bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and Indications for Oxygenator Circuit Replacement in Patients Receiving Venovenous Extracorporeal Membrane Oxygenation
Authors: Vasques Francesco , Sanderson Barnaby , Correa Genex , Collins Patrick , Camarda Valentina , Giosa Lorenzo , Retter Andrew , Meadows Chris , Barrett Nicholas A. , Camporota Luigi
Published: May 2023

In this retrospective observational cohort study, we aimed to describe the rate of extracorporeal membrane oxygenation (ECMO) circuit change, the associated risk factors and its relationship with patient characteristics and outcome in patients receiving venovenous (VV) ECMO at our center between January 2015 and November 2017. Twenty-seven percent of the patients receiving VV ECMO (n = 224) had at least one circuit change, which was associated with lower ICU survival (68% vs 82% p=0.032) and longer ICU stay (30 vs. 17 days p < 0.001). Circuit duration was similar when stratified by gender, clinical severity, or prior circuit change. Hematological abnormalities and increased transmembrane lung pressure (TMLP) were the most frequent indication for circuit change. The change in transmembrane lung resistance (Δ TMLR) gave better prediction of circuit change than TMLP, TMLR, or ΔTMLP. Low postoxygenator PO2 was indicated as a reason for one-third of the circuit changes. However, the ECMO oxygen transfer was significantly higher in cases of circuit change with documented “low postoxygenator PO2” than those without (244 ± 62 vs. 200 ± 57 ml/min; p = 0.009). The results suggest that circuit change in VV ECMO is associated with worse outcomes, that the Δ TMLR is a better predictor of circuit change than TMLP, and that the postoxygenator PO2 is an unreliable proxy for the oxygenator function.
Clinical Decision Support Systems Used in Transplantation: Are They Tools for Success or an Unnecessary Gadget? A Systematic Review
Authors: Wingfield Laura R. , Salaun Achille , Khan Aparajita , Webb Helena , Zhu Tingting , Knight Simon
Published: May 2023

Although clinical decision support systems (CDSSs) have been used since the 1970s for a wide variety of clinical tasks including optimization of medication orders, improved documentation, and improved patient adherence, to date, no systematic reviews have been carried out to assess their utilization and efficacy in transplant medicine. The aim of this study is to systematically review studies that utilized a CDSS and assess impact on patient outcomes. A total of 48 articles were identified as meeting the author-derived inclusion criteria, including tools for posttransplant monitoring, pretransplant risk assessment, waiting list management, immunosuppressant management, and interpretation of histopathology. Studies included 15 984 transplant recipients. Tools aimed at helping with transplant patient immunosuppressant management were the most common (19 studies). Thirty-four studies (85%) found an overall clinical benefit following the implementation of a CDSS in clinical practice. Although there are limitations to the existing literature, current evidence suggests that implementing CDSS in transplant clinical settings may improve outcomes for patients. Limited evidence was found using more advanced technologies such as artificial intelligence in transplantation, and future studies should investigate the role of these emerging technologies.
Ketamine for depression: a potential role in requests for Medical Aid in Dying?
Authors: Garel Nicolas , Nazon Michka , Naghi Kamran , Willis Elena , Looper Karl , Rej Soham , Greenway Kyle T.
Published: May 2023

Medical Aid in Dying (MAiD) is the act of a healthcare provider ending a patient’s life, at their request, due to unbearable suffering from a grievous and incurable disease. Access to MAiD has expanded in the last decade and, more recently, it has been made available for psychiatric illnesses in a few countries. Recent studies have found that such psychiatric requests are rapidly increasing and primarily involve mood disorders as the primary condition. Nevertheless, MAiD for psychiatric disorders is associated with significant controversy and debate, especially regarding the definition and determination of irremediability – that a given patient lacks any reasonable prospect for recovery. In this article, we report the case of a Canadian patient who was actively requesting Medical Assistance in Dying for severe and prolonged treatment-resistant depression until she experienced remarkable benefits from a course of intravenous ketamine infusions. To our knowledge, this is the first report of ketamine or any other intervention yielding remission in a patient who would have otherwise likely been eligible for MAiD for depression. We discuss implications for the evaluation of similar requests and, more specifically, why a trial of ketamine warrants consideration.
Differential grandparental investment when maternal grandmothers are living versus deceased
Authors: Tanskanen Antti O. , Helle Samuli , Danielsbacka Mirkka
Published: May 2023

Grandparents can increase their inclusive fitness by investing time and resources in their grandchildren. However, not all grandparents make such investments equally, and between-grandparent differences in this regard can be predicted based on paternity uncertainty, lineage and grandparents' sex. Using population-based data for English and Welsh adolescents (n= 1430), we examined whether the death of the most important grandparent (in terms of investment), the maternal grandmother (MGM), changes relative support for existing hypotheses predicting differential grandparental-investment patterns. To contrast the predictions of the grandparental investment hypotheses, we used generalized order-restricted information criterion approximation. We consequently found that, when MGMs are alive, the most-supported hypothesis is ‘discriminative grandparental solicitude’, which ranks grandparental investment as MGMs > maternal grandfathers (MGFs) > paternal grandmothers (PGMs) > paternal grandfathers (PGFs). However, when MGMs are deceased, the paternity uncertainty hypothesis (MGFs = PGMs > PGFs) receives the most support; this is due to increased investment by PGMs. Thus, when the heaviest investors (i.e. MGMs) are deceased, PGM investments are closer to—but do not exceed—MGF investments.
Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH
Authors: Schulte Tim , Panas Marc D. , Han Xiao , Williams Lucy , Kedersha Nancy , Fleck Jonas Simon , Tan Timothy J. C. , Dopico Xaquin Castro , Olsson Anders , Morro Ainhoa Moliner , Hanke Leo , Nilvebrant Johan , Giang Kim Anh , Nygren Per-Åke , Anderson Paul , Achour Adnane , McInerney Gerald M.
Published: May 2023

G3BP is the central node within stress-induced protein–RNA interaction networks known as stress granules (SGs). The SG-associated proteins Caprin-1 and USP10 bind mutually exclusively to the NTF2 domain of G3BP1, promoting and inhibiting SG formation, respectively. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1-derived short linear motif (SLiM). Caprin-1 interacts with His-31 and His-62 within a third NTF2-binding site outside those covered by USP10, as confirmed using biochemical and biophysical-binding assays. Nano-differential scanning fluorimetry revealed reduced thermal stability of G3BP1-NTF2 at acidic pH. This destabilization was counterbalanced significantly better by bound USP10 than Caprin-1. The G3BP1/USP10 complex immunoprecipated from human U2OS cells was more resistant to acidic buffer washes than G3BP1/Caprin-1. Acidification of cellular condensates by approximately 0.5 units relative to the cytosol was detected by ratiometric fluorescence analysis of pHluorin2 fused to G3BP1. Cells expressing a Caprin-1/FGDF chimera with higher G3BP1-binding affinity had reduced Caprin-1 levels and slightly reduced condensate sizes. This unexpected finding may suggest that binding of the USP10-derived SLiM to NTF2 reduces the propensity of G3BP1 to enter condensates.
Low-nutrient diet inDrosophilalarvae stage causes enhancement in dopamine modulation in adult brain due epigenetic imprinting
Authors: Zúñiga-Hernández J. M. , Olivares Gonzalo H. , Olguín Patricio , Glavic Alvaro
Published: May 2023

Nutrient scarcity is a frequent adverse condition that organisms face during their development. This condition may lead to long-lasting effects on the metabolism and behaviour of adults due to developmental epigenetic modifications. Here, we show that reducing nutrient availability during larval development affects adult spontaneous activity and sleep behaviour, together with changes in gene expression and epigenetic marks in the mushroom bodies (MBs). We found that open chromatin regions map to 100 of 241 transcriptionally upregulated genes in the adult MBs, these new opening zones are preferentially located in regulatory zones such as promoter-TSS and introns. Importantly, opened chromatin at the Dopamine 1-like receptor 2 regulatory zones correlate with increased expression. In consequence, adult administration of a dopamine antagonist reverses increased spontaneous activity and diminished sleep time observed in response to early-life nutrient restriction. In comparison, reducingdop1R2expression in MBs also ameliorates these effects, albeit to a lesser degree. These results lead to the conclusion that increased dopamine signalling in the MBs of flies reared in a poor nutritional environment underlies the behavioural changes observed due to this condition during development.
Dynamics of hinged wings in strong upward gusts
Authors: Stevenson Jonathan P. J. , Cheney Jorn A. , Usherwood James R. , Bomphrey Richard J. , Windsor Shane P.
Published: May 2023

A bird's wings are articulated to its body via highly mobile shoulder joints. The joints confer an impressive range of motion, enabling the wings to make broad, sweeping movements that can modulate quite dramatically the production of aerodynamic load. This is enormously useful in challenging flight environments, especially the gusty, turbulent layers of the lower atmosphere. In this study, we develop a dynamics model to examine how a bird-scale gliding aircraft can use wing-root hinges (analogous to avian shoulder joints) to reject the initial impact of a strong upward gust. The idea requires that the spanwise centre of pressure and the centre of percussion of the hinged wing start, and stay, in good initial alignment (the centre of percussion here is related to the idea of a ‘sweet spot’ on a bat, as in cricket or baseball). We propose a method for achieving this rejection passively, for which the essential ingredients are (i) appropriate lift and mass distributions; (ii) hinges under constant initial torque; and (iii) a wing whose sections stall softly. When configured correctly, the gusted wings will first pivot on their hinges without disturbing the fuselage of the aircraft, affording time for other corrective actions to engage. We expect this system to enhance the control of aircraft that fly in gusty conditions.
Hydrodynamic analysis of bioinspired vortical cross-step filtration by computational modelling
Authors: Van Wassenbergh S. , Sanderson S. L.
Published: May 2023

Research on the suspension-feeding apparatus of fishes has led recently to the identification of novel filtration mechanisms involving vortices. Structures inside fish mouths form a series of ‘backward-facing steps' by protruding medially into the mouth cavity. In paddlefish and basking shark mouths, porous gill rakers lie inside ‘slots’ between the protruding branchial arches. Vortical flows inside the slots of physical models have been shown to be important for the filtration process, but the complex flow patterns have not been visualised fully. Here we resolve the three-dimensional hydrodynamics by computational fluid dynamics simulation of a simplified mouth cavity including realistic flow dynamics at the porous layer. We developed and validated a modelling protocol in ANSYS Fluent software that combines a porous media model and permeability direction vector mapping. We found that vortex shape and confinement to the medial side of the gill rakers result from flow resistance by the porous gill raker surfaces. Anteriorly directed vortical flow shears the porous layer in the centre of slots. Flow patterns also indicate that slot entrances should remain unblocked, except for the posterior-most slot. This new modelling approach will enable future design exploration of fish-inspired filters.
The role of the Southern Ocean in the global climate response to carbon emissions
Authors: Williams Richard G. , Ceppi Paulo , Roussenov Vassil , Katavouta Anna , Meijers Andrew J. S.
Published: May 2023

The effect of the Southern Ocean on global climate change is assessed using Earth system model projections following an idealized 1% annual rise in atmospheric CO2. For this scenario, the Southern Ocean plays a significant role in sequestering heat and anthropogenic carbon, accounting for 40% ± 5% of heat uptake and 44% ± 2% of anthropogenic carbon uptake over the global ocean (with the Southern Ocean defined as south of 36°S). This Southern Ocean fraction of global heat uptake is however less than in historical scenarios with marked hemispheric contrasts in radiative forcing. For this idealized scenario, inter-model differences in global and Southern Ocean heat uptake are strongly affected by physical feedbacks, especially cloud feedbacks over the globe and surface albedo feedbacks from sea-ice loss in high latitudes, through the top-of-the-atmosphere energy balance. The ocean carbon response is similar in most models with carbon storage increasing from rising atmospheric CO2, but weakly decreasing from climate change with competing ventilation and biological contributions over the Southern Ocean. The Southern Ocean affects a global climate metric, the transient climate response to emissions, accounting for 28% of its thermal contribution through its physical climate feedbacks and heat uptake, and so affects inter-model differences in meeting warming targets.

This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.
Sailing through the southern seas of air–sea CO
2
flux uncertainty
Authors: Landschützer Peter , Tanhua Toste , Behncke Jacqueline , Keppler Lydia
Published: May 2023

The Southern Ocean is among the largest contemporary sinks of atmospheric carbon dioxide on our planet; however, remoteness, harsh weather and other circumstances have led to an undersampling of the ocean basin, compared with its northern hemispheric counterparts. While novel data interpolation methods can in part compensate for such data sparsity, recent studies raised awareness that we have hit a wall of unavoidable uncertainties in air–sea

CO

2

flux reconstructions. Here, we present results from autonomous observing campaigns using a novel platform to observe remote ocean regions: sailboats. Sailboats are at present a free of charge environmentally friendly platform that recurrently pass remote ocean regions during round-the-globe racing events. During the past 5 years, we collected

>

350
 
000

measurements of the sea surface partial pressure of

CO

2

(p

CO

2

) around the globe including the Southern Ocean throughout an Antarctic circumnavigation during the Vendée Globe racing event. Our analysis demonstrates that the sailboat tracks pass regions where large uncertainty in the air–sea

CO

2

flux reconstruction prevails, with regional oversaturation or undersaturation of the sea surface p

CO

2

. Sailboat races provide an independent cross-calibration platform for autonomous measurement devices, such as Argo floats, ultimately strengthening the entire Southern Ocean observing system.

This article is part of a discussion meeting issue ‘Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities’.
New insights into air-sea fluxes and their role in Subantarctic Mode Water formation
Authors: Tamsitt V.
Published: May 2023

The formation of Subantarctic Mode Water SAMW in the Southern Ocean plays a key role in the global oceanic uptake and storage of anthropogenic heat and carbon. Wintertime ocean surface heat loss is a dominant driver of Subantarctic Mode Water formation and variability, but wintertime air-sea flux observations in the Southern Ocean are extremely sparse. Recent advances in our understanding of the role of air-sea fluxes in Subantarctic Mode Water Formation from novel ocean observations are summarized here, particularly the role of synoptic atmospheric extreme events, and the drivers of interannual variations in SAMW. These advances in understanding have important implications for variability in Southern Ocean heat and carbon uptake, and can inform future Southern Ocean observing system design.

This article is part of a discussion meeting issue ‘Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities’.
Tracing the impacts of recent rapid sea ice changes and the A68 megaberg on the surface freshwater balance of the Weddell and Scotia Seas
Authors: Meredith Michael P. , Povl Abrahamsen E. , Alexander Haumann F. , Leng Melanie J. , Arrowsmith Carol , Barham Mark , Firing Yvonne L. , King Brian A. , Brown Peter , Alexander Brearley J. , Meijers Andrew J. S. , Sallée Jean-Baptiste , Akhoudas Camille , Tarling Geraint A.
Published: May 2023

The Southern Ocean upper-layer freshwater balance exerts a global climatic influence by modulating density stratification and biological productivity, and hence the exchange of heat and carbon between the atmosphere and the ocean interior. It is thus important to understand and quantify the time-varying freshwater inputs, which is challenging from measurements of salinity alone. Here we use seawater oxygen isotopes from samples collected between 2016 and 2021 along a transect spanning the Scotia and northern Weddell Seas to separate the freshwater contributions from sea ice and meteoric sources. The unprecedented retreat of sea ice in 2016 is evidenced as a strong increase in sea ice melt across the northern Weddell Sea, with surface values increasing approximately two percentage points between 2016 and 2018 and column inventories increasing approximately 1 to 2 m. Surface meteoric water concentrations exceeded 4% in early 2021 close to South Georgia due to meltwater from the A68 megaberg; smaller icebergs may influence meteoric water at other times also. Both these inputs highlight the importance of a changing cryosphere for upper-ocean freshening; potential future sea ice retreats and increases in iceberg calving would enhance the impacts of these freshwater sources on the ocean and climate.

This article is part of a discussion meeting issue ‘Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities’.
Inhibition of Proliferation of Acute Lymphocytic Leukemia (ALL) by frequency-specific Oscillating Pulsed Electric Fields (OPEF) broadcast by an enclosed gas plasma antenna
Authors: Holland Anthony , Bare James
Published: May 2023

Frequency-specific Oscillating Pulsed Electric Fields (OPEF) broadcast by an enclosed gas plasma antenna with a frequency of 160kHz from a distance of 18 inches inhibited the proliferation of Acute Lymphocytic Leukemia cells in vitro by up to 44%.
The temporal progression of immune remodeling during metastasis
Authors: McGinnis Christopher S. , Miao Zhuang , Reticker-Flynn Nathan E. , Winker Juliane , Satpathy Ansuman T.
Published: May 2023

Tumor metastasis requires systemic remodeling of distant organ microenvironments which impacts immune cell phenotypes, population structure, and intercellular communication networks. However, our understanding of immune phenotypic dynamics in the metastatic niche remains incomplete. Here, we longitudinally assayed lung immune cell gene expression profiles in mice bearing PyMT-driven metastatic breast tumors from the onset of primary tumorigenesis, through formation of the pre-metastatic niche, to the final stages of metastatic outgrowth. Computational analysis of these data revealed an ordered series of immunological changes that correspond to metastatic progression. Specifically, we uncovered a TLR-NFκB myeloid inflammatory program which correlates with pre-metastatic niche formation and mirrors described signatures of CD14+ ‘activated’ MDSCs in the primary tumor. Moreover, we observed that cytotoxic NK cell proportions increased over time which illustrates how the PyMT lung metastatic niche is both inflammatory and immunosuppressive. Finally, we predicted metastasis-associated immune intercellular signaling interactions involvingIgf1andCcl6which may organize the metastatic niche. In summary, this work identifies novel immunological signatures of metastasis and discovers new details about established mechanisms that drive metastatic progression.

Graphical abstract

In brief

McGinnis et al. report a longitudinal scRNA-seq atlas of lung immune cells in mice bearing PyMT-driven metastatic breast tumors and identify immune cell transcriptional states, shifts in population structure, and rewiring of cell-cell signaling networks which correlate with metastatic progression.

Highlights

Longitudinal scRNA-seq reveals distinct stages of immune remodeling before, during, and after metastatic colonization in the lungs of PyMT mice.

TLR-NFκB inflammation correlates with pre-metastatic niche formation and involves both tissue-resident and bone marrow-derived myeloid cell populations.

Inflammatory lung myeloid cells mirror ‘activated’ primary tumor MDSCs, suggesting that primary tumor-derived cues induceCd14expression and TLR-NFκB inflammation in the lung.

Lymphocytes contribute to the inflammatory and immunosuppressive lung metastatic microenvironment, highlighted by enrichment of cytotoxic NK cells in the lung over time.

Cell-cell signaling network modeling predicts cell type-specificCcl6regulation and IGF1-IGF1R signaling between neutrophils and interstitial macrophages.
Inferring secretory and metabolic pathway activity from omic data with secCellFie
Authors: Masson Helen O. , Samoudi Mojtaba , Robinson Caressa M. , Kuo Chih-Chung , Weiss Linus , Ud Doha Km Shams , Campos Alex , Tejwani Vijay , Dahodwala Hussain , Menard Patrice , Voldborg Bjorn G. , Sharfstein Susan T. , Lewis Nathan E.
Published: May 2023

Understanding protein secretion has considerable importance in the biotechnology industry and important implications in a broad range of normal and pathological conditions including development, immunology, and tissue function. While great progress has been made in studying individual proteins in the secretory pathway, measuring and quantifying mechanistic changes in the pathway’s activity remains challenging due to the complexity of the biomolecular systems involved. Systems biology has begun to address this issue with the development of algorithmic tools for analyzing biological pathways; however most of these tools remain accessible only to experts in systems biology with extensive computational experience. Here, we expand upon the user-friendly CellFie tool which quantifies metabolic activity from omic data to include secretory pathway functions, allowing any scientist to infer protein secretion capabilities from omic data. We demonstrate how the secretory expansion of CellFie (secCellFie) can be used to predict metabolic and secretory functions across diverse immune cells, hepatokine secretion in a cell model of NAFLD, and antibody production in Chinese Hamster Ovary cells.
Connecting higher order interactions with ecological stability in experimental aquatic food webs
Authors: Shen Chenyu , Lemmen Kimberley , Alexander Jake , Pennekamp Frank
Published: May 2023

Community ecology is built on theories that represent the strength of interactions between species as pairwise links. Higher order interactions occur when the presence of a third (or more) species changes the pairwise interaction between a focal pair. Recent theoretical work has highlighted the stabilizing role of higher order interactions for large, simulated communities, yet it remains unclear how important higher order effects are in real communities. Here we used experimental communities of aquatic protists to examine the relationship between higher-order interactions and community stability (as measured by the persistence of species in a community). We cultured a focal pair of consumers in the presence of additional competitors and a predator and collected time series data of their abundances. We then fitted competition models with and without HOIs to measure interaction strength between the focal pair across different community compositions. We used survival analysis to measure the persistence of individual species. We found evidence that additional species positively affected persistence of the focal species and that HOIs were present in most of our communities. However, persistence was only linked to HOIs for one of the focal species. Our results vindicate community ecology theory positing that species interactions may deviate from assumptions of pairwise interactions, opening avenues to consider possible consequences for coexistence and community stability.
Analytical performance and concordance with next-generation sequencing of a rapid multiplexed dPCR panel for the detection of actionable DNA and RNA biomarkers in non-small cell lung cancer
Authors: Cabrera Kerri , Gole Jeffery , Leatham Bryan , Jacky Lucien , Brown Bradley A.
Published: May 2023

Background

Over the last ten years, the discovery and FDA approval of targeted therapies for lung cancer has significantly improved patient survival rates. However, despite these improved survival rates, only 68% of patients receive molecular testing that results in assignment of targeted therapy1,2. Barriers to timely access to biomarker information include no testing ordered3,high nucleic acid input requirements, and problematic turnaround time (TAT) by NGS (> 14 days)4.

Here we report the analytical performance and concordance with next-generation sequencing (NGS) of a highly-multiplexed research use only (RUO) panel using digital PCR (dPCR). The HDPCR NSCLC panel reports the status for variants (SNV, indels, and fusions) in eight actionable genes using amplitude modulation and multi-spectral encoding in dPCR5.

Methods

The panel’s analytical sensitivity and reactivity were determined using DNA and RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue spiked with plasmid DNA or in-vitro transcribed RNA. Concordance was established on 106 FFPE samples previously characterized using the Oncomine Precision Assay® or pathology results. Discordant resolution was resolved with Archer Fusionplex® and Variantplex® panels.

Results

The analytical sensitivity, reported as estimated mutant allele fraction (MAF), for DNA targets (EGFRexon 19 deletions,EGFRexon 20 insertions,EGFRS768I,EGFRL858R,EGFRT790M,EGFRL861Q,BRAFV600E,EGFRG719X,ERBB2exon 20 insertions andKRASG12C) ranged from 0.8% – 4.9% with 40 ng of DNA input, and 2.4% to 10.9% with 15 ng of DNA input. For RNA fusion targets (ALK, RET, ROS, NTRK1/2/3, andMETexon 14 skipping), the analytical sensitivity ranged from 24 - 150 copies with 5 ng of total RNA input. The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and >99.0% in aggregate. The accuracy of the assay was >97% with respect to the comparator method.
Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany
Authors: Buchner Dominik , Sinclair James S. , Ayasse Manfred , Beermann Arne , Buse Jörn , Dziock Frank , Enss Julian , Frenzel Mark , Hörren Thomas , Li Yuanheng , Monaghan Michael T. , Morkel Carsten , Müller Jörg , Pauls Steffen U. , Richter Ronny , Scharnweber Tobias , Sorg Martin , Stoll Stefan , Twietmeyer Sönke , Weisser Wolfgang W. , Wiggering Benedikt , Wilmking Martin , Zotz Gerhard , Gessner Mark O. , Haase Peter , Leese Florian
Published: May 2023

Mitigating ongoing losses of insects and their key functions (e.g., pollination) requires accurately tracking large-scale and long-term community changes. However, doing so has been notoriously hindered by uniquely high insect species diversity that requires prohibitively high investments of time, funding, and taxonomic expertise. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1,815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labor and maintenance. With on average 1.4M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single OTU. We estimated another 21,403 plausible species, which likely either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (∼35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (∼80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.
Key role of down-regulated in adenoma (SLC26A3) chloride/bicarbonate exchanger in linaclotide-stimulated intestinal bicarbonate secretion upon loss of CFTR function
Authors: Sarthi Jessica B. , Trumbull Annie M. , Abazari Shayda M. , van Unen Vincent , Chan Joshua E. , Jiang Yanfen , Gammons Jesse , Anderson Marc O. , Cil Onur , Kuo Calvin J. , Sellers Zachary M.
Published: May 2023

Duodenal bicarbonate secretion is critical to epithelial protection, nutrient digestion/absorption and is impaired in cystic fibrosis (CF). We examined if linaclotide, typically used to treat constipation, may also stimulate duodenal bicarbonate secretion. Bicarbonate secretion was measured in vivo and in vitro using mouse and human duodenum (biopsies and enteroids). Ion transporter localization was identified with confocal microscopy and de novo analysis of human duodenal single cell RNA sequencing (sc-RNAseq) datasets was performed. Linaclotide increased bicarbonate secretion in mouse and human duodenum in the absence of CFTR expression (Cftrknockout mice) or function (CFTRinh-172). NHE3 inhibition contributed to a portion of this response. Linaclotide-stimulated bicarbonate secretion was eliminated by down-regulated in adenoma (DRA, SLC26A3) inhibition during loss of CFTR activity. Sc-RNAseq identified that 70% of villus cells expressedSLC26A3, but notCFTR, mRNA. Loss of CFTR activity and linaclotide increased apical brush border expression of DRA in non-CF and CF differentiated enteroids. These data provide further insights into the action of linaclotide and how DRA may compensate for loss of CFTR in regulating luminal pH. Linaclotide may be a useful therapy for CF individuals with impaired bicarbonate secretion.
Soluble antigen arrays improve the efficacy and safety of peptide-based tolerogenic immunotherapy
Authors: Firdessa-Fite Rebuma , Johnson Stephanie N. , Leon Martin A. , Sestak Joshua O. , Berkland Cory , Creusot Remi J.
Published: May 2023

Autoantigen-specific immunotherapy using peptides offers a more targeted approach to treat autoimmune diseases, but the limitedin vivostability and uptake of peptides impedes clinical implementation. We previously showed that multivalent delivery of peptides as soluble antigen arrays (SAgAs) efficiently protects against spontaneous autoimmune diabetes in the non-obese diabetic (NOD) mouse model. Here, we compared the efficacy, safety, and mechanisms of action of SAgAs versus free peptides. SAgAs, but not their corresponding free peptides at equivalent doses, efficiently prevented the development of diabetes. SAgAs increased the frequency of regulatory T cells among peptide-specific T cells or induce their anergy/exhaustion or deletion, depending on the type of SAgA (hydrolysable (hSAgA) and non-hydrolysable ‘click’ SAgA (cSAgA)) and duration of treatment, whereas their corresponding free peptides induced a more effector phenotype following delayed clonal expansion. Moreover, the N-terminal modification of peptides with aminooxy or alkyne linkers, which was needed for grafting onto hyaluronic acid to make hSAgA or cSAgA variants, respectively, influenced their stimulatory potency and safety, with alkyne-functionalized peptides being more potent and less anaphylactogenic than aminooxy-functionalized peptides. Both SAgA variants significantly delayed anaphylaxis compared to their respective free peptides. The anaphylaxis, which occurred in NOD mice but not in C57BL/6 mice, was dose-dependent but did not correlate with the production of IgG1 or IgE against the peptides. We provide evidence that SAgAs significantly improve the efficacy and safety of peptide-based immunotherapy.

SIGNIFICANCE STATEMENT

Peptide-based immunotherapy has several advantages over using full antigen as they are easy to synthetize, chemically modify and customize for precision medicine. However, their use in the clinic has been limited by issues of membrane impermeability, poor stability and potencyin vivo, and in some cases, hypersensitivity reactions. Here, we provide evidence that soluble antigen arrays and alkyne-functionalization of peptides could be used as strategies to improve the safety and efficacy of peptide-based immunotherapy for autoimmune diseases by influencing the nature and dynamics of immune responses induced by the peptides.
Risk and Loss Aversion and Attitude to COVID and Vaccines in Anxious Individuals
Authors: Ferrari Filippo , Alexander Jesse , Seriès Peggy
Published: May 2023

Anxious individuals are known to show impaired decision-making in economic gambling task and in everyday life decisions. This impairment can be due to aversion to uncertainty about outcomes (risk aversion) and/or aversion to negative outcomes (loss aversion). We investigate how non-clinical individuals with high levels of Generalised Anxiety Disorder (GAD) (N = 54) behave compared to less anxious subjects (N = 61) in a gambling decision-making task delivered online and designed to separate the distinct influences of risk and loss aversion on decision-making. By modelling subjects’ choices using computational models derived from Prospect Theory and fitted using Hierarchical Bayesian methods, we estimate individual levels of risk and loss aversion. Moreover we analyse the reaction times and choice data using Hierarchical Drift Diffusion Models (HDDMs). We also link estimates of these parameters to individual propensity to risk averse behaviours during the COVID pandemic, like wearing safer types of face masks, or completing a COVID vaccination course. We report increased loss aversion in individuals with increased level of GAD compared to less anxious individuals and no differences in risk aversion. The HDDM analysis suggests that high anxiety subjects have a reduced bias towards gambling in trials where there is a risk to loose points, also consistent with them being loss averse. We also report no links between risk and loss aversion and attitudes towards COVID and vaccines. These results shed new light on the interplay of anxiety and risk and loss aversion and they can provide useful directions for clinical intervention.
A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease
Authors: Thomas Tom , Rich-Griffin Charlotte , Pohin Mathilde , Friedrich Matthias , Aschenbrenner Dominik , Pakpoor Julia , Jainarayanan Ashwin , Voda Alexandru , Sanches-Peres Raphael , Nee Eloise , Sathananthan Dharshan , Kotliar Dylan , Turner Jason , Nayar Saba ,   IBD Cohort Investigators,   AMP RA investigators, Zhang Fan , Jonsson Anna , Brenner Michael , Raychaudhuri Soumya , Kulicke Ruth , Ramsdell Danielle , Stransky Nicolas , Pagliarini Ray , Bielecki Piotr , Spies Noah , Wagner Allon , Walsh Alissa , Coles Mark , Jostins-Dean Luke , Powrie Fiona M. , Filer Andrew , Travis Simon , Uhlig Holm H. , Dendrou Calliope A , Buckley Christopher D
Published: May 2023

Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires an understanding of how cellular networks change following therapy. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following anti-tumour necrosis factor (TNF) therapy. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies from 38 patients and three controls, revealing disease- and therapy-specific differences. A systems-biology analysis identified distinct spatially-resolved cellular microenvironments: granuloma signatures in CD and interferon (IFN)-response signatures localising to T-cell aggregates and epithelial damage in CD and UC. Longitudinal comparisons demonstrated that disease progression in non-responders associated with myeloid and stromal cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas informs drug positioning across IMIDs, and suggests a rationale for the use of janus kinase (JAK) inhibition following anti-TNF resistance.
Lactate and Immunomagnetic-purified iPSC-derived Cardiomyocytes Generate Comparable Engineered Cardiac Tissue Constructs
Authors: Rossler Kalina J. , de Lange Willem J. , Mann Morgan W. , Aballo Timothy J. , Melby Jake A. , Zhang Jianhua , Kim Gina , Bayne Elizabeth F. , Zhu Yanlong , Farrell Emily T. , Kamp Timothy J. , Ralphe J. Carter , Ge Ying
Published: May 2023

Three-dimensional engineered cardiac tissue (ECT) using purified human induced pluripotent stem cell–derived cardiomyocytes (hiPSC-CMs) has emerged as an appealing model system for the study of human cardiac biology and disease. A recent study reported widely-used metabolic (lactate) purification of monolayer hiPSC-CM cultures results in an ischemic cardiomyopathy-like phenotype compared to magnetic antibody-based cell sorting (MACS) purification, complicating the interpretation of studies using lactate-purified hiPSC-CMs. Herein, our objective was to determine if use of lactate relative to MACs-purified hiPSC-CMs impacts the properties of resulting hiPSC-ECTs. Therefore, hiPSC-CMs were differentiated and purified using either lactate-based media or MACS. After purification, hiPSC-CMs were combined with hiPSC-cardiac fibroblasts to create 3D hiPSC-ECT constructs maintained in culture for four weeks. There were no structural differences observed, and there was no significant difference in sarcomere length between lactate and MACS hiPSC-ECTs. Assessment of isometric twitch force, Ca2+transients, and β-adrenergic response revealed similar functional performance between purification methods. High-resolution mass spectrometry (MS)-based quantitative proteomics showed no significant difference in any protein pathway expression or myofilament proteoforms. Taken together, this study demonstrates lactate- and MACS-purified hiPSC-CMs generate ECTs with comparable molecular and functional properties, and suggests lactate purification does not result in an irreversible change in hiPSC-CM phenotype.

Graphical Abstract
ZymePackNet: rotamer-sampling free graph neural network method for protein sidechain prediction
Authors: Mukhopadhyay Abhishek , Kadan Amit , McMaster Benjamin , McWhirter J. Liam , Dixit Surjit B.
Published: May 2023

Protein sidechain conformation prediction, or packing, is a key step in many in silico protein modeling and design tasks. Popular protein packing methods typically rely on approximated energy functions and complex algorithms to search dense rotamer libraries. Inspired by the recent success of deep learning in protein modeling tasks, we present ZymePackNet, a graph neural network based protein packing tool that does not require a rotamer library, scoring functions or a search algorithm. We train regression models using protein crystal structures represented as graphs, which are employed sequentially to “germinate” the sidechain starting from atoms anchoring the protein backbone to the sidechains’ termini, followed by an iterative refinement stage. ZymePackNet is fast and accurate compared to state-of-the-art protein packing methods. We validate our model on three native backbone datasets achieving a mean average error of 16.6°, 24.1°, 42.1°, and 53.0° for sidechain dihedral angles (χ1toχ4). ZymePackNet captures complex physical interactions such asπstacking without explicitly accounting for it in the model; such effects are currently lacking in the energy terms used in traditional packing tools.

Contact

abmukho@vt.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Human macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast
Authors: Haase Max A. B. , Lazar-Stefanita Luciana , Ólafsson Guðjón , Wudzinska Aleksandra , Shen Michael J. , Truong David M. , Boeke Jef D.
Published: May 2023

In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones providing additional layers of structural and epigenetic regulation. Here, we systematically replaced individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. Variants H2A.J, TsH2B, and H3.5 complemented for their respective replicative counterparts. However, macroH2A1 failed to complement and its expression was toxic in yeast, negatively interacting with native yeast histones and kinetochore genes. To isolate yeast with “macroH2A1 chromatin” we decoupled the effects of its macro and histone fold domains, which revealed that both domains sufficed to override native yeast nucleosome positioning. Furthermore, both modified constructs of macroH2A1 exhibited lower nucleosome occupancy that correlated with decreased short-range chromatin interactions (<20 Kb), disrupted centromeric clustering, and increased chromosome instability. While supporting viability, macroH2A1 dramatically alters chromatin organization in yeast, leading to genome instability and massive fitness defects.
Linked CD4+/CD8+T cell neoantigen vaccination overcomes immune checkpoint blockade resistance and enables tumor regression
Authors: Dolina Joseph S. , Lee Joey , Brightman Spencer E. , McArdle Sara , Hall Samantha M. , Thota Rukman R. , Lanka Manasa , Premlal Ashmitaa Logandha Ramamoorthy , Greenbaum Jason A. , Cohen Ezra E.W. , Peters Bjoern , Schoenberger Stephen P.
Published: May 2023

Therapeutic benefit to immune checkpoint blockade (ICB) is currently limited to the subset of cancers thought to possess a sufficient tumor mutational burden (TMB) to allow for the spontaneous recognition of neoantigens (NeoAg) by autologous T cells. We explored whether the response of an aggressive low TMB squamous cell tumor to ICB could be improved through combination immunotherapy using functionally defined NeoAg as targets for endogenous CD4+and CD8+T cells. We found that, whereas vaccination with CD4+or CD8+NeoAg alone did not offer prophylactic or therapeutic immunity, vaccines containing NeoAg recognized by both subsets overcame ICB resistance and led to the eradication of large established tumors that contained a subset of PD-L1+tumor-initiating cancer stem cells (tCSC), provided the relevant epitopes were physically linked. Therapeutic CD4+/CD8+T cell NeoAg vaccination produced a modified tumor microenvironment (TME) with increased numbers of NeoAg-specific CD8+T cells existing in progenitor and intermediate exhausted states enabled by combination ICB-mediated intermolecular epitope spreading. The concepts explored herein should be exploited for the development of more potent personalized cancer vaccines that can expand the range of tumors treatable with ICB.
Apoptotic signaling clears engineeredSalmonellain an organ-specific manner
Authors: Abele Taylor J. , Billman Zachary P. , Li Lupeng , Harvest Carissa K. , Bryan Alexia K. , Magalski Gabrielle R , Lopez Joseph P , Larson Heather N. , Yin Xiao-Ming , Miao Edward A.
Published: May 2023

Pyroptosis and apoptosis are two forms of regulated cell death that can defend against intracellular infection. Although pyroptosis and apoptosis have distinct signaling pathways, when a cell fails to complete pyroptosis, backup pathways will initiate apoptosis. Here, we investigated the utility of apoptosis compared to pyroptosis in defense against an intracellular bacterial infection. We previously engineeredSalmonella entericaserovar Typhimurium to persistently express flagellin, and thereby activate NLRC4 during systemic infection in mice. The resulting pyroptosis clears this flagellin-engineered strain. We now show that infection of caspase-1 or gasdermin D deficient macrophages by this flagellin-engineeredS. Typhimurium induces apoptosis in vitro. Additionally, we also now engineerS. Typhimurium to translocate the pro-apoptotic BH3 domain of BID, which also triggers apoptosis in macrophages in vitro. In both engineered strains, apoptosis occurred somewhat slower than pyroptosis. During mouse infection, the apoptotic pathway successfully cleared these engineeredS.Typhimurium from the intestinal niche, but failed to clear the bacteria from the myeloid niche in the spleen or lymph nodes. In contrast, the pyroptotic pathway was beneficial in defense of both niches. In order to clear an infection, distinct cell types may have specific tasks that they must complete before they die. In some cells, either apoptotic or pyroptotic signaling may initiate the same tasks, whereas in other cell types these modes of cell death may lead to different tasks that may not be identical in defense against infection. We recently suggested that such diverse tasks can be considered as different cellular “bucket lists” to be accomplished before a cell dies.
DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment
Authors: Baluszek Szymon , Kober Paulina , Rusetska Natalia , Wągrodzki Michał , Mandat Tomasz , Kunicki Jacek , Bujko Mateusz
Published: May 2023

Chordomas are rare tumors of notochord remnants, occurring mainly in the sacrum and skull base. In spite of slow growth, they are highly invasive what makes the treatment challenging. Because of low incidence the molecular background of chordomas is poorly recognized.

Our study aims to determine role of DNA methylation abnormalities in skull base chordomas including its role in deregulation of gene expression. We subjected 32 tumor and 4 normal nucleus pulposus (NP) samples to profiling of DNA methylation with EPIC microarrays and gene expression with RNAseq.

Genome-wide DNA methylation analysis showed two distinct chordoma clusters (subtypes C and I) with different patterns of aberrant DNA methylation. C Chordomas are characterized by general hypomethylation with hypermethylation of CpG islands, while I chordomas are generally hypermethylated. These differences were reflected by distinct distribution of differentially methylated probes (DMPs). Differentially methylated regions were determined in each chordoma subtype indicating aberrant methylation in known tumor-related genes and regions encoding small RNAs in C chordomas. Correlation between methylation and expression was observed in minority of these genes. Upregulation ofTBXTin chordomas appeared related to lower methylation at tumor-specific DMR in gene promoter.

Gene expression-based clusters of tumor samples did not overlap with DNA methylation subtypes. Nevertheless, the subtypes substantially differ in transcriptomic profile that shows immune activation in I chordomas and enhanced proliferation in C chordomas. Immune enrichment in chordomas I was confirmed with deconvolution methods (cohesively based on methylation and transcriptomic data). Copy number analysis showed higher chromosomal instability in C chordomas. All but one have 9p deletion (CDKN2A/B) and downregulation of genes encoded in related chromosomal band. No significant difference in patients’ survival was observed between tumor subtypes, however, shorter survival was observed in patients with higher number of copy number alterations.