bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.

Summary
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.

Summary
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.
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.
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

AbstractThe 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

ABSTRACTProteins 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 SIGNIFICANCEResponsible 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

AbstractMotivationStrain-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.ResultsMetaQuad 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.AvailabilityMetaQuad is an open-source Python package available viahttps://github.com/holab-hku/MetaQuad.Contactjwkho@hku.hkSupplementary informationSupplementary 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

Abstractα-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

AbstractAutism 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

AbstractBackgroundPost-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.MethodsPlasma 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.ResultsIn 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.ConclusionsAKI 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

ABSTRACTBackgroundThe 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.MethodsResponses 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.ResultsMost 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.ConclusionsThe 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.
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

AbstractThe 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

AbstractInvasive 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.