bluuebunny/crossref_metadata_2025 huggingface dataset:
Developmental Deconvolution for Classification of Cancer Origin
Authors: Moiso Enrico , Farahani Alexander , Marble Hetal , Hendricks Austin , Mildrum Samuel , Levine Stuart , Lennerz Jochen , Garg Salil
Published: November 2021

Cancer is a disease manifesting in abrogation of developmental programs, and malignancies are named based on their cell or tissue of origin. However, a systematic atlas of tumor origins is lacking. Here we map the single cell organogenesis of 56 developmental trajectories to the transcriptomes of over 10,000 tumors across 33 cancer types. We use this map to deconvolute individual tumors into their constituent developmental trajectories. Based on these deconvoluted developmental programs, we construct a Developmental Multilayer Perceptron (D-MLP) classifier that outputs cancer origin. The D-MLP classifier (ROC-AUC: 0.974 for top prediction) outperforms classification based on expression of either oncogenes or highly variable genes. We analyze tumors from patients with cancer of unknown primary (CUP), selecting the most difficult cases where extensive multimodal workup yielded no definitive tumor type. D-MLP revealed insights into developmental origins and diagnosis for most patient tumors. Our results provide a map of tumor developmental origins, provide a tool for diagnostic pathology, and suggest developmental classification may be a useful approach for otherwise unclassified patient tumors.
Cumulative Effects of Resting-state Connectivity Across All Brain Networks Significantly Correlate with ADHD Symptoms
Authors: Mooney Michael A. , Hermosillo Robert J.M. , Feczko Eric , Miranda-Dominguez Oscar , Moore Lucille A. , Perrone Anders , Byington Nora , Grimsrud Gracie , Rueter Amanda , Nousen Elizabeth , Antovich Dylan , Feldstein Ewing Sarah W. , Nagel Bonnie J. , Nigg Joel T. , Fair Damien A.
Published: November 2021

Background

The clinical utility of MRI neuroimaging studies of psychopathology has been limited by a constellation of factors—small sample sizes, small effect sizes, and heterogeneity of methods and samples across studies—that hinder generalizability and specific replication. An analogy is early genomics studies of complex traits, wherein a move to large, multi-site samples and a focus on cumulative effects (polygenic scores) led to reproducible and clinically applicable effects from genome-wide association studies. A similar logic in MRI may provide a way to improve reproducibility, precision, and clinical utility for brain-wide MRI association studies.

Methods

Polyneuro scores (PNS) represent the cumulative effect of brain-wide measures—in the present case, resting-state functional connectivity (rs-fcMRI) associated with ADHD symptoms. These scores were constructed and validated using baseline data from the Adolescent Brain Cognitive Development (ABCD, N=5666) study, with a reproducible matched subset as the discovery cohort (N=2801). Association between the PNS and ADHD symptoms was further tested in an independent case-control cohort, the Oregon-ADHD-1000 (N=533).

Results

The ADHD PNS was significantly associated with ADHD symptoms in both the ABCD and Oregon cohorts after accounting for relevant covariates (p-values < 0.001). While the strongest effects contributing to the PNS were concentrated among connections involving the default mode and cingulo-opercular networks, the most predictive PNS involved connectivity across all brain networks. These findings were robust to stringent motion thresholds. In the longitudinal Oregon-ADHD-1000, non-ADHD comparison youth had significantly lower ADHD PNS (β=-0.309, p=0.00142) than children with persistent ADHD (met diagnostic criteria at two or more time points from age 7 to 19). The ADHD PNS, however, did not reliably mediate polygenic risk for ADHD. Instead, the PNS and an ADHD polygenic score were independently associated with ADHD symptoms.

Conclusions

A polyneuro risk score representing cumulative ADHD-associated resting-state connectivity was robustly associated with ADHD symptoms in two independent cohorts using distinct sampling designs, yet was independent of polygenic liability for ADHD, suggesting the need to examine environmental influences. The polyneuro score approach holds promise for improving the reproducibility of neuroimaging studies, identifying their clinical utility, and unraveling the complex relationships between brain connectivity and the etiology of behavioral disorders.
Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass and reference genome properties
Authors: Schmidt Alexandra , Schneider Clément , Decker Peter , Hohberg Karin , Römbke Jörg , Lehmitz Ricarda , Bálint Miklós
Published: November 2021

Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes and genome assemblies.

We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades and potworms. We shotgun-sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.

We recovered 90% of the species, and observed relatively high false positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g. springtails) consistently attracting more hits than others (e.g. enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships.

The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We provide a roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing, and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
The natural compound TMYX reduces SAN cells rate by antagonizing the cAMP modulation of f-channels
Authors: Piantoni Chiara , Paina Manuel , Molla David , Liu Sheng , Bertoli Giorgia , Jiang Hongmei , Wang Yanyan , Wang Yi , Wang Yi , DiFrancesco Dario , Barbuti Andrea , Bucchi Annalisa , Baruscotti Mirko
Published: November 2021

Tongmai Yangxin (TMYX), is a complex compound of a Traditional Chinese Medicine (TCM) used to treat several cardiac rhythm disorders; however, no information regarding its mechanism of action is available. In this study we provide a detailed characterization of the effects of TMYX on the electrical activity of pacemaker cells and unravel its mechanism of action.

Single-cell electrophysiology revealed that TMYX elicits a reversible and dose-dependent (2/6 mg/ml) slowing of spontaneous action potentials rate (−20.8/-50.2%) by a selective reduction of the diastolic phase (−50.1/-76.0%). This action is mediated by a negative shift of the If activation curve (−6.7/-11.9 mV) and is caused by a reduction of the cAMP-induced stimulation of pacemaker channels. We provide evidence that TMYX acts by directly antagonizes the cAMP-induced allosteric modulation of the pacemaker channels. Noticeably, this mechanism functionally resembles the pharmacological actions of muscarinic stimulation or β-blockers, but it does not require generalized changes in cytoplasmic cAMP levels thus ensuring a selective action on rate.

In agreement with a competitive inhibition mechanism, TMYX exerts its maximal antagonistic action at submaximal cAMP concentrations and then progressively becomes less effective thus ensuring a full contribution of If to pacemaker rate during high metabolic demand and sympathetic stimulation.

Funding sources

This work was supported by grants from Tianjin Zhongxin Pharmaceutical Group Co., Ltd. Le Ren Tang Pharmaceutical Factory P.R. China. The financial supporter played no role in the study design, data collection and analysis, decision to publish, or the preparation of the manuscript.
A prospective study of asymptomatic SARS-CoV-2 infection among individuals involved in academic research under limited operations during the COVID-19 pandemic
Authors: Pettifor Audrey , DiPrete Bethany L. , Shook-Sa Bonnie E. , Premkumar Lakshmanane , Kuczynski Kriste , Dittmer Dirk , Aiello Allison , Wallet Shannon , Maile Robert , Tan Joyce , Jadi Ramesh , Pluta Linda , de Silva Aravinda M. , Weber David J. , Kim Min , Seña Arlene C. , Jones Corbin D.
Published: November 2021

Background

Early in the pandemic, transmission risk from asymptomatic infection was unclear making it imperative to monitor infection in workplace settings. Further, data on SARS-CoV-2 seroprevalence within university populations has been limited.

Methods

We performed a longitudinal study of University research employees on campus July-December 2020. We conducted questionnaires on COVID-19 risk factors, RT-PCR testing, and SARS-CoV-2 serology using an in-house spike RBD assay, laboratory-based Spike NTD assay, and standard nucleocapsid platform assay. We estimated prevalence and cumulative incidence of seroconversion with 95% confidence intervals using the inverse of the Kaplan-Meier estimator.

Results

910 individuals were included in this analysis. At baseline, 6.2% (95% CI 4.29-8.19) were seropositive using the spike RBD assay; four (0.4%) were seropositive using the nucleocapsid assay, and 44 (4.8%) using the Spike NTD assay. Cumulative incidence was 3.61% (95% CI: 2.04-5.16). Six asymptomatic individuals had positive RT-PCR results.

Conclusions

Prevalence and incidence of SARS-CoV-2 infections was low; however differences in target antigens of serological tests provided different estimates. Future research on appropriate methods of serological testing in unvaccinated and vaccinated populations is needed. Frequent RT-PCR testing of asymptomatic individuals is required to detect acute infections, and repeated serosurveys are beneficial for monitoring subclinical infection.
Experiences of staff providing specialist palliative care during COVID-19A multiple qualitative case study
Authors: Bradshaw Andy , Dunleavy Lesley , Garner Ian , Preston Nancy , Bajwah Sabrina , Cripps Rachel , Fraser Lorna K , Maddocks Matthew , Hocaoglu Mevhibe , Murtagh Fliss EM , Oluyase Adejoke O , Sleeman Katherine E , Higginson Irene J , Walshe Catherine
Published: November 2021

Objectives

To explore the experiences of, and impact on, staff working in palliative care during the COVID-19 pandemic.

Design

Qualitative multiple case study using semi-structured interviews between November 2020 and April 2021 as part of the CovPall study. Data were analysed using thematic framework analysis.

Setting

Organisations providing specialist palliative services in any setting.

Participants

Staff working in specialist palliative care, purposefully sampled by the criteria of role, care setting and COVID-19 experience.

Main outcome measures

Experiences of working in palliative care during the COVID-19 pandemic.

Results

Five cases and 24 participants were recruited (n=12 nurses, 4 clinical managers, 4 doctors, 2 senior managers, 1 healthcare assistant, 1 allied healthcare professional). Central themes demonstrate how infection control constraints prohibited and diluted participants’ ability to provide care that reflected their core values, resulting in experiences of moral distress. Despite organisational, team, and individual support strategies, continually managing these constraints led to a ‘crescendo effect’ in which the impacts of moral distress accumulated over time, sometimes leading to burnout. Solidarity with colleagues and making a valued contribution provided ‘moral comfort’ for some.

Conclusions

This study provides a unique insight into why and how healthcare staff have experienced moral distress during the pandemic, and how organisations have responded. Despite their experience of dealing with death and dying, the mental health and well-being of palliative care staff was affected by the pandemic. Organisational, structural, and policy changes are urgently required to mitigate and manage these impacts.
Evaluation of a novel direct capture method for virus concentration n wastewater from COVID-19 infectious ward and correlation analysis with the number of inpatients
Authors: Inaba Manami , Nakao Ryohei , Imamura Fumiko , Nakashima Yutaka , Miyazono Seiji , Akamatsu Yoshihisa
Published: November 2021

The global outbreak of the SARS-CoV-2 pandemic has increased the focus of Wastewater-based epidemiology (WBE) studies as a tool for understanding the epidemic and risk management. A highly sensitive and rapid method for the virus concentration from wastewater is needed to obtain the accurate information for early detection of SARS-CoV-2 outbreak and epidemic. In this study, we evaluated the efficiency of the direct capture method provided from Promega, based on column adsorption using the wastewater from actual infectious diseases ward. The efficiency of the nucleic acid extraction-purification process was also evaluated by Maxwell® RSC instrument (fully automated extraction) and QIAamp Viral RNA mini kit (manual extraction). The obtained SARS-CoV-2 data from wastewater were analyzed with the number of inpatients which is the consideration of the severity and the days of onset. The combination of direct capture and Maxwell’s method (DC-MW) was suggested to be a highly sensitive and simple method with better concentration efficiency and quantification than other methods. Moreover, the inpatient conditions (severity and days of after onset) should be considered to accurately understand the actual status of the correlation between the number of inpatients and SARS-CoV-2 concentration in wastewater. The highly sensitive method of DC-MW was suggested to assess more actual situation of SARS-CoV-2 shedding into the wastewater.
Effects of trust, risk perception, and health behavior on COVID-19 disease burden: Evidence from a multi-state US survey
Authors: Ridenhour Benjamin J. , Sarathchandra Dilshani , Seamon Erich , Brown Helen , Leung Fok-Yan , Johnson-Leon Maureen , Megheib Mohamed , Miller Craig R. , Johnson-Leung Jennifer
Published: November 2021

Early public health strategies to prevent the spread of COVID-19 in the United States relied on non-pharmaceutical interventions (NPIs) as vaccines and therapeutic treatments were not yet available. Implementation of NPIs, primarily social distancing and mask wearing, varied widely between communities within the US due to variable government mandates, as well as differences in attitudes and opinions. To understand the interplay of trust, risk perception, behavioral intention, and disease burden, we developed a survey instrument to study attitudes concerning COVID-19 and pandemic behavioral change in three states: Idaho, Texas, and Vermont. We designed our survey (n= 1034) to detect whether these relationships were significantly different in rural populations. The best fitting structural equation models show that trust indirectly affects protective pandemic behaviors via health and economic risk perception. We explore two different variations of this social cognitive model: the first assumes behavioral intention affects future disease burden while the second assumes that observed disease burden affects behavioral intention. In our models we include several exogenous variables to control for demographic and geographic effects. Notably, political ideology is the only exogenous variable which significantly affects all aspects of the social cognitive model (trust, risk perception, and behavioral intention). While there is a direct negative effect associated with rurality on disease burden, likely due to the protective effect of low population density in the early pandemic waves, we found a marginally significant, positive, indirect effect of rurality on disease burden via decreased trust (p= 0.095). This trust deficit creates additional vulnerabilities to COVID-19 in rural communities which also have reduced healthcare capacity. Increasing trust by methods such as in-group messaging could potentially remove some of the disparities inferred by our models and increase NPI effectiveness.
Broadly-neutralizing antibodies that bind to the influenza hemagglutinin stalk domain enhance the effectiveness of neuraminidase inhibitors via Fc-mediated effector functions
Authors: Zhang Ali , Chaudhari Hanu , Agung Yonathan , D’Agostino Michael R. , Ang Jann C. , Miller Matthew S.
Published: November 2021

The conserved hemagglutinin stalk domain is an attractive target for broadly effective antibody-based therapeutics and next generation universal influenza vaccines. Protection provided by hemagglutinin stalk binding antibodies is principally mediated through activation of immune effector cells. Titers of stalk-binding antibodies are highly variable on an individual level, and tend to increase with age as a result of increasing exposures to influenza virus. In our study, we show that stalk-binding antibodies cooperate with neuraminidase inhibitors to protect against influenza virus infection in an Fc-dependent manner. These data suggest that the effectiveness of neuraminidase inhibitors is likely influenced by an individual’s titers of stalk-binding antibodies, and that neuraminidase inhibitors may enhance the effectiveness of future stalk-binding monoclonal antibody-based treatments.
DeepProjection: Rapid and structure-specific projections of tissue sheets embedded in 3D microscopy stacks using deep learning
Authors: Haertter Daniel , Wang Xiaolei , Fogerson Stephanie M. , Ramkumar Nitya , Crawford Janice M. , Poss Kenneth D. , Di Talia Stefano , Kiehart Daniel P. , Schmidt Christoph F.
Published: November 2021

The efficient extraction of local high-resolution content from massive amounts of imaging data remains a serious and unsolved problem in studies of complex biological tissues. Here we present DeepProjection, a trainable projection algorithm based on deep learning. This algorithm rapidly and robustly extracts image content contained in curved manifolds from time-lapse recorded 3D image stacks by binary masking of background content, stack by stack. The masks calculated for a given movie, when predicted, e.g., on fluorescent cell boundaries on one channel, can subsequently be applied to project other fluorescent channels from the same manifold. We apply DeepProjection to follow the dynamic movements of 2D-tissue sheets in embryonic development. We show that we can selectively project the amnioserosa cell sheet during dorsal closure in Drosophila melanogaster embryos and the periderm layer in the elongating zebrafish embryo while masking highly fluorescent out-of-plane artifacts.
The influence of somatosensory and auditory evoked potentials on concurrent transcranial-magnetic stimulation – electroencephalography recordings
Authors: Chowdhury Nahian S , Rogasch Nigel C , Chiang Alan , Millard Samantha K , Skippen Patrick , Chang Wei-Ju , Bilska Katarzyna , Si E. , Seminowicz David A , Schabrun Siobhan M
Published: November 2021

Background

Transcranial magnetic stimulation (TMS) evoked potentials (TEPs) can be used to index cortical excitability. However, it remains unclear to what extent TEPs reflect somatosensory and auditory-evoked potentials which arise from the scalp sensation and click of the TMS coil, as opposed to transcranial stimulation of cortical circuits.

Objectives

The present study had two aims; a) to determine the extent to which sensory potentials contaminate TEPs using a spatially matched sham condition, and b) to determine whether sensory potentials reflect auditory or somatosensory potentials alone, or a combination of the two.

Methods

Twenty healthy participants received active or sham stimulation, with the latter consisting of the click of a sham coil combined with scalp electrical stimulation. Earplugs/headphones were used to suppress the TMS click noise. Two additional control conditions i) electrical stimulation alone and ii) auditory stimulation alone were included in a subset of 13 participants.

Results

Signals from active and sham stimulation were correlated in spatial and temporal domains, especially >70ms post-stimulation. Relative to auditory or electrical stimulation alone, combined (sham) stimulation resulted in a) larger evoked responses b) stronger correlations with active stimulation and c) a signal that could not be explained by the linear sum of electrical and auditory stimulation alone.

Conclusions

Sensory potentials can confound data interpretations of TEPs at timepoints >70ms post-TMS, while earlier timepoints appear reflective of cortical excitability. Furthermore, contamination of TEPs cannot be explained by auditory or somatosensory potentials alone, but instead reflects a non-linear interaction between both sources. Future studies may benefit from controlling for sensory contamination using sham conditions that are spatially matched to active TMS, and which consist of combined auditory and somatosensory stimulation.
BOXR1030, an anti-GPC3 CAR with exogenous GOT2 expression, shows enhanced T cell metabolism and improved antitumor activity
Authors: Hickman Taylor L. , Choi Eugene , Whiteman Kathleen R. , Muralidharan Sujatha , Pai Tapasya , Johnson Tyler , Parikh Avani , Friedman Taylor , Gilbert Madaline , Shen Binzhang , Barron Luke , McGinness Kathleen E. , Ettenberg Seth A. , Motz Greg T. , Weiss Glen J. , Jensen-Smith Amy
Published: November 2021

Purpose

The solid tumor microenvironment (TME) drives T cell dysfunction and inhibits the effectiveness of immunotherapies such as chimeric antigen receptor-based T cell (CAR T) cells. Early data has shown that modulation of T cell metabolism can improve intratumoral T cell function in preclinical models.

Experimental Design

We evaluated GPC3 expression in human normal and tumor tissue specimens. We developed and evaluated BOXR1030, a novel CAR T therapeutic co-expressing glypican-3 (GPC3)-targeted CAR and exogenous glutamic-oxaloacetic transaminase 2 (GOT2) in terms of CAR T cell function both in vitro and in vivo.

Results

Expression of tumor antigen GPC3 was observed by immunohistochemical staining in tumor biopsies from hepatocellular carcinoma, liposarcoma, squamous lung cancer, and Merkel cell carcinoma patients. Compared to control GPC3 CAR alone, BOXR1030 (GPC3-targeted CAR T cell that co-expressed GOT2) demonstrated superior in vivo efficacy in aggressive solid tumor xenograft models, and showed favorable attributes in vitro including an enhanced cytokine production profile, a less-differentiated T cell phenotype with lower expression of stress and exhaustion markers, an enhanced metabolic profile and increased proliferation in TME-like conditions.

Conclusions

Together, these results demonstrated that co-expression of GOT2 can substantially improve the overall antitumor activity of CAR T cells by inducing broad changes in cellular function and phenotype. These data show that BOXR1030 is an attractive approach to targeting select solid tumors. To this end, BOXR1030 will be explored in the clinic to assess safety, dose- finding, and preliminary efficacy (NCT05120271).
Clinical impact of the rapid molecular detection of RSV and influenza A and B viruses in the emergency department
Authors: Yin Nicolas , Van Nuffelen Marc , Bartiaux Magali , Préseau Thierry , Roggen Inge , Delaunoy Sabrina , Mahadeb Bhavna , Dahma Hafid , Busson Laurent , Vandenberg Olivier , Hallin Marie
Published: November 2021

Introduction

Using respiratory viruses’ rapid diagnostic tests in the emergency department could allow better and faster clinical management. Point-of-care PCR instruments now provide results in less than 30 minutes. The objective of this study was to assess the impact of the use of a rapid molecular diagnostic test, the cobas® Influenza A/B & RSV Assay for use on Roche’s cobas® Liat® instrument, during the clinical management of emergency department patients.

Methods

Patients (adults and children) requiring admission or suffering from an underlying condition at risk of respiratory complication were prospectively recruited in the emergency department of four hospitals in the Brussels region. Physician’s intentions regarding admission, isolation, antibiotic, and antiviral use were collected before and after performing the rapid molecular test. Additionally, a comparison of the analytical performance of this test against antigen rapid tests and viral culture was performed as well as a time-to-result evaluation.

Results

Among 293 patients recruited, 90 had a positive PCR whereas 44 had a positive antigen test. PCR yielded a sensitivity of 100% for all targets. Antigen tests yielded sensitivities ranging from 66.7% for influenza B to 83.3% for the respiratory syncytial virus (RSV). The use of PCR allowed a decrease in the overall need for isolation and treatment by limiting the isolation of negative patients and the antibiotic use for positive patients. Meanwhile, antiviral treatments better targeted patients with a positive influenza PCR.

Conclusion

The use of a rapid influenza and RSV molecular test improves the clinical management of patients admitted to the emergency department by providing a fast and reliable result. Their additional cost compared to antigen tests should be balanced with the benefit of their analytical performance, leading to efficient reductions in the need of isolation and antibiotic use.
Modeling COVID-19 care capacity in a major health system
Authors: Erlendsdottir Margret , Eshghi Soheil , Crawford Forrest
Published: November 2021

Hospital resources, especially critical care beds and ventilators, have been strained by additional demand throughout the COVID-19 pandemic. Rationing of scarce critical care resources may occur when available resource limits are exceeded. However, the dynamic nature of the COVID-19 pandemic and variability in projections of the future burden of COVID-19 infection pose challenges for optimizing resource allocation to critical care units in hospitals. Connecticut experienced a spike in the number of COVID-19 cases between March and June 2020. Uncertainty about future incidence made it difficult to predict the magnitude and duration of the increased COVID-19 burden on the healthcare system. In this paper, we describe a model of COVID-19 hospital capacity and occupancy that generates estimates of the resources necessary to accommodate COVID-19 patients under infection scenarios of varying severity. We present the model structure and dynamics, procedure for parameter estimation, and publicly available web application where we implemented the tool. We then describe calibration using data from over 3,000 COVID-19 patients seen at the Yale-New Haven Health System between March and July 2020. We conclude with recommendations for modeling tools to inform decision-making using incomplete information during future crises.
Parental control: ecology drives plasticity in parental response to offspring signals
Authors: Caro S.M. , Velasco A.C. , van Mastrigt T. , van Oers K. , Griffin A.S. , West S.A. , Hinde C.A.
Published: November 2021

Different bird species have completely different parent-offspring interactions. When food is plentiful, the chicks that are begging the loudest are fed the most. When food is scarce, bird species instead feed the largest offspring. While this variation could be due to parents responding to signalling differently based on food availability, it could equally be due to offspring adjusting their behaviour, or to variation in information availability. We tested between these competing explanations experimentally, by manipulating food availability in a population of wild great tits,Parus major, while standardising offspring behaviour and size. We found that when food was more plentiful, parents were: (1) more likely to preferentially feed the chicks that were begging the most; and (2) less likely to preferentially feed larger chicks. In addition, we consistently found these same patterns, in a meta-analysis across 57 bird species. Overall, our results suggest that parents have more control over food distribution than offspring do, and that they flexibly adjust how they respond to both offspring signals and cues of offspring quality in response to food availability. Consequently, depending upon environmental conditions, predictably different signalling systems are favoured.
High diversity of pimpline parasitoid wasps (Hymenoptera, Ichneumonidae, Pimplinae) from the lowermost Eocene Fur Formation
Authors: Klopfstein Seraina
Published: November 2021

With an estimated 100,000 extant species, Darwin wasps (Ichneumonidae) are more specious than all vertebrates together. However, only 288 fossil species have been described to date, with hundreds more awaiting formal description in palaeontological collections. One of the largest gaps in our knowledge concerns the ~12 million years between the K-PG mass extinction and the late Ypresian, from which only two species have been formally described, including Pimpla stigmatica Henriksen from the Danish Fur Formation (~55 Ma). Ie here redescribe and reclassify this species in the genus Epitheronia Gupta, n. comb., and describe nine new species from this fossil locality that are consistent with a placement in Pimplinae: Crusopimpla collina n. sp., C. elongata n. sp., C. minuta n. sp., C. rettigi n. sp., C. violina n. sp., Theronia? furensis n. sp., T. nigriscutum n. sp., Xanthopimpla ciboisae n. sp., and X. crescendae n. sp. The diagnosis of the genus Crusopimpla Kopylov, Spasojevic & Klopfstein is amend in the light of the new species. By comparing the preserved colouration between and within specimens of different species, we draw conclusions about the taxonomic usefulness of colour patterns observed in Fur Formation ichneumonids. The number of described species of pimpline parasitoid wasps from Fur is very high when compared to any other fossil deposit, but low with respect to numbers of extant species. Further study and excavation of Fur ichneumonids will certainly reveal an even higher diversity.
Validity of freehand three-dimensional ultrasound system in measurement of three-dimensional surface shape of shoulder muscles
Authors: Umehara Jun , Fukuda Norio , Konda Shoji , Hirashima Masaya
Published: November 2021

Freehand three-dimensional ultrasound (3DUS) system is a promising technique for accurately assessing muscle morphology. However, its accuracy has been validated mainly in terms of volume by examining lower limb muscles. This study aimed to validate 3DUS in the measurements of 3D surface shape and volume by comparing them with MRI measurements while ensuring the reproducibility of participant posture by focusing on the shoulder muscles. The supraspinatus, infraspinatus, and posterior deltoid muscles of 10 healthy males were scanned using 3DUS and MRI while secured by an immobilization support customized for each participant. A 3D surface model of each muscle was created from the 3DUS and MRI methods, and the agreement between them was assessed. For the muscle volume, the mean difference between the two models was within −0.51 cm3. For the 3D surface shape, the distances between the closest points of the two models and Dice similarity coefficient were calculated. The results showed that the median surface distance was less than 1.21 mm and Dice similarity coefficient was larger than 0.85. These results suggest that, given the above error is permitted, 3DUS can be used as an alternative to MRI in measuring volume and surface shape, even for the shoulder muscles.
Deciphering a hexameric protein complex with Angstrom optical resolution
Authors: Mazal Hisham , Wieser Franz-Ferdinand , Sandoghdar Vahid
Published: November 2021

Cryogenic optical localization in three dimensions (COLD) was recently shown to resolve up to four binding sites on a single protein. However, because COLD relies on intensity fluctuations that result from the blinking behavior of fluorophores, it is limited to cases, where individual emitters show different brightness. This significantly lowers the measurement yield. To extend the number of resolved sites as well as the measurement yield, we employ partial labeling and combine it with polarization encoding in order to identify single fluorophores during their stochastic blinking. We then use a particle classification scheme to identify and resolve heterogenous subsets and combine them to reconstruct the three-dimensional arrangement of large molecular complexes. We showcase this method (polarCOLD) by resolving the trimer arrangement of proliferating cell nuclear antigen (PCNA) and the hexamer geometry of Caseinolytic Peptidase B (ClpB) ofThermus thermophilusin its quaternary structure, both with Angstrom resolution. The combination of polarCOLD and single-particle cryogenic electron microscopy (cryoEM) promises to provide crucial insight into intrinsic, environmental and dynamic heterogeneities of biomolecular structures. Furthermore, our approach is fully compatible with fluorescent protein labeling and can, thus, be used in a wide range of studies in cell and membrane biology.

Significance statement

Fluorescence super-resolution microscopy has witnessed many clever innovations in the last two decades. Here, we advance the frontiers of this field of research by combining partial labeling and 2D image classification schemes with polarization-encoded single-molecule localization at liquid helium temperature to reach Angstrom resolution in three dimensions. We demonstrate the performance of the method by applying it to trimer and hexamer protein complexes. Our approach holds great promise for examining membrane protein structural assemblies and conformations in challenging native environments. The methodology closes the gap between electron and optical microscopy and offers an ideal ground for correlating the two modalities at the single-particle level. Indeed, correlative light and electron microscopy is an emerging technique that will provide new insight into cell biology.
Differential replay for reward and punishment paths predicts approach and avoidance
Authors: McFadyen Jessica , Liu Yunzhe , Dolan Raymond J
Published: November 2021

Planning is thought to involve neural replay, where states relevant to a task goal are rapidly reactivated in sequence. It remains unclear if, during planning, replay of a path relates to an actual prospective choice. Here, using magnetoencephalography (MEG), we studied participants while they planned to either approach or avoid an uncertain environment that contained paths leading to reward and to punishment. We show significant planning-related forward sequential replay with state-to-state transitions in the range of 20 to 90 ms. Replay of rewarding paths was boosted prior to a decision to avoid, and attenuated prior to a decision to approach. Crucially, a trial-by-trial bias in replaying punishing paths predicted an irrational choice to approach when a prospective environment was more risky, an effect that was particularly marked in more anxious participants. The findings reveal a coupling between the content of forwards replay and rational choice behaviour, such that replay prioritises an online representation of potential reward.
A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions
Authors: Jehle Stefanie , Kunowska Natalia , Benlasfer Nouhad , Woodsmith Jonathan , Weber Gert , Wahl Markus C. , Stelzl Ulrich
Published: November 2021

Protein kinases play an important role in cellular signaling pathways and their dysregulation leads to multiple diseases, making kinases prime drug targets. While more than 500 human protein kinases are known to collectively mediate phosphorylation of over 290,000 S/T/Y sites, the activities have been characterized only for a minor, intensively studied subset. To systematically address this discrepancy, we developed a human kinase array in Saccharomyces cerevisiae as a simple readout tool to systematically assess kinase activities. For this array, we expressed 266 human kinases in four different Saccharomyces cerevisiae strains and profiled ectopic growth as a proxy for kinase activity across 33 conditions. More than half of the kinases showed an activity-dependent phenotype across many conditions and in more than one strain. We then employed the kinase array to identify the kinase(s) that can modulate protein-protein-interactions (PPIs). Two characterized, phosphorylation-dependent PPIs with unknown kinase-substrate relationships were analyzed in a phospho-yeast two-hybrid assay. CK2α1 and SGK2 kinases can abrogate the interaction between the spliceosomal proteins AAR2 and PRPF8 and NEK6 kinase was found to mediate the estrogen receptor (ERα) interaction with 14-3-3 proteins. The human kinase yeast array can thus be used for a variety of kinase activity-dependent readouts.
Mitochondrial dysfunction promotes alternative gasdermin D-mediated inflammatory cell death and susceptibility to infection
Authors: Weindel Chi G. , Zhao Xiao , Martinez Eduardo , Bell Samantha L. , Vail Krystal J. , Coleman Aja K. , VanPortfliet Jordyn J. , Zhao Baoyu , Mabry Cory J. , Li Pingwei , Phillip West A. , Karpac Jason , Patrick Kristin L. , Watson Robert O.
Published: November 2021

Human mutations in mitochondrial-associated genes are associated with inflammatory diseases and susceptibility to infection. However, their mechanistic contributions to immune outcomes remain ill-defined. We discovered that the disease-associated gain-of-function allele Lrrk2G2019S (leucine-rich repeat kinase 2) promotes mitochondrial hyper-fission, depolarization, and oxidative stress in macrophages. In the presence of Lrrk2G2019S-dependent mitochondrial perturbations, AIM2 inflammasome activation promotes more cell death but not more pyroptotic IL-1b release. Instead, inflammasome activation in Lrrk2G2019S macrophages triggers gasdermin D (GSDMD)-mediated mitochondrial pores, driving up ROS-mediated RIPK1/RIPK3/MLKL dependent necroptosis. Consequently, infection of Lrrk2G2019S mice with Mycobacterium tuberculosis elicits hyperinflammation and immunopathology via enhanced neutrophil infiltration. By uncovering that GSDMD promotes non-pyroptotic cell death in Lrrk2G2019S macrophages, our findings demonstrate that altered mitochondrial function can reprogram cell death modalities to elicit distinct immune outcomes. This provides mechanistic insights into why mutations in LRRK2 are associated with susceptibility to chronic inflammatory and infectious diseases.

HIGHLIGHTS

Altered mitochondrial homeostasis reprograms cell death modalities

GSDMD associates with and depolarizes mitochondrial membranes following AIM2 activation

GSDMD initiates a shift from pyroptotic to necroptotic cell death in Lrrk2G2019S macrophages

Lrrk2G2019S elicits hyperinflammation and susceptibility to infection in flies and mice
Prostaglandin PGE2 receptor EP4 regulates microglial phagocytosis and increases susceptibility to diet-induced obesity
Authors: Niraula Anzela , Fasnacht Rachael D. , Ness Kelly M. , Frey Jeremy M. , Dorfman Mauricio D. , Thaler Joshua P.
Published: November 2021

Background

In rodents, susceptibility to diet-induced obesity requires microglial activation, but the molecular components of this pathway remain incompletely defined. Prostaglandin E2 (PGE2) levels increase in the mediobasal hypothalamus during high fat diet (HFD) feeding, and the PGE2 receptor EP4 regulates microglial activation state and phagocytic activity, suggesting a potential role for microglial EP4 signaling in obesity pathogenesis.

Method

Metabolic phenotyping, as assessed by body weight, energy expenditure, glucose, and insulin tolerance, was performed in microglia-specific EP4 knockout (MG-EP4 KO) mice and littermate controls on HFD. Morphological and gene expression analysis of microglia, and a histological survey of microglia-neuron interactions in the arcuate nucleus was performed. Phagocytosis was assessed using in vivo and in vitro pharmacological techniques.

Results

Microglial EP4 deletion markedly reduced weight gain and food intake in response to HFD feeding. In correspondence with this lean phenotype, insulin sensitivity was also improved in the HFD-fed MG-EP4 KO mice though glucose tolerance remained surprisingly unaffected. Mechanistically, EP4-deficient microglia showed an attenuated phagocytic state marked by reduced CD68 expression and fewer contacts with POMC neuron soma and processes. These cellular changes observed in the microglial EP4 knockout mice corresponded with an increased density of POMC neurites extending into the paraventricular nucleus.

Conclusion

These findings reveal that microglial EP4 signaling promotes body weight gain and insulin resistance during HFD feeding. Furthermore, the data suggest that curbing microglial phagocytic function may preserve POMC cytoarchitecture and PVN input to limit overconsumption during diet-induced obesity.
Multitrophic higher-order interactions modulate species persistence
Authors: Buche Lisa , Bartomeus Ignasi , Godoy Oscar
Published: November 2021

There is growing recognition that interactions between species pairs are modified in a multispecies context by the density of a third species. However, how these higher-order interactions (HOIs) affect species persistence remains poorly understood. To explore the effect of HOIs steaming from multiple trophic layers on plant persistence, we experimentally built a mutualistic system containing three plants and three pollinators species with two contrasting network structures. For both structures, we first estimated the statistically supported HOIs on plant species, in addition to the pairwise interactions among plants and plant-pollinators. Following a structuralist approach, we then assessed the effects of the supported HOIs on the persistence probability of each of the three competing plant species and their combinations. HOIs produced substantial effects on the strength and sign of per capita interactions between plant species to such an extent that predictions of species persistence differ from a non-HOIs scenario. Changes in network structure due to removing a plant-pollinator link further modulated the species persistence probabilities by reorganizing per capita interaction strengths of both pairwise interactions and HOIs. Our study provides empirical evidence of the joint importance of HOIs and network structure for determining the probability of species to persist within diverse communities.
Cytotoxicity mechanisms and composition of the glyphosate formulated herbicide RangerPro
Authors: Mesnage Robin , Ferguson Scarlett , Mazzacuva Francesca , Caldwell Anna , Halket John , Antoniou Michael N
Published: November 2021

Understanding the nature of co-formulants and toxic effects of major glyphosate-based herbicide (GBH) formulations is considered a research priority. Indeed, the toxicity of the co-formulants present in GBHs have been widely discussed and the European Union recently banned the co-formulant polyoxyethylene tallow amine (POEA). We provide a foundation for the development of new environmental epidemiological studies by reporting the presence of the most commonly used POEA, known as POE-15 tallow amine, in the widely used US GBH RangerPro. In order to understand if POE-15 tallow amine is present in RangerPro at a concentration at which it can exert toxic effects, we also tested the cytotoxicity of this GBH compared to glyphosate and POE-15 tallow amine in the human epithelial cell line Caco-2, a representative of the human intestinal epithelium, and the first to be exposed from the human diet to glyphosate herbicides. The lethal concentration 50 for each of these substances was 125 μg/ml, 17200 μg/ml, and 5.7 μg/ml, for RangerPro, glyphosate and POE-15, respectively. The Caco-2 cell cytotoxicity assay indicated that RangerPro is more cytotoxic than glyphosate, suggesting that its toxicity can be due to the presence of the POE-15 surfactant. RangerPro and POE-15 tallow amine but not glyphosate exerted cell necrotic effects, but did not induce oxidative stress. We show that RangerPro contains POE-15 tallow amine at a concentration at which it could exert toxic effects, which offers a starting point for conducting surveys of co-formulant exposure in human populations.
Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation
Authors: Benjelloun Badr , Leempoel Kevin , Boyer Frédéric , Stucki Sylvie , Streeter Ian , Orozco-terWengel Pablo , Alberto Florian J. , Servin Bertrand , Biscarini Filippo , Alberti Adriana , Engelen Stefan , Stella Alessandra , Colli Licia , Coissac Eric , Bruford Michael W. , Ajmone-Marsan Paolo , Negrini Riccardo , Clarke Laura , Flicek Paul , Chikhi Abdelkader , Joost Stéphane , Taberlet Pierre , Pompanon François
Published: November 2021

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.