bluuebunny/crossref_metadata_2025 huggingface dataset:
Interventional Neurorehabilitation for Promoting Functional Recovery Post-Craniotomy: A Proof-of-Concept
Authors: Poologaindran Anujan , Profyris Christos , Young Isabella M. , Dadario Nicholas B. , Ahsan Syed A. , Chendeb Kassem , Briggs Robert G. , Teo Charles , Romero-Garcia Rafael , Suckling John , Sughrue Michael E.
Published: July 2021

Purpose

The human brain is a highly plastic ‘complex’ network –it is highly resilient to damage and capable of self-reorganisation after a large perturbation. Clinically, neurological deficits secondary to iatrogenic injury have very few active treatments. New imaging and stimulation technologies, though, offer promising therapeutic avenues to accelerate post-operative recovery trajectories. In this study, we sought to establish the safety profile for ‘interventional neurorehabilitation’: connectome-based therapeutic brain stimulation to drive cortical reorganisation and promote functional recovery post-craniotomy.

Methods

In n=34 glioma patients who experienced post-operative motor or language deficits, we used connectomics to construct single-subject cortical networks. Based on their clinical and connectivity deficit, patients underwent network-specific Transcranial Magnetic Stimulation (TMS) sessions daily over five consecutive days. Patients were then assessed for TMS-related side effects and improvements.

Results

31/34 (91%) patients were successfully recruited and enrolled for TMS treatment within two weeks of glioma surgery. No seizures or serious complications occurred during TMS rehabilitation and one-week post-stimulation. Transient headaches were reported in 4/31 patients but improved after a single session. No neurological worsening was observed while a benefit was noted in 28/31 patients post-TMS. We present two clinical vignettes and a video demonstration of interventional neurorehabilitation.

Conclusions

For the first time, we demonstrate the safety profile and ability to recruit, enrol, and complete TMS acutely post-craniotomy in a high seizure risk population. Given the lack of randomisation and controls in this study, prospective randomised sham-controlled stimulation trials are now warranted to establish the efficacy of interventional neurorehabilitation following craniotomy.
Metal concentrations in breastmilk of Fuzhou nursing mothers associates with dietary and lifestyle factors
Authors: Qi Lin , Chiang Vic Shao-Chih , Lu Qiu-Yan , Wen Jing-yuan , Xu Rongxian
Published: July 2021

Metal intake greatly influences physiological development during infancy. For infants, breastmilk is the major route of metal exposure. The metal status of their nursing mothers is affected by lifestyle and nutritional factors. However, the relationship between these factors and breastmilk metal concentration is largely unknown.

The present study provided food frequency questionnaires to be completed by 113 nursing mothers from Fujian Provincial Hospital. Their breastmilk samples were analysed for the metal concentrations using inductively coupled plasma mass spectrometery (ICP-MS). Based on the outcome of the questionnaires and ICP-MS results, a total of 94 samples were deemed valid for further data analyses.

Results showed levels of breastmilk lead (Pb) and iron (Fe) were outside the reference range from authoritative data. Correlation analyses found Pb levels to negatively associate with dietary fibre intake. Additionally, Fe levels were negatively associated with alcohol and dairy consumption. In terms of Zn levels, it was positively associated with tea and vitamin B1 intake. Zn was also negatively associated with seafood consumption.

The study concluded dietary factors to associate with metal levels within breastmilk. Recommendations were made to increase consumption of dietary fibre, tea and foods rich in vitamin B1 for gestational and postpartum women. Conversely, alcohol consumption continues to be discouraged for this population. Furthermore, careful considerations need to be taken for levels of dairy and seafood intake to minimize metal metabolism disruptions. Infant metal exposure requires critical attention and this needs to be initiated through the diet and lifestyle of their nursing mothers.
Viral loads observed under competing strain dynamics
Authors: Hay James A. , Kennedy-Shaffer Lee , Mina Michael J.
Published: July 2021

A plausible mechanism for the increased transmissibility of SARS-CoV-2 variants of concern (VOCs) results from VOC infections causing higher viral loads in infected hosts. However, investigating this hypothesis using routine RT-qPCR testing data is challenging because the population-distribution of viral loads changes depending on the epidemic growth rate; lower cycle threshold (Ct) values for a VOC lineage may simply reflect increasing incidence relative to preexisting lineages. To understand the extent to which viral loads observed under routine surveillance systems reflect viral kinetics or population dynamics, we used a mathematical model of competing strain dynamics and simulated Ct values for variants with different viral kinetics. We found that comparisons of Ct values obtained under random cross-sectional surveillance were highly biased unless samples were obtained at times when the variants had comparable growth rates. Conversely, comparing Ct values from symptom-based testing was largely unaffected by epidemic dynamics, and accounting for the time between symptom onset and sample collection date further reduced the risk of statistical errors. Finally, we show how a single cross-sectional sample of Ct values can be used to jointly estimate differences in viral kinetics and epidemic growth rates between variants. Epidemic dynamics should be accounted for when investigating strain-specific viral kinetics using virologic surveillance data, and findings should be corroborated with longitudinal viral kinetics studies.
Effect of vaccination and of prior infection on infectiousness of vaccine breakthrough infections and reinfections
Authors: Abu-Raddad Laith J. , Chemaitelly Hiam , Ayoub Houssein H. , Tang Patrick , Coyle Peter , Hasan Mohammad R. , Yassine Hadi M. , Benslimane Fatiha M. , Al Khatib Hebah A. , Kanaani Zaina Al , Kuwari Einas Al , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Nasrallah Gheyath K. , Al Kuwari Mohamed Ghaith , Butt Adeel A. , Al Romaihi Hamad Eid , Khal Abdullatif Al , Al-Thani Mohamed H. , Bertollini Roberto
Published: July 2021

SARS-CoV-2 breakthrough infections in vaccinated individuals and in those who had a prior infection have been observed globally, but the transmission potential of these infections is unknown. The RT-qPCR cycle threshold (Ct) value is inversely correlated with viral load and culturable virus. Here, we investigated differences in RT-qPCR Ct values across Qatar’s national cohorts of primary infections, reinfections, BNT162b2 (Pfizer-BioNTech) breakthrough infections, and mRNA-1273 (Moderna) breakthrough infections. Through matched-cohort analyses of the randomly diagnosed infections, the mean Ct value was higher in all cohorts of breakthrough infections compared to the cohort of primary infections in unvaccinated individuals. The Ct value was 1.3 (95% CI: 0.9-1.8) cycles higher for BNT162b2 breakthrough infections, 3.2 (95% CI: 1.8-4.5) cycles higher for mRNA-1273 breakthrough infections, and 4.0 (95% CI: 3.4-4.6) cycles higher for reinfections in unvaccinated individuals. Assuming a linear relationship between viral load and infectiousness, these differences imply that breakthrough infections are at least 50% less infectious than primary infections in unvaccinated individuals. Public health benefits of vaccination may have been underestimated, as COVID-19 vaccines not only protect against acquisition of infection, but also appear to protect against transmission of infection.
Coronavirus vaccination rates in cultural areas in Germany
Authors: Spahn Claudia , Hipp Anna Maria , Richter Bernhard , Nusseck Manfred
Published: July 2021

Vaccination rates can provide useful information about potential risks of infection in a given population. In this study, the vaccination rates and attitudes toward vaccination in cultural sectors, i.e. music areas, have been investigated. In total, 4341 persons in four different areas including visitors of classical music and musicals as well as professional and amateur musicians participated in this survey. Results showed rates of 86% recovered or vaccinated at least once and 54.5% fully vaccinated. These vaccination rates were considerably higher compared to the general population. Vaccination hesitancy was half that of the general population at 6.4%. The findings of this large sample indicate that in the field of music culture there is a high vaccination rate and a low rejection of vaccination on the part of the audience and the performers. The risk of infection can therefore be assumed as very low and the opening of cultural events can thus be recommended.
Transmission-selective muscle pathology induced by active propagation of mutant huntingtin across the human neuromuscular synapse
Authors: Margarita Dinamarca C. , Colombo Laura , Urszulax Brykczynska , Amandine Grimm , Natalia Tousiaki E. , Isabelle Fruh , Hossain Imtiaz , Daniela Gabriel , Anne Eckert , Matthias Müller , Eline Pecho-Vrieseling
Published: July 2021

A potential explanation for the spatiotemporal accumulation of pathological lesions in the brain of patients with neurodegenerative protein misfolding diseases (PMDs) is cell-to-cell transmission of aggregation-prone, misfolded proteins. Little is known about central to peripheral transmission and its contribution to pathology. We show that transmission of Huntington’s disease- (HD-) associated mutant HTT exon 1 (mHTTEx1) occurs across the neuromuscular junctions in human iPSC cultures and in vivo in wild-type mice. We found that transmission is an active and dynamic process, that happens prior to aggregate formation and is regulated by synaptic activity. Furthermore, we find that transmitted mHTTEx1 causes HD-relevant pathology at a molecular and functional level in human muscle cells, even in the presence of ubiquitous expression mHTTEx1. With this work we uncover a casual-link between mHTTEx1 synaptic transmission and pathology, highlighting the therapeutic potential in blocking toxic protein transmission in PMDs.
“Submandibular Injection of Indoleamine 2,3-Dioxygenase Galectin-3 Fusion Protein Inhibits and Prevents Periodontal Disease Progression Over 12 Weeks”
Authors: Rocha Fernanda , Graves Christina , Altitinchi Ali , Farhadi Shaheen A. , Macias Sabrina L. , Wanchoo Arun , Hudalla Gregory A. , Keselowsky Benjamin G. , Wallet Shannon M.
Published: July 2021

Abstract

A major challenge in the treatment of chronic inflammatory diseases including periodontal diseases is the development of therapeutics to safely and specifically direct resolution of inflammation in a localized manner. Here we demonstrate the efficacy of a novel approach that addresses this unmet clinical need. Using an enzyme fusion protein of indoleamine 2,3-dioxygenase 1 (IDO) and galectin-3 (Gal3) with tissue-anchored and thus localized immunomodulatory properties, we prevented and halted progression of induced polymicrobial periodontal disease. Efficacy was achieved with repeated treatment with IDO-Gal3 and was measured by effects on mandibular bone loss, soft tissue inflammation and local T cell plasticity. Specifically, both prophylactic and therapeutic administration of IDO-Gal3 were effective in reducing vertical mandibular bone loss and loss of mandibular bone volume and bone thickness induced by chronic polymicrobial infection. The efficacy observed is at least in part due to localized regulation of innate immune mediators such as IL-1β, IL-6 and IL-8 as well as chemoattractants including IP-10, MCP-1 and MIP-1α, while enhancing the expression of immunoregulatory cytokines such as IL-10. In addition, IDO-Gal3 treatment suppressed the induction of pathogenic CD4+Th1, CD8+Tc1, CD4+Th1/Th17, and CD8+Tc1/Tc17, while promoting the induction of homeostatic CD4+Th17, CD8+Tc17 and CD4+Tregs. Importantly, the efficacy of prophylactically and therapeutically administered IDO-Gal-3 is not dependent on bacterial burden as there were no appreciable effects on bacterial burden following either method of administration. Lastly, therapeutic rather than prophylactic administration of IDO-Gal3 is most effective in preventing mandibular bone loss through more robust innate and adaptive immune modulation. Together these and our previously published data indicate that therapeutic administration of IDO-Gal3 addresses the clinical needs for adjunctive therapeutics to treat active and/or established periodontal diseases.
Ageing and the ipsilateral M1 BOLD response: a connectivity study
Authors: Tak Yae Won , Knights Ethan , Henson Richard , Zeidman Peter
Published: July 2021

Young people exhibit a negative BOLD response in ipsilateral primary motor cortex (M1) when making unilateral movements, such as button presses. This negative BOLD response becomes more positive as people age. Here we investigated why this occurs, in terms of the underlying effective connectivity and haemodynamics. We applied dynamic causal modelling (DCM) to task fMRI data from 635 participants aged 18-88 from the Cam-CAN dataset, who performed a cued button pressing task with their right hand. We found that connectivity from contralateral supplementary motor area (SMA) and dorsal premotor cortex (PMd) to ipsilateral M1 became more positive with age, explaining 44% of the variability across people in ipsilateral M1 responses. Neurovascular and haemodynamic parameters in the model were not able to explain the age-related shift to positive BOLD. Our results add to a body of evidence implicating neural, rather than vascular factors as the predominant cause of negative BOLD – while emphasising the importance of inter-hemispheric connectivity. This study provides a foundation for investigating the clinical and lifestyle factors that determine the sign and amplitude of the M1 BOLD response, which could serve as a proxy for neural and vascular health, via the underlying neurovascular mechanisms.
Nephrotoxicity of Calcineurin Inhibitors in kidney epithelial cells is independent of Calcineurin and NFAT signaling
Authors: Karolin Andrea , Escher Geneviève , Rudloff Stefan , Sidler Daniel
Published: July 2021

Background

Calcineurin inhibitors (CNI) such as Cyclosporine A (CsA) and Tacrolimus (FK506) are commonly used after renal transplantation in order to suppress the immune system. In lymphoid cells, CsA acts via the Calcineurin-NFAT axis, whereas in non-lymphoid cells, such as kidney epithelial cells, CsA induces Calcineurin inhibitor toxicity (CNT). Up to date, it is unknown via which off-targets CsA induces CNT in kidney epithelial cells.

Methods

In vitro experiments using a surrogate marker to measure CNT induction as well as in vivo studies with acute CNT, were used in order to elucidate the underlying molecular mechanism.

Results

Inhibition of the NFAT axis does not show any nephrotoxicity. However, inhibition of p38 and PI3K/Akt Kinases showed induction of nephrotoxicity.

Conclusions

These findings show that CsA acts NFAT independent on kidney epithelial cells. Moreover, inhibition of certain protein kinases mimic CsA activity on kidney epithelial cells indicating that p38 and PI3K/Akt kinase pathways might be involved in CNT progression on kidney epithelial cells.
Multi-omics investigation of tacrolimus nephrotoxicity
Authors: Aouad Hassan , Faucher Quentin , Sauvage François-Ludovic , Pinault Emilie , Barrot Claire-Cécile , Arnion Hélène , Marquet Pierre , Essig Marie
Published: July 2021

Background

Tacrolimus, an immunosuppressive drug prescribed to a majority of transplanted patients is nephrotoxic, through still unclear mechanisms. This study aims to evaluate the impact of tacrolimus on a lineage of proximal tubular cells using a multi-omics approach.

Methods

LLC-PK1 cells were exposed to 5 M of tacrolimus for 24h. Intracellular proteins and metabolites, and extracellular metabolites were extracted and analysed by LC-MS/MS. The transcriptional expression of the dysregulated proteins PCK-1, FBP1 and FBP2 was measured using RT-qPCR.

Results

In our cell model, tacrolimus impacted different metabolic pathways including those of arginine (e.g., citrulline, ornithine) (p < 0.0001), amino acids (e.g., valine, isoleucine, aspartic acid) (p < 0.0001) and pyrimidine (p<0.01). In addition, it induced oxidative stress (p < 0.01) as shown by a decrease in total cell glutathione quantity. It impacted cell energy through an increase in Krebs cycle intermediates (e.g., citrate, aconitate, fumarate) (p < 0.01) and down-regulation of PCK-1 (p < 0.05) and FPB1 (p < 0.01), which are key enzymes in gluconeogenesis. Apart from glucose synthesis, gluconeogenesis is an important process in kidney mediated acid-base balance control.

Conclusion

The variations found using this multi-omics approach clearly point towards a dysregulation of energy production in epithelial cells of the renal tubule, and potentially of their functions, that may be implicated in tacrolimus nephrotoxicity in the clinics.
Transcription-coupled DNA repair underlies variation in persister awakening and the emergence of resistance
Authors: Dorien Wilmaerts , Charline Focant , Paul Matthay , Jan Michiels
Published: July 2021

Persisters constitute a population of temporarily antibiotic-tolerant variants in an isogenic bacterial population and are considered an important cause of relapsing infections. It is currently unclear how cellular damage inflicted by antibiotic action is reversed upon persister state exit and how this relates to antibiotic resistance development. We demonstrate that persisters, upon fluoroquinolone treatment, accumulate oxidative damage which is repaired through nucleotide excision repair. Detection of the damage occurs via transcription-coupled repair using UvrD-mediated backtracking or Mfd-mediated displacement of the RNA polymerase. This competition results in heterogeneity in persister awakening lags. Most persisters repair the oxidative DNA damage, displaying a mutation rate equal to the untreated population. However, the promutagenic factor Mfd increases the mutation rate in a persister subpopulation. Our data provide in-depth insight in the molecular mechanisms underlying persister survival and pinpoints Mfd as an important molecular factor linking persistence to resistance development.
Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids
Authors: Shirasawa Kenta , Nishio Sogo , Terakami Shingo , Botta Roberto , Torello Marinoni Daniela , Isobe Sachiko
Published: July 2021

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.
Accounting for stimulations that do not elicit motor-evoked potentials when mapping cortical representations of multiple muscles
Authors: Jin Fang , Bruijn Sjoerd M , Daffertshofer Andreas
Published: July 2021

The representation of muscles in the cortex can be mapped using navigated transcranial magnetic stimulation. The mapping can be quantified via measures like the centre of gravity or the size of the region of excitability. Determining these measures typically relies only on stimulation points that yield motor-evoked potentials (MEPs); stimulations that do not elicit an MEP, i.e., non-MEP points, are ignored entirely. In this study, we show how incorporating non-MEP points may affect the estimates of the size and centroid of the excitable area in eight hand and forearm muscles after mono-phasic single-pulse TMS. We performed test-retest assessments in twenty participants and estimated the reliability of centroids and sizes of the corresponding areas using inter-class correlation coefficients. For most muscles, the reliability turned out good, if not excellent. As expected, removing the non-MEP points significantly decreased area sizes and area weights, suggesting that conventional approaches that do not account for non-MEP points are likely to overestimate the regions of excitability.
The transcriptional cofactor IRF2BP2 plays a key role in T cell homeostasis and Treg cell expansion
Authors: Mognol Giuliana P. , Oliveira-Vieira Barbara , Pinheiro-Rosa Natalia , Peixoto Barbara C. , Boroni Marianna , González-Avalos Edahi , Secca Cristiane , Bandukwala Hozefa , Faria Ana Maria C. , Rao Anjana , Viola João P.B.
Published: July 2021

The levels of the co-transcriptional regulator IRF2BP2 (Interferon Regulatory Factor-2 Binding Protein-2) decrease with T cell activation and, when ectopically expressed, it reduces T cell proliferation. To further characterize the function of IRF2BP2 in T cell responses in vivo, we generated a conditional transgenic knock-in mouse that overexpresses IRF2BP2 in T lymphocytes. Overexpression of IRF2BP2 leads to a reduction in the T cell compartment of naive animals, upregulation of Foxp3 and Ifng; an increase in the frequency of regulatory T cells (Tregs), a preferential Th1 differentiation with increase of IFN-γ production and a reduction of T cell proliferation, suggesting a disruption in T cell homeostasis. Interestingly, knock-in mice displayed reduced clinical and inflammatory signs of Experimental Autoimmune Encephalomyelitis (EAE) when compared to the control mice, with an augmented frequency of Treg cells. Altogether, our findings indicate that IRF2BP2 might help to control exacerbated T cell responses and point to a role for IRF2BP2 in preventing T cell autoimmunity.
Semaphorin 3C exacerbates liver fibrosis
Authors: De Angelis Rigotti Francesca , Wiedmann Lena , Hubert Max Ole , Vacca Margherita , Hasan Sana S. , Moll Iris , Carvajal Silvia , Jiménez Wladimiro , Starostecka Maja , Billeter Adrian T , Müller-Stich Beat , Wolff Gretchen , Ekim-Üstünel Bilgen , Herzig Stephan , Mogler Carolin , Fischer Andreas , Rodriguez-Vita Juan
Published: July 2021

Background & Aims

Chronic liver disease is a growing epidemic leading to fibrosis and cirrhosis. TGF-β is the pivotal pro-fibrogenic cytokine which activates hepatic stellate cells (HSC), yet, other molecules can substantially modulate TGF-β signaling in the course of liver fibrosis. Expression of the axon guidance molecules Semaphorins (SEMAs), which signal through Plexins and Neuropilins (NRPs), have been associated with liver fibrosis in HBV-induced chronic hepatitis. This study aims at determining their function in the regulation of HSCs.

Approach & Results

We analyzed publicly available patient databases and liver biopsies. We employed transgenic mice where genes are deleted only in activated HSCs to perform ex vivo analysis and animal models. SEMA3C is the most enriched member of the Semaphorin family in liver samples from cirrhotic patients. Higher expression of SEMA3C in patients with NASH, alcoholic hepatitis or HBV-induced hepatitis discriminates those with a more pro-fibrotic transcriptomic profile. SEMA3C expression is also elevated in different mouse models of liver fibrosis and in isolated HSCs upon activation. In keeping with this, deletion of SEMA3C in activated HSCs reduces myofibroblast marker expression. Conversely, SEMA3C overexpression exacerbates TGF-β-mediated myofibroblast activation, as shown by increased SMAD2 phosphorylation and target gene expression. Among SEMA3C receptors, only NRP2 expression is maintained upon activation of isolated HSCs. Interestingly, lack of NRP2 in those cells reduces myofibroblast marker expression. Finally, deletion of either SEMA3C or NRP2, specifically in activated HSCs, reduces liver fibrosis in mice.

Conclusion

SEMA3C is a novel marker for activated HSCs that plays a fundamental role in the acquisition of the myofibroblastic phenotype and liver fibrosis.
Artificial Neural Networks for classification of single cell gene expression
Authors: Zhong Jiahui , Lyu Minjie , Jin Huan , Cao Zhiwei , Chitkushev Lou T. , Zhang Guanglan , Keskin Derin B. , Brusic Vladimir
Published: July 2021

Background

Single-cell transcriptome (SCT) sequencing technology has reached the level of high-throughput technology where gene expression can be measured concurrently from large numbers of cells. The results of gene expression studies are highly reproducible when strict protocols and standard operating procedures (SOP) are followed. However, differences in sample processing conditions result in significant changes in gene expression profiles making direct comparison of different studies difficult. Unsupervised machine learning (ML) uses clustering algorithms combined with semi-automated cell labeling and manual annotation of individual cells. They do not scale up well and a workflow used on a specific dataset will not perform well with other studies. Supervised ML classification shows superior classification accuracy and generalization properties as compared to unsupervised ML methods. We describe a supervised ML method that deploys artificial neural networks (ANN), for 5-class classification of healthy peripheral blood mononuclear cells (PBMC) from multiple diverse studies.

Results

We used 58 data sets to train ANN incrementally – over ten cycles of training and testing. The sample processing involved four protocols: separation of PBMC, separation of PBMC + enrichment (by negative selection), separation of PBMC + FACS, and separation of PBMC + MACS. The training data set included between 85 and 110 thousand cells, and the test set had approximately 13 thousand cells. Training and testing were done with various combinations of data sets from four principal data sources. The overall accuracy of classification on independent data sets reached 5-class classification accuracy of 94%. Classification accuracy for B cells, monocytes, and T cells exceeded 95%. Classification accuracy of natural killer (NK) cells was 75% because of the similarity between NK cells and T cell subsets. The accuracy of dendritic cells (DC) was low due to very low numbers of DC in the training sets.

Conclusions

The incremental learning ANN model can accurately classify the main types of PBMC. With the inclusion of more DC and resolving ambiguities between T cell and NK cell gene expression profiles, we will enable high accuracy supervised ML classification of PBMC. We assembled a reference data set for healthy PBMC and demonstrated a proof-of-concept for supervised ANN method in classification of previously unseen SCT data. The classification shows high accuracy, that is consistent across different studies and sample processing methods.
Targeted resurrection of chromosomal arm 1RS in two elite wheat lines with 1BL/1RS translocation for improved end-use quality
Authors: Kaur Ramandeep , Dhillon Guriqbal Singh , Kaur Amandeep , Kaur Sarabjit , Kaur Puneetinder , Kaur Diljot , Kumar Aman , Singh Rohtas , Mavi Gurvinder Singh , Grewal Satvir Kaur , Chhuneja Parveen , Kaur Satinder
Published: July 2021

1BL/1RS translocation is widely used around the world to enhance wheat yield potential, resistance to various diseases, and adaptation. However, the translocation is combined with inherent quality problems associated with reduced dough strength and dough stickiness due to the presence ofSec-1on proximal end and absence ofGluB3/GliB1on distal end. Two NILs, one carrying the distal (1RSRW) and the other carrying the proximal (1RSWR) fragment from 1BS, in background of Pavon were used for transferring these two loci in yellow rust resistant version of two elite wheat varieties PBW550+Yr5and DBW17+Yr5. Foreground and background marker assisted selection was done for theSec-1-andGluB3+ alongwithLr26/Yr9/Sr31,Pm8and 1RS loci in the advancing generation. BC2F5:6NILs with absence ofSecalinand presence ofGluB3/GliB1loci were evaluated for two years in replicated yield trial. A positive correlation of thousand grain weight (TGW), harvest index (HI), and tiller number per meter (TNpM) with yield (YD) with significant GxE effect was observed. Further multivariate analysis of these traits contributed maximum to the effective yield. Thirty promising NILs were identified withSec-1-/GluB3+alongwith with high yield contributing parameters.
Deficiency in cytosine DNA methylation leads to high chaperonin expression and tolerance to aminoglycosides in Vibrio cholerae
Authors: Carvalho André , Mazel Didier , Baharoglu Zeynep
Published: July 2021

Antibiotic resistance has become a major global issue. Understanding the molecular mechanisms underlying microbial adaptation to antibiotics is of keen importance to fight Antimicrobial Resistance (AMR). Aminoglycosides are a class of antibiotics that target the small subunit of the bacterial ribosome, disrupting translational fidelity and increasing the levels of misfolded proteins in the cell. In this work, we investigated the role of VchM, a DNA methyltransferase, in the response of the human pathogen Vibrio cholerae to aminoglycosides. VchM is a V. cholerae specific orphan m5C DNA methyltransferase that generates cytosine methylation at 5′-RCCGGY-3′ motifs. We show that deletion of vchM, although causing a growth defect in absence of stress, allows V. cholerae cells to cope with aminoglycoside stress at both sub-lethal and lethal concentrations of these antibiotics. Through transcriptomic and genetic approaches, we show that groESL-2 (a specific set of chaperonin-encoding genes located on the second chromosome of V. cholerae), are upregulated in cells lacking vchM and are needed for the tolerance of vchM mutant to lethal aminoglycoside treatment, likely by fighting aminoglycoside-induced misfolded proteins. Interestingly, preventing VchM methylation of the four RCCGGY sites located in groESL-2 region, leads to a higher expression of these genes in WT cells, showing that VchM modulates the expression of these chaperonins in V. cholerae directly through DNA methylation.

AUTHOR SUMMARY

Bacteria are organisms with a remarkable ability to adapt to several stress conditions, including to the presence of antibiotics. The molecular mechanisms underlying such adaptation lead, very often, to phenomena like antimicrobial tolerance and resistance, responsible for the frequent failure of antibiotic treatment. The study of these molecular mechanisms is thus an important tool to understand development of antimicrobial resistance in bacteria. In this work, we show that abrogating cytosine DNA methylation in Vibrio cholerae increases its tolerance to aminoglycosides, a class of antibiotics that cause protein misfolding. DNA methylation is known to affect gene expression and regulate several cellular processes in bacteria. Here we provide evidence that DNA methylation also has a more direct role in controlling antibiotic susceptibility in bacteria. Consequently, the study of bacterial DNA methyltransferases and DNA methylation should not be overlooked when addressing the problem of antimicrobial tolerance/resistance.
Small extracellular vesicles from young mice prevent frailty, improve healthspan and decrease epigenetic age in old mice
Authors: Sanz-Ros Jorge , Mas-Bargues Cristina , Monleón Daniel , Gordevicius Juozas , Brooke Robert T. , Dromant Mar , Derevyanko Aksinya , Guío-Carrión Ana , Román-Domínguez Aurora , Romero-García Nekane , Inglés Marta , Blasco María A. , Horvath Steve , Viña Jose , Borrás Consuelo
Published: July 2021

Aging is associated with an increased risk of frailty, disability, comorbidities, institutionalization, falls, fractures, hospitalization, and mortality. Searching for strategies to delay the degenerative changes associated with aging and frailty is interesting. We treated old animals intravenously with small extracellular vesicles (sEVs) derived from adipose mesenchymal stem cells (ADSCs) of young animals, and we found an improvement of several functional parameters usually altered with aging, such as motor coordination, grip strength, fatigue resistance, fur regeneration, and renal function. Frailty index analysis showed that 40% of old control mice were frail, whereas none of the old ADSCs-sEVs treated mice were. Molecular and structural benefits in muscle and kidney accompanied this functional improvement. ADSCs-sEVs induced pro-regenerative effects and a decrease in oxidative stress, inflammation, and senescence markers. Moreover, predicted epigenetic age was lower in tissues of old mice treated with ADSCs-sEVs and their metabolome changed to a youth-like pattern. Finally, we gained some insight into the miRNAs contained in sEVs that might be, at least in part, responsible for the effects observed. We propose that young sEVs treatment can be beneficial against frailty and therefore can promote healthy aging.
Detection and Spatiotemporal analysis of in-vitro 3D migratory Triple-Negative Breast cancer cells
Authors: Dimitriou Nikolaos M. , Flores-Torres Salvador , Kinsella Joseph Matthew , Mitsis Georgios D.
Published: July 2021

The invasion of cancer cells into the surrounding tissues is one of the hallmarks of cancer. However, a precise quantitative understanding of the spatiotemporal patterns of cancer cell migration and invasion still remains elusive. A promising approach to investigate these patterns are 3D cell cultures, which provide more realistic models of cancer growth compared to conventional 2D monolayers. Quantifying the spatial distribution of cells in these 3D cultures yields great promise for understanding the spatiotemporal progression of cancer. In the present study, we present an image processing and segmentation pipeline for the detection of 3D GFP-fluorescent Triple-Negative Breast Cancer cell nuclei, and we perform quantitative analysis of the formed spatial patterns and their temporal evolution. The performance of the proposed pipeline was evaluated using experimental 3D cell culture data, and was found to be comparable to manual segmentation, outperforming four alternative automated methods. The spatiotemporal statistical analysis of the detected distributions of nuclei revealed transient, non-random spatial distributions that consisted of clustered patterns across a wide range of neighbourhood distances, as well as dispersion for larger distances. Overall, the implementation of the proposed framework revealed the spatial organization of cellular nuclei with improved accuracy, providing insights into the 3 dimensional inter-cellular organization and its progression through time.
Large herbivorous wildlife and livestock differentially influence the relative importance of different sources of carbon for riverine food webs
Authors: Masese Frank O. , Fuss Thomas , Bistarelli Lukas Thuile , Buchen-Tschiskale Caroline , Singer Gabriel
Published: July 2021

In many regions around the world, large populations of native wildlife have declined or been replaced by livestock grazing areas and farmlands, with consequences on terrestrial-aquatic ecosystems connectivity and trophic resources supporting food webs in aquatic ecosystems. The river continuum concept (RCC) and the riverine productivity model (RPM) predict a shift of carbon supplying aquatic food webs along the river: from terrestrial inputs in low-order streams to autochthonous production in mid-sized rivers. Here, we studied the influence of replacing large wildlife (mainly hippos) with livestock on the relative importance of C3 vegetation, C4 grasses and periphyton on macroinvertebrates in the Mara River, which is an African montane-savanna river known to receive large subsidy fluxes of terrestrial carbon and nutrients mediated by LMH, both wildlife and livestock. Using stable carbon (δ13C) and nitrogen (δ15N) isotopes, we identified spatial patterns of the relative importance of allochthonous carbon from C3 and C4 plants (woody vegetation and grasses, respectively) and autochthonous carbon from periphyton for macroinvertebrates at various sites of the Mara River and its tributaries. Potential organic carbon sources and invertebrates were sampled at 80 sites spanning stream orders 1 to 7, various catchment land uses (forest, agriculture and grasslands) and different loading rates of organic matter and nutrients by LMH (livestock and wildlife, i.e., hippopotamus). The importance of different sources of carbon along the river did not follow predictions of RCC and RPM. First, the importance of C3 and C4 carbon was not related to river order or location along the fluvial continuum but to the loading of organic matter (dung) by both wildlife and livestock. Notably, C4 carbon was important for macroinvertebrates even in large river sections inhabited by hippos. Second, even in small 1st −3rd order forested streams, autochthonous carbon was a major source of energy for macroinvertebrates, and this was fostered by livestock inputs fuelling aquatic primary production throughout the river network. Importantly, our results show that replacing wildlife (hippos) with livestock shifts river systems towards greater reliance on autochthonous carbon through an algae-grazer pathway as opposed to reliance on allochthonous inputs of C4 carbon through a detrital pathway.
Modeling memory T cell states at single-cell resolution identifies in vivo state-dependence of eQTLs influencing disease
Authors: Nathan Aparna , Asgari Samira , Ishigaki Kazuyoshi , Amariuta Tiffany , Luo Yang , Beynor Jessica I. , Baglaenko Yuriy , Suliman Sara , Price Alkes , Lecca Leonid , Murray Megan B. , Moody D. Branch , Raychaudhuri Soumya
Published: July 2021

Many non-coding genetic variants cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by gene-regulation differences between cell states. T cells, for example, have fluid, multifaceted functional states in vivo that cannot be modeled in eQTL studies that aggregate cells. Here, we modeled T cell states and eQTLs at single-cell resolution. Using >500,000 resting memory T cells from 259 Peruvians, we found over one-third of the 6,511 cis-eQTLs had state-dependent effects. By integrating single-cell RNA and surface protein measurements, we defined continuous cell states that explained more eQTL variation than discrete states like CD4+ or CD8+ T cells and could have opposing effects on independent eQTL variants in a locus. Autoimmune variants were enriched in cell-state-dependent eQTLs, such as a rheumatoid-arthritis variant near ORMDL3 strongest in cytotoxic CD8+ T cells. These results argue that fine-grained cell state context is crucial to understanding disease-associated eQTLs.
Robust adaptive distance functions for approximate Bayesian inference on outlier-corrupted data
Authors: Schälte Yannik , Alamoudi Emad , Hasenauer Jan
Published: July 2021

Approximate Bayesian Computation (ABC) is a likelihood-free parameter inference method for complex stochastic models in systems biology and other research areas. While conceptually simple, its practical performance relies on the ability to efficiently compare relevant features in simulated and observed data via distance functions. Complications can arise particularly from the presence of outliers in the data, which can severely impair the inference. Thus, robust methods are required that provide reliable estimates also from outlier-corrupted data.

We illustrate how established ABC distance functions are highly sensitive to outliers, and can in practice yield erroneous or highly uncertain parameter estimates and model predictions. We introduce self-tuned outlier-insensitive distance functions, based on a popular adaptive distance weighting concept, complemented by a simulation-based online outlier detection and downweighting routine. We evaluate and compare the presented methods on six test models covering different model types, problem features, and outlier scenarios. Our evaluation demonstrates substantial improvements on outlier-corrupted data, while giving at least comparable performance on outlier-free data.

The developed methods have been made available as part of the open-source Python package pyABC (https://github.com/icb-dcm/pyabc).
Heme-stress activated NRF2 signaling skews fate trajectories of bone marrow cells from dendritic cells towards red pulp-like macrophages
Authors: Vallelian Florence , Buzzi Raphael M. , Pfefferlé Marc , Yalamanoglu Ayla , Wassmer Andreas , Gentinetta Thomas , Hansen Kerstin , Humar Rok , Schulthess Nadja , Schaer Dominik J.
Published: July 2021

Heme is an erythrocyte-derived toxin that drives disease progression in hemolytic anemias, such as sickle cell disease. During hemolysis, specialized bone marrow-derived macrophages with a high heme-metabolism capacity orchestrate disease adaptation by removing damaged erythrocytes and heme-protein complexes from the blood and supporting iron recycling for erythropoiesis. Since chronic heme-stress is noxious for macrophages, erythrophagocytes in the spleen are continuously replenished from bone marrow-derived progenitors. Here, we hypothesized that adaptation to heme stress progressively shifts differentiation trajectories of BM progenitors to expand the capacity of heme-handling monocyte-derived macrophages at the expense of the homeostatic generation of dendritic cells, which emerge from shared myeloid precursors. This heme-induced redirection of differentiation trajectories may contribute to hemolysis-induced secondary immunodeficiency. We performed single-cell RNA sequencing with directional RNA velocity analysis of GM-CSF-supplemented mouse bone marrow cultures to assess myeloid differentiation under heme stress. We found that heme-activated NRF2 signaling shifted the differentiation of bone marrow cells towards antioxidant, iron-recycling macrophages, suppressing the generation of dendritic cells in heme-exposed bone marrow cultures. Heme eliminated the capacity of GM-CSF-supplemented bone marrow cultures to activate antigen-specific CD4 T cells. The generation of functionally competent dendritic cells was restored by NRF2 loss. The heme-induced phenotype of macrophage expansion with concurrent dendritic cell depletion was reproduced in hemolytic mice with sickle cell disease and spherocytosis and associated with reduced dendritic cell functions in the spleen. Our data provide a novel mechanistic underpinning of hemolytic stress as a driver of hyposplenism-related secondary immunodeficiency.

GRAPHICAL ABSTRACT
Temporal variation in lymphocyte proteomics
Authors: McCown Michaela A. , Allen Carolyn , Machado Daniel D. , Boekweg Hannah , Liang Yiran , Nwosu Andikan J. , Kelly Ryan T. , Payne Samuel H.
Published: July 2021

Chronic Lymphocytic Leukemia (CLL) is a slow progressing disease, characterized by a long asymptomatic stage followed by a symptomatic stage during which patients receive treatment. While proteomic studies have discovered differential pathways in CLL, the proteomic evolution of CLL during the asymptomatic stage has not been studied. In this pilot study, we show that by using small sample sizes comprising ~145 cells, we can detect important features of CLL necessary for studying tumor evolution. Our small samples are collected at two time points and reveal large proteomic changes in healthy individuals over time. A meta-analysis of two CLL proteomic papers showed little commonality in differentially expressed proteins and demonstrates the need for larger control populations sampled over time. To account for proteomic variability between time points and individuals, large control populations sampled at multiple time points are necessary for understanding CLL progression. Data is available via ProteomeXchange with identifier PXD027429.
A machine-learning approach for detection of local brain networks and marginally weak signals identifies novel AD/MCI differentiating connectomic neuroimaging biomarkers
Authors: Li Yanming , Kang Jian , Wu Chong , Dinov Ivo D. , Hu Jinxiang , Chalise Prabhakar , Mahnken Jonathan D. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: July 2021

Introduction

A computationally fast machine learning method is introduced for uncovering the wholebrain voxel-level connectomic spectra that differentiates different status of Alzheimer’s disease (AD). The method is applied to the Alzheimer’s Disease Neuroimaging Initiative (ADNI) Fluorinefluorodeoxyglucose Positron Emission Tomography (FDG-PET) imaging and clinical data and identified novel AD/MCI differentiating connectomic neuroimaging biomarkers.

Methods

A divide-and-conquer algorithm is introduced for detect informative local brain networks at voxel level and whole-brain scale. The connection information within the local networks is integrated into the node voxels, which makes detection of the marginally weak signals possible. Prediction accuracy is significantly improved by incorporating the local brain networks and marginally weak signals.

Results

Brain connectomic structures differentiating AD and mild cognitive impairment (MCI), AD and healthy, and MIC and healthy were discovered. We identified novel AD/MCI-associated neuroimaging biomarkers by integrating local brain networks and marginally weak signals. For example, networkbased signals in paracentral lobule (p-value=6.1e-5), olfactory cortex (p-value=4.6e-5), caudate nucleus (1.8e-3) and precentral gyrus (1.8e-3) are informative in differentiating AD and MCI. Connections between calcarine sulcus and lingual gyrus (p-value=0.049), between parahippocampal gyrus and Amygdala (p-value=0.025), between rolandic opercula and insula lobes (p-values=0.0028 and 0.0026). An overall prediction accuracy of 95.3% was achieved by integrating the selected local brain networks and marginally weak signals, compared to 84.0% by not considering the inter-voxel connections and using marginally strong signals only.

Conclusion

(i) The connectomic structures differentiating AD and MCI are significantly different to that differentiating MCI and healthy, which may indicate different neuronal etiology for AD and MCI. (ii) Many neuroimaging biomarkers exert their effects on the outcome diseases through their connections to other markers. Integrating such connections can help identify novel neuroimaging biomarkers and improve disease prediction accuracy.
Outer hair cell electro-mechanical power conversion
Authors: Rabbitt Richard D.
Published: July 2021

Outer hair cells are the cellular motors in the mammalian inner ear responsible for sensitive high-frequency hearing. Motor function requires expression of the protein prestin in the OHC lateral membrane and mechano-electrical transduction in the apical hair bundle. In the present report, electrical power consumption and mechanical power output are determined using previously published voltage clamp data from isolated OHCs and membrane patches. Results reveal that power output by the prestin-motor complex peaks at a best frequency much higher than implied by the low-pass character of nonlinear capacitance, and much higher than the whole-cell resistive-capacitive corner frequency. High frequency power output is enabled by a −90° shift in the phase of prestin-dependent electrical charge displacement, manifested electrically as emergence of imaginary-valued nonlinear capacitance.