bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic Sleep Stage Classification with Optimized Selection of EEG Channels
Authors: Stenwig Håkon , Soler Andres , Furuki Junya , Suzuki Yoko , Abe Takashi , Molinas Marta
Published: June 2022

Visual inspection of Polysomnography (PSG) recordings by sleep experts based on established guidelines has been the gold standard in sleep stage classification. This approach is expensive, time consuming and mostly limited to experimental research and clinical cases of major sleep disorders. Various automatic approaches to sleep scoring have been emerging in the past years and are opening the way to a quick computational assessment of sleep architecture that may find its way to the clinics. With the hope to make sleep scoring a fully automated process in the clinics, we report here an ensemble algorithm that aims at not only predicting sleep stages but of doing so with an optimized minimal number of EEG channels. For that, we combine a genetic algorithm based optimization with a classification framework that minimizes the number of channels used by the machine learning algorithm to quantify sleep stages. This resulted in a scoring with an F1 score of 0.793 for the fully automatic model and 0.806 for the model trained on 10 percent of the unseen subject, both with only 3 EEG channels. The ensemble algorithm is based on a combination of extremely randomized trees and MiniRocket classifiers. The algorithm was trained, validated and tested on night sleep PSG data collected from 7 subjects. The novelty of our approach lies on the use of the minimum information needed for automated sleep scoring, based on a systematic search that concurrently selects the optimal-minimum number of EEG channels and the best performing features for the machine learning classifier. The optimization framework presented in this work may enable new designs for sleep scoring devices suited to studies in the comfort of the homes, easily and inexpensively and in this way facilitate experimental and clinical studies in large populations.
Sparse Dimensionality Reduction Approaches in Mendelian Randomization with highly correlated exposures
Authors: Karageorgiou Vasilios , Gill Dipender , Bowden Jack , Zuber Verena
Published: June 2022

Multivariable Mendelian randomization (MVMR) is an instrumental variable technique that generalizes the MR framework for multiple exposures. Framed as a linear regression problem, it is subject to the pitfall of multi-collinearity. The bias and efficiency of MVMR estimates thus depends on the correlation of exposures. Dimensionality reduction techniques such as principal component analysis (PCA) provide transformations of all the included variables that are effectively uncorrelated. We propose the use of sparse PCA (sPCA) algorithms that create principal components of subsets of the exposures and may provide more interpretable and reliable MR estimates. The approach consists of three steps. We first apply a sparse dimension reduction method and transform the variant-exposure summary statistics to principal components. We then choose a subset of the principal components based on data-driven cutoffs, and estimate their strength as instruments with an adjusted F-statistic. Finally, we perform MR with these transformed exposures. This pipeline is demonstrated in a simulation study of highly correlated exposures and an applied example using summary data from a genome-wide association study of 118 highly correlated lipid metabolites. As a positive control, we tested the causal associations of the transformed exposures on CHD. Compared to the conventional inverse-variance weighted MVMR method and a weak-instrument robust MVMR method (MR GRAPPLE), sparse component analysis achieved a superior balance of sparsity and biologically insightful grouping of the lipid traits.

Key Messages

In multivariable MR, investigation of multiple highly correlated exposures can hinder the efficiency of the estimators and mask true associations.

Dimensionality reduction approaches such as principal component analysis (PCA) appear to be effective in summarising the variant-exposure summary statistics data in an example of correlated metabolite data.

Sparse PCA approaches have the additional benefit of providing interpretable PCs as only a few exposures contribute to each. This benefit is shown in simulation studies where there is a gain in accuracy over PCA.

In a positive control analysis, the sparse PCs were representing biologically meaningful groups of metabolites (VLDL, LDL, HDL) and in general were associated with coronary heart disease in an anticipated mannert.
Important Role of Hematopoietic Proteoglycan Serglycin in Liver Hepatocellular Carcinoma Associated with Tumor Microenvironment
Authors: Zou Zengcheng , Xie Heping , Guo Wenhai , Li Yue , Zhang Jiongshan , Li Yongwei
Published: June 2022

Background

Serglycin (SRGN) is a prominent hematopoietic proteoglycan that regulates tumorigenesis; however, its role in tumor immunity is unclear.

Materials and methods

We investigated the expression and prognostic potential of SRGN in liver hepatocellular cancer (LIHC) in the context of pan-cancer (for showing the similarity and heterogeneity) using the PrognoScan, GEPIA, Kaplan–Meier Plotter, and TIMER bioinformatics databases. HepG2 cells were transfected with an SRGN over-expression vector, and their proliferation, invasion, sorafenib resistance, and vasculature were examinedin vitro. A subcutaneous xenograft tumor model was created in nude mice.

Results

SRGN expression was prominent in M2 macrophages in LIHC. The Kaplan–Meier Plotter indicated that SRGN RNA was a favorable prognostic factor after correcting for clinical factors. TIMER 2.0 showed that the immune infiltrates of CD8+ T cells, M1 and M2 macrophages, and endothelial cells were strongly correlated with SRGN RNA expression (r=0.552, P=5.79e-29; r=0.517, P=5.84e-25; r=0.696, P=3.26e51; and r=0.522, P=1.67e-25, respectively), and had prognostic potential in LIHC in patients with low or high levels of SRGN, in addition to resting memory CD4+ T cells, hematopoietic stem cells (HSCs), and myeloid-derived suppressor cells (MDSCs). SRGN promoted the proliferation of HepG2 cellsin vitroandin vivo, and was associated with weak sorafenib resistance, invasion, and vasculature. CD206 and CD80 were up-regulated and down-regulated, respectively, in subcutaneous tumor tissues.

Conclusions

The results comprehensively revealed relationships between SRGN and tumor microenvironment(TME)-infiltrating cells, especially monocyte/macrophage subsets. These may constitute an important TME because the pro-tumorigenicity of SRGN in liver cancer.
Comparison between an exact and a heuristic neural mass model with second order synapses
Authors: Clusella Pau , Köksal-Ersöz Elif , Garcia-Ojalvo Jordi , Ruffini Giulio
Published: June 2022

Neural mass models (NMMs) are designed to reproduce the collective dynamics of neuronal populations. A common framework for NMMs assumes heuristically that the output firing rate of a neural population can be described by a static nonlinear transfer function (NMM1). However, a recent exact mean-field theory for quadratic integrate-and-fire (QIF) neurons challenges this view by showing that the mean firing rate is not a static function of the neuronal state but follows two coupled non-linear differential equations (NMM2). Here we analyze and compare these two descriptions in the presence of second-order synaptic dynamics. First, we derive the mathematical equivalence between the two models in the infinitely slow synapse limit, i.e., we show that NMM1 is an approximation of NMM2 in this regime. Next, we evaluate the applicability of this limit in the context of realistic physiological parameter values by analyzing the dynamics of models with inhibitory or excitatory synapses. We show that NMM1 fails to reproduce important dynamical features of the exact model, such as the self-sustained oscillations of an inhibitory interneuron QIF network. Furthermore, in the exact model but not in the limit one, stimulation of a pyramidal cell population induces resonant oscillatory activity whose peak frequency and amplitude increase with the self-coupling gain and the external excitatory input. This may play a role in the enhanced response of densely connected networks to weak uniform inputs, such as the electric fields produced by non-invasive brain stimulation.
Valproic Acid Affects Neuronal Specification and Differentiation During Early Optic Tectum Development of Zebrafish
Authors: Dixon Sierra C. , Calder Bailey J. , Lilya Shane M. , Davies Brandon M. , Martin Annalie , Peterson Maggie , Hansen Jason M. , Suli Arminda
Published: June 2022

The mammalian superior colliculus and its non-mammalian homolog, the optic tectum (OT), are midbrain structures that integrate multimodal sensory inputs and guide non-voluntary movements in response to prevalent stimuli. Recent studies have implicated this structure as a possible site affected in Autism Spectrum Disorder (ASD). Interestingly, fetal exposure to valproic acid (VPA) has also been associated with an increased risk of ASD in humans and animal models. Therefore, we took the approach of determining the effects of VPA treatment on zebrafish OT development as a first step in identifying the mechanisms that allow its formation. We describe the normal OT development during the first 5 days of development and show that in VPA treated embryos, while proliferation of the OT neuroepithelium continued, neuronal specification stalled. This was followed by impairment of neurite extension and complexity, suggesting that in addition to neurogenesis, VPA treatment affects axonogenesis and dendritogenesis. VPA treatment was most detrimental during the first three days of development and did not appear to be linked to oxidative stress. In conclusion, our work provides a foundation for research into mechanisms driving OT development, as well as the relationship between the OT, VPA, and ASD.
Relating pupil diameter and blinking to cortical activity and hemodynamics across arousal states
Authors: Turner Kevin L. , Gheres Kyle W. , Drew Patrick J.
Published: June 2022

Arousal state affects neural activity and vascular dynamics in the cortex, with sleep associated with large changes in the local field potential (LFP) and increases in cortical blood flow. We investigated the relationship between pupil diameter and blink rate with neural activity and blood volume in the somatosensory cortex in male and female unanesthetized, head-fixed mice. We monitored these variables while the mice were awake, during periods of rapid eye movement (REM), and non-rapid eye movement (NREM) sleep. Pupil diameter was smaller during sleep than in the awake state. Changes in pupil diameter were coherent with both gamma-band power and blood volume in the somatosensory cortex, but the strength and sign of this relationship varied with arousal state. We observed a strong negative correlation between pupil diameter and both gamma-band power and blood volume during periods of awake rest and NREM sleep, though the correlations between pupil diameter and these signals became positive during periods of alertness, active whisking, and REM. Blinking was associated with increases in arousal and decreases in blood volume when the mouse was asleep. Bilateral coherence in gamma-band power and in blood volume dropped following awake blinking, indicating a ‘reset’ of neural and vascular activity. Using only eye metrics (pupil diameter and eye motion), we could determine the mouse’s arousal state (‘Awake’, ‘NREM’, ‘REM’) with greater than 90% accuracy with a 5 second resolution. There is a strong relationship between pupil diameter and hemodynamics signals in mice, reflecting the pronounced effects of arousal on cerebrovascular dynamics.

Significance Statement

Determining arousal state is a critical component of any neuroscience experiment. Pupil diameter and blinking are influenced by arousal state, as are hemodynamics signals in the cortex. We investigated the relationship between cortical hemodynamics and pupil diameter and found that pupil diameter was strongly related to the blood volume in the cortex. Mice were more likely to be awake after blinking than before, and blinking ‘resets’ neural activity. Pupil diameter and eye motion can be used as a reliable, non-invasive indicator of arousal state. As mice transition from wake to sleep and back again over a timescale of seconds, monitoring pupil diameter and eye motion permits the non-invasive detection of sleep events during behavioral or resting-state experiments.
Relationship between national changes in mobility due to non-pharmaceutical interventions and emergency department visits due to pediatric acute respiratory infections during the COVID-19 pandemic
Authors: Díaz Franco , Carvajal Cristóbal , Gatica Sebastian , Vásquez-Hoyos Pablo , Jabornisky Roberto , Moltke Richard Von , Jaramillo-Bustamante Juan Camilo , Pizarro Federico , Cruces Pablo
Published: June 2022

Background

Strong social distancing measures were quickly implemented in Chile during the SARS-CoV-2 outbreak. One of the aims of non-pharmaceutical interventions (NPI) mandates was to decrease overcrowding, thus is usually measured as mobility changes.

Methods

we gather data from national health statistics for pediatric emergency (PED) visits for acute respiratory infection (ARI) in children younger than 15. We defined a historical cohort, including data from 2016 to 2019, and compared them with 2020 and 2021 pandemic years. Also, Chile’s national mobility reports from the online google database were downloaded. We tested the correlation between changes in mobility and relative reduction in PED-ARI by Spearman’s Rank Test.

Results

Historical data showed a mean of 46863 ± 3071 PED-ARI weekly visits with a high seasonal variation, with two peaks in weeks 20 and 28 and weeks 32 to 36. This transient drop was temporally associated with the mid-winter 2-week holiday of schools. The usual PED visits peaks did not occur in 2020 and 2021. Mobility declined from week 9, reaching lower than historical data from week 12 and a minimum of 43% in week 15 of 2020 (Figure 1).

The correlation between mobility and PED-ARI visits showed a strong monotonic relationship (quadratic) with a Spearman’s rho of 0.80 (95% CI 0.75 to 0.86) (Figure 2).

Conclusion

NPI resulting in a decrease in mobility should be considered a robust public health measure to relieve the winter’s collapse of the national health system, decreasing morbimortality in children due to PED-ARI.

WHAT’S KNOWN ON THIS SUBJECT

A remarkable decrease in pediatric respiratory infections has been described during the pandemic, although the causes are still poorly understood.

WHAT THIS STUDY ADDS

In a historical cohort before the pandemic, we observed a temporal association between mid-winter holidays and the gap between the two peaks of acute pediatric respiratory infections. We found a strong correlation between national mobility changes due to non-pharmaceutical interventions and acute pediatric respiratory infections during the pandemic. Therefore, timely implementation of non-pharmaceutical interventions might be considered as a robust public health measure to attenuate the seasonal epidemic of non-COVID viral acute respiratory infections. With these data, we wonder if the time has come to implement non-pharmaceutical interventions to mitigate the stress, and frequently collapse, of national health systems due to the increase in pediatric acute respiratory infection, placing children as a priority, and provide the best care to this vulnerable population.
Exploring Polygenic Neuroimaging Derived Scores in a Longitudinal Attention-deficit/hyperactivity disorder Sample
Authors: van der Es Tim , Sprooten Emma , Soheili-Nezhad Sourena , Damatac Christienne G , Franke Barbara , Buitelaar Jan , Mota Nina Roth
Published: June 2022

Genome-wide association studies (GWAS) indicate neuropsychiatric disorders to be highly polygenic. Polygenicity refers to the additive influence of multiple genes on variation in a disorder. GWAS have identified many single-nucleotide polymorphisms (SNPs) across the genome associated with neuropsychiatric disorders, each explaining a very small part of individual variance within a trait. This complicates the understanding of the genetic architecture and biological mechanisms underlying these disorders. Previous studies have successfully used common genetic variants associated psychiatric disorders to generate Polygenic Risk scores (PRS). PRSs estimate the aggregate genetic liability of an individual for a particular disorder or trait based on a genome-wide association study (GWAS) of said trait. Here, we present a novel bottom-up approach to polygenic scoring that starts at the brain, rather than at behavior or clinical diagnosis. We used GWAS of structural brain imaging derived phenotypes (IDPs) from the UK Biobank as a basis to generate polygenic imaging derived scores (PIDS). As a proof-of-concept of its application, we applied PIDS to quantify differences in the genetic influence on brain structure between persons with ADHD and unaffected controls. 94 IDPs were selected using the subcortical segmentation atlas and the Desikan-Killiany cortical atlas from FreeSurfer. In the polygenic model training stage, 72 out 94 PIDS were associated with their respective IDP in an independent sample. Global measures such as cerebellum white matter, cerebellum cortex and cerebral white matter ranked amongst the highest in variance explained ranging between 3% and 5.7%. Our results indicate that a majority of GWAS of structural neuroimaging traits are becoming sufficiently powered to enable reliable and meaningful use of polygenic scoring applications that accurately reflect the underlying polygenic architecture well. Larger discovery GWAS will further improve upon this. Conversely, our associations with ADHD were relatively weak. Larger target samples are required to establish robust links of PIDS with behavioral or clinical traits like ADHD. With this novel approach to polygenic risk scoring we provide a new tool for other researchers to build on in the field of psychiatric genetics.
Disease stages and therapeutic hypotheses in two decades of neurodegenerative disease clinical trials
Authors: Mortberg Meredith A. , Vallabh Sonia M. , Minikel Eric Vallabh
Published: June 2022

Structured Abstract

Background

Neurodegenerative disease is increasing in prevalence and remains without disease-modifying therapies, and most trials of new drugs fail. Proposed solutions include aiming upstream: targeting molecular root causes of disease and testing therapies earlier, even at pre-symptomatic stages. We sought to understand what disease stages were eligible to enroll in neurodegenerative disease clinical trials in recent years and what molecular targets were tested in these trials.

Methods

We combined automated analysis and manual curation of trial registrations from ClinicalTrials.gov for Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia / amyotrophic lateral sclerosis, and Huntington’s disease.

Findings

3,241 trials from 2000-2020 were curated. Industry-sponsored drug trials, a minority (34%) of trials but a majority (61%) of patient-years, were more likely to complete, to have specified phase, and to have placebo or standard-of-care control arms. The mean number of inclusion and exclusion criteria more than doubled over this period, and eligible score ranges shrank. Trials have shifted towards less severely impaired participants, but only 2.7% of trials were open to pre-symptomatic individuals and these were depleted for industry sponsors (OR = 0.32) and for drug trials (OR = 0.59), instead being enriched for behavioral interventions (OR = 3.1). 16 novel, genetically supported therapeutic hypotheses have been tested in drug trials, with a mean lag of 13 years from genetic association to first trial. Such trials comprised just 18% of patient-years.

Interpretation

Eligibility criteria for trials have shifted towards earlier, milder disease stages but are still overwhelmingly focused on symptomatic patients, particularly for industry-sponsored drug trials. Drugs targeting disease genes supported by human genetics comprise just a fraction of drug development effort, and their success may be hindered by a focus on symptomatic patients, where the relevance of the target to the rate of disease progression is less clear.
Strategies for using antigen rapid diagnostic tests to reduce transmission of SARS-CoV-2 in low- and middle-income countries: a mathematical modelling study applied to Zambia
Authors: Han Alvin X. , Girdwood Sarah , Khan Shaukat , Sacks Jilian A. , Toporowski Amy , Huq Naushin , Hannay Emma , Russell Colin A. , Nichols Brooke E.
Published: June 2022

Background

Increasing the availability of antigen rapid diagnostic tests (Ag-RDTs) in low- and middle-income countries (LMICs) is key to alleviating global SARS-CoV-2 testing inequity (median testing rate in December 2021-March 2022 when the Omicron variant was spreading in multiple countries; high-income countries=600 tests/100,000 people/day; LMICs=14 tests/ 100,000 people/day). However, target testing levels and effectiveness of asymptomatic community screening to impact SARS-CoV-2 transmission in LMICs are unclear.

Methods

We used PATAT, an LMIC-focused agent-based model to simulate COVID-19 epidemics, varying the amount of Ag-RDTs available for symptomatic testing at healthcare facilities and asymptomatic community testing in different social settings. We assumed that testing was a function of access to healthcare facilities and availability of Ag-RDTs. We explicitly modelled symptomatic testing demand from non-SARS-CoV-2 infected individuals and measured impact based on the number of infections averted due to test-and-isolate.

Results

Testing symptomatic individuals yields greater benefits than any asymptomatic community testing strategy until most symptomatic individuals who sought testing have been tested.

Meeting symptomatic testing demand likely requires at least 200-400 tests/100,000 people/day on average as symptomatic testing demand is highly influenced by non-SARS-CoV-2 infected individuals. After symptomatic testing demand is satisfied, excess tests to proactively screen for asymptomatic infections among household members yields the largest additional infections averted.

Conclusions

Testing strategies aimed at reducing transmission should prioritize symptomatic testing and incentivizing test-positive individuals to adhere to isolation to maximize effectiveness.
The seroprevalence of neutralizing antibodies against the adeno-associated virus capsids in Japanese hemophiliacs
Authors: Kashiwakura Yuji , Baatartsogt Nemekhbayar , Yamazaki Shoji , Nagao Azusa , Amano Kagehiro , Suzuki Nobuaki , Matsushita Tadashi , Sawada Akihiro , Higasa Satoshi , Yamazaki Naoya , Fujii Teruhisa , Ogura Taemi , Takedani Hideyuki , Taki Masashi , Matsumoto Takeshi , Yamanouchi Jun , Sakai Michio , Nishikawa Masako , Yatomi Yutaka , Yada Koji , Nogami Keiji , Watano Ryota , Hiramoto Takafumi , Hayakawa Morisada , Kamoshita Nobuhiko , Kume Akihiro , Mizukami Hiroaki , Ishikawa Shizukiyo , Sakata Yoichi , Ohmori Tsukasa
Published: June 2022

Adeno-associated virus (AAV) vectors are promising modalities of gene therapy to address unmet medical needs. However, anti-AAV neutralizing antibodies (NAbs) hamper the vector-mediated therapeutic effect. Therefore, the NAb prevalence in the target population is vital in designing clinical trials with AAV vectors. Hence, updating the seroprevalence of anti-AAV NAbs, herein we analyzed sera from 100 healthy individuals and 216 hemophiliacs in Japan. In both groups, the overall seroprevalence against various AAV serotypes was 20%–30%, and the ratio of NAb-positive population increased with age. The seroprevalence did not differ between healthy participants and hemophiliacs and was not biased by the concomitant blood-borne viral infections. The high neutralizing activity, which strongly inhibits the transduction with all serotypesin vitro, was mostly found in the 60s or older age. The multivariate analysis suggested that “60s or older age” was the only independent factor related to the high titer of NAbs. Conversely, a large proportion of younger hemophiliacs was seronegative, rendering them eligible for AAV-mediated gene therapy in Japan. Compared with our previous study, the peak of seroprevalences has shifted to older populations, indicating natural AAV exposure in the elderly has occurred in their youth but not during the last decade.
An update on oral clinical courses among patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: A clinical follow-up (a prospective prevalent cohort) study
Authors: Gebretsadik Heron Gezahegn
Published: June 2022

Introduction

Contemporary literature has revealed that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes acute sialadenitis and related symptoms, such as discomfort, pain, swelling, and secretory dysfunction in salivary glands. The secretory dysfunction is due to SARS-CoV-2 infection-induced xerostomia and other associated clinical courses such as sore tongue, mucosal ulcer, and gingivitis in the oral cavity. Furthermore, it has been reported that COVID-19 causes the development of other oral manifestations.

Materials and Methods

A prospective clinical follow-up (a prevalent cohort) study was conducted to identify the possible oral manifestations of SARS-CoV-2 infection among patients admitted at the Eka General Hospital COVID-19 treatment center. Furthermore, the study aimed to calculate the prevalence rate of oral clinical courses in the cohorts. The study had two follow-up phases: Hospital and patient-home-based.

Results

A total of 55 patients (36 males and 19 females) met the inclusion criteria and were followed for 7.5 weeks. The 3.5 weeks’ hospital-based prospective follow-up study documented an 18% (n=10) prevalence rate of oral clinical courses among the cohorts. Twelve oral symptoms appeared in these ten patients. The manifested oral symptoms were oral mucosal lesions (n=6), xerostomia (n=5), and thickening of saliva (n=1). The oral mucosal lesions per se consisted of aphthous lesions (n=3), candidiasis (n=1), geographic tongue (n=1), and localized gingivitis (n=1). On the other hand, the four weeks’ home-based follow-up study disclosed four newly manifested oral symptoms: hemorrhagic crust, bulla, buccal mucositis, and petechiae. These manifestations appeared among six patients (four males and two females) who had not manifested any oral symptoms during the hospital-based follow-up. Accordingly, the overall prevalence of oral clinical courses among patients presented with SARS-CoV-2 is raised from 18% (n=10) to 29% (n=16). Similarly, the number of clinical courses increased from 12 to 16 after four additional weeks of follow-up.

Discussion

The study’s findings suggest the importance of initiating oral health care for patients with COVID-19. Therefore, multidisciplinary healthcare approaches should be delivered to assure optimal health outcomes. Accordingly, oral health professionals must be a substantial part of the interdisciplinary approach in caring for patients with COVID-19.
Disrupting cellular memory to overcome drug resistance
Authors: Harmange Guillaume , Reyes Hueros Raúl A. , Schaff Dylan , Emert Benjamin , Saint-Antoine Michael , Nellore Shivani , Fane Mitchell E. , Alicea Gretchen M. , Weeraratna Ashani T. , Singh Abhyudai , Shaffer Sydney M.
Published: June 2022

Plasticity enables cells to change their gene expression state in the absence of a genetic change. At the single-cell level, these gene expression states can persist for different lengths of time which is a quantitative measurement referred to as gene expression memory. Because plasticity is not encoded by genetic changes, these cell states can be reversible, and therefore, are amenable to modulation by disrupting gene expression memory. However, we currently do not have robust methods to find the regulators of memory or to track state switching in plastic cell populations. Here, we developed a lineage tracing-based technique to quantify gene expression memory and to identify single cells as they undergo cell state transitions. Applied to human melanoma cells, we quantified long-lived fluctuations in gene expression that underlie resistance to targeted therapy. Further, we identified the PI3K and TGF-β pathways as modulators of these state dynamics. Applying the gene expression signatures derived from this technique, we find that these expression states are generalizable to in vivo models and present in scRNA-seq from patient tumors. Leveraging the PI3K and TGF-β pathways as dials on memory between plastic states, we propose a “ pretreatment” model in which we first use a PI3K inhibitor to modulate the expression states of the cell population and then apply targeted therapy. This plasticity informed dosing scheme ultimately yields fewer resistant colonies than targeted therapy alone. Taken together, we describe a technique to find modulators of gene expression memory and then apply this knowledge to alter plastic cell states and their connected cell fates.
A role for axon-glial interactions and Netrin-G1 signaling in the formation of low-threshold mechanoreceptor end organs
Authors: Meltzer Shan , Comeau Katelyn , Osei-Asante Emmanuella , Handler Annie , Zhang Qiyu , Sano Chie , Itohara Shigeyoshi , Ginty David D.
Published: June 2022

Low-threshold mechanoreceptors (LTMRs) and their cutaneous end organs convert light mechanical forces acting on the skin into electrical signals that propagate to the central nervous system. In mouse hairy skin, hair follicle-associated longitudinal lanceolate complexes, which are end organs comprising of LTMR axonal endings that intimately associate with terminal Schwann cell (TSC) processes, mediate LTMR responses to hair deflection and skin indentation. Here, we characterized developmental steps leading to the formation of Aβ RA-LTMR and Aδ-LTMR lanceolate complexes. During early postnatal development, Aβ RA-LTMRs and Aδ-LTMRs extend and prune cutaneous axonal branches in close association with nascent TSC processes. Netrin-G1 is expressed in these developing Aβ RA-LTMR and Aδ-LTMR lanceolate endings, and Ntng1 ablation experiments indicate that Netrin-G1 functions in sensory neurons to promote lanceolate ending elaboration around hair follicles. The Netrin-G ligand (NGL-1), encoded by Lrrc4c, is expressed in TSCs, and ablation of Lrrc4c phenocopies the lanceolate complex deficits observed in Ntng1 mutants. Moreover, NGL-1–Netrin-G1 signaling is a general mediator of LTMR end organ formation across diverse tissue types demonstrated by the fact that Aβ RA-LTMR endings associated with Meissner corpuscles and Pacinian corpuscles are also compromised in the Ntng1 and Lrrc4c mutant mice. Thus, axon-glia interactions mediated by NGL-1–Netrin-G1 signaling promote LTMR end organ formation.

Significance statement

Our sense of touch is essential for fundamental tasks ranging from object recognition to social exchange. Yet, touch remains one of the least understood senses at the developmental level. Here, we investigate the formation of lanceolate complexes, which are mechanosensory end organs associated with hair follicles. The axons of touch sensory neurons innervating hairy skin extend into the skin at late embryonic and neonatal times, prune excessive branches during early postnatal development, and closely associate with non-myelinating glial cells, called terminal Schwann cells (TSCs) during formation of mature endings around hair follicles. Moreover, NGL-1 and its receptor Netrin-G1 mediate a molecular dialogue between nascent TSCs and sensory neuron axonal endings to promote mechanosensory end organ formation in both hairy and non-hairy (glabrous) skin.
Mutant SF3B1 promotes PDAC malignancy through TGF-β resistance
Authors: Simmler Patrik T. , Mengis Tamara , Lehmann Kjong-Van , Kahles André , Thomas Tinu , Rätsch Gunnar , Stoffel Markus , Schwank Gerald
Published: June 2022

The splicing factor SF3B1 is recurrently mutated in various tumors, including pancreatic ductal adenocarcinoma (PDAC). The impact of the hotspot mutation SF3B1K700E on the PDAC pathogenesis, however, remains elusive. Here, we demonstrate that Sf3b1K700E alone is insufficient to induce malignant transformation of the murine pancreas, but increases aggressiveness of PDAC if it co-occurs together with mutated KRAS and p53. We further demonstrate that SF3B1K700E reduces epithelial–mesenchymal transition (EMT) and confers resistance to TGF-β1-induced cell death, and provide evidence that this phenotype is in part mediated through aberrant splicing of Map3k7. Taken together, our work suggests that SF3B1K700E acts as an oncogenic driver in PDAC through enhancing resistance to the tumor suppressive effects of TGF-β.
Depletion of FH, an essential TCA cycle enzyme, drives proliferation in a two-step model
Authors: Solaimuthu Balakrishnan , Lichtenstein Michal , Hayashi Arata , Khatib Anees , Plaschkes Inbar , Nevo Yuval , Tanna Mayur , Lavi Shirel , Pines Ophry , Shaul Yoav D.
Published: June 2022

Several tumor suppressor genes do not follow the canonical function of cell cycle repressors. For example, fumarate hydratase (FH) is an evolutionary conserved TCA cycle enzyme that reversibly catalyzes the hydration of fumarate to L-malate and has a moonlight function in the DNA damage response (DDR). Interestingly, despite this enzyme’s essential role in central carbon metabolism, FH is inactive or absent in several tumors, such as hereditary leiomyomatosis and renal cell cancer (HLRCC). Accordingly, FH has a contradictory cellular function, as it is pro-survival through its role in the TCA cycle, yet its loss can drive tumorigenesis. These observations have supported the role of FH as a tumor suppressor. Here, we solved this contradiction by determining the molecular mechanisms that allow the cells to survive and even proliferate upon FH loss. We found that the cells’ response to FH loss is separated into two distinct time frames based on cell proliferation and DNA damage repair. During the early stages of FH loss, the cells’ proliferation and DNA damage repair are inhibited. However, over time the cells overcome the FH loss and form knockout clones, indistinguishable from WT cells in their proliferation rate. Due to the FH loss effect on DNA damage repair, we assumed that the recovered cells bear adaptive mutations. Therefore, we applied whole-exome sequencing to identify such mutated genes systematically. Indeed, we identified recurring mutations in genes belonging to the central oncogenic signaling pathways, such as JAK/STAT, which we validated to be impaired in FH-KO clones. Intriguingly, we demonstrated that these adaptive mutations are responsible for FH-KO cell proliferation under TCA cycle malfunction.
Engineered bacteria recruit and orchestrate anti-tumor immunity
Authors: Savage Thomas M. , Vincent Rosa L. , Rae Sarah S. , Huang Lei Haley , Ahn Alexander , Pu Kelly , Li Fangda , Coker Courtney , Danino Tal , Arpaia Nicholas
Published: June 2022

Tumors employ multiple mechanisms to actively exclude or suppress adaptive immune cells involved in anti-tumor immunity. Strategies focused on overcoming these immunosuppressive or exclusion signals – through localized delivery of chemokines that directly recruit immune cells into the tumor microenvironment – remain limited due to an inability to target therapeutics specifically to the tumor. Synthetic biology enables engineering of cells and microbes for tumor localized delivery, offering therapeutic candidates previously unavailable using conventional systemic administration techniques. Here, we engineer bacteria to produce and intratumorally release chemokines to attract adaptive immune cells into the tumor environment. Intravenous or intratumoral delivery of bacteria expressing an activating mutant of the human chemokine CXCL16 (hCXCL16K42A) leads to the recruitment of activated T cells within tumors and offers therapeutic benefit in multiple mouse tumor models. Furthermore, we rationally target an additional step in the immune activation cascade – specifically, the presentation of tumor-derived antigens by dendritic cells – using a second engineered bacterial strain expressing CCL20. This combined targeting approach led to the recruitment of type 1 conventional dendritic cells and effectively synergized with hCXCL16K42A-induced T cell recruitment to provide additional therapeutic benefit. In summary, we engineer bacteria to cooperatively recruit and activate both innate and adaptive anti-tumor immune responses, offering a new cancer immunotherapy strategy.
Multimodal monitoring of human cortical organoids implanted in mice using transparent graphene microelectrodes reveal functional connection between organoid and mouse visual cortex
Authors: Wilson Madison N. , Thunemann Martin , Liu Xin , Lu Yichen , Puppo Francesca , Adams Jason W. , Kim Jeong-Hoon , Pizzo Donald P. , Djurovic Srdjan , Andreassen Ole A. , Mansour Abed A. , Gage Fred H. , Muotri Alysson R. , Devor Anna , Kuzum Duygu
Published: June 2022

Human cortical organoids, three-dimensional neuronal cell cultures derived from human induced pluripotent stem cells, have recently emerged as promising models of human brain development and dysfunction. Transplantation of human brain organoids into the mouse brain has been shown to be a successful in vivo model providing vascularization for long term chronic experiments. However, chronic functional connectivity and responses evoked by external sensory stimuli has yet to be demonstrated, due to limitations of chronic recording technologies. Here, we develop an experimental paradigm based on transparent graphene microelectrode arrays and two-photon imaging for longitudinal, multimodal monitoring of human organoids transplanted in the mouse cortex. The transparency of graphene microelectrodes permits visual and optical inspection of the transplanted organoid and the surrounding cortex throughout the chronic experiments where local field potentials and multi-unit activity (MUA) are recorded during spontaneous activity and visual stimuli. These experiments reveal that visual stimuli evoke electrophysiological responses in the organoid, matching the responses from the surrounding cortex. Increases in the power of the gamma and MUA bands as well as phase locking of MUA events to slow oscillations evoked by visual stimuli suggest functional connectivity established between the human and mouse tissue. Optical imaging through the transparent microelectrodes shows vascularization of the organoids. Postmortem histological analysis exhibits morphological integration and synaptic connectivity with surrounding mouse cortex as well as migration of organoid cells into the surrounding cortex. This novel combination of stem cell and neural recording technologies could serve as a unique platform for comprehensive evaluation of organoids as models of brain development and dysfunction and as personalized neural prosthetics to restore lost, degenerated, or damaged brain regions.
Investigation of neurobiological responses to Theta Burst Stimulation during recovery from mild traumatic brain injury (mTBI)
Authors: Coyle Hannah L. , Bailey Neil W. , Ponsford Jennie , Hoy Kate E.
Published: June 2022

The ability of the brain to recover following neurological insult is of considerable interest in mild traumatic brain injury (mTBI) populations. To date, a limited amount of research has examined changes in brain function over time following mTBI. Investigating whether non-invasive brain stimulation (NIBS) can modulate neurophysiology and cognitive performance is particularly relevant for therapeutic targeting post injury. The purpose of the current study was to investigate the neurobiological effects of a single session of intermittent theta burst stimulation (iTBS) applied to the dorsolateral prefrontal cortex (DLPFC) in participants with mTBI during recovery. Changes to neurophysiology were assessed with electroencephalography (EEG) and transcranial magnetic stimulation combined with EEG (TMS-EEG). Digit span working memory accuracy was assessed as a marker of cognitive performance. 30 patients in the subacute phase following mTBI (within one month post-injury) and 26 demographically matched controls were assessed. Participants also completed 3-month (mTBI: N = 21, control: N = 26) and 6-month (mTBI: N = 15, control: N = 24) follow up sessions. Cluster-based analyses demonstrated iTBS did not reliably modulate neurophysiological activity, and no differences were found in cognitive performance in either mTBI or control group participants across any of the assessment time points. The factors that may have contributed to our results are unclear, and possible limitations to our experimental design are discussed. Our findings highlight additional research is required to establish the effects of iTBS on plasticity and cognition in a mTBI population prior to therapeutic application.
Peripheral signature of altered synaptic integrity in young onset Cannabis Use Disorder: A proteomic study of circulating extracellular vesicles
Authors: Ganesh Suhas , Lam TuKiet T. , Garcia-Milian Rolando , D’Souza Deepak , Nairn Angus C. , Elgert Katya , Eitan Erez , Ranganathan Mohini
Published: June 2022

Background

The prevalence of cannabis use and Cannabis Use Disorder (CUD) are highest amongst adolescents and young adults. A lack of brain tissues from patients with CUD limits the ability to examine the molecular basis of cannabis related neuropathology. Proteomic studies of neuron-derived extracellular vesicles (NDEs) isolated from the biofluids may reveal markers of neuropathology in CUD.

Methods

NDEs were extracted using ExoSORT, an immunoaffinity method, from plasma samples of 10 patients with young onset CUD and 10 matched controls. Differential proteomic profiles of NDEs between groups was explored with Label Free Quantification (LFQ) mass spectrometry. Selected differentially abundant proteins were validated using orthogonal methods.

Results

A total of 231 (+/- 10) unique proteins were identified in NDE preparations of which 28 were differentially abundant between groups. The difference in abundance properdin, encoded by the CFP gene surpassed the significance threshold after false discovery rate correction.

Notably, SHANK1 (SH3 and multiple ankyrin repeat domains protein 1), an adapter protein at the post-synaptic density, was found to be depleted in the CUD compared to control NDE preparations.

Discussion

The study shows that LFQ mass spectrometry proteomic analysis of NDEs derived from plasma may yield important insights into the synaptic pathology associated with CUD. Optimization of this approach may lead to a novel assay to study altered proteomic signalling in the brain using liquid biopsy in diverse neuropsychiatric syndromes.
Is COVID-19 seasonal? A time series modeling approach
Authors: Wiemken Timothy L , Khan Farid , Nguyen Jennifer L , Jodar Luis , McLaughlin John M
Published: June 2022

Background

Determining whether SARS-CoV-2 is or will be seasonal like other respiratory viruses is critical for public health planning, including informing vaccine policy regarding the optimal timing for deploying booster doses. To help answer this urgent public health question, we evaluated whether COVID-19 case rates in the United States and Europe followed a seasonal pattern using time series models.

Methods

We analyzed COVID-19 data from Our World in Data from Mar 2020 through Apr 2022 for the United States (and Census Region) and five European countries (Italy, France, Germany, Spain, and the United Kingdom). For each, anomalies were identified using Twitter’s decomposition method and Generalized Extreme Studentized Deviate tests. We performed sensitivity analyses to determine the impact of data source (i.e., using US Centers for Disease Control and Prevention [CDC] data instead of OWID) and whether findings were similar after adjusting for multiple covariates. Finally, we determined whether our time series models accurately predicted seasonal influenza trends using US CDC FluView data.

Results

Anomaly plots detected COVID-19 rates that were higher than expected between November and March each year in the United States and Europe. In the US Southern Census Region, in addition to seasonal peaks in the fall/winter, a second peak in Aug/Sep 2021 was identified as anomalous. Results were robust to sensitivity analyses.

Conclusions

Our results support employing annual protective measures against SARS-CoV-2 such as administration of seasonal booster vaccines or other non-pharmaceutical interventions in a similar timeframe as those already in place for influenza prevention.

Summary of the Main Point

Although SARS-CoV-2 continues to cause morbidity and mortality year-round due to its high transmissibility and rapid viral evolution, our results suggest that COVID-19 activity in the United States and Europe peaks during the traditional winter viral respiratory season.
Rethinking the Human Resource Crisis in Africa’s Health Systems: Evidence across Ten Countries
Authors: Sheffel Ashley , Andrews Kathryn G. , Conner Ruben , Giorgio Laura Di , Evans David K. , Gatti Roberta , Lindelow Magnus , Sharma Jigyasa , Svensson Jakob , Wane Waly , Welander Anna
Published: June 2022

Sub-Saharan Africa has fewer medical workers per capita than any region of the world, and that shortage has been highlighted consistently as a critical constraint to improving health outcomes in the region. This paper draws on newly available, systematic, comparable data from ten countries in the region to explore the dimensions of this shortage. We find wide variation in human resources performance metrics, both within and across countries. Many facilities are barely staffed, and effective staffing levels fall further when adjusted for absenteeism. However, caseloads—while also varying widely within and across countries—are also low in many settings, suggesting that even within countries, deployment rather than shortages, together with barriers to demand, may be the principal challenges. Beyond raw numbers, we observe significant proportions of health workers with very low levels of clinical knowledge on standard maternal and child health conditions. This work demonstrates that countries may need to invest broadly in health workforce deployment, improvements in capacity and performance of the health workforce, and on addressing demand constraints, rather than focusing narrowly on increases in staffing numbers.

Key messages

This study analyzed health worker surveys from ten countries in Sub-Saharan Africa for a deeper understanding of human resource challenges.

Average staffing across facilities is far below the stated staffing norms for each country.

Half of health centers and health posts have one or fewer clinical staff assigned to them.

Staffing is even lower when adjusted for absence, which is highest in small facilities and public facilities.

Massive within-country variation in caseload suggests that staffing problems may be solved in part by reallocation of clinical staff.

Health workers lack basic clinical competencies, caseloads are imbalanced, and there is substantial absence of workers from health facilities.