bluuebunny/crossref_metadata_2025 huggingface dataset:
Gastroesophageal resuscitative occlusion of the aorta prolongs survival in a lethal liver laceration model
Authors: McCracken Brendan M. , Tiba Mohamad Hakam , Colmenero Mahmood Carmen I. , Leander Danielle C. , Greer Nicholas L. , Plott Jeffery S. , Shih Albert J. , Wang Stewart C. , Eliason Jonathan L. , Ward Kevin R.
Published: October 2021

BACKGROUND

Noncompressible torso hemorrhage management remains a challenge especially in the prehospital setting. We evaluated a device designed to occlude the aorta from the stomach (gastroesophageal resuscitative occlusion of the aorta [GROA]) for its ability to stop hemorrhage and improve survival in a swine model of lethal liver laceration and compared its performance to resuscitative endovascular balloon occlusion of the aorta (REBOA) and controls.

METHODS

Swine (n = 24) were surgically instrumented and a 30% controlled arterial hemorrhage over 20 minutes was followed by liver laceration. Animals received either GROA, REBOA, or control (no treatment) for 60 minutes. Following intervention, devices were deactivated, and animals received whole blood and crystalloid resuscitation. Animals were monitored for an additional 4 hours.

RESULTS

The liver laceration resulted in the onset of class IV shock. Mean arterial blood pressure (MAP) (standard deviation) decreased from 84.5 mm Hg (11.69 mm Hg) to 27.1 mm Hg (5.65 mm Hg) at the start of the intervention. Seven of eight control animals died from injury prior to the end of the intervention period with a median survival (interquartile) time of 10.5 minutes (12 minutes). All GROA and REBOA animals survived the duration of the intervention period (60 minutes) with median survival times of 86 minutes (232 minutes) and 79 minutes (199 minutes) after resuscitation, respectively. The GROA and REBOA animals experienced a significant improvement in survival compared with controls (p = 0.01). Resuscitative endovascular balloon occlusion of the aorta resulted in higher MAP at the end of intervention 114.6 mm Hg (22.9 mm Hg) compared with GROA 88.2 mm Hg (18.72 mm Hg) (p = 0.024), as well as increased lactate compared with GROA 13.2 meq·L−1 (1.56 meq·L−1) versus 10.5 meq·L−1 (1.89 meq·L−1) (p = 0.028). Histological examination of the gastric mucosa in surviving animals revealed mild ischemic injury from both GROA and REBOA.

CONCLUSION

The GROA and REBOA devices were both effective at temporarily stanching lethal noncompressible torso hemorrhage of the abdomen and prolonging survival.
Motor Evoked Potentials in Newly Diagnosed and Treated Patients With Wilson Disease
Authors: Bembenek Jan P. , Kurczych Katarzyna , Kłysz Bożena , Smoliński Łukasz , Litwin Tomasz , Członkowska Anna
Published: October 2021

Purpose:

To investigate whether patients with Wilson disease have abnormal motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation.

Methods:

In a prospective, observational, single-center study, transcranial magnetic stimulation was used to examine MEPs recorded from the abductor digiti minimi in 24 newly diagnosed treatment-naive patients and 21 treated patients with Wilson disease.

Results:

Motor evoked potentials were recorded in 22 (91.7%) newly diagnosed treatment-naive patients and in 20 (95.2%) treated patients. Abnormal MEP parameters were found in a similar proportion of newly diagnosed and treated patients: MEP latency (38% vs. 29%), MEP amplitude (21% vs. 24%), central motor conduction time (29% vs. 29%), and resting motor threshold (68% vs. 52%). Abnormal MEP amplitude (P= 0.044) and resting motor threshold (P= 0.011) were more frequent in treated patients with brain MRI abnormalities but not in newly diagnosed patients. We did not observe significant improvement in MEPs parameters after 1 year of treatment introduction in eight examined patients. However, in one patient where MEPs were initially nondetectable, they were present 1 year after treatment introduction with zinc sulfate, although MEPs were not in the normal range.

Conclusions:

Motor evoked potential parameters did not differ between newly diagnosed and treated patients. There was no significant improvement in MEP parameters one year after treatment introduction. Further studies conducted on large cohorts are necessary to determine the usefulness of MEPs in detecting pyramidal tract damage and improvement after anticopper treatment introduction in Wilson disease.
Late Component of the Trigemino-Cervical Reflex: Clinical and Neuroradiological Correlations
Authors: Asan Furkan , Gündüz Ayşegül , Kızıltan Meral E.
Published: October 2021

Introduction:

The authors aimed to analyze the possible relationship of the late response of trigemino-cervical reflex (TCR) with various clinical conditions having brainstem lesions and lesion localizations in the brainstem.

Methods:

The authors enrolled 30 healthy subjects, 16 patients with stroke, 14 patients with multiple sclerosis (MS), and 9 patients with neuro-Behçet disease. All patients had at least one MRI, and lesion localization was classified into midbrain, pons, medulla oblongata, or their combinations. The TCR was recorded simultaneously from bilateral sternocleidomastoid and splenius capitis muscles.

Results:

There was no significant difference based on lesion localization within the brainstem. Trigemino-cervical reflex latency was significantly longer in patients with MS compared with all other groups (P < 0.005 for each comparison). The Receiver Operating Characteristic curve analysis of sternocleidomastoid showed a cut-off value of 76.9 ms with 44% sensitivity and 92.7% specificity to predict MS. Similarly, the authors determined a cut-off value of 61.5 ms of splenius capitis latency with 38.5% sensitivity and 91.5% specificity to predict MS.

Conclusions:

This study showed that TCR might be abnormal in a given patient with one brainstem lesion, independently from the lesion localization. This may be attributed to a broad network of TCR at the brainstem. Thus, abnormally delayed TCR responses can be used as a tool for the discrimination of MS among other brainstem lesions.
Winged Scapula: Clinical and Electrophysiological Features and Common Causes Based on 20 Years of Experience in a Referral Center in Turkey
Authors: Azman Filiz , Yildiz Fatma Gokcem , Temucin Cagri Mesut
Published: October 2021

Purpose:

Winged scapula (WS) is a functionally disabling problem and it occurs because of neurogenic causes frequently. The authors aimed to assess WS patients by physical and electrodiagnostic examinations as well as some further investigations and define the common causes of WS.

Methods:

The authors reviewed clinical and neurophysiological findings of 52 patients who were referred for electrodiagnostic examination because of WS in the period of 20 years.

Results:

The mean age was 39 (range, 11–73) years and 32 were male patients. Right side was involved in 60% of patients (n = 31). According to electrodiagnostic examinations, 44 patients (85%) had neurogenic causes; 29 spinal accessory nerve palsy (17 occurred after surgical procedure), nine long thoracic nerve palsy (four occurred after strenuous activity), two dorsal scapular nerve (both neuralgic amyotrophy), one long thoracic nerve and spinal accessory nerve (relevant with strenuous trauma), one spinal accessory nerve and dorsal scapular nerve palsies (after surgical procedure and radiotherapy), one C5-7 radiculopathy (avulsion), and one brachial plexopathy (obstetric trauma). Five patients (10%) had muscle-related findings (four facio-scapulo-humeral dystrophy and one Duchenne muscular dystrophia) and three patients (5%) had normal findings (bone-joint related).

Conclusions:

This study presents a relatively large series of patients with WS because of several causes from a referral tertiary EMG laboratory. The authors found that spinal accessory nerve palsy after neck surgery is the most common cause and long thoracic nerve palsy is the second common cause of unilateral WS. Electrodiagnostic examinations should be performed in WS patients to establish exact diagnosis and reveal some coexistence of WS causes.
Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov
Authors: Teo Wee Fei Aaron , Tan Geok Yuan Annie , Li Wen-Jun
Published: October 2021

The taxonomic positions of members within the familyPseudonocardiaceaewere assessed based on phylogenomic trees reconstructed using core-proteome and genomeblastdistance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the familyPseudonocardiaceaewere analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values. The familyPseudonocardiaceaeconsists of the type genusPseudonocardia, as well as the generaActinoalloteichus,Actinocrispum,Actinokineospora,Actinomycetospora,Actinophytocola,Actinopolyspora,Actinorectispora,Actinosynnema,Allokutzneria,Allosaccharopolysporagen. nov.,Amycolatopsis,Bounagaea,Crossiella,Gandjariella,Goodfellowiella,Haloactinomyces,Haloechinothrix,Halopolyspora,Halosaccharopolysporagen. nov.,Herbihabitans,Kibdelosporangium,Kutzneria,Labedaea,Lentzea,Longimycelium,Prauserella,Saccharomonospora,Saccharopolyspora,Saccharothrix,Salinifilum,Sciscionella,Streptoalloteichus,Tamaricihabitans,Thermocrispum,ThermotunicaandUmezawaea. The G+C contents of thePseudonocardiaceaegenomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the namesAllosaccharopolyspora corallicomb. nov.,Halosaccharopolyspora lacisalsicomb. nov. andActinoalloteichus caeruleuscomb. nov. are proposed. This study revealed thatActinokineospora mzabensisis a heterotypic synonym ofActinokineospora spheciospongiae,Lentzea desertiis a heterotypic synonym ofLentzea atacamensis,Prauserella endophyticais a heterotypic synonym ofPrauserella coralliicola, andPrauserella flavaandPrauserella sediminisare heterotypic synonyms ofPrauserella salsuginis. This study addresses the nomenclature conundrums ofActinoalloteichus cyanogriseusandStreptomyces caeruleusas well asMicropolyspora internatusandSaccharomonospora viridis.
Mobility network reveals the impact of spatial vaccination heterogeneity on COVID-19
Authors: Yuan Yuan , Jahani Eaman , Zhao Shengjia , Ahn Yong-Yeol , Pentland Alex
Published: October 2021

Mass vaccination is one of the most effective epidemic control measures. Because one’s vaccination decision is shaped by social processes, the pattern of vaccine uptake tends to show strong social and spatial heterogeneity, such as urban-rural divide and clustering. Examining through network perspectives, we develop a framework for estimating the impact of spatial vaccination heterogeneity on epidemic outbreaks. Leveraging fine-grained mobility data and computational models, we investigate two network effects—the “hub effect” (vaccinating mobility hubs reduces transmission) and the “homophily effect” (stronger homophily in vaccination rates increases transmission). Applying Bayesian deep learning and fine-grained epidemic simulations, our study suggests a negative effect of homophily and a positive effect of highly vaccinated hubs on reducing case counts for both the synthetic network and the U.S. mobility network. Our framework enables us to evaluate outcomes from various hypothetical spatial vaccine distributions and to study a hypothetical vaccination campaign strategy that targets a small number of regions with the largest gain in protective power using the data from January 2022. Our simulation suggests that our strategy can potentially prevent about 2.5 times more cases than a uniform strategy with an additional 1% of the population vaccinated. Notably, our simulation also shows that this strategy could even better protect vulnerable or disadvantaged communities through network effects than strategies that directly target them. Our study suggests that we need to examine the interplay between vaccination patterns and mobility networks beyond the overall vaccination rate, and that understanding geographical pattern of vaccine uptake could be just as important as improving the overall vaccination rate.
Dampening of the respiratory cytokine storm is promoted by inhaled budesonide in patients with early COVID-19
Authors: Baker Jonathan R , Mahdi Mahdi , Nicolau Dan V , Ramakrishnan Sanjay , Barnes Peter J , Simpson Jodie L , Cass Steven P , Russell Richard EK , Donnelly Louise E , Bafadhel Mona
Published: October 2021

Vaccinations against SARS-CoV-2 are effective in COVID-19. However, with limited vaccine access, vaccine hesitancy and variant breakthroughs, there is still a need for effective and safe early treatments. Two community-based clinical trials of the inhaled corticosteroid, budesonide, have recently been published showing and improvement in patients with COVID-19 treated early with budesonide1,2. To understand mechanistically how budesonide was beneficial, inflammatory mediators were assessed in the nasal mucosa of patients recruited to the Steroids in COVID (STOIC1) trial and a cohort of SARS-CoV-2 negative individuals. Here we show that in early COVID-19, elevation in viral response proteins and Th1 and Th2 inflammation occurs. Longitudinal sampling in the natural course of COVID-19 showed persistently high interferon levels and elevated concentrations of the eosinophil chemokine, CCL11. In patients who deteriorate, the initial nasal mucosal signal is characterised by a marked suppression of the early inflammatory response, with reduced concentrations of interferon and inflammatory cytokines, but elevated eosinophil chemokines. Systemic inflammation remained altered in COVID-19 patients, implying that even after symptom resolution, changes in immunological mediators do not resolve. Budesonide treatment decreased IL-33 and IFN-γ, implying a reduction in epithelial damage and dampening of the interferon response. Budesonide treatment also increased CCL17 concentrations, suggesting an improved T-cell response; and significantly alters inflammatory pathways giving further insight into how this treatment can accelerate patient recovery.

Abstract Figure
A miniature kinematic coupling device for mouse head fixation
Authors: Kim Su Jin , Slocum Alexander H. , Scott Benjamin B.
Published: October 2021

Head-fixation is a common technique in the preparation of subjects for neuroscience experiments. Accurate alignment, stability, and repeatability during fixation provide experimental consistency, thus enabling the subject to return to the same position over time to provide meaningful data. Head restraint systems inspired by kinematic clamps have been developed to allow micron scale repositioning across imaging epochs in rats. Here we report the development of a light-weight, implantable kinematic coupling (clamp) system that is wearable by mice, and enables repeated positioning to submicron accuracy across imaging epochs. This system uses a stainless steel headplate and a Maxwell-style three-groove kinematic mounting system with magnetic force clamping load. Spheres on the dorsal surface of the headplate provide contact points for vee-groove kinematic features machined into a tabletop mount. Evaluation of the clamp using multiphoton microscopy revealed submicron precision in registration accuracy and stability, allowing cellular resolution calcium imaging in awake, behaving mice. These results indicate that miniaturized implantable kinematic clamps for mice could be valuable for future experiments which require repositioning of subjects across time and different instruments.

Highlights

Development of a kinematic clamp for mice for precise repositioning in chronic studies.

Headplate and clamp provide stability for cellular resolution imaging during behavior.

Ruby contact features enable submicron registration repeatability.
Spatial-temporal analysis of nanoparticles in live tumor spheroids impacted by cell origin and density
Authors: Ahmed-Cox Aria , Pandzic Elvis , Johnston Stuart T. , Heu Celine , McGhee John , Mansfeld Friederike M. , Crampin Edmund J. , Davis Thomas P. , Whan Renee M. , Kavallaris Maria
Published: October 2021

Nanoparticles hold great preclinical promise in cancer therapy but continue to suffer attrition through clinical trials. Advanced, three dimensional (3D) cellular models such as tumor spheroids can recapitulate elements of the tumor environment and are considered the superior model to evaluate nanoparticle designs. However, there is an important need to better understand nanoparticle penetration kinetics and determine how different cell characteristics may influence this nanoparticle uptake. A key challenge with current approaches for measuring nanoparticle accumulation in spheroids is that they are often static, losing spatial and temporal information which may be necessary for effective nanoparticle evaluation in 3D cell models. To overcome this challenge, we developed an analysis platform, termed the Determination of Nanoparticle Uptake in Tumor Spheroids (DONUTS), which retains spatial and temporal information during quantification, enabling evaluation of nanoparticle uptake in 3D tumor spheroids. Outperforming linear profiling methods, DONUTS was able to measure silica nanoparticle uptake to 10 µm accuracy in both isotropic and irregularly shaped cancer cell spheroids. This was then extended to determine penetration kinetics, first by a forward-in-time, center-in-space model, and then by mathematical modelling, which enabled the direct evaluation of nanoparticle penetration kinetics in different spheroid models. Nanoparticle uptake was shown to inversely relate to particle size and varied depending on the cell type, cell stiffness and density of the spheroid model. The automated analysis method we have developed can be applied to live spheroids in situ, for the advanced evaluation of nanoparticles as delivery agents in cancer therapy.
Electro-mechanical transfection for non-viral primary immune cell engineering
Authors: Sido Jessica M. , Hemphill James B. , McCormack Rameech N. , Beighley Ross D. , Grant Bethany F. , Buie Cullen R. , Garcia Paulo A.
Published: October 2021

Non-viral approaches to transfection have emerged a viable option for gene transfer. Electro-mechanical transfection involving use of electric fields coupled with high fluid flow rates is a scalable strategy for cell therapy development and manufacturing. Unlike purely electric field-based or mechanical-based delivery methods, the combined effects result in delivery of genetic material at high efficiencies and low toxicity. This study focuses on delivery of reporter mRNA to show electro-mechanical transfection can be used successfully in human T cells. Rapid optimization of delivery to T cells was observed with efficiency over 90% and viability over 80%. Confirmation of optimized electro-mechanical transfection parameters was assessed in multiple use cases including a 50-fold scale up demonstration. Transcriptome and ontology analysis show that delivery, via electro-mechanical transfection, does not result in gene dysregulation. This study demonstrates that non-viral electro-mechanical transfection is an efficient and scalable method for cell and gene therapy engineering and development.

One Sentence Summary

This study demonstrates that non-viral electro-mechanical transfection is an efficient and scalable method for development of engineered cellular therapies.
Fruit flies subjected to TBI exhibit genotype-dependent changes in seizure incidence and duration
Authors: Krcmarik Tori R , Willes Ashley M , Yang A , Weber Sydney L , Brusich Douglas J
Published: October 2021

Traumatic brain injury (TBI) is common and often debilitating. One complication following TBI is post-traumatic seizures (PTS). However, there is a poor understanding of PTS, in part, because it is challenging to model. We sought to develop a fly model of PTS. We used a high-impact trauma (HIT) device to inflict TBI and followed this with behavioral, bang-testing methods to assess seizure behavior. Our results showed PTS incidence was sensitive to genetic background. We also found seizure duration was most pronounced at 30 minutes after injury. Our findings support the efficacy of our fly model for coarse screening of seizure behavior. We expect this model will be useful in first-pass screens intended to identify modifiers of seizure risk following TBI.
Brain-inspired spiking neural network controller for a neurorobotic whisker system
Authors: Antonietti Alberto , Geminiani Alice , Negri Edoardo , D’Angelo Egidio , Casellato Claudia , Pedrocchi Alessandra
Published: October 2021

It is common for animals to use self-generated movements to actively sense the surrounding environment. For instance, rodents rhythmically move their whiskers to explore the space close to their body. The mouse whisker system has become a standard model to study active sensing and sensorimotor integration through feedback loops. In this work, we developed a bioinspired spiking neural network model of the sensorimotor peripheral whisker system, modelling trigeminal ganglion, trigeminal nuclei, facial nuclei, and central pattern generator neuronal populations. This network was embedded in a virtual mouse robot, exploiting the Neurorobotics Platform, a simulation platform offering a virtual environment to develop and test robots driven by brain-inspired controllers. Eventually, the peripheral whisker system was properly connected to an adaptive cerebellar network controller. The whole system was able to drive active whisking with learning capability, matching neural correlates of behaviour experimentally recorded in mice.
Pharmacological impacts on schizophrenia functional analysis: a postmortem proteome study
Authors: Alnafisah Rawan S. , Reigle James , O’Donovan Sinead M , Funk Adam J. , Meller Jaroslaw , Mccullumsmith Robert E. , Shukla Rammohan
Published: October 2021

Schizophrenia (SCZ) is a severe and debilitating mental illness. Antipsychotic drugs (APDs) are used to treat both positive and negative SCZ symptoms, by influencing the cellular, subcellular-synaptic, and molecular processes. We posit that these effects influence our understanding of SCZ. To address this, we analyzed postmortem dorsolateral prefrontal cortex grey matter samples from control and SCZ subjects (n=10/group) using liquid-chromatography mass-spectrometry-based proteomics. We retrieved SCZ-altered and APD-influenced proteome-sets using linear and mixed linear models, respectively, and validated them experimentally using independent cohorts and insilico using published datasets. Functional analysis of proteome-sets was contrasted at the biological pathway, cell-type, subcellular-synaptic, and drug-target levels. The SCZ-altered proteome was conserved across several studies from DLPFC and other brain areas and was dependent on drug effect. At the pathway level, we observed an aberrant extracellular event and, except for homeostasis, signal-transduction, cytoskeleton, and dendrites associated downregulated changes, the APDs compensated for the majority of the SCZ-altered pathways. At the cell-type level, the up-and down-regulated SCZ-altered events were associated with two different subsets of striatum projecting layer-5 pyramidal-neurons regulating dopaminergic secretion. At the subcellular synaptic level, compensatory pre- and post-synaptic events were observed. At the drug target level, dopaminergic processes influence the SCZ-altered up-regulated proteome, whereas non-dopaminergic and a diverse array of non-neuromodulatory mechanisms influence the SCZ-altered down-regulated proteome. While these findings are dependent on pharmacological effects, they are also consistent with previous SCZ studies, implying the need to re-evaluate previous results. We discuss our findings in the context of cortico-striatal influence in SCZ-pathology.
FiberNeat: Unsupervised White Matter Tract Filtering
Authors: Chandio Bramsh Qamar , Chattopadhyay Tamoghna , Owens-Walton Conor , Reina Julio E. Villalon , Nabulsi Leila , Thomopoulos Sophia I. , Garyfallidis Eleftherios , Thompson Paul M.
Published: October 2021

Whole-brain tractograms generated from diffusion MRI digitally represent the white matter structure of the brain and are composed of millions of streamlines. Such tractograms can have false positive and anatomically implausible streamlines. To obtain anatomically relevant streamlines and tracts, supervised and unsupervised methods can be used for tractogram clustering and tract extraction. Here we propose FiberNeat, an unsupervised white matter tract filtering method. FiberNeat takes an input set of streamlines that could either be unlabeled clusters or labeled tracts. Individual clusters/tracts are projected into a latent space using nonlinear dimensionality reduction techniques, t-SNE and UMAP, to find spurious and outlier streamlines. In addition, outlier streamline clusters are detected using DBSCAN and then removed from the data in streamline space. We performed quantitative comparisons with expertly delineated tracts. We ran FiberNeat on 131 participants’ data from the ADNI3 dataset. We show that applying FiberNeat as a filtering step after bundle segmentation improves the quality of extracted tracts and helps improve tractometry.
Single nuclear transcriptional signatures of dysfunctional brain vascular homeostasis in Alzheimer’s disease
Authors: Tsartsalis Stergios , Fancy Nurun , Smith Amy M. , Khozoie Combiz , Yang Xin , Davey Karen , Willumsen Nanet , McGarry Aisling , Muirhead Robert C. J. , Debette Stephanie , Owen David R. , Matthews Paul M.
Published: October 2021

Brain perfusion and normal blood brain barrier integrity are reduced early in Alzheimer’s disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and control brains to characterise pathological transcriptional signatures. We found that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. EC transcriptional signatures identified mechanisms for impaired β-amyloid clearance. Evidence for immune activation was found with upregulation of interferon signalling genes in EC and in pericytes (PC). Transcriptional signatures suggested dysregulation of vascular homeostasis and angiogenesis with upregulation of pro-angiogenic signals (HIF1A) and metabolism in EC, but downregulation of homeostatic growth factor pathways (VEGF, EGF, insulin) in EC and PC and of extracellular matrix genes in fibroblasts (FB). Our genomic dissection of vascular cell risk gene enrichment suggests a potentially causal role for EC and defines transcriptional signatures associated with microvascular dysfunction in AD.
Chronumental: time tree estimation from very large phylogenies
Authors: Sanderson Theo
Published: October 2021

Phylogenetic trees are an important tool for interpreting sequenced genomes, and their interrelationships. Estimating the date associated with each node of such a phylogeny creates a “time tree”, which can be especially useful for visualising and analysing evolution of organisms such as viruses. Several tools have been developed for time-tree estimation, but the sequencing explosion in response to the SARS-CoV-2 pandemic has created phylogenies so large as to prevent the application of these previous approaches to full datasets. Here we introduce Chronumental, a tool that can rapidly infer time trees from phylogenies featuring large numbers of nodes. Chronumental uses stochastic gradient descent to identify lengths of time for tree branches which maximise the evidence lower bound under a probabilistic model, implemented in a framework which can be compiled into XLA for rapid computation. We show that Chronumental scales to phylogenies featuring millions of nodes, with chronological predictions made in minutes, and is able to accurately predict the dates of nodes for which it is not provided with metadata.
Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Authors: Sereika Mantas , Kirkegaard Rasmus Hansen , Karst Søren Michael , Michaelsen Thomas Yssing , Sørensen Emil Aarre , Wollenberg Rasmus Dam , Albertsen Mads
Published: October 2021

Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-perfect genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-perfect microbial genomes from isolates or metagenomes without shortread or reference polishing.
Balancing memory fidelity and representational stability in the female mouse accessory olfactory bulb
Authors: Yoles-Frenkel Michal , Shea Stephen D. , Davison Ian G. , Ben-Shaul Yoram
Published: October 2021

Sensory systems must balance the value of efficient coding schemes against the need to update specific memorized representations without perturbing other memories. Here we describe a unique solution to this challenge that is implemented by the vomeronasal system (VNS) to encode and remember multiple conspecific individuals as part of the Bruce Effect (BE). In the BE, exposure of a pregnant female mouse to the odors of an unfamiliar male leads to failure of the pregnancy (‘pregnancy block’) via the VNS. Following mating and sensory exposure, however, the female becomes protected from a pregnancy block by the stud individual. While this form of natural learning has been proposed to depend on changes in the representation of his odors in her accessory olfactory bulb (AOB), a key VNS structure, there are no direct comparisons of in vivo sensory responses before and after imprinting. It has further been suggested that these changes simply render the AOB insensitive to stud odors. However, the combinatorial odor code used by the AOB and the significant overlap in the odor composition of different males means that silencing responses to one individual is likely to degrade responses to others, posing potential problems for more general sensory encoding. To identify the neuronal correlates of learning in the context of the BE, we recorded extracellular responses of AOB neurons in vivo in mated and unmated female mice upon controlled presentation of urinary chemosignals, including urine from both the stud and males of a distinct strain. We find that while initial sensory responses in the AOB (within a timescale required to guide social interactions) remain stable, responses to extended stimulation (as required for eliciting the pregnancy block) display selective attenuation of stud-responsive neurons. Based on our results, we propose a model that reconciles the formation of strong, selective memories with the need to sustain robust representational bandwidth by noting a distinction between the representations of brief and extended stimuli. This temporal disassociation allows attenuation of slow-acting endocrine processes in a stimulus-specific manner, without compromising consistent ongoing representations of stimuli that guide behavior.
Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor
Authors: Eckenrode Kelly B. , Righelli Dario , Ramos Marcel , Argelaguet Ricard , Vanderaa Christophe , Geistlinger Ludwig , Culhane Aedin C. , Gatto Laurent , Carey Vincent , Morgan Martin , Risso Davide , Waldron Levi
Published: October 2021

Background

The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes.

Results

We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via theMultiAssayExperimentBioconductor class, document and re-distribute datasets as theSingleCellMultiModalpackage in Bioconductor’s Cloud-basedExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor’s ecosystem of hundreds of packages for single-cell and multimodal data.

Conclusions

We provide two examples of integrative analyses that are greatly simplified bySingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.

Author Summary

Experimental data packages that provide landmark datasets have historically played an important role in the development of new statistical methods in Bioconductor by lowering the barrier of access to relevant data, providing a common testing ground for software development and benchmarking, and encouraging interoperability around common data structures. In this manuscript, we review major classes of technologies for collecting multimodal data including genomics, transcriptomics, epigenetics, proteomics, and spatial information at the level of single cells. We present the SingleCellMultiModal R/Bioconductor package that provides single-command access to landmark datasets from seven different technologies, storing datasets using HDF5 and sparse arrays for memory efficiency and integrating data modalities via the MultiAssayExperiment class. We demonstrate two integrative analyses that are greatly simplified by SingleCellMultiModal. The package facilitates development and benchmarking of bioinformatic and statistical methods to integrate molecular layers at the level of single cells with phenotypic outputs including cell differentiation, activity, and disease, within Bioconductor’s ecosystem of hundreds of packages for single-cell and multimodal data.
Qualitative and quantitative top-down proteomics of human colorectal cancer cell lines identified 23000 proteoforms and revealed drastic proteoform-level differences between metastatic and non-metastatic cancer cells
Authors: McCool Elijah N. , Xu Tian , Chen Wenrong , Beller Nicole C. , Nolan Scott M. , Hummon Amanda B. , Liu Xiaowen , Sun Liangliang
Published: October 2021

Understanding cancer metastasis at the proteoform level is crucial for discovering new protein biomarkers for cancer diagnosis and drug development. Proteins are the primary effectors of function in biology and proteoforms from the same gene can have drastically different biological functions. Here, we present the first qualitative and quantitative top-down proteomics (TDP) study of a pair of isogenic human metastatic and non-metastatic colorectal cancer (CRC) cell lines (SW480 and SW620). This study pursues a global view of human CRC proteome before and after metastasis in a proteoform specific manner. We identified 23,319 proteoforms of 2,297 genes from the CRC cell lines using capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS), representing nearly one order of magnitude improvement in the number of proteoform identifications from human cell lines compared to literature data. We identified 111 proteoforms containing single amino acid variants (SAAVs) using a proteogenomic approach and revealed drastic differences between the metastatic and non-metastatic cell lines regarding SAAVs profiles. Quantitative TDP analysis unveiled statistically significant differences in proteoform abundance between the SW480 and SW620 cell lines on a proteome scale for the first time. Ingenuity Pathway Analysis (IPA) disclosed that many differentially expressed genes at the proteoform level had diversified functions and were closely related to cancer. Our study represents a milestone in TDP towards the definition of human proteome in a proteoform specific manner, which will transform basic and translational biomedical research.

For TOC only
Translating outcomes from the clinical setting to preclinical models: chronic pain and functionality in chronic musculoskeletal pain
Authors: Lenert Melissa E. , Gomez Rachelle , Lane Brandon T. , Dailey Dana L. , Vance Carol G.T. , Rakel Barbara A. , Crofford Leslie J. , Sluka Kathleen A. , Merriwether Ericka N. , Burton Michael D.
Published: October 2021

Fibromyalgia (FM) is a chronic pain disorder characterized by chronic widespread musculoskeletal pain (CWP), tenderness, and fatigue, which interferes with daily functioning and quality of life. In clinical studies, this symptomology is assessed, while preclinical models of CWP are limited to nociceptive assays. The aim of the study was to investigate the human-to-model translatability of clinical behavioral assessments for pain and muscle function in a preclinical model of CWP. We assessed correlations between pain behaviors and muscle function in a preclinical model of CWP and in women with fibromyalgia to examine whether similar relationships between outcomes existed in both settings, for usability of clinical assays in model systems. For preclinical measures, the acidic saline model of FM which induces widespread muscle pain, was used in adult female mice. Two gastrocnemius injections of acidic or physiological pH saline were given following baseline measures, five days apart. An array of adapted pain measures and functional assays were assessed for three weeks. For clinical measures, pain and functional assays were assessed in adult women with FM. For both preclinical and clinical outcomes, movement-evoked pain (MEP) was associated with mechanical pain sensitivity. Mechanical sensitivity was correlated to shifts in weight-bearing preclinically and was predictive of functionality in patients. Preclinically, it is imperative to expand how the field assesses pain behaviors when studying multi- symptom disorders like FM. Targeted pain assessments to match those performed clinically is an important aspect of improving preclinical to clinical translatability of animal models.

Preclinical assessments of chronic musculoskeletal pain recapitulate several outcome measures for clinical assessment of patients with FM, particularly prolonged resting pain, and MEP.
Multi-‘omics of host-microbiome interactions in short- and long-term Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
Authors: Xiong Ruoyun , Gunter Courtney , Fleming Elizabeth , Vernon Suzanne D. , Bateman Lucinda , Unutmaz Derya , Oh Julia
Published: October 2021

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system, debilitating disability manifesting as severe fatigue and post-exertional malaise. The chronic dysfunctions in ME/CFS are increasingly recognized as significant health factors with potential parallels with ‘long COVID’. However, the etiology of ME/CFS remains elusive with limited high-resolution human studies. In addition, reliable biomarker-based diagnostics have not been well-established, but may assist in disease classification, particularly during different temporal phases of the disease. Here, we performed deep multi-‘omics (shotgun metagenomics of gut microbiota and plasma metabolomics) and clinical phenotyping of healthy controls (n=79) vs. two cohorts of ME/CFS patients – those with short-term disease (<4 years, n=75), and patients with long-term disease (>10y, n=79). Overall, ME/CFS was characterized by reduced gut microbiome diversity and richness with high heterogeneity, and depletion of sphingomyelins and short-chain fatty acids in the plasma. We found significant differences when stratifying by cohort; short-term ME/CFS was associated with more microbial dysbiosis, but long-term ME/CFS was associated with markedly more severe phenotypic and metabolic abnormalities. We identified a reduction in the gene-coding capacity (and relative abundance of butyrate producers) of microbial butyrate biosynthesis together with a reduction in the plasma concentration of butyrate, especially in the short-term group. Global co-association and detailed gene pathway correlation analyses linking the microbiome and metabolome identified additional potential biological mechanisms underlying host-microbiome interactions in ME/CFS, including bile acids and benzoate pathways. Finally, we built multiple state-of-the-art classifiers to identify microbes, microbial gene pathways, metabolites, and clinical features that individually or together, were most able to differentiate short or long-term MECFS, or MECFS vs. healthy controls. Taken together, our study presents the highest resolution, multi-cohort and multi-‘omics analysis to date, providing an important resource to facilitate mechanistic hypotheses of host-microbiome interactions in ME/CFS.
FEMA: Fast and efficient mixed-effects algorithm for large sample whole-brain imaging data
Authors: Parekh Pravesh , Fan Chun Chieh , Frei Oleksandr , Palmer Clare E. , Smith Diana M. , Makowski Carolina , Iversen John R. , Pecheva Diliana , Holland Dominic , Loughnan Robert , Nedelec Pierre , Thompson Wesley K. , Hagler Donald J. , Andreassen Ole A. , Jernigan Terry L. , Nichols Thomas E. , Dale Anders M.
Published: October 2021

The linear mixed-effects model (LME) is a versatile approach to account for dependence among observations. Many large-scale neuroimaging datasets with complex designs have increased the need for LME, however LME has seldom been used in whole-brain imaging analyses due to its heavy computational requirements. In this paper, we introduce a fast and efficient mixed-effects algorithm (FEMA) that makes whole-brain vertex-wise, voxel-wise, and connectome-wide LME analyses in large samples possible. We validate FEMA with extensive simulations, showing that the estimates of the fixed effects are equivalent to standard maximum likelihood estimates but obtained with orders of magnitude improvement in computational speed. We demonstrate the applicability of FEMA by studying the cross-sectional and longitudinal effects of age on region-of-interest level and vertex-wise cortical thickness, as well as connectome-wide functional connectivity values derived from resting state functional MRI, using longitudinal imaging data from the Adolescent Brain Cognitive DevelopmentSMStudy release 4.0. Our analyses reveal distinct spatial patterns for the annualized changes in vertex-wise cortical thickness and connectome-wide connectivity values in early adolescence, highlighting a critical time of brain maturation. The simulations and application to real data show that FEMA enables advanced investigation of the relationships between large numbers of neuroimaging metrics and variables of interest while considering complex study designs, including repeated measures and family structures, in a fast and efficient manner. The source code for FEMA is available via:https://github.com/cmig-research-group/cmig_tools/.
Loss-of-Function FLNC Variants are Associated with Arrhythmogenic Cardiomyopathy Phenotypes when Identified through Exome Sequencing of a General Clinical Population
Authors: Carruth Eric D. , Qureshi Maria , Alsaid Amro , Kelly Melissa A. , Calkins Hugh , Murray Brittney , Tichnell Crystal , Sturm Amy C. ,   Regeneron Genetics Center, Baras Aris , Kirchner H. Lester , Fornwalt Brandon K. , James Cynthia A. , Haggerty Christopher M.
Published: October 2021

Background

The FLNC gene has recently garnered attention as a likely cause of arrhythmogenic cardiomyopathy (ACM), which is considered an actionable genetic condition. However, the association with disease in an unselected clinical population is unknown. We hypothesized that individuals with loss-of-function variants in FLNC (FLNCLOF) would have increased odds for ACM-associated phenotypes versus variant-negative controls in the Geisinger MyCode cohort.

Methods

We identified rare, putative FLNCLOF among 171,948 individuals with exome sequencing linked to health records. Associations with ACM phenotypes from available diagnoses and cardiac evaluations were investigated.

Results

Sixty individuals (0.03%; median age 58 years [47–70 IQR], 43% male) harbored 27 unique FLNCLOF. These individuals had significantly increased odds ratios (OR) for dilated cardiomyopathy (OR:4.9, [95% confidence interval: 2.6–7.6]; p<0.001), supraventricular tachycardia (OR:3.2, [1.1–5.6]; p=0.01), defibrillator implantation (OR:4.6, [1.9–8.4]; p<0.001), and left-dominant ACM (OR:4.2, [1.4–7.9]; p=0.003). Echocardiography revealed reduced left ventricular ejection fraction (52±13% vs. 57±9%; p=0.001) associated with FLNCLOF. Overall, at least 9% of FLNCLOF carriers demonstrated evidence of penetrant disease.

Conclusions

FLNCLOF variants are associated with increased odds of ventricular arrhythmia and dysfunction in an unselected clinical population. These findings support genomic screening of FLNC for actionable secondary findings.
Prostate-specific membrane antigen is a biomarker for residual disease following neoadjuvant intense androgen deprivation therapy in prostate cancer
Authors: Bright John R. , Lis Rosina T. , Ku Anson T. , Terrigino Nicholas T. , Trostel Shana Y. , Carrabba Nicole V. , Harmon Stephanie A. , Turkbey Baris , Wilkinson Scott , Sowalsky Adam G.
Published: October 2021

Neoadjuvant intense androgen deprivation therapy can exert a wide range of histologic responses, which in turn are reflected in the final prostatectomy specimen. Accurate identification and measurement of residual tumor volumes are critical for tracking and stratifying patient outcomes. The goal of this current study was to evaluate the ability of antibodies against prostate-specific membrane antigen (PSMA) to detect residual tumor in a cohort of 35 patients treated with androgen deprivation therapy plus enzalutamide for six months prior to radical prostatectomy. Residual carcinoma was detected in 31 patients, and PSMA reacted positively with tumor in all cases. PSMA staining was 95.5% sensitive for tumor, with approximately 81.6% of benign regions showing no reactivity. By contrast, PSMA positively reacted with 72.2% of benign regions in a control cohort of 37 untreated cases, resulting in 27.8% specificity for tumor. PSMA further identified highly dedifferentiated prostate carcinomas including tumors with evidence of neuroendocrine differentiation. We propose that anti-PSMA immunostaining be a standardized marker for identifying residual cancer in the setting of neoadjuvant intense androgen deprivation therapy.