bluuebunny/crossref_metadata_2025 huggingface dataset:
An integrated map of cell type-specific gene expression in pancreatic islets
Authors: Elgamal Ruth M , Kudtarkar Parul , Melton Rebecca L , Mummey Hannah M , Benaglio Paola , Okino Mei-Lin , Gaulton Kyle J
Published: February 2023

Pancreatic islets are comprised of multiple endocrine cell types that produce hormones required for glucose homeostasis, and islet dysfunction is a major factor in the development of type 1 and type 2 diabetes (T1D, T2D). Numerous studies have generated gene expression profiles in individual islet cell types using single cell assays. However, there is no canonical reference of gene expression in islet cell types in both health and disease that is also easily accessible for researchers to access, query, and use in bioinformatics pipelines. Here we present an integrated reference map of islet cell type-specific gene expression from 192,203 cells derived from single cell RNA-seq assays of 65 non-diabetic, T1D autoantibody positive (Aab+), T1D, and T2D donors from the Human Pancreas Analysis Program. We identified 10 endocrine and non-endocrine cell types as well as sub-populations of several cell types, and defined sets of marker genes for each cell type and sub-population. We tested for differential expression within each cell type in T1D Aab+, T1D, and T2D states, and identified 1,701 genes with significant changes in expression in any cell type. Most changes were observed in beta cells in T1D, and, by comparison, there were almost no genes with changes in T1D Aab+. To facilitate user interaction with this reference, we provide the data using several single cell visualization and reference mapping tools as well as open-access analytical pipelines used to create this reference. The results will serve as a valuable resource to investigators studying islet biology and diabetes.
μCas, a novel class of miniature type-V Cas12f nucleases with diverse PAM
Authors: Sharrar Allison , Arake de Tacca Luisa , Collingwood Trevor , Meacham Zuriah , Rabuka David , Staples-Ager Johanna , Schelle Michael
Published: February 2023

Small CRISPR-Cas effectors are key to developing gene editing therapies due to the packaging constraints in viral vectors. While Cas9 and Cas12a CRISPR-Cas effectors have advanced into select clinical applications, their size is prohibitive for efficient delivery of both nuclease and guide RNA in a single viral vector. Type-V Cas12f effectors present a solution given their small size. Here we describe μCas, a novel class of miniature (<490AA) type-V Cas12f nucleases that cleave double stranded DNA in human cells. We determined their optimal trans-activating RNA (tracrRNA) empirically through rational modifications which resulted in an optimal single guide RNA (sgRNA). We show that the μCas nucleases have broader PAM preferences than previously known Cas12f effectors. The unique characteristics of these novel nucleases add to the diversity of the miniature CRISPR-Cas toolbox while the expanded PAM allows for the editing of genomic locations that could not be accessed with existing Cas12f nucleases.
Seroreversion toChlamydia trachomatisPgp3 antigen among children in a hyperendemic region of Amhara, Ethiopia
Authors: Tedijanto Christine , Aragie Solomon , Gwyn Sarah , Wittberg Dionna M. , Zeru Taye , Tadesse Zerihun , Chernet Ambahun , Thompson Isabel J.B. , Nash Scott D. , Lietman Thomas M. , Martin Diana L. , Keenan Jeremy D. , Arnold Benjamin F.
Published: February 2023

Monitoring trachoma transmission with antibody data requires characterization of decay in IgG toChlamydia trachomatisantigens. In a three-year longitudinal cohort in a high transmission setting, we estimated a median IgG half-life of 3 years and a seroreversion rate of 2.5 (95% CI: 1.6, 3.5) per 100 person-years.
Impact of human CD8+ T cell senescence on89Zr radiolabelling and homing properties
Authors: Bystrom Jonas , Carrascal-Miniño Amaia , Keeling George P , Pham Truc , Ketchley Conor Garrod- , Schroth Johannes , De Rosales Rafael T. M. , Terry Samantha YA , Henson Sian M.
Published: February 2023

The ability of CD8+ T cells to protect against infection and malignant transformation diminishes with age. Novel means to assess cellular functional deficitsin vivoare being made available such as total-body positron emission tomography (PET) and radiotracers with long half-lives. Here, we determined radiolabeled human CD8+ T cells isolated from young and old individuals with zirconium-89 (89Zr) and assessed their biological statusin vitroand distributionin vivo.

Methods

Fresh and cryopreserved CD8+ T cells from young and old individuals were labelled with varying activities of [89Zr]Zr-oxine and assessed for DNA damage and survival, subsequent toin vitroculture in the presence or absence of antioxidants.89Zr-labelled CD8+ T cells were injected intravenously in NSG mice and whole-body cell migration assessed using PET imaging.

Results

Fresh and cryopreserved CD8+ T cells showed no difference in ability to be labelled with89Zr, radionuclide retention, or CD8+ T cell phenotype.89Zr induced partial cell death and DNA damage, which was no longer detectable visible after four days. The level of DNA repair observed in old samples was highly variable.89Zr efflux from cells, seenin vitro, did not occurin vivo. Longitudinal PET imaging indicated that CD8+ T cells from old individuals accumulated in tissues at a slower rate than those isolated from young individuals.

Conclusion

We have established a strategy to label and track the biodistribution of cryopreserved CD8+T cells. Further study is required to understand differences in migratory behaviour of CD8+ T cells isolated from old and young individuals.
Understanding the Impact of Social Engagement Activities, Health Protocol Maintenance, and Social Interaction on Depression During Covid-19 Pandemic Among Older Americans
Authors: Ahmmad Roungu , Burns Paul A. , Alam Ashraful , Simino Jeannette , Yimer Wondwosen , Faruque Fazlay
Published: February 2023

Objectives

Depression is a critical public health concern among older Americans. However, little is known about how older adults’ social engagement activities, health protocol maintenance, and social interaction (both physically and virtually) potentially contribute to their feelings of depression.

Methods

Data were collected from the Covid-19 supplement to the National Health and Aging Trend Study (NHATS) and core longitudinal follow-up study. A total of 3,181 Medicare-eligible older adults between June and December 2020 were examined how self-reported depression is related to social engagement activities, health protocols, social interaction with friends and family (F&F), and doctors using multiple logistic regression.

Results

This study reveals that the lack of social engagement activities, such as birthday parties and long-term care visits significantly contributes to older adults’ depression (OR: 1.34, 90% CI: 1.07-1.68, p=0.012, and OR: 1.28, 90% CI: 1.01-1.65, p=0.053 respectively). Subsequently, health protocols compliance with washing hands and wearing masks in public places were more likely 2.36 times and 3.44 times higher symptoms of depression for the older adults than those who were not maintaining those protocols (OR: 2.36, 90% CI: 1.24-4.57, p=0.009, OR: 3.44, 90% CI: 1.97-6.17, p<0.001 respectively). Furthermore, the lack of virtual social interaction via phone and text message with F&F is significantly related to depression whereas email or video call are not significantly related to depression for older adults. During Covid-19 pandemic, in-person visits with doctors significantly reduced patients’ depression on the other hand email communication significantly increased. However other virtual interactions with doctors did not significantly associate with patients’ depression.

Conclusion

The lack of social engagement, maintaining health protocols, and lacking virtual interactions over the phone significantly increase depression symptoms for older adults during the Covid-19 pandemic. Therefore, it would be beneficial to take initiative to engage older adults in a variety of social activities to make them feel more connected to their community. The older population should be contacted by phone during the Covid-19 pandemic with encouraging messages and informed of the importance of maintaining health protocols.
Constrained dynamics of oligonucleotides in the phase-separated droplets
Authors: Singh Anupam , Thutupalli Shashi , Kumar Manoj , Ameta Sandeep
Published: February 2023

Phase-separated droplets are excellent means of compartmentalizing functional molecules and have been shown as excellent models for protocells. Although complex functions based on oligonucleotides have been studied, we still lack an understanding of how the oligonucleotide dynamics are affected by the condensed internal environment of these droplets. Particularly, we lack high-resolution experimental measurements of the dynamical parameters that control oligonucleotide diffusion inside the phase-separated droplets. In addition, there is no clarity on how these dynamical parameters differ in the charged (coacervates)vsnon-charged (aqueous two-phase system, ATPS) environment of these droplets. In this study, using fluorescence correlation spectroscopy (FCS), we demonstrate the constrained dynamics of oligonucleotides inside membraneless phase-separated droplets at an unprecedented resolution. We further compare transport properties at different lengths of oligonucleotides as well as salt concentrations. We observe that among all the parameters the oligonucleotide’s caging (spatial restriction in the movement) inside the matrix has a considerable impact on the diffusive dynamics. Our study provides a way of unravelling, quantifying and understanding physical parameters governing the polymer transport dynamics inside the phase-separated droplets.
Functional anomaly mapping lateralizes temporal lobe epilepsy with high accuracy in individual patients
Authors: Gholipour Taha , DeMarco Andrew , You Xiaozhen , Englot Dario J , Turkeltaub Peter E , Koubeissi Mohamad Z , Gaillard William D. , Morgan Victoria L
Published: February 2023

Objective

Mesial temporal lobe epilepsy (mTLE) is associated with variable dysfunction beyond the temporal lobe. We used functional anomaly mapping (FAM), a multivariate machine learning approach to resting state fMRI analysis to measure subcortical and cortical functional aberrations in patients with mTLE. We also examined the value of individual FAM in lateralizing the hemisphere of seizure onset in mTLE patients. Methods: Patients and controls were selected from an existing imaging and clinical database. After standard preprocessing of resting state fMRI, time-series were extracted from 400 cortical and 32 subcortical regions of interest (ROIs) defined by atlases derived from functional brain organization. Group-level aberrations were measured by contrasting right (RTLE) and left (LTLE) patient groups to controls in a support vector regression models, and tested for statistical reliability using permutation analysis. Individualized functional anomaly maps (FAMs) were generated by contrasting individual patients to the control group. Half of patients were used for training a classification model, and the other half for estimating the accuracy to lateralize mTLE based on individual FAMs. Results: Thirty-two right and 14 left mTLE patients (33 with evidence of hippocampal sclerosis on MRI) and 94 controls were included. At group levels, cortical regions affiliated with limbic and somatomotor networks were prominent in distinguishing RTLE and LTLE from controls. At individual levels, most TLE patients had high anomaly in bilateral mesial temporal and medial parietooccipital default mode regions. A linear support vector machine trained on 50% of patients could accurately lateralize mTLE in remaining patients (median AUC =1.0 [range 0.97-1.0], median accuracy = 96.87% [85.71-100Significance: Functional anomaly mapping confirms widespread aberrations in function, and accurately lateralizes mTLE from resting state fMRI. Future studies will evaluate FAM as a non-invasive localization method in larger datasets, and explore possible correlations with clinical characteristics and disease course.
At the core of salinity: convergent and divergent transcriptome response pathways to neutral and alkaline salinity in natural populations ofArabidopsis thaliana
Authors: Almira-Casellas Maria , Busoms Sílvia , Pérez-Martín Laura , Escolà Glòria , López-Valiñas Álvaro , Garcia-Molina Antoni , Llugany Mercè , Poschenrieder Charlotte
Published: February 2023

More than 70% of land’s cultivated area is affected by alkaline salinity stress. As 98% of plants are glycophytes – unable to successfully reproduce under salinity – our previous research focused on comparative studies ofArabidopsis thalianademes with differential performance under neutral and alkaline salinity(neuSALandalkSAL) due to local adaptation processes. Here, an integrated analysis on leaf tissue was performed, including physiological indicators, nutritional status, endogenous phytohormonal concentration and transcriptome profiling, to further understand differences in molecular mechanisms underlyingneuSALandalkSALresponses. The results support thatalkSALis more detrimental to plant performance thanneuSALand indicate higher sensitivity toalkSALin demes locally adapted to coastal siliceous soils. A decreased internal Fe use efficiency in coastal demes underalkSALis proposed to be the driver of their enhanced sensitivity, and sequence variation at β-CA1 and α-CA1 locus is hypothesized to contribute to the imbalance of Fe homeostasis. Dissection on the down-regulated transcripts shared byneuSALandalkSALconfirmed enhanced inhibition of central features on primary and secondary metabolism in coastal individuals underalkSAL. The cell wall and vacuolar β-galactosidaseBGAL4was revealed as a candidate for conferring tolerance toneuSALby favoring stress-regulated cell wall rearrangement, but not toalkSAL, probably due to pH-restricted enzymatic activity. In addition, differential modulation of endogenous phytohormonal cues was reported among salinity types and demes, by which higher alteration of the auxinic, ethylene and jasmonic acid signaling pathways was exerted by alkSAL but sustained ABA biosynthesis was detected only in coastal plants under neuSAL. Weighted correlation network analysis (WGCNA) confirmed the involvement of the identified candidate genes in co-expression modules significantly correlating with favorable responses toneuSALandalkSAL. Overall, the present study provides useful insights into key targets for breeding improvement in alkaline saline soils.
FGF independent MEK1/2 signalling is essential for male fetal germline development in mice
Authors: Blücher Rheannon O. , Lim Rachel S. , Jarred Ellen G. , Ritchie Matthew E. , Western Patrick S.
Published: February 2023

Background

Germline development provides the founding cells for spermatogenesis and oogenesis in males and females, respectively. Disrupted germline differentiation or compromised testis development can lead to subfertility or infertility and are strongly associated with testis cancer in humans. In mice, SRY and SOX9 induce expression of a range of genes, includingFgf9,that promote Sertoli cell differentiation and testis development. FGF9 is also thought to promote male germline differentiation but the pathway through which it signals is unknown. As FGFs signal through Mitogen-Activated Protein Kinases (MAPKs) in other tissues, we explored whether FGF9 regulates male germline development through MAPK by inhibiting either FGF or MEK1/2 signalling in fetal testis cultures from embryonic day (E)12.5, immediately after gonadal sex determination and testis cord formation, but prior to male germline commitment.

Results

Inhibition of MEK1/2 disrupted mitotic arrest, dysregulated a broad range of male germline development genes and prevented the upregulation of key male germline markers DPPA4 and DNMT3L. In contrast, when FGF signalling was inhibited, the male germline specific transcriptional program and the expression of male germline markers DPPA4 and DNMT3L were unaffected, and germ cells entered mitotic arrest normally. While male germline development was not disrupted by FGF inhibition, some genes were commonly altered after 24h of FGF or MEK1/2 inhibition including genes involved in maintenance, germline stem cells, Nodal signalling, proliferation, and germline cancer.

Conclusions

Together, these data demonstrate a novel and essential role for MEK1/2 signalling in male germline differentiation, but a more limited role for FGF signalling. Our data strongly indicate that additional ligands act through MEK1/2 to promote male germline differentiation and highlight a need for further mechanistic understanding of male germline development.
Comparison of coil placement approaches targeting dorsolateral prefrontal cortex in depressed adolescents receiving repetitive transcranial magnetic stimulation: an electric field modeling study
Authors: Deng Zhi-De , Robins Pei L. , Dannhauer Moritz , Haugen Laura M. , Port John D. , Croarkin Paul E.
Published: February 2023

Background

A promising treatment option for adolescents with treatment-resistant depression is high-frequency repetitive transcranial magnetic stimulation (rTMS) delivered to the left dorsolateral prefrontal cortex (L-DLPFC). Conventional coil placement strategies for rTMS in adults include the 5-cm rule, the Beam F3 method, and the magnetic resonance imaging (MRI) neuronavigation method. The purpose of this study was to compare the three targeting approaches to a computational E-field optimization coil placement method in depressed adolescents.

Methods

Ten consenting and assenting depressed adolescents (4 females, age: 15.9 ± 1.1) participated in an open-label rTMS treatment study. Participants were offered MRI-guided rTMS 5 times per week over 6–8 weeks. To compute the induced E-field, a head model was generated based on MRI images, and a figure-8 TMS coil (Neuronetics) was placed over the L-DLPFC using the four targeting approaches.

Results

Results show that there was a significant difference in the induced E-field at the L-DLPFC between the four targeting methods (χ2= 24.7,p <0.001).Post hocpairwise comparisons show that there was a significant difference between any two of the targeting methods (Holm adjustedp <0.05), with the 5-cm rule producing the weakest E-field (46.0 ± 17.4 V/m), followed by the F3 method (87.4 ± 35.4 V/m), followed by the MRI-guided (112.1 ± 14.6 V/m), and followed by the computationally optimized method (130.1 ± 18.1 V/m). The Bartlett test of homogeneity of variances show that there was a significant difference in sample variance between the groups (K2= 8.0,p <0.05), with F3 having the largest variance. In participants who completed the full course of treatment, the median E-field strength in the L-DLPFC was correlated with the change in depression severity (r=–0.77,p <0.05).

Conclusions

The E-field models revealed inadequacies of scalp-based targeting methods compared to MRI-guidance. Computational optimization may further enhance E-field dose delivery to the treatment target.
Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients
Authors: Bodansky Aaron , Wang Chung-Yu , Saxena Aditi , Mitchell Anthea , Takahashi Saki , Anglin Khamal , Huang Beatrice , Hoh Rebecca , Lu Scott , Goldberg Sarah A. , Romero Justin , Tran Brandon , Kirtikar Raushun , Grebe Halle , So Matthew , Greenhouse Bryan , Durstenfeld Matthew S. , Hsue Priscilla Y. , Hellmuth Joanna , Kelly J. Daniel , Martin Jeffrey N. , Anderson Mark S. , Deeks Steven G. , Henrich Timothy J. , DeRisi Joseph L. , Peluso Michael J.
Published: February 2023

Some individuals do not return to baseline health following SARS-CoV-2 infection, leading to a condition known as Long COVID. The underlying pathophysiology of Long COVID remains unknown. Given that autoantibodies have been found to play a role in severity of COVID infection and certain other post-COVID sequelae, their potential role in Long COVID is important to investigate. Here we apply a well-established, unbiased, proteome-wide autoantibody detection technology (PhIP-Seq) to a robustly phenotyped cohort of 121 individuals with Long COVID, 64 individuals with prior COVID-19 who reported full recovery, and 57 pre-COVID controls. While a distinct autoreactive signature was detected which separates individuals with prior COVID infection from those never exposed to COVID, we did not detect patterns of autoreactivity that separate individuals with Long COVID relative to individuals fully recovered from SARS-CoV-2 infection. These data suggest that there are robust alterations in autoreactive antibody profiles due to infection; however, no association of autoreactive antibodies and Long COVID was apparent by this assay.
Patterns of testing in the extensive Danish national SARS-CoV-2 test set-up
Authors: Gram Mie Agermose , Steenhard Nina , Cohen Arieh Sierra , Vangsted Anne-Marie , Mølbak Kåre , Gorm Jensen Thøger , Hansen Christian Holm , Ethelberg Steen
Published: February 2023

Background

The Danish national SARS-CoV-2 mass test system was among the most ambitious worldwide. We describe its set-up and analyse differences in patterns of testing per demography and time period in relation to the three waves of SARS-CoV-2 transmission in Denmark.

Methods

We included all reported PCR- and rapid antigen-tests performed between 27 February 2020 and 10 March 2022 among all residents aged 2 years or above. Descriptive statistics and Poisson regression models were used to analyse characteristics of individuals tested for SARS-CoV-2 using a national cohort study design.

Results

A total of 63.7 million PCR-tests and 60.0 million antigen-tests were performed in the study period, testing 91.1% and 79.2% of the Danish population at least once by PCR or antigen, respectively. Female sex, younger age, Danish heritage and living in the capital area were all factors positively associated with the frequency of PCR-testing. The association between COVID-19 vaccination and PCR-testing changed from negative to positive over time.

Conclusion

We provide details of the widely available, free-of-charge, national SARS-CoV-2 test system, which served to identify infected individuals, assist isolation of infectious individuals and contact tracing, and thereby mitigating the spread of SARS-CoV-2 in the Danish population. The test system was utilized by nearly the entire population at least once, and widely accepted across different demographic groups. However, demographic differences in the test uptake did exist and should be considered in order not to cause biases in studies related to SARS-CoV-2, e.g., studies of transmission and vaccine effectiveness.
Left bundle branch pacing with and without anodal capture: impact on ventricular activation pattern and acute hemodynamics
Authors: Ali Nadine , Saqi Khulat , Arnold Ahran D. , A.Miyazawa Alejandra , Keene Daniel , Chow Ji-Jian , Little Ian , Peters Nicholas S. , Kanagaratnam Prapa , Qureshi Norman , Ng Fu Siong , Linton Nick W. F , Lefroy David C. , Francis Darrel P. , Lim PB , Tanner Mark A. , Muthumala Amal , Shun-Shin Matthew J. , Cole Graham D. , Whinnett Zachary I.
Published: February 2023

Introduction

Left bundle branch pacing (LBBP) can deliver physiological left ventricular activation, but typically at the cost of delayed right ventricular (RV) activation. A proposed solution is to advance RV activation through anodal capture, but there is uncertainty regarding the mechanism by which early RV activation is achieved (capture of right bundle or RV myocardial capture) and it is not known whether this produces hemodynamic benefit.

Methods

We recruited patients with LBBP leads in whom anodal capture eliminated the terminal R wave in lead V1.

Ventricular activation pattern, timing and high precision acute hemodynamic response were studied during LBBP with and without anodal capture.

Results

We recruited 21 patients, mean age 67 years, 14 were males. We measured ECG timings and hemodynamics in all patients and in 15 we also performed non-invasive mapping. Ventricular epicardial propagation maps demonstrated that right ventricular septal myocardial capture, rather than right bundle capture, was the mechanism for earlier RV activation. With anodal capture, QRS duration was shorter (116 ± 12ms versus 129 ± 14ms, p < 0.01), and total ventricular activation time was shorter (83 ± 18ms versus 90 ± 15ms, p = 0.01). This required higher outputs (3.6 ± 1.9V versus 0.6 ± 0.2V, p <0.01) but did not provide additional hemodynamic benefit (mean difference −0.2 ± 3.8 mmHg compared to pacing without anodal capture, p = 0.2).

Conclusion

Left bundle pacing with anodal capture advances right ventricular activation as a result of stimulation of the RV septal myocardium. However, this requires higher outputs and did not improve acute hemodynamics. Aiming for anodal capture may therefore not be necessary.
Soluble suppression of tumorigenicity-2 (sST2) predicts mortality and right heart failure in LVAD patients
Authors: Numan Lieke , Aarts Emmeke , Ramjankhan Faiz , Oerlemans Marish I.F. , van der Meer Manon G. , de Jonge Nicolaas , Oppelaar Anne-Marie , Kemperman Hans , Asselbergs Folkert W. , Van Laake Linda W.
Published: February 2023

Background

Soluble suppression of tumorigenicity-2 (sST2) predicts mortality in heart failure patients. The predictive value of sST2 in left ventricular assist device (LVAD) patients remains unknown. Therefore, we studied the relationship between sST2 and outcome after LVAD implantation.

Methods

Patients implanted between January 2015 and December 2022 were included. Survival of patients with normal and elevated pre-operative sST2 levels was compared using Kaplan-Meier analysis. The relationship between post-operative sST2, survival and right heart failure (RHF) was evaluated using a Joint Model (JM). Multivariate JM analysis adjusted for serially measured NT-proBNP was performed.

Results

The median follow-up was 25 months, during which 1573 post-operative sST2 levels were measured in 199 patients, with a median of 29 ng/ml. Survival in patients with normal or elevated pre-operative sST2 levels (n=86) did not differ significantly (p=0.22). Time-dependent post-operative sST2 levels were significantly associated with mortality, with a hazard ratio (HR) of 1.20 (95% CI: 1.10-1.30, p<0.01) and a HR of 1.22 (95% CI: 1.07-1.39, p=0.01) for RHF, both per 10 unit sST2 increase. The sST2 instantaneous change was not predictive for survival or RHF (p=0.99, p=0.94 respectively). Multivariate JM analysis showed a significant relationship between sST2 with mortality adjusted for NT-proBNP with HR 1.19 (95% CI: 1.00-1.42, p=0.05), while the HR of RHF was not significant (1.22, 95% CI: 0.94-1.59, p=0.14), both per 10 unit sST2 increase.

Conclusion

Time-dependent post-operative sST2 predicts all-cause mortality after LVAD implantation independently of NT-proBNP. Future research is warranted into possible target interventions and the optimal monitoring frequency.
Loss of Y is associated with multi-omic changes in immune cells from Alzheimer’s disease patients
Authors: Jąkalski Marcin , Rychlicka-Buniowska Edyta , Davies Hanna , Sarkisyan Daniil , Siedlar Maciej , Baran Jaroslaw , Węglarczyk Kazimierz , Jaszczynski Janusz , Ryś Janusz , Gedraitis Vilmantas , Klich-Rączka Alicja , Kilander Lena , Ingelsson Martin , Dumanski Jan P. , Mieczkowski Jakub
Published: February 2023

Alzheimer’s disease (AD) is a common and increasing societal problem due to the extending human lifespan. In males, loss of Y (LOY) in leukocytes is more prevalent in AD patients. We studied DNA methylation, gene expression and other epigenetic changes in monocytes and granulocytes with and without LOY from male AD patients and controls. New candidate genes were identified and numerous genes already implicated in AD pathogenesis were confirmed. We show that multi-omics of leukocytes can define AD candidate genes and we strengthen the role of LOY in disease development. The LOY-associated differences in DNA methylation levels were predominantly observed in regulatory regions, and supported by expression analysis showing down-regulation of immune genes. The single-cell transcriptomics highlighted that the AD patient-specific immune activation dominates over LOY-specific activation. Our findings agree with the hypothesis that age-related dysfunction of immune cells contribute to AD and that LOY is reflected by higher-level epigenetic changes with an AD-specific pattern.
Improving sleep after stroke: a randomised controlled trial of digital cognitive behavioural therapy for insomnia
Authors: Fleming Melanie K , Smejka Tom , Macey Ellie , Luengo-Fernandez Ramon , Henry Alasdair L , Robinson Barbara , Kyle Simon D , Espie Colin A , Johansen-Berg Heidi
Published: February 2023

Stroke is frequently accompanied by long-term sleep disruption. We therefore aimed to assess the efficacy of digital cognitive behavioural therapy (dCBT) for insomnia to improve sleep after stroke. A parallel group randomised controlled trial was conducted remotely in participant’s homes/online. Randomisation was online with minimisation of between-group differences in age and baseline Sleep Condition Indicator (SCI-8) score. In total, 86 community dwelling stroke survivors consented, of whom 84 completed baseline assessments (39 female, mean 5.5 years post-stroke, mean 59 years of age) and were randomised to dCBT or control (sleep hygiene information). Follow-up was completed at post-intervention (mean 75 days after baseline) and 8-weeks later. The primary outcome was self-reported insomnia symptoms, as per the SCI-8 (range 0-32, lower numbers indicate more severe insomnia, reliable change 7-points) at post-intervention. There were significant improvements in SCI-8 for dCBT compared to control (intention-to-treat, dCBT n=48, control n=36, 5 imputed datasets, effect of group p≤0.02, ηp2=0.07–0.12, pooled mean difference=-3.35). Additionally, secondary outcomes showed shorter self-reported sleep onset latencies and better mood for the dCBT group, but no significant differences for self-efficacy, quality of life, or actigraphy-derived sleep parameters. Cost-effectiveness analysis found that dCBT dominates over control (non-significant cost savings and higher quality adjusted life years). No related serious adverse events were reported to the researchers. Overall, dCBT for insomnia effectively improves sleep after stroke. Future research is needed to assess earlier stages post-stroke, with a longer follow-up period to determine whether it should be included as part of routine post-stroke care.

Clinicaltrials.govNCT04272892
Family Income and Utilization Disparities for Dental Access of Minority Children: A Cross-Sectional Study
Authors: Okuji David , Wei Tianqi , Lee Myeonggyun
Published: February 2023

Purpose

Through the use Minorities’ Diminished Return theory, this study aimed to assess the concepts of the theory for access to and utilization of dental care of minority children, compared to White children, when all race/ethnicity groups achieve higher socioeconomic status.

Methods

This study was designed cross-sectionally from 21,599 subjects responding to the 2017 National Survey of Children’s Health. The outcome variables of access to and utilization of dental care were compared across Hispanic and non-Hispanic White, Black, Asian, and Multi-race children. Logistic regression models estimated the effects of race/ethnicity on each outcome, with adjustments for child sex, parental education, child age, and income-to-needs ratio.

Results

The findings showed that compared to White children, when all racial/ethnic groups increased family income and socioeconomic status, Black and Multi-race children received less health gains in the outcomes of access to and utilization of dental care; and Hispanic children experienced less access to dental care.

Conclusions

Minorities’ Diminished Return theory provides evidence of structural barriers which negatively impact the health gains from higher socioeconomic status for access to and utilization of dental care for Black, Hispanic, and Multi-race children. Dentists and policymakers must address systemic racism and structural barriers for oral health equity among all children.
Incorporating data from multiple endpoints in the analysis of clinical trials: example from RSV vaccines
Authors: Prunas Ottavia , Willemsen Joukje E. , Bont Louis , Pitzer Virginia E. , Warren Joshua L. , Weinberger Daniel M.
Published: February 2023

Background

To achieve licensure, interventions typically must demonstrate efficacy against a primary outcome in a randomized clinical trial. However, selecting a single primary outcomea prioriis challenging. Incorporating data from multiple and related outcomes might help to increase statistical power in clinical trials. Inspired by real-world clinical trials of interventions against respiratory syncytial virus (RSV), we examined methods for analyzing data on multiple endpoints.

Method

We simulated data from three different populations in which the efficacy of the intervention and the correlation among outcomes varied. We developed a novel permutation-based approach that represents a weighted average of individual outcome test statistics (varP) to evaluate intervention efficacy in a multiple endpoint analysis. We compared the power and type I error rate of this approach to two alternative methods: the Bonferroni correction (bonfT) and another permutation-based approach that uses the minimum P-value across all test statistics (minP).

Results

When the vaccine efficacy against different outcomes was similar,VarPyielded higher power thanbonfTandminP;in some scenarios the improvement in power was substantial. In settings where vaccine efficacy was notably larger against one endpoint compared to the others, all three methods had similar power.

Conclusions

Analyzing multiple endpoints using a weighted permutation method can increase power while controlling the type I error rate in settings where outcomes share similar characteristics, like RSV outcomes. We developed an R package,PERMEATE, to guide selection of the most appropriate method for analyzing multiple endpoints in clinical trials.
Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops
Authors: Kavaliauskaite Gabija , Madsen Jesper Grud Skat
Published: February 2023

Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei, which enables unbiased characterization of cell types and states in tissues. However, the isolation of cells or nuclei for sxRNA-seq can introduce artifacts, such as cell damage and transcript leakage. This can distort biological signals and introduce contamination from debris. Thus, the identification of barcodes con-taining high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, which is a novel data-adaptive method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with biological distinct signals. We benchmark valiDrops and existing methods and find that the biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops. Finally, we show that valiDrops can be used to predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to remove barcodes associated with low quality cells or nuclei from sxRNA-seq datasets, thereby improving data quality and biological interpretation. Our method is openly available as an R package atwww.github.com/madsen-lab/valiDrops.
Phantom touch illusion, an unexpected phenomenological effect of tactile gating in the absence of tactile stimulation
Authors: Pilacinski Artur , Metzler Marita , Klaes Christian
Published: February 2023

We report the presence of a tingling sensation perceived during self touch without physical stimulation. We used immersive virtual reality scenarios in which subjects touched their body using a virtual object. This touch resulted in a tingling sensation corresponding to the location touched on the virtual body. We called it “phantom touch illusion” (PTI). Interestingly the illusion was also present when subjects touched invisible (inferred) parts of their limb. We reason that this PTI results from tactile gating process during self-touch. The reported PTI when touching invisible body parts indicates that tactile gating is not exclusively based on vision, but rather on multi-sensory, top-down input involving body schema. This finding shows that representations of own body are defined top-down, beyond the available sensory information.
Rigosertib promotes anti-tumor immunity via autophagic degradation of PD-L1 in colorectal cancer cells
Authors: Zhou Xinyi , Fu Dongliang , Yang Hang , Le Chenqin , Lu Yier , Wei Jingsun , Tang Yang , Zhang Jiawei , Yuan Ying , Ding Kefeng , Xiao Qian
Published: February 2023

Rigosertib (RGS) is a benzyl styryl sulfone which exhibits impressive cytotoxicity in cancer cells. However, its modulating effect on tumor immune microenvironment remains elusive. In our experiments, compared with immunodeficient mouse model, increased tumor growth arrest and robust anti-tumor immunity were observed in RGS-treated colorectal cancer (CRC) xenograft tumors in immunocompetent mice.

Intriguingly, RGS markedly down-regulated programmed cell death ligand 1 (PD-L1) expression in both vivo and in vitro. Meanwhile, RGS increased autophagic vacuole number in CRC cells as seen by transmission electron microscopy and immunofluorescence. Moreover, increased LC3-II level and tandem- mRFP- GFP- LC3 labeled vacuole accumulation demonstrated RGS-induced autophagic flux.

Mechanistically, it is the activation of AMP-activated protein kinase-UNC-51-like kinase 1 (AMPK-ULK1) axis, rather than the canonical mTOR signaling pathway, that plays a pivotal role in RGS-induced autophagy. AMPK-ULK1 dependent autophagy inhibition, by either short interfering RNA or chemical inhibitors, blocked RGS-induced PD-L1 degradation. Finally, RGS exhibited synergistic anti-tumor activity with cytotoxic T-lymphocyte-associated protein 4 monoclonal antibody in the CRC xenograft model. Furthermore, apart from the immunomodulatory effect, we also confirmed the direct cytotoxicity of RGS in inducing mitochondria-related apoptosis. Altogether, considering its PD-L1 inhibitory and cytotoxic effects, RGS could be a promising drug for CRC therapy.
The dual role of the angiosperm radiation on insect diversification
Authors: Peris David , Condamine Fabien L.
Published: February 2023

Most of the animal pollination is realized by insects, interactions between them and flowering plants have been hypothesized to be important drivers of diversification. Yet, there is weak support for coevolutionary diversification in plant–pollinator interactions. Macroevolutionary studies on insect and plant diversities support the hypothesis that angiosperms evolved after an insect diversity peak in the Early Cretaceous, suggesting that gymnosperm pollinators may have been accessible for angiosperms when they evolved. We examined fossil and phylogenetic evidence documenting this hypothesis and provide new clues on the impact of angiosperm radiation on insect diversification. Using the family-level fossil record of insects and a Bayesian process-based approach, we estimated diversification rates and the role of six different variables on insect macroevolutionary history. We found that, among the six tested variables, angiosperms had a dual role that has changed through time with an attenuation of insect extinction in the Cretaceous and a driver of insect origination in the Cenozoic. However, increasing insect diversity, spore plants and global temperature also showed strong positive correlation with both origination and extinction rates of insects, suggesting that different drivers had important effect on insect evolution, not just angiosperms, which would deserve further studies.
Coordination between endoderm progression and gastruloid elongation controls endodermal morphotype choice
Authors: Farag Naama , Schiff Chen , Nachman Iftach
Published: February 2023

Embryos mostly follow a single morphogenetic trajectory, where variability is largely quantitative with no qualitative differences. This robustness stands in contrast to in-vitro embryo-like models, which, like most organoids, display a high degree of variability. What makes embryonic morphogenesis so robust is unclear.

We use the gastruloid model to study the morphogenetic progression of definitive endoderm (DE) and its divergence. We first catalog the different morphologies and characterize their statistics. We then learn predictive models for the lineage morphotype based on earlier expression and morphology measurements. Finally, we analyze these models to identify key drivers of morphotype variability, and devise personalized (gastruloid-specific) as well as global interventions that will lower this variability and steer morphotype choice. In the process we identify two types of coordination that are lacking in the in-vitro model but are required for robust gut tube formation.

We expect the insights obtained here will improve the quality and usability of 3D embryo-like models, chart a methodology extendable to other organoids for controlling variability, and will also shed light on the factors that provide the embryo its morphogenetic robustness.
Wnt activity reveals context-specific genetic effects on gene regulation in neural progenitors
Authors: Matoba Nana , Le Brandon D , Valone Jordan M , Wolter Justin M , Mory Jessica , Liang Dan , Aygün Nil , Broadaway K Alaine , Bond Marielle L , Mohlke Karen L , Zylka Mark J , Love Michael I , Stein Jason L
Published: February 2023

Gene regulatory effects in bulk-post mortem brain tissues are undetected at many non-coding brain trait-associated loci. We hypothesized that context-specific genetic variant function during stimulation of a developmental signaling pathway would explain additional regulatory mechanisms. We measured chromatin accessibility and gene expression following activation of the canonical Wnt pathway in primary human neural progenitors from 82 donors. TCF/LEF motifs, brain structure-, and neuropsychiatric disorder-associated variants were enriched within Wnt-responsive regulatory elements (REs). Genetically influenced REs were enriched in genomic regions under positive selection along the human lineage. Stimulation of the Wnt pathway increased the detection of genetically influenced REs/genes by 66.2%/52.7%, and led to the identification of 397 REs primed for effects on gene expression. Context-specific molecular quantitative trait loci increased brain-trait colocalizations by up to 70%, suggesting that genetic variant effects during early neurodevelopmental patterning lead to differences in adult brain and behavioral traits.
IQGAP2 regulates blood-brain barrier immune dynamics
Authors: Katdare Ketaki A. , Kjar Andrew , O’Brown Natasha M. , Neal Emma H. , Sorets Alexander G. , Shostak Alena , Romero-Fernandez Wilber , Kwiatkowski Alexander J. , Mlouk Kate , Kim Hyosung , Cowell Rebecca P. , Schwensen Katrina R. , Horner Kensley B. , Wilson John T. , Schrag Matthew S. , Megason Sean G. , Lippmann Ethan S.
Published: February 2023

Brain endothelial cells (BECs) play an important role in maintaining central nervous system (CNS) homeostasis through blood-brain barrier (BBB) functions. BECs express low baseline levels of adhesion receptors, which limits entry of leukocytes. However, the molecular mediators governing this phenotype remain mostly unclear. Here, we explored how infiltration of immune cells across the BBB is influenced by the scaffold protein IQ motif containing GTPase activating protein 2 (IQGAP2). In mice and zebrafish, we demonstrate that loss of Iqgap2 increases infiltration of peripheral leukocytes into the CNS under homeostatic and inflammatory conditions. Using single-cell RNA sequencing and immunohistology, we further show that BECs from mice lacking Iqgap2 exhibit a profound inflammatory signature, including extensive upregulation of adhesion receptors and antigen-processing machinery. Human tissue analyses also reveal that Alzheimer’s disease is associated with reduced hippocampal IQGAP2. Overall, our results implicate IQGAP2 as an essential regulator of BBB immune privilege and immune cell entry into the CNS.
Diminishing neuronal acidification by channelrhodopsins with low proton conduction
Authors: Hayward Rebecca Frank , Brooks F. Phil , Yang Shang , Gao Shiqiang , Cohen Adam E
Published: February 2023

Many channelrhodopsins are permeable to protons. We found that in neurons, activation of a high-current channelrhodopsin, CheRiff, led to significant acidification, with faster acidification in the dendrites than in the soma. Experiments with patterned optogenetic stimulation in monolayers of HEK cells established that the acidification was due to proton transport through the opsin, rather than through other voltage-dependent channels. We identified and characterized two opsins which showed large photocurrents, but small proton permeability, PsCatCh2.0 and ChR2-3M. PsCatCh2.0 showed excellent response kinetics and was also spectrally compatible with simultaneous voltage imaging with QuasAr6a. Stimulation-evoked acidification is a possible source of disruptions to cell health in scientific and prospective therapeutic applications of optogenetics. Channelrhodopsins with low proton permeability are a promising strategy for avoiding these problems.

Statement of Significance

Acidification is an undesirable artifact of optogenetic stimulation. Low proton-permeability opsins minimize this artifact while still allowing robust optogenetic control.
Artificial physics engine for real-time inverse dynamics of arm and hand movement
Authors: Manukian Mykhailo , Bahdasariants Serhii , Yakovenko Sergiy
Published: February 2023

Simulating human body dynamics requires detailed and accurate mathematical models. When solved inversely, these models provide a comprehensive description of force generation that evaluates subject morphology and can be applied to control real-time assistive technology, for example, orthosis or muscle/nerve stimulation. Yet, model complexity hinders the speed of its computations and may require approximations as a mitigation strategy. Here, we use machine learning algorithms to provide a method for accurate physics simulations and subject-specific parameterization. Several types of artificial neural networks (ANNs) with varied architecture were tasked to generate the inverse dynamic transformation of realistic arm and hand movement (23 degrees of freedom). Using a physical model to generate the training and testing sets for the limb workspace, we developed the ANN transformations with low torque errors (less than 0.1 Nm). Multiple ANN implementations using kinematic sequences solved accurately and robustly the high-dimensional kinematic Jacobian and inverse dynamics of arm and hand. These results provide further support for the use of ANN architectures that use temporal trajectories of time-delayed values to make accurate predictions of limb dynamics.