bluuebunny/crossref_metadata_2025 huggingface dataset:
Increasing emergency department referral of chest pain patients for non-invasive cardiac testing does not improve two-year clinical outcomes
Authors: Mark Dustin G. , Huang Jie , Ballard Dustin W. , Vinson David R. , Rana Jamal S. , Sax Dana R. , Rauchwerger Adina S. , Reed Mary E. ,   the Kaiser Permanente CREST Network Investigators
Published: August 2023

Background

Non-invasive cardiac testing (NICT) has been associated with decreased long-term risks of major adverse cardiac events (MACE) among emergency department (ED) patients at high coronary risk. It is unclear whether this association extends to patients without evidence of myocardial injury on initial electrocardiogram and cardiac troponin testing.

Methods

Retrospective cohort study of patients presenting with chest pain between 2013-2019 to 21 EDs within an integrated health care system, excluding patients with ST-elevation myocardial infarction or myocardial injury by serum troponin testing. To account for confounding by indication, we grouped patient encounters by the NICT referral rate of the initially assigned emergency physician, relative to local peers within discrete time periods. The primary outcome was MACE within two years. Secondary outcomes were coronary revascularization and MACE inclusive of all-cause mortality (MACE-ALL). Associations between NICT referral group (low, intermediate, or high) and outcomes were assessed using risk-adjusted proportional hazards methods with censoring for competing events.

Results

Among 144,577 eligible patient encounters, 30-day NICT referral was 13.0%, 19.9% and 27.8% in low, intermediate, and high NICT referral groups, respectively, with good balance of baseline covariates between groups. Compared with the low group, there was no significant decrease in the adjusted hazard ratio (aHR) of MACE within the intermediate (aHR 1.08, 95% CI 1.02-1.14, adjusted p = 0.024) or high (aHR 1.05, 95% CI 0.99-1.11, adjusted p = 0.13) NICT referral groups. Results were similar for MACE-ALL and coronary revascularization, as well as subgroup analyses stratified by estimated risk (HEART score; 48.2% low-risk, 49.2% moderate-risk, 2.7% high-risk).

Conclusion

Increased NICT referral was not associated with a decreased hazard of MACE within two years following ED visits for chest pain without evidence of acute myocardial injury. These findings further highlight the need for evidence-based guidance regarding appropriate use of NICT in this population.

What is Known

In emergency department patients with chest pain but no evidence of acute myocardial injury, referral for non-invasive cardiac testing is not associated with improved outcomes within 6 to 12 months.

There is some evidence that non-invasive cardiac testing may improve longer-term outcomes, especially among patients at moderate to high risk of coronary disease.

What the Study Adds

Higher non-invasive cardiac testing was not associated with improved outcomes within two years following emergency department visits for chest pain, absent evidence of acute myocardial injury.

This finding was most evident among patients at low to moderate predicted coronary risk.
Linking cognitive integrity to working memory dynamics in the aging human brain
Authors: Monov G , Stein H , Klock L , Gallinat J , Kühn S , Lincoln T , Krkovic K , Murphy PR , Donner TH
Published: August 2023

Aging is accompanied by a decline of multiple cognitive capacities, including working memory: the ability to maintain information online for the flexible control of behavior. Working memory involves stimulus-selective neural activity, persisting after stimulus presentation in widely distributed cortical areas. Here, we unraveled the mechanisms of working memory in healthy older adults and patients with mild cognitive impairment (MCI), a condition associated with increased risk of developing dementia. We studied a sample of 19 older adults diagnosed with MCI and 20 older healthy controls using a combination of model-based behavioral psychophysics, neuropsychological assessment, and magnetoencephalographic (MEG) recordings of brain activity. Twenty-one younger healthy adults were studied with model-based behavioral psychophysics only. All subjects performed a visuo-spatial delayed-match-to-sample working memory task under systematic manipulation of the temporal delay and the spatial distance between successively presented sample and test stimuli. We developed a computational model of the latent dynamics underlying task behavior and fit this to individual behavior. In the model, working memory representations diffused over time, a threshold was applied to produce a match/non-match decision about sample and test locations, and occasional lapses produced random decisions. For the older participants, we related the individual model parameters to a summary measure of individual cognitive integrity obtained from a large neuropsychological test battery, as well as to cortical MEG activity during the delay interval of the working memory task. For all groups, task accuracy decreased with delay duration and sample-test distance. When sample/test distances were small, older adults exhibited larger false alarm rates than younger adults. The behavioral effects were well captured by the model, which explained the age-related differences in terms of a deterioration of the quality of working memory representations, rather than differences in task strategy (i.e., threshold parameter). Task accuracy as well as the parameters governing behavioral stochasticity (diffusion noise and lapse rate combined) were correlated with overall cognitive integrity in the MCI group, but not in the older healthy controls. Individual task accuracy and stochasticity parameters (diffusion noise and lapse rate) were also correlated with stimulus-selective cortical activity during the delay interval, as assessed by decoding of the MEG signals, corroborating their validity as markers of cortical working memory mechanisms. Our findings provide insight into the mechanistic basis of aging-related changes in working memory maintenance and reveal a link between individual working memory dynamics and cognitive integrity in MCI.
Parallel trophic diversifications in polyploid cyprinid fish from East Africa: from preadaptive polymorphism to trophic specialization
Authors: Levin Boris A. , Komarova Aleksandra S. , Tiunov Alexei V. , Golubtsov Alexander S.
Published: August 2023

Trophic diversification is one of the main mechanisms driving the adaptive radiation. The polyploid lineage of the cyprinid genusLabeobarbusrepresent an excellent model for studying the trophically-based adaptive radiation in either lacustrine or riverine environments. Recently discovered four diversifications in rivers of the Ethiopian Highlands (East Africa) demonstrate independently evolved repeated mouth polymorphisms each represented by four core mouth phenotypes: (i) generalized, (ii) thick-lipped, (iii) scraping, and iv) large-mouthed. Mouth phenotypes in some radiations can be further divided to subtypes representing from four to eight sympatric ecomorphs. Using the stable isotope and gut content analyses we tested hypothesis on trophic resource partitioning within each radiation, revealed disparity in degree of diversification between radiations and tried to reconstruct the process of trophic diversification. Three of four radiations demonstrated partitioning of trophic resources within five trophic niches: i) detritophagy, ii) macrophytophagy, iii) invertivorous benthophagy, iv) periphyton feeding, and v) piscivory. The studied riverine radiations were likely at the different stages of the diversification. One radiation having a similar set of mouth phenotypes was not trophically divergent displaying a remarkable decouple of form and function. A unique case of ecologically non-functional mouth polymorphism at an incipient stage of trophic diversification supports a concept of the plasticity-first evolution. This phenomenon stems from the pre-existing genomic templates of mouth polymorphism ancestrally inherited upon the allopolyploid origin of theLabeobarbuslineage. The predetermined and preadaptive mouth polymorphism can be considered a key innovation of theLabeobarbusthat promoted to resource-based diversification via adaptive radiation.
An extracellular vesicle delivery platform based on the PTTG1IP protein
Authors: Perez Carla Martin , Liang Xiuming , Gupta Dhanu , Conceição Mariana , Mäger Imre , Andaloussi Samir EL , Wood Matthew J.A. , Roberts Thomas C.
Published: August 2023

Extracellular vesicles (EVs) hold great promise as therapeutic delivery vehicles, although their potential is limited by a lack of efficient EV engineering strategies to enhance loading and functional delivery of therapeutic cargo. Here, we identified N-glycosylation as a putative EV- sorting feature using a novel bioinformatics analysis strategy. We exploited this finding to develop a platform for EV-mediated delivery of macromolecular cargoes based on PTTG1IP, a small N- glycosylated, single spanning transmembrane protein. We demonstrate that PTTG1IP EV enrichment is dependent on its N-glycosylation at two sites, and that PTTG1IP is a suitable scaffold for EV loading of therapeutic cargoes. To achieve functional delivery, cargoes were fused to PTTG1IP, separated by various self-cleaving sequences intended to promote cargo release from the scaffold after EV loading. In addition, the fusogenic VSVG protein was co-expressed to enhance endosomal escape. This PTTG1IP-based strategy enabled highly efficient functional delivery of Cre protein to recipient cells and mouse xenograft tumors, as well as Cas9 and Cas9/sgRNA complex delivery to reporter cells. Importantly, PTTG1IP exhibited improved protein delivery potential relative to a scaffold based on CD63 (a common EV marker). Moreover, we developed various PTTG1IP variants with improved properties, demonstrating the versatility of PTTG1IP as an EV scaffold. The EV-loading platform described in this study offers significant advantages over other strategies, such as favourable membrane topology, the potential for further engineering, and functional delivery capability, which will enable the development of improved EV-based therapeutics.
Consensus prediction of cell type labels with popV
Authors: Ergen Can , Xing Galen , Xu Chenling , Jayasuriya Michael , McGeever Erin , Pisco Angela Oliveira , Streets Aaron , Yosef Nir
Published: August 2023

Cell-type classification is a crucial step in single-cell analysis. To facilitate this, several methods have been proposed for the task of transferring a cell-type label from an annotated reference atlas to unannotated query data sets. Existing methods for transferring cell-type labels lack proper uncertainty estimation for the resulting annotations, limiting interpretability and usefulness. To address this, we propose popular Vote (popV,https://github.com/YosefLab/popV), an ensemble of prediction models with an ontology-based voting scheme. PopV achieves accurate cell-type labeling and provides effective uncertainty scores. In multiple case studies, popV confidently annotates the majority of cells while highlighting cell populations that are challenging to annotate. This additional step helps to reduce the load of manual inspection, which is often a necessary component of the annotation process, and enables one to focus on the most problematic parts of the annotation, streamlining the overall annotation process.
Longevity Bottlenecks
Authors: Florea Michael , Hamalainen Mark , Seebold Patrick , Cheng Nathan , Murray Paul , Colville Alex James , Zheng Sally , Ingham Dylan , Kantelal Ridhi , De Sicilia Rose ,   (Longevity Biotech Fellowship consortium)
Published: August 2023

The longevity field has received an influx of capital and talent over the past 5 years, but it is unclear where directing these resources would result in the biggest positive impact. We aimed to establish a systematic, rigorous and unbiased way to identify the areas where increased investment would accelerate progress across the whole longevity field the most. To do so, we surveyed ∼400 participants across various sectors of longevity, asking them to 1) identify the major bottlenecks they are experiencing, 2) list their most needed solution, and 3) rate the potential efficacy and barriers to development of various aging intervention strategies. We built a classification system of Bottlenecks and Solutions based on grouping related answers and found the most frequently listed bottlenecks to be 1) lack of validated aging biomarkers; 2) an overall lack of funding; and 3) lack of good models for aging studies. Surprisingly, the most wanted solution was greater availability of large public datasets. Indeed, a common theme across all answers was the need for a new data-centric structure of scientific research, where large datasets are routinely gathered and made available, access walls are removed, protocols are standardized, negative and unpublished data are shared, and AI systems are released on the data for automated discovery. Finally, a lack of regulatory clarity was listed as the biggest barrier to development across all interventions, whereas cellular reprogramming, organ replacement, and genetic medicine (gene therapies and gene editing) were perceived as the intervention strategies with the highest potential for increasing healthy lifespan. We provide these data as a resource for funding agencies, philanthropists, entrepreneurs and newcomers to the field as a means to identify high impact areas to fund and work on.

Key takeaways

395 Participants were surveyed for their biggest bottlenecks and most needed solutions

Top Bottlenecks: lack of Validated Biomarkers; Overall lack of Funding and Slow & Expensive Models.

Top proposed Solutions: more Public Datasets; improved Regulatory Path; and Overall More Funding.

Bottlenecks and Solutions vary substantially across industry areas.

Rapamycin and calorie restriction are perceived as the most efficacious interventions in the near term.

Somatic reprogramming, organ replacement, and genetic medicine are perceived as the most efficacious interventions in the long term (25 years).

Sirtuin and NAD targeting therapies are seen as the least efficacious interventions in all time-frames.

Across all interventions, Regulatory Issues are perceived as the most severely inhibiting factor in the development of the intervention.
Hippocampal hub failure is linked to long-term memory impairment in anti-NMDA-receptor encephalitis - Insights from structural connectome graph theoretical network analysis
Authors: Hechler André , Kuchling Joseph , Müller-Jensen Leonie , Klag Johanna , Paul Friedemann , Prüss Harald , Finke Carsten
Published: August 2023

Introduction

Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is characterized by distinct structural and functional brain alterations, predominantly affecting the medial temporal lobes and the hippocampus. Structural connectome analysis with graph-based investigations of network properties allows for an in-depth characterization of global and local network changes and their relationship with clinical deficits in NMDAR encephalitis.

Objective

To investigate changes in structural connectivity and network efficiency in NMDAR encephalitis by use of probabilistic whole-brain tractography and graph theoretical analysis of structural brain networks.

Methods

Structural networks from sixty-one NMDAR encephalitis patients in the post-acute stage (median time from acute hospital discharge: 18 months) and sixty-one age- and sex-matched healthy controls (HC) were analyzed using diffusion-weighted imaging (DWI)-based probabilistic anatomically-constrained tractography and spherical deconvolution-informed filtering of tractograms. We calculated global, modular, and nodal graph measures indicative of structural connectivity and network reorganization with special focus on default-mode network, medial temporal lobe, and hippocampus. Pathologically altered metrics were included in multiple regression analyses to investigate their potential association with clinical course, disease severity, and cognitive outcome.

Results

Patients with NMDAR encephalitis showed regular global graph metrics, but bilateral reductions of hippocampal node strength (left:p=0.049; right:p=0.013) and increased node strength of right precuneus (p=0.013) compared to HC. Betweenness centrality was decreased for left-sided entorhinal cortex (p=0.042) and left caudal middle frontal gyrus (p = 0.037). Correlation analyses showed a significant association between reduced left hippocampal node strength and verbal long-term memory impairment (p=0.021)

Conclusion

Focal network property changes of the medial temporal lobes indicate hippocampal hub failure that is associated with memory impairment in NMDAR encephalitis at the post-acute stage, while global structural network properties remain unaltered. Graph theory analysis provides new pathophysiological insight into structural network changes and their association with persistent cognitive deficits in NMDAR encephalitis.
Partial Anchored Capture and Long-Read Sequencing (PACLseq) Enable a Stand-alone Diagnostic Method for Ph-like Acute Lymphoblastic Leukemia
Authors: Zhang Hang , Yu Huan , Chen Yanmei , Jiang Kai , Huo Beibei , Li Jialin , Liu Ting , Xie Dan
Published: August 2023

Fusion genes play a crucial role in the development of Philadelphia chromosome–like acute lymphoblastic leukemia (Ph-like ALL). Timely and accurate determination of malgenic fusion transcripts that cause Ph-like ALL is essential for guiding treatment decisions. However, due to the complexity of possible gene fusion combination of Ph-like ALL, prevailing molecular diagnostic methods for Ph-like ALL are inefficient and lack of standardization, resulting in a slow diagnostic process. We introduce Partial Anchored Capture and Long-Read Sequencing (PACLseq), a nanopore-sequencing-technology-based approach, which enables fast stand-alone identification of fusion genes with a mere 10ng of input RNA. With extensive testing using BCR-ABL1 standards and 47 clinical samples to validate the efficacy of PACLseq, we demonstrated that PACLseq performs excellently in target region coverage and fusion gene detection accuracy, achieving a sensitivity of 93.33% and specificity of 100%. These findings highlight the reliability and versatility of PACLseq as a streamlined method for the clinical diagnosis of Ph-like ALL. By offering rapid and accurate fusion gene detection, PACLseq has the potential to significantly improve diagnostic efficiency, facilitate timely treatment decisions, and enhance patient outcomes in the management of Ph-like ALL.
Nigral volume loss in prodromal, early, and moderate Parkinson’s disease
Authors: Langley Jason , Hwang Kristy S. , Huddleston Daniel E. , Hu Xiaoping P.
Published: August 2023

The loss of melanized neurons in the substantia nigra pars compacta (SNc) is a hallmark pathology in Parkinson’s disease (PD). Melanized neurons in SNc can be visualizedin vivousing magnetization transfer (MT) effects. Nigral volume was extracted in data acquired with a MT-prepared gradient echo sequence in 33 controls, 83 non-manifest carriers (42 LRRK2 and 41 GBA nonmanifest carriers), 65 prodromal hyposmic participants, 105de novoPD patients and 26 48-month PD patients from the Parkinson’s Progressive Markers Initiative. No difference in nigral volume was seen between controls and LRRK2 and GBA non-manifest carriers (F=0.076;P=0.927). A significant main effect in group was observed between controls, prodromal hyposmic participants, and overt PD patients (F=5.192;P=0.002). Longer disease duration significantly correlated with lower nigral volume (r=-0.252;P=0.010). This study shows that nigral depigmentation can be robustly detected in prodromal hyposmic participants and overt PD patients.
Protocol on Establishing a National Disease Registry – Swiss Pediatric Inflammatory Brain Disease Registry
Authors: Hulliger Lorena Freya , Tscherter Anne , Kühni Claudia , Bigi Sandra
Published: August 2023

Background

Pediatric-onset inflammatory brain diseases are a group of potentially life-threatening central nervous system disorders. Overall, pediatric-onset inflammatory brain diseases are rare and therefore difficult to study. Patient registries are well suited to study the natural history of (rare) diseases and have markedly advanced the knowledge on pediatric-onset inflammatory brain diseases in other countries. Following their example, we established a national pediatric-onset inflammatory brain disease registry in Switzerland (Swiss-Ped-IBrainD).

Aims

The Registry aims to describe epidemiology, demographics, diagnostics, management, and treatment, since these areas remain understudied in Switzerland. Additionally, we want to promote research by fostering the knowledge exchange between study centers and setting up studies such as national quality of life surveys. We further aim to facilitate the access to national and international studies for patients with a pediatric-onset inflammatory brain disease living and/or treated in Switzerland.

Methods

The Swiss-Ped-IBrainD is a multicentric, population-based, observational cohort study (IRB number: 2019-00377) collaborating with 11 neuropediatric centers in Switzerland. Patient screening, information and recruitment is mainly conducted by the local principal investigators. The data collection is organized centrally by the Executive Office of the registry. The collected data is purely observational. Medical records are the primary data source. All patients who have been diagnosed with a pediatric-onset inflammatory brain disease since 2005 are eligible. We aim to include all pediatric-onset inflammatory brain disease patients living and/or treated in Switzerland who meet the inclusion criteria. Considering existing literature and our single-center experience we anticipate 300-400 eligible patients.

Status

Currently, all 11 neuropediatric centers have been initiated and are recruiting. As of the first of May 2023, we have identified 275 eligible participants and obtained informed consent from 101 patients and/or families. None of the informed patients and/or families have refused participation.
The effect of recall period on reported out-of-pocket health expenditure in Ghana
Authors: Agorinya Isaiah Awintuen , Ross Amanda , Flores Gabriela , Akazili James , Edejer Tessa Tan-torres , van Wilgenburg Kim , Dalaba Maxwell , Mensah Nathan , Lan Le My , Bacha YadetaDassie , Sumboh Jemima , Tediosi Fabrizio
Published: August 2023

Background

Out-of-pocket health payments (OOPs) are a key indicator of health financing systems’ performance. Measuring OOPs through household surveys is challenging and yet it is the primary source of information in the absence of comprehensive data on user charges in the public sector and market data from the private sector. The choice of the recall period has been identified as a source of bias in previous studies. This study investigates the effect of two different types of recall periods on the agreement between OOPs reported by households and providers.

Methods

Households were sampled for the community survey from the Navrongo Health and Demographic Surveillance System, Ghana. Two versions of a health expenditure module were developed differing only in the recall periods, “shorter recall periods”2weeks for medicines and outpatient care, 3monthsfor preventive care and 6months for inpatient care and medical products. The longer recall periods were 4 weeks, 6months and 12months.Households from both community and provider sampling were randomly assigned to the two questionnaires. The providers included the hospital, one clinic and health facilities and drug shops in the area. We estimated the ratio between the overall mean household OOPs and overall mean provider OOPs. We assessed agreement between the individual matched household-provider OOPs using the Bland-Altman analysis.

Findings

The short and long recall period versions of the questionnaires were administered to746 and 480 households with matching success to provider records of 72% and 84%, respectively. The most common spending categories were inpatient care and medicines in this sample. The overall mean OOPs reported by the households were higher than provider records for both recall periods. For matched household-provider data, there was no evidence of a difference in the agreement between the household and provider OOPs for inpatient care, the ratio of household to provider for the 12 months recall was estimated to be 0.74 (95% CI 0.45, 1.19; p=0.22) that of the ratio of household to provider for the 6-month period, where less than 1 indicates better agreement. For medicines, the ratio of 4 weeks to 2 weeks was 1.26 (0.93, 1.39; p=0.39).

Conclusion

There were considerable challenges in using provider data to assess the accuracy of reported OOPs in this setting. There was no evidence from this study that the agreement between household and provider data differed by recall period, however the confidence intervals of the effect were wide, and an effect cannot be ruled out.
A thrombus is formed by a gradient of platelet activation and procoagulant endothelium
Authors: Carminita Estelle , Tourn Julie , Crescence Lydie , Brouilly Nicolas , Merrill-Skoloff Glenn , Mazharian Alexandra , Dubois Christophe , Panicot-Dubois Laurence
Published: August 2023

Introduction

The contribution of platelets in thrombosis within microcirculation has been extensively documented in the literature. We previously showed,in vivo,that platelet activation revealed by intracellular calcium mobilization was a crucial step in the growth of thrombi following laser-induced injury, a model of thromboinflammation.

Aim

We employed a multimodal, correlative microscopy approach and computational biology to investigate the extent of platelet activation and the spatial distribution of platelets throughout a growing thrombus.

Results

We observed a reversible intracellular platelet calcium mobilization that correlates with the time a platelet resides during thrombus growth. Our bioinformatics analysis displayed three distinct platelet subpopulations resident within a thrombus:(1)resting,(2)partially activated, and(3)“fully” activated platelets. The spatial distribution of the platelet subpopulations in the thrombus creates a double gradient in both the transversal and longitudinal axis, with the maximal percentage of fully activated platelets close to the site of injury. However, these activated platelets did not express negative phospholipids. The injured endothelium was identified to play a vital role in activating the blood coagulation cascade in this model of thrombosis.

Conclusion

Following a laser-induced injury, thrombi are formed by a gradient of activated platelets from the injury site to the periphery of the thrombus. These different activation states of platelets throughout the thrombi regulate the biomechanics of the thrombus. The injured endothelium, rather than platelets, was identified to play a key role in the activation of the blood coagulation cascade in this model of thromboinflammation.

Essentials

Computational biology was used to analyze thrombosis.

Non-activated, low- and fully-activated platelets are part of a thrombus.

The activation of the platelets forms a gradient from the site of injury to the periphery.

The endothelium, and not platelets, expressed negative phospholipids.

Graphical abstract

A thrombus is formed by a gradient of platelet activation and procoagulant endothelium
Acylation of MLKL impacts its function in necroptosis
Authors: Pradhan Apoorva J. , Chitkara Shweta , Ramirez Ricardo X. , Monje-Galvan Viviana , Sancak Yasemin , Atilla-Gokcumen G. Ekin
Published: August 2023

Mixed lineage kinase domain-like (MLKL) is a key signaling protein of necroptosis. Upon activation by phosphorylation, MLKL translocates to the plasma membrane and induces membrane permeabilization which contributes to the necroptosis-associated inflammation. Membrane binding of MLKL is initially initiated by the electrostatic interactions between the protein and membrane phospholipids. We previously showed that MLKL and its phosphorylated form (pMLKL) areS-acylated during necroptosis. Here, we characterize acylation sites of MLKL and identify multiple cysteines that can undergo acylation with an interesting promiscuity at play. Our results show that MLKL and pMLKL undergo acylation at a single cysteine, C184, C269 and C286 are the possible acylation sites. Using all atom molecular dynamic simulations, we identify differences that the acylation of MLKL causes at the protein and membrane level. Through systematic investigations of theS-palmitoyltransferases that might acylate MLKL in necroptosis, we showed that zDHHC21 activity has the strongest effect on pMLKL acylation, inactivation of which profoundly reduced the pMLKL levels in cells and improved membrane integrity. These results suggest that blocking the acylation of pMLKL destabilizes the protein at the membrane interface and causes its degradation, ameliorating necroptotic activity. At a broader level, our findings shed light on the effect ofS-acylation on MLKL functioning in necroptosis and MLKL-membrane interactions mediated by its acylation.
Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain inC. crescentus
Authors: Ahmed Yasin M , Bowman Grant R
Published: August 2023

Asymmetric cell division in bacteria is achieved through cell polarization, where regulatory proteins are directed to specific cell poles. Curiously, both poles contain a membraneless microdomain, established by the polar assembly hub PopZ, through most of the cell cycle, yet many PopZ clients are unipolar and transiently localized. We find that PopZ’s interaction with the response regulator CpdR is controlled by phosphorylation, via the histidine kinase CckA. Phosphorylated CpdR does not interact with PopZ and is not localized to cell poles. At poles where CckA acts as a phosphatase, de-phosphorylated CpdR binds directly with PopZ and subsequently recruits ClpX, substrates, and other members of a protease complex to the cell pole. We also find that co-recruitment of protease components and substrates to polar microdomains enhances their coordinated activity. This study connects phosphosignaling with polar assembly and the activity of a protease that triggers cell cycle progression and cell differentiation.
Genome-wide Bioinformatics Analysis of Human Protease Specificity Identified Potential Cathepsin L Cleavage Site at K790 Position of the SARS-CoV-2 Spike Glycoprotein
Authors: Matveev Eugenii V. , Ponomarev Gennady V. , Kazanov Marat D.
Published: August 2023

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) primarily enters the cell by binding the virus’s spike (S) glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor on the cell surface, followed by proteolytic cleavage by host proteases. Studies have identified furin and TMPRSS2 proteases in priming and triggering cleavages of the S glycoprotein, converting it into a fusion-competent form and initiating membrane fusion, respectively. Alternatively, SARS-CoV-2 can enter the cell through the endocytic pathway, where activation is triggered by lysosomal cathepsin L. However, other proteases are also suspected to be involved in both entry routes. In this study, we conducted a genome-wide bioinformatics analysis to explore the capacity of human proteases in hydrolyzing peptide bonds of the S glycoprotein. Predictive models of sequence specificity for 169 human proteases were constructed and applied to the S glycoprotein together with the method for predicting structural susceptibility to proteolysis of protein regions. After validating our approach on extensively studied S2’ and S1/S2 cleavage sites, we applied our method to each peptide bond of the S glycoprotein across all 169 proteases. Our results indicate that various members of the PCSK, TTSP, and kallikrein families, as well as specific coagulation factors, are capable of cleaving S2’ or S1/S2 sites. We have also identified a potential cleavage site of cathepsin L at the K790 position within the S2’ loop. Structural analysis suggests that cleavage of this site induces conformational changes similar to the cleavage at the R815 (S2’) position, leading to the exposure of the fusion peptide and subsequent fusion with the membrane. Other potential cleavage sites and the influence of mutations in common SARS-CoV-2 variants on proteolytic efficiency are discussed.
Striatal dopamine release reflects a domain-general prediction error
Authors: Costa Kauê Machado , Raheja Nishika , Mirani Jash , Sercander Courtney , Schoenbaum Geoffrey
Published: August 2023

Dopamine is classically thought to drive learning based on errors in the prediction of rewards and punishments1. However, animals also learn to predict cues with no intrinsic value2, and it is unclear if such latent learning also relies on dopaminergic prediction errors. Here, we tested this by recording dopamine release in the nucleus accumbens and dorsomedial striatum while rats executed a sensory preconditioning task that incorporates both types of learning3. We found that dopamine release in both regions correlated with errors in predicting value-neutral cues during latent learning and with errors in predicting reward during reward-based conditioning. Moreover, dopamine in the nucleus accumbens reflected inferred value in the probe test, supported by orbitofrontal cortex activity. Our findings suggest that dopamine signals a domain- general, multi-factorial prediction error, capable of supporting model-based learning.
No evidence for enhanced disease with polyclonal SARS-CoV-2 antibody in the ferret model
Authors: Reed Douglas S. , McElroy Anita K. , Barbeau Dominique J. , McMillen Cynthia M. , Tilston-Lunel Natasha L. , Nambulli Shamkumar , Cottle Emily , Gilliland Theron C. , Rannulu Hasala , Lundy Jeneveve , Olsen Emily L. , O’Malley Katherine J. , Xia Mengying , Hartman Amy L. , Luke Thomas C , Egland Kristi , Bausch Christoph , Wu Hua , Sullivan Eddie J. , Klimstra William B. , Duprex W. Paul
Published: August 2023

Since SARS-CoV-2 emerged in late 2019, it spread from China to the rest of the world. An initial concern was the potential for vaccine- or antibody-enhanced disease (AED) as had been reported with other coronaviruses. To evaluate this, we first developed a ferret model by exposing ferrets to SARS-CoV-2 by either mucosal inoculation (intranasal/oral) or inhalation using a small particle aerosol. Mucosal inoculation caused a mild fever and weight loss that resolved quickly; inoculation via either route resulted in virus shedding detected in the nares, throat, and rectum for 7-10 days post-infection. To evaluate the potential for AED, we then inoculated groups of ferrets intravenously with 0.1, 0.5, or 1 mg/kg doses of a human polyclonal anti-SARS-CoV-2 IgG from hyper-immunized transchromosomic bovines (SAB-185). Twelve hours later, ferrets were challenged by mucosal inoculation with SARS-CoV-2. We found no significant differences in fever, weight loss, or viral shedding after infection between the three antibody groups or the controls. Signs of pathology in the lungs were noted in infected ferrets but no differences were found between control and antibody groups. The results of this study indicate that healthy, young adult ferrets of both sexes are a suitable model of mild COVID-19 and that low doses of specific IgG in SAB-185 are unlikely to enhance the disease caused by SARS-CoV-2.
Phospholipase A2activity is required for immune defense of European (Apis mellifera) and Asian (Apis cerana) honeybees against the American foulbrood pathogen,Paenibacillus larvae
Authors: Jin Gahyeon , Hrithik Md Tafim Hossain , Mandal Eeshita , Kil Eui-Joon , Jung Chuleui , Kim Yonggyun
Published: August 2023

Honeybees require a functioning immune system to defend against microbial pathogens. The American foulbrood pathogen,Paenibacillus larvae, is lethal to honeybees and one of the main causes of colony collapse. This study investigated the immune responses ofApis melliferaandApis ceranahoneybees against the bacterial pathogenP. larvae. Both species of honeybee larvae exhibited significant mortalities even at 102∼ 103cfu/mL ofP. larvaeby diet-feeding, althoughA. melliferaappeared to be more tolerant to the bacterial pathogen thanA. cerana. Upon bacterial infection, the two honeybee species expressed both cellular and humoral immune responses. Hemocytes of both species exhibited characteristic spreading behaviors by cytoskeletal extension along with F-actin growth, and formed nodules uponP. larvaeinfection. Larvae of both species also expressed an antimicrobial peptide called apolipophorin III (ApoLpIII) in response to bacterial infection. However, these immune responses were significantly suppressed by a specific inhibitor to phospholipase A2(PLA2). Each honeybee genome encodes four PLA2genes (PLA2A∼PLA2D), representing four orthologous combinations between the two species. In response toP. larvaeinfection, both species significantly up-regulated PLA2enzyme activities and the expression of all four PLA2genes. To determine the roles of the four PLA2s in the immune responses, RNA interference (RNAi) was performed by injecting gene-specific double stranded RNAs (dsRNAs). All four RNAi treatments significantly suppressed the immune responses, and specific inhibition of the two secretory PLA2s (PLA2AandPLA2B) potently suppressed nodule formation andApoLpIIIexpression. These results demonstrate the cellular and humoral immune responses ofA. melliferaandA. ceranaagainstP. larvae. This study suggests that eicosanoids play a crucial role in mediating common immune responses in two closely related honeybees.
Spatial Transcriptomics Reveals Alterations in Perivascular Macrophage Lipid Metabolism: Insights into the onset of Wooden Breast Myopathy in Broiler Chickens
Authors: Wang Ziqing , Khondowe Paul , Brannick Erin , Abasht Behnam
Published: August 2023

This study aims to use spatial transcriptomics to characterize the cell-type-specific expression profile associated with the microscopic features observed in Wooden Breast myopathy. 1 cm3muscle sample was dissected from the cranial part of the right pectoralis major muscle from three randomly sampled broiler chickens at 23 days post-hatch and processed with Visium Spatial Gene Expression kits (10X Genomics), followed by high-resolution imaging and sequencing on the Illumina Nextseq 2000 system. WB classification was based on histopathologic features identified. Sequence reads were aligned to the chicken reference genome (Galgal6) and mapped to histological images. Unsupervised K-means clustering and Seurat integrative analysis differentiated histologic features and their specific gene expression pattern, including lipid laden macrophages (LLM), unaffected myofibers, myositis and vasculature. In particular, LLM exhibited reprogramming of lipid metabolism with up-regulated lipid transporters and genes in peroxisome proliferator-activated receptors pathway, possibly through CD36-mediated signaling. Moreover, overexpression of fatty acid binding protein 5 could enhance fatty acid uptake in adjacent veins. In myositic regions, increased expression of cathepsins may play a role in muscle homeostasis and repair by mediating lysosomal activity and apoptosis. A better knowledge of different cell-type interactions at early stages of WB is essential in developing a comprehensive understanding.
Method to Test Etiologic Heterogeneity Among Non-Competing Diagnoses that Accrue Over Time: Application to Discriminating the Impact of Perinatal Exposures on Autism and Attention Deficit Hyperactivity Disorder
Authors: Kalkbrenner Amy E. , Zheng Cheng , Yu Justin , Jenson Tara E. , Kuhlwein Thomas , Ladd-Acosta Christine , Grove Jakob , Schendel Diana
Published: August 2023

Background

Testing etiologic heterogeneity – whether a disorder subtype is more or less impacted by a risk factor, is important toward understanding causal pathways and optimizing statistical power. The study of mental health disorders especially benefits from strategic sub-categorization because these disorders are heterogenous and frequently co-occur. Existing methods to quantify etiologic heterogeneity are not appropriate for non-competing events in an open cohort of variable-length follow-up. Thus, we developed a new method.

Methods

We estimated risks from urban residence, maternal smoking during pregnancy, and parental psychiatric history, with subtypes defined by the presence or absence of a co-diagnosis: autism alone, attention deficit hyperactivity disorder (ADHD) alone, and joint diagnoses of autism+ADHD. To calculate the risk of a single diagnosis (e.g. autism alone), we subtracted the risk for autism+ADHD from the risk for autism overall. We tested the equivalency of average risk ratios over time, using a Wald-type test and bootstrapped standard errors.

Results

Urban residence was most strongly linked with autism+ADHD and least with ADHD only; maternal smoking was associated with ADHD only but not autism only; and parental psychiatric history exhibited similar associations with all subgroups.

Conclusions

Our method allowed the calculation of appropriate p values to test strength of association, showing etiologic heterogeneity wherein 2 of these 3 risk factors exhibited different impacts across diagnostic subtypes. The method used all available data, avoided neurodevelopmental outcome misclassification, exhibited robust statistical precision, and is applicable to similar heterogeneous complex conditions using common diagnostic data with variable follow-up.
Blunted glucocorticoid responsiveness to stress causes behavioral and biological alterations that lead to posttraumatic stress disorder vulnerability
Authors: Monari Silvia , Guillot de Suduiraut Isabelle , Grosse Jocelyn , Zanoletti Olivia , Walker Sophie E. , Mesquita Michel , Wood Tobias C. , Cash Diana , Astori Simone , Sandi Carmen
Published: August 2023

BACKGROUND

Understanding why only a subset of trauma-exposed individuals develop posttraumatic stress disorder (PTSD) is critical for advancing clinical strategies. A few behavioral (deficits in fear extinction) and biological (blunted glucocorticoid levels, small hippocampal size, and rapid-eye movement sleep (REMS) disturbances) traits have been identified as potential vulnerability factors. However, whether and to what extent these traits are interrelated and whether one of them could causally engender the others are not known.

METHODS

In a genetically selected rat model of reduced corticosterone responsiveness to stress, we explored PTSD-related biobehavioral traits usingex vivomagnetic resonance imaging, cued fear conditioning, and polysomnographic recordings combined within vivophotometric measurements.

RESULTS

We showed that genetic selection for blunted glucocorticoid responsiveness leads to a correlated multitrait response, including impaired fear extinction, small hippocampal volume, and REMS disturbances, supporting their interrelatedness. Fear extinction deficits and concomitant disruptions in REMS could be normalized through postextinction corticosterone administration, causally implicating glucocorticoid deficiency in two core PTSD-related risk factors and manifestations. Furthermore, reduced REMS was accompanied by higher norepinephrine levels in the hippocampal dentate gyrus that were also reverted by postextinction corticosterone treatment.

CONCLUSIONS

Our results indicate a predominant role for glucocorticoid deficiency over the contribution of reduced hippocampal volume in engendering both REMS alterations and associated deficits in fear extinction consolidation, and causally implicate blunted glucocorticoids in sustaining neurophysiological disturbances leading to fear extinction deficits.
Transcriptome analyses of mouse cardiac myocytes and non-cardiomyocytes: postmitotic vs. proliferative cells
Authors: Takenaka Yasuhiro , Hirasaki Masataka , Inoue Ikuo , Ikeda Masaaki , Ohata Hisayuki , Kakinuma Yoshihiko
Published: August 2023

Adult heart mostly contains long-lived postmitotic cardiomyocytes and non-cardiomyocytes that have proliferative potential. Here, we isolated cardiomyocytes and non-cardiomyocytes from young and aged mouse heart, and performed transcriptome analyses by RNA sequencing to understand the differences of gene expression in postmitotic and proliferative cells. Gene ontology analyses revealed that genes associated with inflammatory response were upregulated in aged cardiac myocytes, whereas genes including two ATP synthases in mitochondrial respiratory complex V (Atp5landAtp5J2) and two NADH dehydrogenases in complex I (Ndufa11andNdufv3) were significantly downregulated. In aged non-cardiomyocytes, genes related to inflammatory responses were also upregulated, while genes involved in cell cycle and DNA replication process were downregulated. We also found that the expression levels of some small nucleolar RNAs (snoRNAs) are decreased cardiomyocytes with aging. snoRNAs are deeply involved in RNA modification such as pseudouridylation stabilizing ribosomal RNA (rRNA) and mRNA splicing. Therefore, the age-related reduction in snoRNA expression may lead to the destabilization of rRNA, splicing dysfunction, and ultimately a decrease in protein synthesis capacity. A comparison with transcriptome results obtained for non-cardiomyocytes suggests that the decline in the expression of mitochondria-related genes and snoRNAs accompanying aging is specific to cardiomyocytes, implying their potential utility as one of novel aging markers in postmitotic cells.
Red light perception by the root is essential for gibberellin-induced primary-root elongation in tomato
Authors: Ramon Uria , Adiri Amit , Cheriker Hadar , Nir Ido , Burko Yogev , Weiss David
Published: August 2023

The promoting effect of gibberellin (GA) on primary-root elongation is well-documented in several plant species, yet its influence in others, including tomato (Solanum lycopersicum), remains unclear.

The role of GA in primary-root elongation has been studied in tomato using the GA-deficient mutantsgib-1andga20-oxidase(ga20ox1) and various growth systems, including Dark (D)-root and D-shoot plates.

GA application to these mutants following germination on vermiculite, promoted primary-root elongation. However, when the roots grew deeper into the dark environment the hormone had no effect. RNA-seq analysis of dark-grown roots, treated with GA, revealed typical transcriptional responses, but the output for cell expansion remained unaffected. When dark-grown roots were illuminated deep in the ground, the hormone promoted their elongation. The results suggest that activation of Phytochrome B (PhyB) in the root, by red light, is essential for GA-induced elongation.

We propose that GA promotes tomato root elongation after germination, when roots are exposed to low light underground and this contributes to rapid seedling establishment. As roots penetrate deeper into the soil, insensitivity to GA due to the lack of light may be important for sustained root growth under fluctuating water availability, given that water deficiency suppresses GA accumulation.