ong Yee T. , Roback John D. , Alter David N. , Holter Jan C. , Karlsen Tom H. , Sacchi Nicoletta , Romero‐Gómez Manuel , Invernizzi Pietro , Fernández Javier , Buti Maria , Albillos Agustin , Julià Antonio , Valenti Luca , Asselta Rosanna , Banales Jesus M. , Bujanda Luis , de Cid Rafael , Franke André ,   for the Severe COVID‐19 GWAS group, Sarafianos Stefan G. , Hong Jeong S. , Sorscher Eric J. , Ehrhardt Annette
Published: October 2023

Patients with cystic fibrosis (CF) exhibit pronounced respiratory damage and were initially considered among those at highest risk for serious harm from SARS‐CoV‐2 infection. Numerous clinical studies have subsequently reported that individuals with CF in North America and Europe—while susceptible to severe COVID‐19—are often spared from the highest levels of virus‐associated mortality. To understand features that might influence COVID‐19 among patients with cystic fibrosis, we studied relationships between SARS‐CoV‐2 and the gene responsible for CF (i.e., the cystic fibrosis transmembrane conductance regulator, CFTR). In contrast to previous reports, we found no association between CFTR carrier status (mutation heterozygosity) and more severe COVID‐19 clinical outcomes. We did observe an unexpected trend toward higher mortality among control individuals compared with silent carriers of the common F508del CFTR variant—a finding that will require further study. We next performed experiments to test the influence of homozygous CFTR deficiency on viral propagation and showed that SARS‐CoV‐2 production in primary airway cells was not altered by the absence of functional CFTR using two independent protocols. On the contrary, experiments performed in vitro strongly indicated that virus proliferation depended on features of the mucosal fluid layer known to be disrupted by absent CFTR in patients with CF, including both low pH and increased viscosity. These results point to the acidic, viscous, and mucus‐obstructed airways in patients with cystic fibrosis as unfavorable for the establishment of coronaviral infection. Our findings provide new and important information concerning relationships between the CF clinical phenotype and severity of COVID‐19.
The Versatility of the Lateral-based Mammary Flap as an “Auto-implant” for Enhancing Breast Mound for Patients Undergoing Primary Mastopexy
Authors: Megahed Mohamed Ahmed , Alkandary Qutiba , Abdelaty Mahmoud Ahmed , Ismail Mohammad Samir , Makkar Rami Magdi , AboShaban Mohammed Saad
Published: October 2023

Background:

The demand for augmentation-mastopexy surgery without using implants has significantly increased over the years. Fat transfer offers an alternative method, but some patients do not favor this procedure either. The purpose of this study was to evaluate the versatility of using a lateral-based mammary flap as an “auto-implant” for enhancing the breast mound for patients undergoing primary mastopexy.

Method:

This retrospective study was performed between February 2016 and April 2019, including 36 female patients (72 breasts). Our technique involves using the inferior breast tissue by elevating the lateral-based dermoglandular flap that was moved cranially with a 90 degree rotation in a conical shape within the created pocket to refill the superior and central mound.

Result:

The mean nipple projection was 11.2 after 36 months postoperative compared with 5.2 before surgery. The mean ± SD of pre- and postoperative measurements for the lower pole zone were 80.2 ± 10.5 and 50.1 ± 6.4, and those for the upper pole zone were 40.3 ± 9.5 and 63.9 ± 6.5, respectively. The distance of breast mound elevation after the surgical procedure ranged from 5.30 to 9.55 cm, with a mean of 7.90 cm.

Conclusions:

The lateral-based mammary flap acts like an implant that helps shape and augment the breast, enhances the mammary projection, and restores the breast contour without requiring a synthetic implant or fat grafting. It is a reliable technique with high patient satisfaction but is unsuitable for patients with insufficient breast volume.
Investigation Into Potentially Inappropriate Prescribing Patterns of Loop Diuretics in a Nationally Representative Outpatient Population
Authors: Fosnight Steven , Soric Mate Michael , Smearman Jacob , Graves Emily , Vazquez Melvin , Herrington Zachary , Palladino Carl , Costello Matthew , Knauss Abby
Published: October 2023

Background:

Loop diuretic therapy effectively treats edema related to heart failure, chronic kidney disease, and liver impairment; however, evidence supporting other indications is lacking. For indications such as hypertension or dependent edema or treatment of adverse events associated with other medications, the benefits likely do not outweigh the risks, putting patients at an unacceptably high risk of poor outcomes.

Study Question:

What is the proportion of loop diuretic prescribing that occurs in the absence of a diagnosis of heart failure, chronic kidney disease, liver impairment, or other evidence-based indications?

Study Design:

This was a national, retrospective, cross-sectional investigation conducted using the National Ambulatory Care Survey from 2013 to 2016. Outpatient visits for patients aged 18 years or older prescribed with loop diuretics were included.

Measures and Outcomes:

The primary end point was the frequency of potentially inappropriate loop diuretic prescribing. The secondary end point was a multivariable regression model that identified predictors of potentially inappropriate loop diuretic utilization.

Results:

This analysis identified 5261 outpatient visits conducted during the study period in which loop diuretics were prescribed. Of these, 3648 visits (65.8% of weighted visits) were of patients without a history of heart failure, chronic kidney disease, or liver impairment. Positive predictors included age older than 65 years (odds ratio [OR] 1.71; 95% confidence interval [CI] 1.38–2.13), concomitant calcium channel blocker (OR 1.42; 95% CI, 1.09–1.84), sodium-containing medication use (OR 2.78; 95% CI, 1.23–6.25), and office visit with a cardiology specialist (OR 2.84; 95% CI, 2.31–3.50).

Conclusions:

This analysis identified that loop diuretics are prescribed in the absence of evidence-based indications more frequently than they are prescribed for them. This prescribing pattern creates a unique opportunity for clinicians to optimize patient care. Further study of the outcomes associated with this prescribing pattern is warranted.
Angiopoietin-like 3 inhibition and the liver: less is more?
Authors: Oostveen Reindert F. , Hovingh G. Kees , Stroes Erik S.G.
Published: October 2023

Purpose of review

The aim of this study was to discuss the potential mechanisms and implications of the opposing liver safety results from recent angiopoietin-like 3 (ANGPTL3) inhibition studies.

Recent findings

The clinical development of vupanorsen, a N-acetylgalactosamine (GalNAc) antisense targeting hepatic ANGPTL3, was recently discontinued due to a significant signal of liver transaminase increase. Vupanorsen elicited a dose-dependent increase in hepatic fat fraction up to 75%, whereas the small interfering RNA (siRNA) ARO-ANG3, has reported preliminary evidence of a dose-dependent decrease in hepatic fat fraction up to 30%.

ANGPTL3 inhibition is an attractive therapeutic target to reduce all apoB-containing lipoproteins. The discrepancy in liver signal results between the antisense and siRNA approach may be explained by the level of target inhibition. An alternative explanation may relate to off-target effects of vupanorsen, which have a molecule- and/or platform-specific origin. For intrahepatic strategies, highly potent ANGPTL3 inhibition will for now require special attention for liver safety.
Realities and challenges of head and neck free flap reconstruction in sub-Saharan Africa
Authors: Okerosi Samuel , Nkya Aslam , Fagan Johan , Xu Mary Jue
Published: October 2023

Purpose of review

With an increased need to decentralize and train more head and neck ablative and reconstructive surgeons in sub-Saharan Africa, we assess the realities and challenges of free flap reconstruction in sub–Saharan Africa to provide context of its use as a reconstructive option.

Recent findings

Head and neck free flap reconstruction has been performed by local teams as well as visiting teams in Sub Saharan Africa with good results. Free flap success rates are similar to high income regions at 89% vs. 85–100%. However, flap salvage rates are significantly lower (45% compared to 64.1% reported in high income regions). This has been attributed to resource constraints.

With increasing efforts to increase free flap reconstructive capacity in sub-Saharan Africa, these efforts need to be in the context of available healthcare resources including infrastructure and workforce outside of the surgical team. As training of head and neck ablative and reconstructive surgeons is expanded, reconstructive training needs take the healthcare resource availability into account.
Current opinion in otolaryngology and head and neck surgery: the role of the otolaryngologist in the management of pediatric dysphagia
Authors: Farrell Annie , Raol Nikhila
Published: October 2023

Purpose of review

Dysphagia affects at least 1% of the pediatric population. This prevalence further increases in patients who are born prematurely or who have underlying neuromuscular or cardiopulmonary disorders. A multidisciplinary team approach, including an Otolaryngologist, can help promote an expedited diagnosis and therapeutic regimen, ensuring that the patient receives adequate nutrition needed for growth and development.

Recent findings

The development and growth of multidisciplinary aerodigestive clinics have improved outcomes in pediatric patients with dysphagia. If a structural concern is noted on examination, there remain a multitude of medical and surgical options to help improve patient outcomes and swallow. These treatment options are usually multimodality and specific interventions may be employed to target a specific and notable abnormality.

Pediatric dysphagia is a complex concern. For the otolaryngologist, etiologies with surgical targets may include ankyloglossia, tonsillar hypertrophy, laryngomalacia, laryngo-esophageal cleft, vocal fold movement impairment, and cricopharyngeal achalasia. The development and formalization of a multidisciplinary approach has streamlined and broadened treatment options for these patients. An otolaryngologist is integral as part of the treatment team of these patients.
Intracapsular tonsillectomy: setting a new standard
Authors: Bassett Ethan
Published: October 2023

Purpose of review

Tonsillectomy is one of the most common surgical procedures performed on children in the United States. Since 2002, the intracapsular technique has been studied as a safer and less painful alternative to total tonsillectomy. Concerns have been raised, however, as to the potential for regrowth and long-term outcomes regarding this technique.

Recent findings

Studies support the use of intracapsular tonsillectomy in the management of sleep disordered breathing, including in syndromic populations, as well as for tonsillitis. In addition, safety profiles continue to be improved over that of extracapsular dissection. While the incidence of regrowth ranges depending on the study and duration of follow up, it remains acceptably low. The most consistent independent risk factor for revision surgery includes young age.

While total tonsillectomy is more thoroughly studied historically, an important absence in the literature is a definitive superiority over the intracapsular technique. With continued high-level studies, as well as additional examination of long-term outcomes, we should continue to see greater acceptance of intracapsular tonsillectomy as a standard of practice in a vulnerable population.
Velopharyngeal Insufficiency After Botox Injection for Persistent Bruxism
Authors: Evin Nuh , Sifil Melih K. , Aghazada Turan M. , Özcan Ebru D. , Guneren Ethem
Published: October 2023

Botulinum toxin type-A (BTX-A) injections have emerged as a promising treatment for bruxism and temporomandibular joint (TMJ) disorders. However, there is a need for further exploration of optimal dosage, injection techniques, and intervals to maximize treatment effectiveness. Complications, such as velopharyngeal insufficiency, can occur after BTX-A injections, emphasizing the importance of precautionary measures. The utilization of ultrasound guidance and electromyography assistance can aid in precise injections and minimize the risk of complications. In addition, patients should receive appropriate medication and adhere to post-treatment instructions to alleviate symptoms. Follow-up procedures are essential to monitor potential complications, and in some cases, professional mental health care may be required. Further research is warranted to establish the safety and efficacy of BTX-A injections for the treatment of bruxism and TMJ disorders. This case study presents the development velopharyngeal insufficiency in a patient with chronic bruxism 3 days after receiving a BTX-A injection.
Shortened Motor Evoked Potential Latency in the Epileptic Hemisphere of Children With Focal Epilepsy
Authors: Liu Jingjing , Tsuboyama Melissa , Jannati Ali , Kaye Harper Lee , Hipp Joerg F. , Rotenberg Alexander
Published: October 2023

Purpose:

Motor evoked potential (MEP) amplitude and latency are acquired routinely during neuronavigated transcranial magnetic stimulation, a method of functional mapping of the motor cortex before epilepsy surgery. Although MEP amplitude is routinely used to generate a motor map, MEP latency in patients with focal epilepsy has not been studied systematically. Given that epilepsy may alter myelination, we tested whether intrinsic hand muscle MEPs obtained from the hemisphere containing a seizure focus differ in latency from MEPs collected from the opposite hemisphere.

Methods:

Latencies of abductor pollicis brevis MEPs were obtained during routine motor mapping by neuronavigated transcranial magnetic stimulation in children with intractable, unihemispheric focal epilepsy. The primary motor cortex was stimulated bilaterally in all cases. Only data from patients without a lesion involving the corticospinal tract were included. We tested whether abductor pollicis brevis MEP latency varied as a function of seizure focus lateralization.

Results:

In the 17 patients who met the inclusion criteria, the mean latency of MEPs with amplitudes in the top and bottom quartiles was shorter in the epileptic hemisphere. Interhemispheric latency difference was greater in patients with lesional epilepsy than in those with nonlesional epilepsy (0.7 ± 0.4 vs. 0.1 ± 0.6 milliseconds, P = 0.02).

Conclusions:

Motor evoked potential latency was shortened in the epileptic hemisphere of children with focal epilepsy.
Succinate-mediated reactive oxygen species production in the anoxia-tolerant epaulette (
Hemiscyllium ocellatum
) and grey carpet (
Chiloscyllium punctatum
) sharks
Authors: Devaux Jules B. L. , Hickey Anthony J. R. , Renshaw Gillian M. C.
Published: October 2023

Anoxia/re-oxygenation (AR) results in elevated unchecked oxidative stress and mediates irreversible damage within the brain for most vertebrates. Succinate accumulation within mitochondria of the ischaemic brain appears to increase the production of reactive oxygen species (ROS) upon re-oxygenation. Two closely related elasmobranchs, the epaulette shark (
Hemiscyllium ocellatum
) and the grey carpet shark (
Chiloscyllium punctatum
) repeatedly experience near anoxia and re-oxygenation in their habitats and have adapted to survive AR at tropical temperatures without significant brain injuries. However, these anoxia-tolerant species display contrasting strategies to survive AR, with only
H. ocellatum
having the capacity to supress metabolism and
H. ocellatum
mitochondria the capacity to depress succinate oxidation post-AR. We measured oxygen consumption alongside ROS production mediated by elevated succinate in mitochondria of permeabilized cerebellum from both shark species. Although mitochondrial respiration remained similar for both species, the ROS production in
H. ocellatum
was half that of
C. punctatum
in phosphorylating and non-phosphorylating mitochondria. Maximum ROS production in
H. ocellatum
was mediated by succinate loads 10-fold higher than in
C. punctatum
mitochondria. The contrasting survival strategies of anoxia-tolerant sharks reveal the significance of mitigating ROS production under elevated succinate load during AR, shedding light on potential mechanisms to mitigate brain injury.
A primer on correlation-based dimension reduction methods for multi-omics analysis
Authors: Downing Tim , Angelopoulos Nicos
Published: October 2023

The continuing advances of omic technologies mean that it is now more tangible to measure the numerous features collectively reflecting the molecular properties of a sample. When multiple omic methods are used, statistical and computational approaches can exploit these large, connected profiles. Multi-omics is the integration of different omic data sources from the same biological sample. In this review, we focus on correlation-based dimension reduction approaches for single omic datasets, followed by methods for pairs of omics datasets, before detailing further techniques for three or more omic datasets. We also briefly detail network methods when three or more omic datasets are available and which complement correlation-oriented tools. To aid readers new to this area, these are all linked to relevant R packages that can implement these procedures. Finally, we discuss scenarios of experimental design and present road maps that simplify the selection of appropriate analysis methods. This review will help researchers navigate emerging methods for multi-omics and integrating diverse omic datasets appropriately. This raises the opportunity of implementing population multi-omics with large sample sizes as omics technologies and our understanding improve.
Information theory-based direct causality measure to assess cardiac fibrillation dynamics
Authors: Shi Xili , Sau Arunashis , Li Xinyang , Patel Kiran , Bajaj Nikesh , Varela Marta , Wu Huiyi , Handa Balvinder , Arnold Ahran , Shun-Shin Matthew , Keene Daniel , Howard James , Whinnett Zachary , Peters Nicholas , Christensen Kim , Jensen Henrik Jeldtoft , Ng Fu Siong
Published: October 2023

Understanding the mechanism sustaining cardiac fibrillation can facilitate the personalization of treatment. Granger causality analysis can be used to determine the existence of a hierarchical fibrillation mechanism that is more amenable to ablation treatment in cardiac time-series data. Conventional Granger causality based on linear predictability may fail if the assumption is not met or given sparsely sampled, high-dimensional data. More recently developed information theory-based causality measures could potentially provide a more accurate estimate of the nonlinear coupling. However, despite their successful application to linear and nonlinear physical systems, their use is not known in the clinical field. Partial mutual information from mixed embedding (PMIME) was implemented to identify the direct coupling of cardiac electrophysiology signals. We show that PMIME requires less data and is more robust to extrinsic confounding factors. The algorithms were then extended for efficient characterization of fibrillation organization and hierarchy using clinical high-dimensional data. We show that PMIME network measures correlate well with the spatio-temporal organization of fibrillation and demonstrated that hierarchical type of fibrillation and drivers could be identified in a subset of ventricular fibrillation patients, such that regions of high hierarchy are associated with high dominant frequency.
A supergene in seaweed flies modulates male traits and female perception
Authors: Enge Swantje , Mérot Claire , Mozūraitis Raimondas , Apšegaitė Violeta , Bernatchez Louis , Martens Gerrit A. , Radžiutė Sandra , Pavia Henrik , Berdan Emma L.
Published: October 2023

Supergenes, tightly linked sets of alleles, offer some of the most spectacular examples of polymorphism persisting under long-term balancing selection. However, we still do not understand their evolution and persistence, especially in the face of accumulation of deleterious elements. Here, we show that an overdominant supergene in seaweed flies,
Coelopa frigida
, modulates male traits, potentially facilitating disassortative mating and promoting intraspecific polymorphism. Across two continents, the
Cf-Inv(1)
supergene strongly affected the composition of male cuticular hydrocarbons (CHCs) but only weakly affected CHC composition in females. Using gas chromatography–electroantennographic detection, we show that females can sense male CHCs and that there may be differential perception between genotypes. Combining our phenotypic results with RNA-seq data, we show that candidate genes for CHC biosynthesis primarily show differential expression for
Cf-Inv(1)
in males but not females. Conversely, candidate genes for odorant detection were differentially expressed in both sexes but showed high levels of divergence between supergene haplotypes. We suggest that the reduced recombination between supergene haplotypes may have led to rapid divergence in mate preferences as well as increasing linkage between male traits, and overdominant loci. Together this probably helped to maintain the polymorphism despite deleterious effects in homozygotes.
Musculature of an Early Cambrian cycloneuralian animal
Authors: Zhang Huaqiao , Xiao Shuhai , Eriksson Mats E. , Duan Baichuan , Maas Andreas
Published: October 2023

Cycloneuralians are ecdysozoans with a fossil record extending to the Early Cambrian Fortunian Age and represented mostly by cuticular integuments. However, internal anatomies of Fortunian cycloneuralians are virtually unknown, hampering our understanding of their functional morphology and phylogenetic relationships. Here we report the exceptional preservation of cycloneuralian introvert musculature in Fortunian rocks of South China. The musculature consists of an introvert body-wall muscular grid of four circular and 36 radially arranged longitudinal muscle bundles, as well as an introvert circular muscle associated with 19 roughly radially arranged, short retractors. Collectively, these features support at least a scalidophoran affinity, and the absence of muscles associated with a mouth cone and scalids further indicates a priapulan affinity. As in modern scalidophorans, the fossil musculature, and particularly the introvert circular muscle retractors, may have controlled introvert inversion and facilitated locomotion and feeding. This work supports the evolution of scalidophoran-like or priapulan-like introvert musculature in cycloneuralians at the beginning of the Cambrian Period.
Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development
Authors: Cutter Asher D.
Published: October 2023

Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.
On the relationship between protist metabarcoding and protist metagenome-assembled genomes
Authors: Zavadska Daryna , Henry Nicolas , Auladell Adrià , Berney Cédric , Richter Daniel J.
Published: October 2023

Abstract

The two most commonly used approaches to study the composition of environmental protist communities are marker gene metabarcoding and whole genome analysis through metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches have been developed to assemble metagenomic sequence reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. Due to the nature of their construction, MAGs do not contain the most commonly used barcoding loci, meaning that sequence homology approaches cannot be used to match OTUs and MAGs.

We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from theTaraOceans expedition (2009-2013) based on the correspondence of their relative abundances across the same set of samples. We evaluated the performance of several methods for detecting correspondence between features in these two compositional datasets and developed a series of controls to filter artefacts of data structure and processing. After selecting the best-performing correspondence metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs.

In a subset of cases, V9 OTUs and MAGs could be successfully matched with one another with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: Scenario I - one V9 OTU matches more than one MAG; Scenario II - more than one V9 OTU matches more than one MAG; Scenario III - more than one V9 OTU matches one MAG; Scenario IV - one V9 OTU matches one MAG.

These diverse scenarios for V9 OTU-MAG matches illustrate the complex nature of the OTU/MAG relationship. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity that they represent.
Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET
Authors: Zagotta William N. , Evans Eric G. B. , Eggan Pierce , Tessmer Maxx H. , Shaffer Kyle D. , Petersson E. James , Stoll Stefan , Gordon Sharona E.
Published: October 2023

Proteins are the workhorses of biology, orchestrating a myriad of cellular functions through intricate conformational changes. Protein allostery, the phenomenon where binding of ligands or environmental changes induce conformational rearrangements in the protein, is fundamental to these processes. We have previously shown that transition metal Förster resonance energy transfer (tmFRET) can be used to interrogate the conformational rearrangements associated with protein allostery and have recently introduced novel FRET acceptors utilizing metal-bipyridyl derivatives to measure long (>20 Å) intramolecular distances in proteins. Here, we combine our tmFRET system with fluorescence lifetime measurements to measure the distances, conformational heterogeneity, and energetics of maltose binding protein (MBP), a model allosteric protein. Time-resolved tmFRET captures near-instantaneous snapshots of distance distributions, offering insights into protein dynamics. We show that time-resolved tmFRET can accurately determine distance distributions and conformational heterogeneity of proteins. Our results demonstrate the sensitivity of time-resolved tmFRET in detecting subtle conformational or energetic changes in protein conformations, which are crucial for understanding allostery. In addition, we extend the use of metal-bipyridyl compounds, showing Cu(phen)2+can serve as a spin label for pulse dipolar electron paramagnetic resonance (EPR) spectroscopy, a method which also reveals distance distributions and conformational heterogeneity. The EPR studies both establish Cu(phen)2+as a useful spin label for pulse dipolar EPR and validate our time-resolved tmFRET measurements. Our approach offers a versatile tool for deciphering conformational landscapes and understanding the regulatory mechanisms governing biological processes.

STATEMENT OF SIGNIFICANCE

Responsible for the regulation of virtually all biological processes, allosteric proteins are fundamental to all life. To understand the mechanisms for their vital functions, we must determine the structure and energetics of these proteins under physiological conditions. In this work, we have developed a fluorescence method that allows for the simultaneous measurement of protein structure and energetics under physiological conditions. These studies pave the way for future advances in physiology and medicine.
MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples
Authors: Xu Sheng , Morgan Daniel C. , Qian Gordon , Huang Yuanhua , Ho Joshua W. K.
Published: October 2023

Motivation

Strain-level analysis of metagenomic data has garnered significant interest in recent years. Microbial single nucleotide polymorphisms (SNPs) are genomic variants that can reflect strain-level differences within a microbial species. The diversity and emergence of SNPs in microbial genomes may reveal evolutionary history and environmental adaptation in microbial populations. However, efficient discovery of shared polymorphic variants in a large collection metagenomic samples remains a computational challenge.

Results

MetaQuad employs a density-based clustering technique to efficiently differentiate shared variants from non-polymorphic sites using shotgun metagenomic data. Empirical comparisons with other state-of-the-art methods show that MetaQuad significantly reduces the number of false-positive SNPs without greatly affecting the true-positive rate. We used MetaQuad to identify antibiotic-associated variants in patients who underwentHelicobacter pylorieradication therapy. MetaQuad detected 7,591 variants across 529 antibiotic resistance genes. The nucleotide diversity of some genes is increased six weeks after antibiotic treatment, potentially indicating the role of these genes in specific antibiotic treatments.

Availability

MetaQuad is an open-source Python package available viahttps://github.com/holab-hku/MetaQuad.

Contact

jwkho@hku.hk

Supplementary information

Supplementary data are available atXXXXonline.
Single-nucleus transcriptomics reveals disease- and pathology-specific signatures in α-synucleinopathies
Authors: Nido Gonzalo S , Castelli Martina , Mostafavi Sepideh , Rubiolo Anna , Shadad Omnia , Alves Guido , Tysnes Ole-Bjørn , Dölle Christian , Tzoulis Charalampos
Published: October 2023

α-synucleinopathies are severe neurodegenerative disorders characterized by intracellular aggregation of α-synuclein, yet their molecular pathogenesis remains unknow. Here, we explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single-nucleus RNA sequencing (snRNA-seq) on nearly 300,000 nuclei from the prefrontal cortex of individuals with idiopathic Parkinson’s disease (iPD), Parkinson’s disease caused byLRRK2mutations (LRRK2-PD), multiple system atrophy (MSA) and healthy controls. iPD and LRRK2-PD exhibit a largely overlapping cell type-specific signature, which is distinct from that of MSA, and includes an overall decrease of the transcriptional output in neurons. Notably, most of the differential expression signal in iPD and LRRK2-PD is concentrated in a specific deep cortical neuronal subtype expressing adrenoceptor alpha 2A. While most differentially expressed genes are highly cell type- and disease-specific,PDE10Ais found consistently downregulated in most cortical neurons, and across all three diseases. Finally, exploiting the variable presence and/or severity of α-synuclein pathology in LRRK2-PD and iPD, we identify cell type-specific signatures associated with α-synuclein pathology, including a neuronal upregulation of theSNCAgene itself, encoding α-synuclein. Our findings provide novel insights into the cell-specific transcriptional landscape of the α-synucleinopathy spectrum.
Maintenance of Heterochromatin links Chromatin Modifiers and Neurodevelopment in Autism Spectrum Disorder
Authors: Garvin Michael R. , Kainer David
Published: October 2023

Autism spectrum disorder (ASD) is a highly heritable and highly heterogeneous neuropsychiatric condition whose cause is still unknown because there are no recurrent genes found among diagnosed individuals. One of the most common functional properties of the many reported risk-genes for autism is “chromatin modification” but it is not known how this biological process relates to neurodevelopment and autism. We recently reported frequent, recurrent genomic structural variants (SVs) in two cohorts of individuals with autism that were identified using non-Mendelian inheritance (NMI) patterns in family trios. The genes harboring the SVs participate in neurodevelopment, glutamate signaling, and chromatin modification, confirming previous reports and providing greater detail for these processes in ASD. The majority of these ASD-associated SVs (ASD-SV) were found in non-coding regions of the genome and were enriched for expression quantitative trait loci (eQTL) suggesting that gene dysregulation results from these genomic disruptions rather than alteration of proteins. Here, we intersect the ASD-SV from our earlier work with different gene regulatory and epigenetic multiomic layers to understand how they may function to produce autism. Our results indicate that the core of ASD resides in the dysregulation of a process called RNA-induced Initiation of Transcriptional gene Silencing (RITS) that is meant to maintain heterochromatin and produces SVs in the genes within these chromosomal regions, resulting in alterations in brain development. This finally links reported ASD-risk genes involved in chromatin remodeling with neurodevelopment. In addition, it may explain the role ofde novomutations in ASD and provide a framework for more accurate diagnostics and endophenotypes.
Acute kidney injury after cardiac surgery is associated with platelet activation
Authors: Brown Naomi , Sullo Nikol , Tyson Nathan , Eagle-Hemming Bryony , Lai Florence Y. , Sheikh Sophia , Tomkova Kristina , Joel-David Lathishia , Kumar Tracy , Aujla Hardeep , Goodall Alison H , Murphy Gavin J , Woźniak Marcin J
Published: October 2023

Background

Post-cardiac surgery acute kidney injury (AKI) is common, with high rates of mortality and morbidity. Despite extensive research, the AKI pathogenesis is still unknown. We hypothesised that platelet activation, circulating extracellular vesicles (EV) and micro-RNA levels associate with post-surgery AKI.

Methods

Plasma samples were collected from 95 patients recruited to the MaRACAS study before, immediately after and 6-12, 24 and 48 hours after cardiac surgery. Platelet responsiveness was measured with Multiplate. Flow cytometry was used to measure platelet and leukocyte activation and EV derivation, while EV size distribution and concentrations were measured using NanoSight. Circulating soluble biomarkers were measured by immunoassays. Micro-RNA was measured by TaqMan arrays, validated by qPCR.

Results

In the 57% (54/95) of patients who developed AKI post-surgery, the numbers of platelet-derived EVs were higher 24 hours after surgery. Platelets in AKI patients were desensitised to ADP 6-12 hours after surgery, independent of the administration of aspirin or P2Y12 antagonists. AKI patients also had more activated platelets 6-12 hours after surgery, more circulating platelet-granulocyte aggregates before and 6-12 and 24 hours after surgery and higher levels of sICAM1 before and 48 hours after surgery. TaqMan arrays identified miR-668 downregulated before and miR-92a-1, –920, –518a-3p, –133b and –1262 upregulated after surgery in AKI patients. qRT-PCR confirmed these differences for miR-1262.

Conclusions

AKI is associated with increased platelet activation during cardiac surgery, indicating that alternative platelet inhibition treatments may be renoprotective. Studies in larger cohorts are required to validate these findings.
Perceptions of access to harm reduction services during the COVID-19 pandemic among people who inject drugs in Chicago
Authors: Kristensen Kathleen , Boodram Basmattee , Avila Wendy , Pineros Juliet , Latkin Carl , Mackesy-Amiti Mary-Ellen
Published: October 2023

Background

The COVID-19 pandemic amplified the risk environment for people who inject drugs (PWID), making continued access to harm reduction services imperative. Research has shown that some harm reduction service providers were able to continue to provide services throughout the pandemic. Most of these studies, however, focused on staff perspectives, not those of PWID. Our study examines changes in perceptions of access to harm reduction services among PWID participating in a longitudinal study conducted through the University of Illinois-Chicago’s Community Outreach Intervention Project field sites during the COVID-19 pandemic.

Methods

Responses to a COVID-19 module added to the parent study survey that assessed the impact of COVID-19 on PWID participating in an ongoing longitudinal study were analyzed to understand how study participants’ self-reported access to harm reduction services changed throughout the pandemic. Mixed effects logistic regression was used to examine difficulty in syringe access as an outcome of COVID-19 phase.

Results

Most participants reported that access to syringes and naloxone remained the same as prior to the pandemic. Participants had significantly higher odds of reporting difficulty in accessing syringes earlier in the pandemic.

Conclusions

The lack of perceived changes in harm reduction access by PWID and the decrease in those reporting difficulty accessing syringes as the pandemic progressed suggests the efficacy of adaptations to harm reduction service provision (e.g., window and mobile service) during the pandemic. Further research is needed to understand how the COVID-19 pandemic may have impacted PWIDs’ engagement with harm reduction services.
Interface-aware molecular generative framework for protein-protein interaction modulators
Authors: Wang Jianmin , Mao Jiashun , Li Chunyan , Xiang Hongxin , Wang Xun , Wang Shuang , Wang Zixu , Chen Yangyang , Li Yuquan , No Kyoung Tai , Song Tao , Zeng Xiangxiang
Published: October 2023

Protein-protein interactions (PPIs) play a crucial role in numerous biochemical and biological processes. Although several structure-based molecular generative models have been developed, PPI interfaces and compounds targeting PPIs exhibit distinct physicochemical properties compared to traditional binding pockets and small-molecule drugs. As a result, generating compounds that effectively target PPIs, particularly by considering PPI complexes or interface hotspot residues, remains a significant challenge. In this work, we constructed a comprehensive dataset of PPI interfaces with active and inactive compound pairs. Based on this, we propose a novel molecular generative framework tailored to PPI interfaces, named GENiPPI. Our evaluation demonstrates that GENiPPI captures the implicit relationships between the PPI interfaces and the active molecules, and can generate novel compounds that target these interfaces. Moreover, GENiPPI can generate structurally diverse novel compounds with limited PPI interface modulators. To the best of our knowledge, this is the first exploration of a structure-based molecular generative model focused on PPI interfaces, which could facilitate the design of PPI modulators. The PPI interface-based molecular generative model enriches the existing landscape of structure-based (pocket/interface) molecular generative model.
Quinoa as Functional Food? Urinary elimination of ecdysterone after consumption of quinoa alone and in combination with spinach
Authors: Isenmann Eduard , Yuliandra Tasha , Touvleliou Konstantina , Broekmann Matthias , Torre Xavier de la , Botrè Francesco , Diel Patrick , Parr Maria Kristina
Published: October 2023

The phytosteroid ecdysterone is included on the monitoring list of the World Anti-Doping Agency. Therefore, the consumption of food rich in ecdysterone is the focus of a lively debate. Thus, urinary excretion of ecdysterone and its metabolites in humans was investigated following quinoa consumption alone and in combination with spinach.

After intake of both preparations, ecdysterone and two metabolites were excreted in urine. Maximum concentrations of ecdysterone ranged from 0.44–5.50µg/mL after quinoa and 0.34– 4.09µg/mL after quinoa with spinach. The total urinary excreted amount as parent drug plus metabolites was 2.60(1.09)% following quinoa and 1.71(0.86)% after combination. Significant differences were found in total urinary excreted amounts of ecdysterone, 14-deoxy-ecdysterone, and 14-deoxy-poststerone. In conclusion, only small proportions of ecdysterone from quinoa and the combination with spinach were excreted in urine. The results indicate that both, quinoa and spinach, are poor sources of ecdysterone.
Acute exposure to caffeine improves navigation in an invasive ant
Authors: Galante Henrique , De Agrò Massimo , Koch Alexandra , Kau Stefanie , Czaczkes Tomer J.
Published: October 2023

Invasive alien species are a major and growing problem, devastating ecosystems and costing billions of euros in damage and control efforts. Argentine ants,Linepithema humile, are particularly concerning, with control efforts often falling short likely due to a lack of sufficient bait consumption. Using neuroactives to manipulate ant navigation and learning could increase recruitment and consumption, ultimately leading to more efficient control strategies. Caffeine is naturally occurring, cheap, and has been found to cause motivational and cognitive improvements in bees. Here, we subjectL. humileto a wide range of caffeine concentrations and a complex but ecologically relevant task: an open landscape foraging experiment. Without caffeine, we find no effect of consecutive foraging visits on the time the ants take to reach a reward, suggesting a failure to learn the reward’s location. However, low (25ppm) to intermediate (250ppm) concentrations of caffeine lead to a decrease of up to 38% in the time taken to find the reward during each consecutive visit, implying that caffeine boosts learning. Interestingly, such improvements are lost at high (2000ppm) doses. In contrast, caffeine appears to have no impact on the ants’ homing behaviour, as the time required to reach the nest was similar across treatments. The effect of caffeine is thus not only dose-dependent, but also differentially targets neurologically distinct navigational mechanisms. Adding moderate levels of caffeine to baits could be a simple way to improve ant’s ability to learn its location, potentially leading to increased recruitment to, and consumption of, the toxicant.
Epigenetic insights into GABAergic development in Dravet Syndrome iPSC and therapeutic implications
Authors: Schuster Jens , Lu Xi , Dang Yonglong , Klar Joakim , Wenz Amelie , Dahl Niklas , Chen Xingqi
Published: October 2023

Dravet syndrome (DS) is a devastating early onset refractory epilepsy syndrome caused by variants in theSCN1Agene. A disturbed GABAergic interneuron function is implicated in the progression to DS but the underlying developmental and pathophysiological mechanisms remain elusive, in particularly at the chromatin level. In this study, we utilized induced pluripotent stem cells (iPSCs) derived from DS cases and healthy donors to model disease- associated epigenetic abnormalities of GABAergic development. Employing the ATAC-Seq technique, we assessed chromatin accessibility at multiple time points (Day 0, Day 19, Day 35, and Day 65) of GABAergic differentiation. Additionally, we elucidated the effects of the commonly used anti-seizure drug valproic acid (VPA) on chromatin accessibility in GABAergic cells. The distinct dynamics in chromatin profile of DS iPSC predicted accelerated early GABAergic development, evident at D19, and diverged further from the pattern in control iPSC with continued differentiation, indicating a disrupted GABAergic maturation. Exposure to VPA at D65 reshaped the chromatin landscape at a variable extent in different iPSC-lines and rescued the observed dysfunctional development in some DS iPSC-GABA. This study provides the first comprehensive investigation on the chromatin landscape of GABAergic differentiation in DS-patient iPSC, offering valuable insights into the epigenetic dysregulations associated with interneuronal dysfunction in DS. Moreover, our detailed analysis of the chromatin changes induced by VPA in iPSC-GABA holds the potential to improve development of personalized and targeted anti-epileptic therapies.