bluuebunny/crossref_metadata_2025 huggingface dataset:
Physiological (TCR-like) regulated lentiviral vectors for the generation of improved CAR-T cells
Authors: Tristán-Manzano María , Maldonado-Pérez Noelia , Justicia-Lirio Pedro , Muñoz Pilar , Cortijo-Gutiérrez Marina , Pavlovic Kristina , Jiménez-Moreno Rosario , Nogueras Sonia , Carmona MDolores , Sánchez-Hernández Sabina , Aguilar-González Araceli , Castella María , Juan Manel , Marañón Concepción , Benabdellah Karim , Herrera Concha , Martin Francisco
Published: March 2021

Background

Chimeric antigen receptor (CAR) T cells directed against CD19 have achieved impressive outcomes for the treatment of relapsed/refractory B lineage lymphoid neoplasms. However, CAR-T therapy still has important limitations due to severe side effects and the lack of efficiency in 40-50% of the patients. Most CARs-T products are generated using retroviral vectors with strong promoters. However, high CAR expression levels can lead to tonic signalling, premature exhaustion and over-stimulation of CAR-T cells, reducing efficacy and increasing side effects. TCR-like expression of the CAR through genome editing resulted in enhanced anti-tumour potency, reducing tonic signalling and improving CAR-T phenotype. In this manuscript, we searched for LVs that mimic the TCR expression pattern as a closer-to-clinic alternative for the generation of improved CAR-T cells.

Methods

Different LVs containing viral and human promoters were analysed to select those that closely mimic a TCR-like kinetic profile upon T-cell activation. WAS gene proximal promoter-driven LVs (AW-LVs) were selected to express a second generation 4-1BB aCD19 CAR (ARI-0001) into T cells to generate AWARI CAR-T cells. TCR-like AWARI and EF1α-driven ARI CAR T cells were analysed for in vitro and in vivo killing efficiency using leukaemia and lymphoma cellular models. Tonic signalling, exhaustion markers and phenotype were determined by flow cytometry. Large-scale automated manufacturing of AWARI CAR-T cells was performed in a CliniMACs Prodigy bioreactor.

Results

Our data showed that LVs expressing the transgene through the WAS gene proximal promoter mimic very closely the TCR (CD3) expression pattern kinetic upon TCR stimulation or antigen encounter. Compared to EF1α-driven ARI CAR-T cells, AWARI CAR-T cells exhibited a higher proportion of naïve/stem cell memory T cells with less exhausted phenotype after efficient killing of CD19+ cells both in vitro and in vivo. AWARI CAR-T cells also showed lower tonic signalling and reduced secretion of pro-inflammatory cytokines and were efficiently manufactured in large-scale GMP-like conditions.

Conclusions

WAS-gene-promoter driven LVs can be used to generate physiological 4-1BB-CAR-T cell products with lower tonic signalling, improved phenotype and a safer profile. We propose the use of TCR-like LVs as an alternative to strong-promoter driven LVs for the generation of CAR-T products.
Predicting adult Attention Deficit Hyperactivity Disorder (ADHD) using vocal acoustic features
Authors: von Polier Georg G. , Ahlers Eike , Amunts Julia , Langner Jörg , Patil Kaustubh R. , Eickhoff Simon B. , Helmhold Florian , Langner Daina
Published: March 2021

Background

It is a key concern in psychiatric research to investigate objective measures to support and ultimately improve diagnostic processes. Current gold standard diagnostic procedures for attention deficit hyperactivity disorder (ADHD) are mainly subjective and prone to bias. Objective measures such as neuropsychological measures and EEG markers show limited specificity. Recent studies point to alterations of voice and speech production to reflect psychiatric symptoms also related to ADHD. However, studies investigating voice in large clinical samples allowing for individual-level prediction of ADHD are lacking. The aim of this study was to explore a role of prosodic voice measures as objective marker of ADHD.

Methods

1005 recordings were analyzed from 387 ADHD patients, 204 healthy controls, and 100 clinical (psychiatric) controls. All participants (age range 18-59 years, mean age 34.4) underwent an extensive diagnostic examination according to gold standard methods and provided speech samples (3 min in total) including free and given speech. Paralinguistic features were calculated, and random forest based classifications were performed using a 10-fold cross-validation with 100 repetitions controlling for age, sex, and education. Association of voice features and ADHD-symptom severity assessed in the clinical interview were analyzed using random forest regressions.

Results and Conclusion

ADHD was predicted with AUC = 0.76. The analysis of a non-comorbid sample of ADHD resulted in similar classification performance. Paralinguistic features were associated with ADHD-symptom severity as indicated by random forest regression. In female participants, particularly with age < 32 years, paralinguistic features showed the highest classification performance (AUC = 0.86).

Paralinguistic features based on derivatives of loudness and fundamental frequency seem to be promising candidates for further research into vocal acoustic biomarkers of ADHD. Given the relatively good performance in female participants independent of comorbidity, vocal measures may evolve as a clinically supportive option in the complex diagnostic process in this patient group.
Essential Emergency and Critical Care – a consensus among global clinical experts
Authors: Schell Carl Otto , Khalid Karima , Wharton-Smith Alexandra , Oliwa Jacquie Narotso , Sawe Hendry Robert , Roy Nobhojit , Sanga Alex , Marshall John C. , Rylance Jamie , Hanson Claudia , Kayambankadzanja Raphael Kazidule , Wallis Lee A. , Jirwe Maria , Baker Tim ,   the EECC Collaborators
Published: March 2021

Background

Globally, critical illness results in millions of deaths every year. Although many of these deaths are potentially preventable, the basic, life-saving care of critically ill patients are often overlooked in health systems. Essential Emergency and Critical Care (EECC) has been devised as the care that should be provided to all critically ill patients in all hospitals in the world. EECC includes the effective care of low cost and low complexity for the identification and timely treatment of critically ill patients across all medical specialities. This study aimed to specify the content of EECC and additionally, given the surge of critical illness in the ongoing pandemic, the essential diagnosis-specific care for critically ill patients with COVID-19.

Methods

A Delphi process was conducted to seek consensus (>90% agreement) in a diverse panel of global clinical experts. The panel was asked to iteratively rate proposed treatments and actions based on previous guidelines and the WHO/ICRC’s Basic Emergency Care. The output from the Delphi was adapted iteratively with specialist reviewers into a coherent and feasible EECC package of clinical processes plus a list of hospital resource requirements.

Results

The 269 experts in the Delphi panel had clinical experience in different acute medical specialties from 59 countries and from all resource settings. The agreed EECC package contains 40 clinical processes and 67 hospital readiness requirements. The essential diagnosis-specific care of critically ill COVID-19 patients has an additional 7 clinical processes and 9 hospital readiness requirements.

Conclusion

The study has specified the content of the essential emergency and critical care that should be provided to all critically ill patients. Implementation of EECC could be an effective strategy to reduce preventable deaths worldwide. As critically ill patients have high mortality rates, especially where trained staff or resources are limited, even small improvements would have a large impact on survival. EECC has a vital role in the effective scale-up of oxygen and other care for critically ill patients in the COVID-19 pandemic. Policy makers should prioritise EECC, increase its coverage in hospitals, and include EECC as a component of universal health coverage.
Uncertainty extraction and verification for the Common Conditions Affecting the Hand and Wrist Priority Setting Partnership: A proposed methodology for Priority Setting Partnerships with the James Lind Alliance
Authors: Grindlay DJC , Davis TRC , Kennedy D , Larson D , Furniss D , Cowan K , Giddins G , Jain A , Trickett RW , Karantana A
Published: March 2021

Objective

To report our recommended methodology for extracting and confirming published research uncertainties during a broad scope Priority Setting Partnership (PSP) with the James Lind Alliance.

Setting

This process was completed in the UK as part of the PSP for “Common Conditions Affecting the Hand and Wrist”, comprising of health professionals, patients and carers.

Design and Data Extraction

We applied best practice in systematic review methodology and reporting, including independent screening and data extraction by multiple researchers and use of a PRISMA flowchart, alongside steering group consensus processes.

Data Sources

Cochrane Systematic Reviews and Protocols, NICE (National Institute for Health and Care Excellence) Guidelines, and SIGN (Scottish Intercollegiate Guidelines Network) Guidelines.

Selection Criteria

Selection of research uncertainties was guided by the scope of the Common Conditions Affecting the Hand and Wrist PSP which focused on “common hand conditions routinely treated by hand specialists, including hand surgeons and hand therapists limited to identifying questions concerning the results of intervention, and not the basic science or epidemiology behind disease.

Results

Of 2358 records identified after duplicate extraction which entered the screening process, 186 records were presented to the PSP steering group for eligibility assessment; 79 were deemed within scope and included for the purpose of research uncertainty extraction (45 full Cochrane Reviews, 18 Cochrane Review protocols, 16 Guidelines). These yielded 89 research uncertainties, which were compared to the stakeholder survey, and added to the longlist where necessary; before derived uncertainties were checked against non-Cochrane published systematic reviews.

Conclusions

In carrying out this work, beyond reporting on output of the Common Conditions Affecting the Hand and Wrist PSP, we detail the methodology and processes we hope can inform and facilitate the work of future PSPs and other evidence reviews, especially those with a broader scope beyond a single disease or condition.

Strengths and Limitations

–

This is a novel and rigorous approach to uncertainty extraction and verification in the setting of a James Lind Alliance Priority Setting Partnership.

–

The detailed methodology provides transparency regarding the extraction and verification of uncertainties.

–

The uncertainty extraction and verification relied upon the HandSRev database – similar resources may not be available for other Priority Setting Partnerships.
Intensity of COVID-19 in care homes following Hospital Discharge in the early stages of the UK epidemic
Authors: Hollinghurst Joe , North Laura , Emmerson Chris , Akbari Ashley , Torabi Fatemeh , Lyons Ronan A , Hawkes Alan G , Bennett Ed , Gravenor Mike B , Fry Richard
Published: March 2021

Background

A defining feature of the COVID-19 pandemic in many countries was the tragic extent to which care home residents were affected, and the difficulty preventing introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was transfer of patients from hospitals, which were experiencing high levels of nosocomial events.

Methods

We tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in cases rates following exposure to a hospital discharge using multi-level hierarchical logistic regression, and a novel stochastic Hawkes process outbreak model.

Findings

In regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected.

Interpretation

There is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.
Vision-to-value transformations in artificial neural networks and human brain
Authors: Pham Trung Quang , Yoshimoto Takaaki , Niwa Haruki , Takahashi Haruka K , Uchiyama Ryutaro , Matsui Teppei , Anderson Adam K , Sadato Norihiro , Chikazoe Junichi
Published: March 2021

Humans and now computers can derive subjective valuations from sensory events although such transformation process is essentially unknown. In this study, we elucidated unknown neural mechanisms by comparing convolutional neural networks (CNNs) to their corresponding representations in humans. Specifically, we optimized CNNs to predict aesthetic valuations of paintings and examined the relationship between the CNN representations and brain activity via multivoxel pattern analysis. Primary visual cortex and higher association cortex activities were similar to computations in shallow CNN layers and deeper layers, respectively. The vision-to-value transformation is hence proved to be a hierarchical process which is consistent with the principal gradient that connects unimodal to transmodal brain regions (i.e. default mode network). The activity of the frontal and parietal cortices was approximated by goal-driven CNN. Consequently, representations of the hidden layers of CNNs can be understood and visualized by their correspondence with brain activity–facilitating parallels between artificial intelligence and neuroscience.
Auditory mismatch responses are differentially sensitive to changes in muscarinic acetylcholine versus dopamine receptor function
Authors: Weber Lilian A. , Tomiello Sara , Schöbi Dario , Wellstein Katharina V. , Müller Daniel , Iglesias Sandra , Stephan Klaas E.
Published: March 2021

The auditory mismatch negativity (MMN) has been proposed as a biomarker of NMDA receptor (NMDAR) dysfunction in schizophrenia. Pathophysiological theories suggest that such dysfunction might be partially caused by aberrant interactions of different modulatory neurotransmitters with NMDARs, which could explain heterogeneity among patients with schizophrenia and their treatment response. Understanding the differential impact of different neuromodulators on readouts of NMDAR function is therefore of high clinical relevance.

Here, we report results from two studies (N=81 each) which systematically tested whether the MMN is sensitive to diminishing and enhancing cholinergic vs. dopaminergic function. Both studies used a double-blind, placebo-controlled between-subject design and monitored individual drug plasma levels. Using a novel variant of the auditory oddball paradigm, we contrasted phases with stable versus volatile probabilities of tone switches. In the first study, we found that the muscarinic acetylcholine receptor antagonist biperiden reduced and/or delayed mismatch responses, particularly during stable phases of the experiment, whereas this effect was absent for amisulpride, a dopamine D2/D3 receptor antagonist. The direct comparison between biperiden and amisulpride indicated a significant drug × mismatch interaction. In the second study, neither elevating acetylcholine nor dopamine levels via administration of galantamine and levodopa, respectively, exerted significant effects on MMN.

Overall, our results indicate differential sensitivity of the MMN to changes in cholinergic (muscarinic) versus dopaminergic receptor function. This finding may prove useful for developments of future tools for predicting individual treatment responses in disorders that show abnormal MMN, such as schizophrenia.
Inferring causality in biological oscillators
Authors: Tyler Jonathan , Forger Daniel , Kim Jae Kyoung
Published: March 2021

A fundamental goal of biological study is to identify regulatory interactions among components. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulatory networks computationally. However, when the components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test whether time series are reproducible with a specific model but require inefficient simulations and have limited applicability. Here, we develop an inference method based on a general model of molecular, neuronal, and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability, and usability. Our method successfully infers the positive and negative regulations of various oscillatory networks, including the repressilator and a network of cofactors of pS2 promoter, outperforming popular inference methods. We also provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to decipher the mechanisms by which diverse systems generate oscillations.
Analysis of correlation and trail coefficients for componentperformance s in nine experimental tomato lines
Authors: Choque Gonzalo Quispe
Published: March 2021

The objective of the research was to analyze the main variables related to tomato yield, and guide the selection of materials for the INIAF vegetable improvement program. The experiment was carried out in the open field using nine tomato lines on the grounds of the National Vegetable Seed Production Center, during the 2017-2018 agricultural campaign. A randomized complete block experimental design was used, with three repetitions and 10 plants per experimental unit. For the analysis of the data, the variable yield was considered as dependent and the variables number of flowers per inflorescence, number of clusters per plant, number of fruits per plant, weight of fruit, equatorial and polar diameter as independent variables. Analysis of variance, phenotypic correlations and path coefficients were performed. The performance of the L015 line was 80. 79 t ha-1 higher than the L014, L019 and Rio Grande lines. The fruit yield had a significant correlation with the weight of fruit per plant followed by the polar diameter, equatorial diameter, number of fruits per plant and weight of fruit. The analysis of path coefficients showed that the number of fruits per plant had the highest direct positive effect on the fruit yield, fruit weight and equatorial diameter that have a significant correlation and a direct effect on the fruit yield, emerged as the components with coefficients of 0.96 and 0.52 respectively. These characters may be relevant within the selection criteria in the development of new varieties. number of fruits per plant and weight of fruit. The analysis of path coefficients showed that the number of fruits per plant had the highest direct positive effect on the fruit yield, fruit weight and equatorial diameter that have a significant correlation and a direct effect on the fruit yield, emerged as the components with coefficients of 0.96 and 0.52 respectively. These characters may be relevant within the selection criteria in the development of new varieties. number of fruits per plant and weight of fruit. The analysis of path coefficients showed that the number of fruits per plant had the highest direct positive effect on the fruit yield, fruit weight and equatorial diameter that have a significant correlation and a direct effect on the fruit yield, emerged as the components with coefficients of 0.96 and 0.52 respectively. These characters may be relevant within the selection criteria in the development of new varieties.
Convergent Usage of Amino Acids in Human Cancers as a Reversed Process of Tissue Development
Authors: Luo Yikai , Liang Han
Published: March 2021

Genome and transcriptome-wide amino acid usage preference across different species is a well-studied phenomenon in molecular evolution, but its characteristics and implication in cancer evolution and therapy remain largely unexplored. Here, we analyzed large-scale transcriptome/proteome profiles such as TCGA, GTEx, and CPTAC and found that compared to normal tissues, different cancer types showed a convergent pattern towards using biosynthetically low-cost amino acids. Such a pattern can be accurately captured by a single index based on the average biosynthetic energy cost of amino acids, termed Energy Cost Per Amino Acid (ECPA). With this index, we further compared the trends of amino acid usage and the contributing genes in cancer and tissue development and revealed their reversed patterns. Finally, focusing on the liver, a tissue with a dramatic increase in ECPA during development, we found that EPCA represented a powerful biomarker that could distinguish liver tumors from normal liver samples consistently across 11 independent patient cohorts (AUROC = ~0.99) and outperformed any index based on single genes. Our study reveals an important principle underlying cancer evolution and suggests the global amino acid usage as a system-level biomarker for cancer diagnosis.
Growth of Lahontan Cutthroat Trout from multiple sources reintroduced into Sagehen Creek, CA
Authors: Stead Jonathan E. , Boucher Virginia L. , Moyle Peter B. , Rypel Andrew L.
Published: March 2021

Lahontan Cutthroat TroutOncorhynchus clarkii henshawihave experienced massive declines in their native range and are now a threatened species under the US Endangered Species Act. A key management goal for this species is re-establishing extirpated populations using translocations and conservation hatcheries. In California USA, two broodstocks (Pilot Peak and Independence Lake) are available for translocation, in addition to potential wild sources. Yet suitability of these sources for re-introduction in different ecosystem types and regions remains an open and important topic. We conducted growth experiments using Lahontan Cutthroat Trout stocked into Sagehen Creek, CA USA. Experiments evaluated both available broodstocks and a smaller sample of wild fish translocated from a nearby creek. Fish from the Independence Lake source had significantly higher growth in weight and length compared to the other sources. Further, Independence Lake fish were the only stock that gained weight on average over the duration of the experiment. Our experiments suggest fish from the Independence Lake brood stock may be useful for re-introduction efforts into small montane headwater streams in California.
Predicting activatory and inhibitory drug–target interactions based on mol2vec and genetically perturbed transcriptomes
Authors: Lee Won-Yung , Lee Choong-Yeol , Kim Chang-Eop
Published: March 2021

A computational approach to identifying drug–target interactions (DTIs) is a credible strategy for accelerating drug development and understanding the mechanisms of action of small molecules. However, current methods are limited to providing simple DTIs without mode of action (MoA), or they show unsatisfactory performance for a limited range of compounds and targets. Here, we propose AI-DTI, a novel method that predicts activatory and inhibitory DTIs by combining the mol2vec and genetically perturbed transcriptomes. We trained the model on large-scale DTIs with MoA and found that our model outperformed a previous model that predicted activatory and inhibitory DTIs. To extend the applicability, we applied the inferential method for the target vector so that our method can learn and predict a wider range of targets. Our method achieved satisfactory performance in an independent dataset where the target was unseen in the training set and a high-throughput screening dataset where positive and negative samples were explicitly defined. Finally, our method successfully rediscovered approximately half of the DTIs for drugs used in the treatment of COVID-19. These results indicate that AI-DTI is a practically useful tool for guiding drug discovery processes and generating plausible hypotheses that can reveal unknown mechanisms of drug action.
Impact of anaesthesia on static and dynamic functional connectivity in mice
Authors: Tsurugizawa Tomokazu , Yoshimaru Daisuke
Published: March 2021

A few studies have compared the static functional connectivity between awake and anaesthetized states in rodents by resting-state fMRI. However, impact of anaesthesia on static and dynamic fluctuations in functional connectivity has not been fully understood. Here, we developed a resting-state fMRI protocol to perform awake and anaesthetized functional MRI in the same mice. Static functional connectivity showed a widespread decrease under anaesthesia, such as when under isoflurane or a mixture of isoflurane and medetomidine. Several interhemispheric connections were key connections for anaesthetized condition from awake. Dynamic functional connectivity demonstrates the shift from frequent broad connections across the cortex, the hypothalamus, and the auditory-visual cortex to frequent local connections within the cortex only. Fractional amplitude of low frequency fluctuation in the thalamic nuclei decreased under both anaesthesia. These results indicate that typical anaesthetics for functional MRI alters the spatiotemporal profile of the dynamic brain network in subcortical regions, including the thalamic nuclei and limbic system.

Highlights

Resting-state fMRI was compared between awake and anaesthetized in the same mice.

Anaesthesia induced a widespread decrease of static functional connectivity.

Anaesthesia strengthened local connections within the cortex.

fALFF in the thalamus was decreased by anaesthesia.
The Human Milk Oligosaccharide 3’Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice
Authors: Pessentheiner Ariane R. , Spann Nathanael J. , Autran Chloe A. , Ramms Bastian , Chiang Austin W.T. , Grunddal Kaare V. , Wang Yiwen , Quach Anthony , Booshehri Laela M. , Hammond Alexandra , Tognaccini Chiara , Latasiewicz Joanna , Witztum Joseph L. , Hoffman Hal M. , Lewis Nathan E. , Glass Christopher K. , Bode Lars , Gordts Philip L.S.M.
Published: March 2021

Macrophages contribute to the induction and resolution of inflammation and play a central role in the chronic low-grade inflammation in cardiovascular diseases caused by atherosclerosis. Human milk oligosaccharides (HMOs) are complex unconjugated glycans unique to human milk that benefit infant health and act as innate immune modulators. Here, we identify the HMO 3’sialyllactose (3’SL) as a natural inhibitor of TLR4-induced low-grade inflammation in macrophages and endothelium. Transcriptome analysis in macrophages revealed that 3’SL attenuates a selected set of inflammatory gene expression and promotes activity of LXR and SREBP. These acute anti-inflammatory effects of 3’SL were associated with reduced histone H3K27 acetylation at a subset of LPS-inducible enhancers distinguished by preferential enrichment for CTCF, IRF2, BCL6, and other transcription factor recognition motifs. In a murine atherosclerosis model, both subcutaneous and oral administration of 3’SL significantly reduced atherosclerosis development and the associated inflammation. This study provides evidence that 3’SL attenuates inflammation by a transcriptional mechanism to reduce atherosclerosis development in the context of cardiovascular disease.
Loss of Endothelial HIF-Prolyl hydroxylase 2 (PHD2) Induces Cardiac Hypertrophy and Fibrosis
Authors: Dai Zhiyu , Cheng Jianding , Liu Bin , Yi Dan , Feng Anlin , Wang Ting , Gao Chen , Wang Yibin , Zhu Maggie M. , Zhang Xianming , Zhao You-Yang
Published: March 2021

Background

Cardiac hypertrophy and fibrosis are common adaptive responses to injury and stress, eventually leading to heart failure. Hypoxia signaling is important to the (patho)physiological process of cardiac remodeling. However, the role of endothelial Prolyl-4 hydroxylase 2 (PHD2)/hypoxia inducible factors (HIFs) signaling in the pathogenesis of heart failure remains elusive.

Methods and Results

Mice withTie2-Cre-mediated deletion ofEgln1(encoding PHD2) (Egln1Tie2Cre) exhibited left ventricular (LV) hypertrophy evident by increased thickness of anterior and posterior wall and LV mass, as well as cardiac fibrosis. Tamoxifen-induced endothelialEgln1deletion in adult mice also induced LV hypertrophy and fibrosis. Additionally, we observed a marked decrease of PHD2 expression in heart tissues and cardiovascular endothelial cells from patients with cardiomyopathy. Moreover, genetic ablation ofHif2abut notHif1ainEgln1Tie2Cremice normalized cardiac size and function. RNA sequencing analysis also demonstrated HIF-2α as a critical mediator of signaling related to cardiac hypertrophy and fibrosis. Pharmacological inhibition of HIF-2α attenuated cardiac hypertrophy and fibrosis inEgln1Tie2Cremice.

Conclusions

The present studies define for the first time an unexpected role of endothelial PHD2 deficiency in inducing cardiac hypertrophy and fibrosis in a HIF-2α dependent manner. PHD2 was markedly decreased in cardiovascular endothelial cells in patients with cardiomyopathy. Thus, targeting PHD2/HIF-2α signaling may represent a novel therapeutic approach for the treatment of pathological cardiac hypertrophy and failure.
GABAergic signaling in human and murine NK cells upon challenge withToxoplasma gondii
Authors: Bhandage Amol K. , Friedrich Laura M. , Kanatani Sachie , Jakobsson-Björkén Simon , Escrig-Larena J. Ignacio , Wagner Arnika K. , Chambers Benedict J. , Barragan Antonio
Published: March 2021

Protective cytotoxic and proinflammatory cytokine responses by natural killer (NK) cells impact the outcome of infections byToxoplasma gondii, a common parasite in humans and other vertebrates. However,T. gondiican also sequester within NK cells and downmodulate their effector functions. Recently, the implication of γ–aminobutyric acid (GABA) signaling in infection and inflammation-related responses of mononuclear phagocytes and T cells has become evident. Yet, the role of GABAergic signaling in NK cells has remained unknown. Here, we report that human and murine NK cells synthesize and secrete GABA in response to infection challenge. Parasitized NK cells secreted GABA while activation stimuli, such as IL-12/IL-18 or parasite lysates, failed to induce GABA secretion. GABA secretion by NK cells was associated to a transcriptional upregulation of GABA synthesis enzymes (GAD65/67) and was abrogated by GAD-inhibition. Further, NK cells expressed GABA-A receptor subunits and GABA signaling regulators, with transcriptional modulations taking place upon challenge withT. gondii. Exogenous GABA and GABA-containing supernatants from parasitized dendritic cells (DCs) impacted NK cell function by reducing the degranulation and cytotoxicity of NK cells. Conversely, GABA-containing supernatants from NK cells enhanced the migratory responses of parasitized DCs. This enhanced DC migration was abolished by GABA-A receptor antagonism or GAD-inhibition and was reconstituted by exogenous GABA. Jointly, the data show that NK cells are GABAergic cells and that GABA hampers NK cell cytotoxicityin vitro. We hypothesize that GABA secreted by parasitized immune cells modulates the immune responses toT. gondiiinfection.

Summary sentence

In response to infection challenge, NK cells synthesize and secreteγ-aminobutyric acid (GABA), which impacts NK cell and dendritic cell functions via GABA-A receptors.
Machine learning prediction of Antibody-Antigen binding: dataset, method and testing
Authors: Ye Chao , Hu Wenxing , Gaeta Bruno
Published: March 2021

DNA sequencing technologies are providing new insights into the immune response by allowing the large scale sequencing of rearranged immunoglobulin gene present in an individual, however the applications of this approach are limited by the lack of methods for determining the antigen(s) that an immunoglobulin encoded by a given sequence binds to. Computational methods for predicting antibody-antigen interactions that leverage structure prediction and docking have been proposed, however these methods require knowledge of the 3D structures.

As a step towards the development of a machine learning method suitable for predicting antibody-antigen binding affinities from sequence data, a weighted nearest neighbor machine learning approach was applied to the problem. A prediction program was coded in Python and evaluated using cross-validation on a dataset of 600 antibodies interacting with 50 antigens. The classification predicting accuracy was around 76% for this dataset. These results provide a useful frame of reference as well as protocols and considerations for machine learning and dataset creation in this area.

Both the dataset (in csv format) and the machine learning program (coded in python) are freely available for download.
γδ-Thymocyte Maturation and Emigration
Authors: Joannou K. , Golec D.P. , Wang H. , Henao-Caviedes L.M. , May J.F. , Kelly R.G. , Chan R. , Jameson S.C. , Baldwin T.A.
Published: March 2021

The thymus is the site of both αβ and γδ-T cell development. After several unique waves of γδ-T cells are generated in, and exported from, the fetal/neonatal thymus, the adult thymus continues to produce a stream of γδ-T cells throughout life. One intriguing feature of γδ T cell development is the coordination of differentiation and acquisition of effector function within the fetal thymus, however, it is less clear whether this paradigm holds true in adult animals. To investigate the relationship between maturation and time since V(D)J recombination in adult-derived γδ-thymocytes, we used the Rag2pGFP model. Immature (CD24+) γδ-thymocytes expressed high levels of GFP while only a small minority of mature (CD24-) γδ-thymocytes were GFP+. Similarly, most GFP+γδ-splenocytes were immature, while some were mature. Analysis of γδ-recent thymic emigrants (RTEs) indicated that most γδ-T cell RTEs were CD24+and GFP+and adoptive transfer experiments showed that immature γδ-thymocytes could be maintained in the periphery for at least 3 days over which time they matured. With respect to the mature γδ-thymocytes that were GFP-, parabiosis experiments demonstrated that mature γδ-T cells did not recirculate from the periphery. Instead, a population of mature γδ-thymocytes remained resident in the thymus for at least 60 days while mature γδ-thymocytes derived solely from adult hematopoiesis were mostly lost from the thymus within 60 days. Collectively, these data demonstrate two streams of actively developing γδ-T cells in adult mice: an immature subset that quickly leaves the thymus and matures in the periphery, and one that completes maturation within the thymus over a longer period of time. Furthermore, there is a fetal-derived and heterogeneous population of resident γδ-thymocytes of unknown functional importance.
Optogenetic manipulation of individual or whole populationCaenorhabditis elegansworms with an under hundred-dollar tool: the OptoArm
Authors: Koopman M. , Janssen L. , Nollen E.A.A.
Published: March 2021

Abstract

Optogenetic tools have revolutionized the study of neuronal circuits inCaenorhabditis elegans.The expression of light-sensitive ion channels or pumps under specific promotors allows researchers to modify the behavior of excitable cells. Several optogenetic systems have been developed to spatially and temporally photoactivate light-sensitive actuators inC. elegans. Nevertheless, their high costs and low flexibility have limited wide access to optogenetics. Here, we developed an inexpensive, easy-to-build, and adjustable optogenetics device for use on different microscopes and worm trackers, called the OptoArm. The OptoArm allows for single- and multiple-worm illumination and is adaptable in terms of light intensity, lighting profiles and light-color. We demonstrate the OptoArm’s power in a population-based study on contributions of motor circuit cells to age-related motility decline. We find that functional decline of cholinergic neurons mirrors motor decline, while GABAergic neurons and muscle cells are relatively age-resilient, suggesting that rate-limiting cells exist and determine neuronal circuit aging.
A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity
Authors: Nakajima Souta , Sueyoshi Masanao , Hirota Shun K. , Ishiyama Nobuo , Matsuo Ayumi , Suyama Yoshihisa , Nakamura Futoshi
Published: March 2021

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpinCottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded unexpected results and provided important insights for conservation.
APOE4is associated with elevated blood lipids and lower levels of innate immune biomarkers in a tropical Amerindian subsistence population
Authors: Garcia Angela R , Finch Caleb E , Gatz Margaret , Kraft Thomas S , Cummings Daniel , Charifson Mia , Rodriguez Daniel Eid , Buetow Kenneth , Beheim Bret , Allayee Hooman , Thomas Gregory S , Stieglitz Jonathan , Gurven Michael , Kaplan Hillard , Trumble Benjamin C
Published: March 2021

In post-industrial settings,APOE4is associated with increased cardiovascular and neurological disease risk. However, the majority of human evolutionary history occurred in environments with higher pathogenic diversity and low cardiovascular risk. We hypothesize that in high-pathogen and energy-limited contexts, theAPOE4allele confers benefits by reducing baseline innate inflammation when uninfected, while maintaining higher lipid levels that buffer costs of immune activation during infection. Among Tsimane forager-farmers of Bolivia (N=1266),APOE4is associated with 30% lower C-reactive protein, and higher total cholesterol and oxidized-LDL. Blood lipids were either not associated, or negatively associated with inflammatory biomarkers, except for associations of oxidized-LDL and inflammation which were limited to obese adults. Further,APOE4carriers maintain higher levels of total and LDL cholesterol at low BMIs. These results suggest the relationship betweenAPOE4and lipids is likely beneficial for pathogen-driven immune responses, and unlikely to increase cardiovascular risk in an active subsistence population.
Bumblebees can detect floral humidity
Authors: Harrap Michael J. M. , de Ibarra Natalie Hempel , Knowles Henry D. , Whitney Heather M. , Rands Sean A.
Published: March 2021

Floral humidity, a region of elevated humidity proximal to the flower, occurs in many plant species and may add to their multimodal floral displays. So far, the ability to detect and respond to floral humidity cues has been only established for hawkmoths when they locate and extract nectar while hovering in front of some moth-pollinated flowers. To test whether floral humidity can be used by other more widespread generalist pollinators, we designed artificial flowers that presented biologically-relevant levels of humidity similar to those shown by flowering plants. Bumblebees showed a spontaneous preference for flowers which produced higher floral humidity. Furthermore, learning experiments showed that bumblebees are able to use differences in floral humidity to distinguish between rewarding and nonrewarding flowers. Our results indicate that bumblebees are sensitive to different levels of floral humidity. In this way floral humidity can add to the information provided by flowers and could impact pollinator behaviour more significantly than previously thought.

Summary statement

We demonstrate for the first time that bumblebees show a preference to elevated floral humidity and can learn to distinguish flowers that differ in floral humidity levels.
Representation learning of RNA velocity reveals robust cell transitions
Authors: Qiao Chen , Huang Yuanhua
Published: March 2021

Abstract

RNA velocity is a promising technique to reveal transient cellular dynamics among a heterogeneous cell population and quantify their transitions from single-cell transcriptome experiments. However, the cell transitions estimated from high dimensional RNA velocity are often unstable or inaccurate, partly due to the high technical noise and less informative projection. Here, we present VeloAE, a tailored representation learning method to learn a low-dimensional representation of RNA velocity on which cell transitions can be robustly estimated. From various experimental datasets, we show that VeloAE can both accurately identify stimulation dynamics in time-series designs and effectively capture the expected cellular differentiation in different biological systems. VeloAE therefore enhances the usefulness of RNA velocity for studying a wide range of biological processes.
Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach
Authors: Sonnenkalb Lindsay , Carter Joshua , Spitaleri Andrea , Iqbal Zamin , Hunt Martin , Malone Kerri , Utpatel Christian , Cirillo Daniela Maria , Rodrigues Camilla , Nilgiriwala Kayzad S. ,   the CRyPTIC Consortium, Fowler Philip W. , Merker Matthias , Niemann Stefan
Published: March 2021

Bedaquiline (BDQ) and clofazimine (CFZ) are core drugs for treatment of multidrug resistant tuberculosis (MDR-TB), however, our understanding of the resistance mechanisms for these drugs is sparse which is hampering rapid molecular diagnostics. To address this, we employed a unique approach using experimental evolution, protein modelling, genome sequencing, and minimum inhibitory concentration data combined with genomes from a global strain collection of over 14,151Mycobacterium tuberculosiscomplex isolates and an extensive literature review. Overall, 230 genomic variants causing elevated BDQ and/or CFZ MICs could be discerned, with 201 (87.4%) variants affecting the transcriptional repressor (Rv0678) of an efflux system (mmpS5-mmpL5). Structural modelling of Rv0678 suggests four major mechanisms that confer resistance: impairment of DNA binding, reduction in protein stability, disruption of protein dimerization, and alteration in affinity for its fatty acid ligand. These modelling and experimental techniques will improve personalized medicine in an impending drug resistant era.
Seqpac: A New Framework for small RNA analysis in R using Sequence-Based Counts
Authors: Skog Signe , Örkenby Lovisa , Kugelberg Unn , Tariq Kanwal , Farrants Ann-Kristin Östlund , Öst Anita , Nätt Daniel
Published: March 2021

Small RNA sequencing (sRNA-seq) has become important for studying regulatory mechanisms in many cellular processes. Data analysis remains challenging, mainly because each class of sRNA—such as miRNA, piRNA, tRNA- and rRNA-derived fragments (tRFs/rRFs)—needs special considerations. Analysis therefore involves complex workflows across multiple programming languages, which can produce research bottlenecks and transparency issues. To make analysis of sRNA more accessible and transparent we present seqpac: a tool for advanced group-based analysis of sRNA completely integrated in R. This opens advanced sRNA analysis for Windows users—from adaptor trimming to visualization. Seqpac provides a framework of functions for analyzing a PAC object, which contains 3 standardized tables: sample phenotypic information (P), sequence annotations (A), and a counts table with unique sequences across the experiment (C). By applying a sequence-based counting strategy that maintains the integrity of the fastq sequence, seqpac increases flexibility and transparency compared to other workflows. It also contains an innovative targeting system allowing sequence counts to be summarized and visualized across sample groups and sequence classifications. Reanalyzing published data, we show that seqpac’s fastq trimming performs equal to standard software outside R and demonstrate how sequence-based counting detects previously unreported bias. Applying seqpac to new experimental data, we discovered a novel rRF that was down-regulated by RNA pol I inhibition (anticancer treatment), and up-regulated in previously published data from tumor positive patients. Seqpac is available on github (https://github.com/Danis102/seqpac), runs on multiple platforms (Windows/Linux/Mac), and is provided with a step-by-step vignette on how to analyze sRNA-seq data.
Molecular basis for recognition of the Group A Carbohydrate backbone by the PlyC streptococcal bacteriophage endolysin
Authors: King Harley , Castro Sowmya Ajay , Pohane Amol Arunrao , Scholte Cynthia M. , Fischetti Vincent A. , Korotkova Natalia , Nelson Daniel C. , Dorfmueller Helge C.
Published: March 2021

Endolysins are peptidoglycan (PG) hydrolases that function as part of the bacteriophage (phage) lytic system to release progeny phage at the end of a replication cycle. Notably, endolysins alone can produce lysis without phage infection, which offers an attractive alternative to traditional antibiotics. Endolysins from phage that infect Gram-positive bacterial hosts contain at least one enzymatically active domain (EAD) responsible for hydrolysis of PG bonds and a cell wall binding domain (CBD) that binds a cell wall epitope, such as a surface carbohydrate, providing some degree of specificity for the endolysin. Whilst the EADs typically cluster into conserved mechanistic classes with well-defined active sites, relatively little is known about the nature of the CBDs and only a few binding epitopes for CBDs have been elucidated. The major cell wall components of many streptococci are the polysaccharides that contain the polyrhamnose (pRha) backbone modified with species-specific and serotype-specific glycosyl side chains. In this report, using molecular genetics, microscopy, flow cytometry and lytic activity assays, we demonstrate the interaction of PlyCB, the CBD subunit of the streptococcal PlyC endolysin, with the pRha backbone of the cell wall polysaccharides, Group A Carbohydrate (GAC) and serotypec-specific carbohydrate (SCC) expressed by the Group A Streptococcus andStreptococcus mutans, respectively.