bluuebunny/crossref_metadata_2025 huggingface dataset:
Phospholipase D3 contributes to Alzheimer’s disease risk via disruption of Aβ clearance and microglia response to amyloid plaques
Authors: Rosene Matthew J. , Hsu Simon , You Shih Feng , Brase Logan , Verbeck Anthony , Martinez Rita , Wallace Clare E. , Li Zeran , Yan Ping , Dräger Nina M. , Sattler Sydney M. , Iyer Abhirami K , Macauley Shannon L , Holtzman David M. , Benitez Bruno A. , Kampmann Martin , Cruchaga Carlos , Harari Oscar , Cirrito John R. , Lee Jin-Moo , Goate Alison M. , Karch Celeste M.
Published: February 2022

Alzheimer’s disease (AD) is characterized by the accumulation of amyloid-β (Aβ) plaques and neurofibrillary tangles in the brain. AD is also the result of complex genetic architecture that can be leveraged to understand pathways central to disease processes. We have previously identified coding variants in the phospholipase D3 (PLD3) gene that double the late-onset AD risk. However, the mechanism by which PLD3 impacts AD risk is unknown. One AD risk variant, PLD3 p.A442A, disrupts a splicing enhancer-binding site and reduces PLD3 splicing in human brains. Using differentiated induced pluripotent stem cells from a PLD3 p.A442A carrier and CRISPR-reverted, isogenic control, we show that PLD3 p.A442A cortical neurons exhibit a PLD3 splicing defect and a significant increase in Aβ42 and Aβ40, both of which are corrected upon reversion of the risk allele in isogenic control neurons. Thus, PLD3 p.A442A is sufficient to alter PLD3 splicing and Aβ metabolism. While the normal function of PLD3 is poorly understood, PLD3 is highly expressed in neurons and brain regions most susceptible to amyloid pathology. PLD3 expression is significantly lower in AD brains than controls, suggesting that PLD3 may play a role in sporadic AD. Thus, we sought to determine whether PLD3 contributes to Aβ accumulation in AD. In a mouse model of amyloid accumulation, loss of Pld3 increases interstitial fluid (ISF) Aβ and reduces Aβ turnover. AAV-mediated overexpression of PLD3 in the hippocampus decreased ISF Aβ levels and accelerated Aβ turnover. To determine whether PLD3-mediated reduction of ISF Aβ impacts amyloid accumulation, we measured amyloid plaque abundance and size after significant Aβ deposition. We found that in the absence of Pld3, amyloid plaques were less compact and more diffuse. Additionally, we observed reduced recruitment of microglia to amyloid plaques in the absence of Pld3. PLD3 may impact amyloid accumulation and AD risk through disrupted microglia function as PLD3 is enriched in disease associated microglia in human brains. Together, our findings demonstrate that PLD3 regulates Aβ clearance through cell-autonomous and non-cell-autonomous pathways in a manner that likely contributes to AD risk.
Patterns of Medication Use and Prescription Fills for Cardioprotective Anti-Hyperglycemic Agents in the United States
Authors: Nargesi Arash A , Clark Callahan , Chen Lian , Liu Mengni , Reddy Abraham , Amodeo Samuel , Oikonomou Evangelos K , Suchard Marc A , McGuire Darren K , Lin Zhenqiu , Inzucchi Silvio , Khera Rohan
Published: February 2022

Importance

Selected glucagon-like peptide-1 receptor agonists (GLP-1RAs) and sodium glucose cotransporter-2 inhibitors (SGLT2i) have cardioprotective effects in patients with type 2 diabetes and elevated cardiovascular risk. Prescription of these agents by clinicians and their consistent use by patients are essential to realize their benefits.

Objective

To assess the patterns of use and prescription fills of GLP-1RAs and SGLT-2i.

Design

Cross-sectional for medication use and prospective for prescription fills in 2018-2020

Setting

Nationwide de-identified US administrative claims database of Medicare Advantage and commercially insured adults.

Participants

Individuals 18 years of age and older with type 2 diabetes

Exposures

Comorbidities representing guideline-directed indications of atherosclerotic cardiovascular disease (ASCVD) for GLP-1RAs, and ASCVD, heart failure, and diabetic nephropathy for SGLT2i.

Main Outcomes and Measures

Medication use and monthly fill rates for 12 months following initiation of therapy by calculating the proportion of days with consistent medication use.

Results

Among 587,657 individuals with type 2 diabetes, 80,196 (13.6%) were prescribed GLP-1RAs and 68,149 (11.5%) SGLT2i during 2018-2020. This represented 12.9% and 10.5% of individuals with indications for each medication, respectively. Based on monthly counts of new prescriptions, there were no changes in the uptake of either drug class during 2019-2020. Among new initiators, fill rate was 52.5% for GLP-1RAs and 52.9% for SGLT2i one year after initiation. One-year fill rates were higher for patients with commercial insurance than those with Medicare Advantage plans for both GLP-1RAs (59.3% vs 51.0%, p-value<0.001) and SGLT2i (63.4% vs 50.3%, p-value<0.001). After adjusting for comorbidity profile, there were higher prescription fills for patients with commercial insurance (versus Medicare Advantage, OR 1.17, 95% CI [1.06-1.29] for GLP-1RAs, and 1.59 [1.42-1.77] for SGLT2i); and higher income (top quartile versus others, OR 1.09 [1.06-1.12] for GLP-1RAs, and 1.06 [1.03-1.10] for SGLT2i).

Conclusions and Relevance

In 2018-2020, use of GLP-1RAs and SGLT2i remained limited to fewer than 1 in 8 individuals with type 2 diabetes meeting criteria for evidence-based guideline and professional society recommendations, with one-year fill rates around 50%. The low and inconsistent use of these medications compromises their longitudinal health outcomes benefits in a period of expanding indications for their use.
Comparison of BinaxNOW TM and SARS-CoV-2 qRT-PCR detection of the Omicron Variant from Matched Anterior Nares Swabs
Authors: Landaverde Lena , Turcinovic Jacquelyn , Doucette-Stamm Lynn , Gonzales Kevin , Platt Judy , Connor John H. , Klapperich Catherine M.
Published: February 2022

The COVID-19 pandemic has increased the use of rapid antigen tests such as the Abbott BinaxNOWTM COVID-19 Antigen Self-Test. In winter of 2021-2022, the omicron variant surge made it quickly apparent that although rapid diagnostic tests (RDTs) are less sensitive than qRT-PCR, the accessibility, ease of use, and rapid read-outs of RDTs made them a sought after and often sold-out item at local suppliers. Here, we sought to qualify the BinaxNOWTM test for use in our university testing program as a method to rule-in positive or rule-out negative individuals quickly when they seek care at our priority qRT-PCR testing site. To perform this qualification study, we collected matched additional swabs from individuals attending this test site for standard of care qRT-PCR testing. All matched swabs were tested using the BinaxNOWTM RDT. Initially as part of a feasibility study, test period 1 (n=110) samples were put in cold storage prior to testing. In follow-on test period (n=209), we tested samples real-time at the test facility. Combined, 102 of 319 samples tested positive for SARS-CoV-2. All samples for which genome sequence could be collected were omicron (n=92). We observed a calculated sensitivity of 53.9%, specificity of 100%, a positive predictive value (PPV) of 100%, and a negative predictive value (NPV) of 82.2% for the BinaxNOWTM tests (n=319). Sensitivity improved (75.3%) by changing the qRT-PCR positivity threshold from a CT of 40 to a CT of 30. The ROC curve shows that for qRT-PCR positive CT values between 24-40, the BinaxNOWTM test is of limited value diagnostically. Our results suggest that RDT tests could be used in our setting to confirm SARS-CoV-2 infection in individuals with substantial viral load, but that a significant fraction of infected individuals would be missed if we used RDT tests exclusively to rule out infection.
Number of plasma exchanges and outcome in myasthenic crisis
Authors: Hansen Michael , Neilson Lee , Parikh Melanie , Katirji Bashar
Published: February 2022

Background

Plasma exchange is an effective therapy for myasthenic crisis (MC); yet the number of exchanges needed is unknown. We set out to examine the relationship between the number of plasma exchanges and clinical outcome in patients experiencing MC.

Methods

We retrospectively reviewed patient episodes with ICD 9 and ICD 10 codes for myasthenia gravis and myasthenia gravis exacerbation/crisis in patients admitted to a single center tertiary care referral center from July 2008 to July 2017. These episodes were screened for patients with impending myasthenia gravis crisis and manifest crisis who received plasmapheresis during their hospital course. We performed statistical analyses to determine if increased number of plasma exchanges improves the primary outcome (hospital length of stay), as well as the secondary outcome (disposition to home, skilled nursing facility, long term acute care hospital, or death).

Results

There is neither clinically observable nor statistically significant improvement in length of stay or disposition on discharge in patients who received six or greater sessions of plasmapheresis.

Conclusions

This study provides class IV evidence that extending the number of plasma exchanges beyond five does not correlate with decreased hospital length of stay or improved discharge disposition in patients experiencing myasthenic crisis.
Extension of Community Healthcare Outcomes in Parkinson Disease (Parkinson ECHO): A Feasibility Study
Authors: Neilson Lee E. , Wilhelm Jennifer , McDonnell Margaret McLain , Mann Lisa , Kraakevik Jeff A.
Published: February 2022

Parkinson’s disease is the second most common neurodegenerative disorder and presents with a heterogeneous group of symptoms. Managing these symptoms requires coordinated care from a neurology specialist and a primary care provider. Access to neurology care is limited for those patients with Parkinson’s disease who reside in rural areas given financial and mobility constraints along with the rarity of specialty providers. To close this gap, we developed and implemented a telehealth-based Project ECHO® (Extension for Community Healthcare Outcomes) program, “Parkinson ECHO,” to provide education and support for rural clinicians and allied health members. We assessed the feasibility of this tele-mentoring educational offering and the effect it had on clinician confidence in diagnosing and treating Parkinson’s disease. Participants from across Oregon (n=33), of whom 70% served rural and/or medically underserved communities, attended the biweekly sessions. The sessions focused on a topic within Parkinson’s disease diagnosis or management followed by case discussions. We assessed clinician confidence and acceptability using surveys before and after their participation in the program. The COVID-19 pandemic was an unexpected obstacle in executing this project, delaying the program by several months and likely accounting for a lower number of attendees for the last two sessions. Nevertheless, we found Parkinson ECHO did significantly increase participant confidence levels in diagnosing and managing Parkinson’s disease.
Coagulation abnormalities in children with uncorrected congenital heart defects seen at a teaching hospital in a developing country
Authors: Majiyagbe Omotola O. , Akinsete Adeseye M. , Adeyemo Titilayo A. , Ekure Ekanem N. , Okoromah Christy A. N.
Published: February 2022

Background

Coagulation abnormality is a significant complication and cause of mortality in children with uncorrected congenital heart defects (CHD). The aim of this study was to determine the prevalence of coagulation abnormalities and the associated factors in children with uncorrected CHD.

Method

A cross sectional study conducted to determine the prevalence of coagulation abnormalities among 70 children with uncorrected CHD aged six months to 17 years and 70 age and sex matched apparently healthy controls. Coagulation abnormality was determined using complete blood count, prothrombin time, activated partial thromboplastin time and D-dimer assay.

Results

The prevalence of coagulation abnormalities among children with CHD and controls was 37.1% and 7.1% respectively. Children with Cyanotic CHD had a significantly higher prevalence of coagulation abnormalities compared to children with Acyanotic CHD (57.1% versus 17.1%). Haematocrit and oxygen saturation levels were significantly associated with coagulation abnormalities.

Conclusion

This study affirms that coagulation abnormality is high in children with uncorrected CHD. Oxygen saturation and haematocrit are factors of coagulation abnormalities. Routine coagulation screening is recommended especially in children with cyanotic congenital heart defects to improve their quality of life and reduce morbidity and mortality while awaiting definitive surgeries.
Embodiment of Supernumerary Robotic Limbs in Virtual Reality
Authors: Arai Ken , Saito Hiroto , Fukuoka Masaaki , Ueda Sachiyo , Sugimoto Maki , Kitazaki Michiteru , Inami Masahiko
Published: February 2022

The supernumerary robotic limb system expands the motor function of human users by adding extra artificially designed limbs. It is important for us to embody the system as if it is a part of one’s own body and to maintain cognitive transparency in which the cognitive load is suppressed. Embodiment studies have been conducted with an expansion of bodily functions through a “substitution” and “extension.” However, there have been few studies on the “addition” of supernumerary body parts. In this study, we developed a supernumerary robotic limb system that operates in a virtual environment, and then evaluated whether the extra limb can be regarded as a part of one’s own body using a questionnaire and whether the perception of peripersonal space changes with a visuotactile crossmodal congruency task. We found that the participants can embody the extra-limbs after using the supernumerary robotic limb system. We also found a positive correlation between the perceptual change in the crossmodal congruency task and the subjective feeling that the number of one’s arms had increased (supernumerary limb sensation). These results suggest that the addition of an extra body part may cause the participants to feel that they had acquired a new body part that differs from their original body part through a functional expansion.
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context
Authors: Marchiano Fabio , Haering Margaux , Habermann Bianca Hermine
Published: February 2022

Mitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterised by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It however lacked functions aimed at integrating mitochondria in the cellular context and thus, identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade we implemented two novel integrative functions, Network Analysis and the transcription factor- (TF-) Enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualisation, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species as well as an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in 3 specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.
Seasonal IVIG contains high infectivity neutralizing and hemagglutination inhibition activity against seasonal flu virus strains selected for vaccines (2020-22)
Authors: Díez José María , Casals Daniel , Romero Carolina , Gajardo Rodrigo
Published: February 2022

IVIG solutions (10%) were tested for infectivity neutralization and hemagglutination inhibition against the influenza strains (two A and two B) recommended by the WHO for inclusion in vaccines for Northern and Southern hemispheres 2020-2022. The IVIG batches used were manufactured (June 2020) from plasma pools collected in the US. Potent neutralization and inhibition of hemagglutination were seen with these IVIG batches. This raises the possibility that IVIG could be added to existing therapies, especially in immunocompromised patients, to fight serious influenza infections. Further study of the potential of IVIG in influenza is warranted.
A model of autonomous interactions between hippocampus and neocortex driving sleep-dependent memory consolidation
Authors: Singh Dhairyya , Norman Kenneth A. , Schapiro Anna C.
Published: February 2022

How do we build up our knowledge of the world over time? Many theories of memory formation and consolidation have posited that the hippocampus stores new information, then “teaches” this information to neocortex over time, especially during sleep. But it is unclear, mechanistically, how this actually works — how are these systems able to interact during periods with virtually no environmental input to accomplish useful learning and shifts in representation? We provide a framework for thinking about this question, with neural network model simulations serving as demonstrations. The model contains hippocampus and neocortical areas, which replay memories and interact with one another completely autonomously during simulated sleep. Oscillations are leveraged to support error-driven learning that leads to useful changes in memory representation and behavior. The model has a non-Rapid Eye Movement (NREM) sleep stage, where dynamics between hippocampus and neocortex are tightly coupled, with hippocampus helping neocortex to reinstate high-fidelity versions of new attractors, and a REM sleep stage, where neocortex is able to more freely explore existing attractors. We find that alternating between NREM and REM sleep stages, which alternately focuses the model’s replay on recent and remote information, facilitates graceful continual learning. We thus provide an account of how the hippocampus and neocortex can interact without any external input during sleep to drive useful new cortical learning and to protect old knowledge as new information is integrated.
Anatomical variability, multi-modal coordinate systems, and precision targeting in the marmoset brain
Authors: Ose Takayuki , Autio Joonas A. , Ohno Masahiro , Frey Stephen , Uematsu Akiko , Kawasaki Akihiro , Takeda Chiho , Hori Yuki , Nishigori Kantaro , Nakako Tomokazu , Yokoyama Chihiro , Nagata Hidetaka , Yamamori Tetsuo , Van Essen David C. , Glasser Matthew F. , Watabe Hiroshi , Hayashi Takuya
Published: February 2022

Localising accurate brain regions needs careful evaluation in each experimental species due to their individual variability. However, the function and connectivity of brain areas is commonly studied using a single-subject cranial landmark-based stereotactic atlas in animal neuroscience. Here, we address this issue in a small primate, the common marmoset, which is increasingly widely used in systems neuroscience. We developed a non-invasive multi-modal neuroimaging-based targeting pipeline, which accounts for intersubject anatomical variability in cranial and cortical landmarks in marmosets. This methodology allowed creation of multi-modal templates (MarmosetRIKEN20) including head CT and brain MR images, embedded in coordinate systems of anterior and posterior commissures (AC-PC) and CIFTI grayordinates. We found that the horizontal plane of the stereotactic coordinate was significantly rotated in pitch relative to the AC-PC coordinate system (10 degrees, frontal downwards), and had a significant bias and uncertainty due to positioning procedures. We also found that many common cranial and brain landmarks (e.g., bregma, intraparietal sulcus) vary in location across subjects and are substantial relative to average marmoset cortical area dimensions. Combining the neuroimaging-based targeting pipeline with robot-guided surgery enabled proof-of-concept targeting of deep brain structures with an accuracy of 0.2 mm. Altogether, our findings demonstrate substantial intersubject variability in marmoset brain and cranial landmarks, implying that subject-specific neuroimaging-based localization is needed for precision targeting in marmosets. The population-based templates and atlases in grayordinates, created for the first time in marmoset monkeys, should help bridging between macroscale and microscale analyses.

Highlights

Achieved sub-millimeter localization accuracy of subject-wise brain region

Propose a dedicated non-invasive multi-modal subject-specific registration pipeline

Construct brain coordinate system in AC-PC and grayordinate spaces

Establish multi-modal MRI and CT brain and cortical templates, MarmosetRIKEN20

Quantify intersubject variabilities in marmoset brain

Significant bias and uncertainty exist in marmoset stereotactic positioning
Increased academic performance and prolonged career duration among principal investigators in ecology and evolutionary biology in Taiwan
Authors: Hsu Gen-Chang , Lin Wei-Jiun , Sun Syuan-Jyun
Published: February 2022

Academic job markets have become increasingly challenging worldwide, yet it remains poorly characterized how competitively-successful candidates should be and what the underlying determinants of their success are. Focusing on the field of ecology and evolutionary biology, we analyzed the academic performance (measured as h-index) as well as the duration before recruitment as a new faculty member and promotion to full professor of 145 principal investigators (PI) over the past 34 years in Taiwan. We found that PIs had higher performance and longer duration before recruitment more recently. Performance before promotion remained stable, whereas the duration increased over time. The origin and prestige of doctorate had no effect on the performance or duration either before recruitment or before promotion. We also found that the difference in performance before and after recruitment (“After” performance — “Before” performance) decreased in recent years, with PIs recruited in earlier years maintaining their performance after recruitment while those recruited in later years exhibiting a performance drop. While PIs performed equally well before and after recruitment irrespective of doctorate origin, those with domestic PhD degrees showed a decrease in performance after promotion compared to their counterparts with foreign degrees. Taken together, our findings reveal a prolonged career duration for researchers as a result of intensifying competition in academia, and highlight the increasingly crucial role of academic performance, rather than PhD degree itself, in determining academic success.
Surface engineering enhances the therapeutic potential of extracellular vesicles following acute myocardial infarction
Authors: Mentkowski Kyle I. , Tarvirdizadeh Touba , Manzanero Cody A. , Eagler Lisa A. , Lang Jennifer K.
Published: February 2022

Structured Abstract

Objectives

The objective of the study was to assess the therapeutic efficacy of targeting remote zone cardiomyocytes with cardiosphere-derived cell (CDC) extracellular vesicles (EVs) in acute myocardial infarction.

Background

Cardiomyocyte (CM) cell death plays a significant role in left ventricular (LV) remodeling and cardiac dysfunction following myocardial infarction (MI). While EVs secreted by CDCs have shown efficacy in promoting cardiac repair in preclinical models of MI, their translational potential is limited by their biodistribution. We hypothesized that targeting therapeutic EVs to CMs would result in further reduction of cardiomyocyte (CM) cell death in vivo and improvement in cardiac function post-MI.

Methods

CDC-derived EVs were engineered to express a CM-specific binding peptide (CMP) on their surface and characterized for size, morphology, and protein expression. Mice with acute MI underwent delivery of human CDC EVs, CMP-EVs and placebo in a double-blind study. LVEF was assessed by echo at 1- and 28-days post-MI and tissue samples processed for assessment of EV biodistribution and histological endpoints.

Results

CMP-EVs demonstrated superior cardiac targeting and retention when compared with control EVs 24 hours post MI. While intramyocardial administered CDC-EVs improved LVEF compared with placebo at 4 weeks, mice treated with CMP-EVs demonstrated a significant improvement in LVEF compared with non-targeted EVs. Likely accounting for their augmented therapeutic efficacy, CMP-EVs demonstrated enhanced reduction of remote zone cardiomyocyte apoptosis.

Conclusions

Targeting CMP-EVs to CMs post-MI improved cardiac function compared with unmodified EVs demonstrating a strategy to further optimize therapeutic EV delivery to increase efficacy and decease off-target effects.

Condensed Abstract

Extracellular vesicles (EVs) offer several potential advantages over small molecule therapeutics for cardiovascular disease (CVD). However, their potential is limited by their biodistribution and lack of specificity. We engineered cardiosphere-derived cells (CDCs) to express Lamp2b fused to a cardiomyocyte specific peptide (CMP), generating EVs with increased cardiomyocyte uptake and cardiac retention. CMP-EVs enhanced cardiac function following acute MI and further reduced remote zone apoptosis when compared with unmodified CDC-EVs. This work highlights a role for targeting therapeutic EVs to cardiomyocytes following injury and serves as a proof-of-concept study for the utility of EV surface engineering in the treatment of CVD.
Identification of significant molecules and signaling pathways between 2D and 3D culture methods of renal cancer cells
Authors: Wang Mengyao , Guo Hongmei , Gu Hanming , Zhang Mason
Published: February 2022

The majority of cancer studies are conducted with the two-dimensional (2D) culture method, which does not reflect tumor in vivo structure. The 3D culture method can form free bundles of cancer cells and spheroid, which mimics the tumor microenvironment in vivo. However, the molecules and signaling pathways between the 2D and 3D culture methods are still unknown. In this study, we aim to identify the key molecules and signaling pathways by analyzing the RNA-seq data. The GSE190296 was created by the BGISEQ-500 (Homo sapiens). The KEGG and GO analyses indicated sulfur compound metabolic process and regulation of leukocyte mediated immunity are the major differences between 2D and 3D renal cancer cell cultures. Moreover, we figured out several interactive genes including MYC, EGF, VEGFA, STAT3, NOTCH1, CAT, CCND1, HSPA8, DLG4, and HSPA5. Our study may provide new knowledge on the differences between 2D and 3D cancer cell cultures.
AlphaFold2 and RoseTTAFold Predict Posttranslational modifications. Chromophore Formation in GFP-like Proteins
Authors: Hartley Sophia M. , Tiernan Kelly A. , Ametaj Gjina , Cretu Adriana , Zhuang Yan , Zimmer Marc
Published: February 2022

AlphaFold2 and RoseTTAfold are able to predict, based solely on their sequence whether GFP-like proteins will post-translationally form a chromophore or not. Their training has not only taught them protein structure and folding, but also chemistry. The structures of 21 sequences of GFP-like fluorescent proteins that will post-translationally form a chromophore and of 23 GFP-like non-fluorescent proteins that do not have the residues required to form a chromophore were determined by AlphaFold2 and RoseTTAfold. The resultant structures were mined for a series of geometric measurements that are crucial to chromophore formation. Statistical analysis of these measurements showed that both programs conclusively distinguished between chromophore forming and non-chromophore forming proteins. A clear distinction between sequences capable of forming a chromophore and those that do not have the residues required for chromophore formation can be obtained by examining a single measurement - the RMSD of the overlap of the central alpha helices of the crystal structure of S65T GFP and the AlphaFold2 determined structure.
A high-quality genome assembly and annotation of the European earwig Forficula auricularia
Authors: Bhattarai Upendra R. , Katuwal Mandira , Poulin Robert , Gemmell Neil J. , Dowle Eddy
Published: February 2022

The European earwig Forficula auricularia is an important model for studies of maternal care, sexual selection, sociality and host-parasite interactions. However, detailed genetic investigations of this species are hindered by a lack of genomic resources. Here we present a high-quality hybrid genome assembly for F. auricularia. The genome was assembled using nanopore long-reads and 10x chromium link-reads. The final assembly is 1.06Gb in length with 31.03% GC content. It consists of 919 scaffolds with an N50 of 12.55Mb. Half of the genome is present in only 20 scaffolds. Benchmarking Universal Single-Copy Orthologs scores are ~90% from three sets of single-copy orthologs (eukaryotic, insect, and arthropod). The total repeat elements in the genome are 64.62%. The MAKER2 pipeline annotated 12,876 protein-coding genes and 21,031 mRNAs. A phylogenetic analysis revealed the isolate used in our genomic analysis belongs to Subspecies B, one of the two known genetic subspecies of F. auricularia. The genome assembly, annotation, and associated resources will be of high value to a large and diverse group of researchers working on Dermapterans.
ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data
Authors: Ford Michael , Hari Ananth , Rodriguez Oscar , Xu Junyan , Lack Justin , Oguz Cihan , Zhang Yu , Weber Sarah , Magglioco Mary , Barnett Jason , Xirasagar Sandhya , Samuel Smilee , Imberti Luisa , Bonfanti Paolo , Biondi Andrea , Dalgard Clifton L. , Chanock Stephen , Rosen Lindsey , Holland Steven , Su Helen , Notarangelo Luigi ,   NIAID COVID Consortium, Vishkin Uzi , Watson Corey , Sahinalp S. Cenk
Published: February 2022

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which, together with the joining genes (IGHJ), diversity genes (IGHD), constant genes (IGHC) and immunoglobulin light chains, code for antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype through the use of standard short read sequencing technologies. Here we introduce ImmunoTyper-SR, an algorithmic method for genotype and CNV analysis of the germline IGHV genes using Illumina whole genome sequencing (WGS) data. ImmunoTyper-SR is based on a novel combinatorial optimization formulation that aims to minimize the total edit distance between reads and their assigned IGHV alleles from a given database, with constraints on the number and distribution of reads across each called allele. We have validated ImmunoTyper-SR on 12 individuals with Illumina WGS data from the 1000 Genomes Project, whose IGHV allele composition have been studied extensively through the use of long read and targeted sequencing platforms, as well as nine individuals from the NIAID COVID Consortium who have been subjected to WGS twice. We have then applied ImmunoTyper-SR on 585 samples from the NIAID COVID Consortium to investigate associations between distinct IGHV alleles and anti-type I IFN autoantibodies which have been linked to COVID-19 severity.
Acarbose suppresses symptoms of mitochondrial disease in a mouse model of Leigh Syndrome
Authors: Bitto Alessandro , Grillo Anthony S. , Stanaway Ian B. , Nguyen Bao M. G. , Ying Kejun , Tung Herman , Smith Kaleb , Tran Ngoc , Velikanje Gunnar , Urfer Silvan R. , Snyder Jessica M. , Kayser Ernst-Bernhard , Wang Lu , Smith Daniel L. , Thompson J. Will , DuBois Laura , DePaolo William , Kaeberlein Matt
Published: February 2022

Mitochondrial diseases represent a spectrum of disorders caused by impaired mitochondrial function ranging in severity from mortality during infancy to progressive adult-onset disease. Mitochondrial dysfunction is also recognized as a molecular hallmark of the biological aging process. Rapamycin, a drug that increases lifespan and health during normative aging also increases survival and reduces neurological symptoms in a mouse model of the severe mitochondrial disease Leigh Syndrome. The Ndufs4 knockout (Ndufs4-/-) mouse lacks the complex I subunit NDUFS4 and shows rapid onset and progression of neurodegeneration mimicking patients with Leigh Syndrome. Here we show that another drug that extends lifespan and delays normative aging in mice, acarbose, also suppresses symptoms of disease and improves survival of Ndufs4-/- mice. Unlike rapamycin, acarbose rescues disease phenotypes independently of mTOR inhibition. Furthermore, rapamycin and acarbose have additive effects in delaying neurological symptoms and increasing maximum lifespan in Ndufs4-/- mice. We find that acarbose remodels the intestinal microbiome and alters the production of short chain fatty acids. Supplementation with tributyrin, a source of butyric acid, recapitulates some effects of acarbose on lifespan and disease progression. This study provides the first evidence that alteration of the gut microbiome may impact severe mitochondrial disease and provides further support for the model that biological aging and severe mitochondrial disorders share underlying common mechanisms.
Three models of vaccination strategies against cryptococcosis in immunocompromised hosts using heat-killedCryptococcus neoformansΔsgl1
Authors: Normile Tyler G. , Del Poeta Maurizio
Published: February 2022

Vaccines are one of the greatest medical accomplishments to date, yet no fungal vaccines are currently available in humans mainly because opportunistic mycoses generally occur during immunodeficiencies necessary for vaccine protection. In previous studies, a live, attenuatedCryptococcus neoformansΔsgl1mutant accumulating sterylglucosides was found to be avirulent and protected mice from a subsequent lethal infection even in absence of CD4+T cells, a condition most associated with cryptococcosis (e.g., HIV). Here, we tested three strategies of vaccination against cryptococcosis. First, in our preventative model, protection was achieved even after a 3-fold increase of the vaccination window. Second, because liveC. neoformansΔsgl1-vaccinated mice challenged more than once with WT strain had a significant decrease in lung fungal burden, we testedC. neoformansΔsgl1as an immunotherapeutic. We found that therapeutic administrations of HKC. neoformansΔsgl1subsequent to WT challenge significantly improve the lung fungal burden. Similarly, therapeutic administration of HKC. neoformansΔsgl1post WT challenge resulted in 100% or 70% survival depending on the time of vaccine administration, suggesting that HK Δsgl1is a robust immunotherapeutic option. Third, we investigated a novel model of vaccination in preventing reactivation from lung granuloma usingC. neoformansΔgcs1. Remarkably, we show that administration of HK Δsgl1prevents mice from reactivating Δgcs1upon inducing immunosuppression with corticosteroids or by depleting CD4+T cells. Our results suggest that HK Δsgl1represents a clinically relevant, efficacious vaccine that confers robust host protection in three models of vaccination against cryptococcosis even during CD4-deficiency.

Importance

Cryptococcosis results in ∼180,000 global deaths per year in immunocompromised individuals. Current antifungal treatment options are potentially toxic, lacking in areas of need, and exhibit limited efficacy. In addition to these lackluster therapeutic options, no fungal vaccines are currently available for clinical use. Due to the increasing rate of immunocompromised individuals, there is a dire need for the development of improved antifungal therapeutics. Presently, we have demonstrated the high efficacy of a clinically relevant heat-killed mutant strain ofCryptococcus neoformansin inducing advantageous host protection in three models of vaccination against cryptococcosis during immunodeficiencies most associated with this disease.
Robotic-Assisted Gait for lower-limb Rehabilitation: Evidence of Altered Neural Mechanisms in Stroke
Authors: Mayor-Torres Juan Manuel , O’Callaghan Ben , Korik Attila , Del Felice Alessandra , Coyle Damien , Murphy Sean , Lennon Olive
Published: February 2022

Robotic-Assisted Gait training (RAGT) offers an innovative therapeutic option for restoration of functional gait in stroke survivors, complementing existing physical rehabilitation strategies. However, there is a limited understanding of the neurophysiological response induced by this training in end-users. Neural desynchronization and Cortico-Muscular Coherence (CMC) are two biomarkers that define the level of muscle-cortex association during gait phases and can be used to estimate induced user’s adaptation during RAGT. In this study, we measure Event-Related Spectral Perturbation (ERSP) and CMC from three healthy individuals and three stroke survivors during overground-gait with and without an exoskeleton. Results show that (1) the use of the exoskeleton in healthy individuals is associated with a different and more refined motor-control represented in a highθ-desynchronization, (2) altered and noisy ERSP and lower and non-focalβ-CMC patterns are observed in Stroke patients when performing overground-gait both with and without the Exoskeleton, and (3) Exoskeleton use in stroke survivors is associated with a reduction in swing-time during gait-cycle, but this effect is not correlated with an increment ofθ-desynchronization and/orβ-CMC. ERSP and CMC demonstrated evidence of neural modulation in able-bodied users during RAGT, which could not be detected in subacute stroke survivors during RAGT. These results suggest that the gait-parameters changes observed during exoskeleton use in subacute stroke survivors are unlikely to be neurally driven.
Diagnostic Utility of Exome Sequencing for Polycystic Kidney Disease
Authors: Chang Alexander R. , Moore Bryn , Luo Jonathan Z. , Sartori Gino , Fang Brian , Jacobs Steven , Abdalla Yoosif , Taher Mohammed ,   Regeneron Genetics Center, Carey David J. , Triffo William , Singh Gurmukteshwar , Mirshahi Tooraj
Published: February 2022

Importance

Most studies of ADPKD genetics have used select cohorts, focusing onPKD1andPKD2and more recently several other cystic genes. However, the population prevalence of ADPKD and the contribution of each cystic gene to ADPKD are not well understood.

Objective

Determine the prevalence of ADPKD, contribution ofPKD1, PKD2, and other cystic genes to ADPKD in a large, unselected cohort.

Design, Setting, and Participants

We determined the prevalence of ADPKD In an unselected health system-based cohort of 173,954 subjects with the existing exome sequencing and extensive electronic health records, including abdominal imaging. The presence of genetic variants inPKD1, PKD2, and eleven other cystic genes was evaluated. Rare genetic variants were identified in patients with chart review confirmed diagnosis of ADPKD.

Main Outcomes

Diagnosis of ADPKD and presences of rare (AF<0.0001) missense, protein-truncating variants (PTVs), or copy number variants deletions (CNV) inPKD1, PKD2, or PTVs and CNVs in the following 11 genes:ALG8, ALG9, DNAJB11, GANAB, HNF1B, IFT140, LRP5, PKHD1, PRKCSH, SEC61B, andSEC63.

Results

Among 173,954 patients, there were 235 patients with chart review confirmed ADPKD (0.135%). Among patients with PTV or CNV inPKD1, 66/70 (94.2%) had ADPKD and 43/44 (97.7%) of patients with PTV or CNV inPKD2had ADPKD. In contrast, only 24/77 (31.2%) patients with a PKD1 missense variant previously classified as “likely pathogenic” had ADPKD. A rare variant was identified in a cystic gene in 180/235 (76.6%) of ADPKD patients, with the most common genes implicatedPKD1(127) andPKD2(34) and thenIFT140(7),PKHD1(3),GANAB(4),HNF1B(2),ALG8(1),ALG9(1),IFT140+PKHD1(1). The yield for a genetic determinant of ADPKD was 91.3% among those with a family history compared to 50.6% among those without a family history (p<0.0001). We report several previously unreported variants where pedigree data suggest pathogenicity. Atypical cystic genesALG8, ALG9, GANAB, HNF1B, IFT140, andSEC63were associated with having any kidney or liver cystic ICD code, but not diagnosed ADPKD.

Conclusions

Exome sequencing established the molecular diagnosis for the vast majority of patients with ADPKD, revealed a wider range of ADPKD with atypical cystic genes. Additional population-based research cohorts are needed to carefully curate missensePKD1variants and variants in atypical cystic genes.
Aberrant naive CD4+ T Cell differentiation in systemic juvenile idiopathic arthritis is committed to B cell help
Authors: Kuehn Julia , Schleifenbaum Susanne , Hellige Antje , Park Carolin , Hinze Claas , Wittkowski Helmut , Holzinger Dirk , Foell Dirk , Kessel Christoph
Published: February 2022

Objective

Systemic juvenile idiopathic arthritis (sJIA) features characteristics of autoinflammation and autoimmunity, culminating in chronic arthritis. Previous work indicated decreased IFNγ-expression by T helper (Th) cells in sJIA. Here, we hypothesized this to result from aberrant or incomplete Th cell polarization.

Methods

Cells or sera were obtained from healthy controls (HC, n=26) and sJIA patients (n=61). Isolated naïve Th cells were cultured under Th1, Th17, and T follicular or T peripheral helper (Tf/ph) polarizing conditions and were partly co-cultured with allogenic memory B cells. Surface marker, transcription factor, and/or cytokine expression in peripheral or polarized Th cells or sera as well as B cellular plasma blast generation were studied by flow cytometry, multiplexed bead array assays, ELISA and retrospective RNA profiling analyses.

Results

SJIA naive Th cell differentiation towards Th1 resulted in low IFNγ and Eomesodermin expression. Instead, developing sJIA Th1 cells revealed elevated IL-21 release that negatively correlated with cellular IFNγ and Eomesodermin expression. Both In vitro and ex vivo, IL-21 together with PD-1, ICOS and CXCR5 expression indicated naïve sJIA Th cell differentiation to rather polarize towards a Tf/ph phenotype. Retrospective analysis of whole blood RNA sequencing data demonstrated sJIA-specific overexpression of Bcl-6 as respective master transcription factor. Compared to controls, in vitro generated sJIA Tf/ph cells promoted enhanced B cellular plasma-blast generation.

Conclusion

In sJIA pathogenesis skewing of sJIA naïve Th cell differentiation towards a Tf/ph phenotype may represent an echo of autoimmunity, which could shed light on the mechanisms driving the progression towards chronic destructive arthritis.
Predicting Respiratory Decompensation in Mechanically Ventilated Adult ICU Patients
Authors: Tan Yvette , Young Michael , Girish Akanksha , Hu Beini , Kurian Zina , Greenstein Joseph L , Kim Han , Winslow Raimond , Fackler James , Bergmann Jules
Published: February 2022

Background

Mechanical ventilation is a life-saving treatment in the Intensive Care Unit (ICU), but often causes patients to be at risk of further respiratory complication. We created a statistical model utilizing electronic health record and physiologic vitals data to predict the Center for Disease Control and Prevention (CDC) defined Ventilator Associated Complications (VACs).

Methods

We constructed a random forest model to predict occurrence of VACs using health records and chart events from adult patients in the Medical Information Mart for Intensive Care III (MIMIC-III) database. We trained the machine learning models on two patient populations of 1921 and 464 based on low and high frequency data availability. Model features were generated using both basic statistical summaries and tsfresh, an automated python feature generation library. Classification to determine whether a patient will experience VAC one hour after 36 hours of ventilation was performed using a random forest classifier. Two different sample spaces conditioned on five varying feature extraction techniques were evaluated to identify the most optimal selection of features resulting in the best VAC discrimination. Each dataset was assessed using K-folds cross-validation (k = 10), giving average area under the receiver operating curves (AUROC) s and accuracies.

Findings

After feature selection, hyperparameter tuning, and feature extraction, the best performing model used automatically generated features on high frequency data and achieved an average Area Under Receiver Operating Characteristic Curve (AUC) of 0·83 ± 0·11 and an average accuracy of 0·69 ± 0·10.

Interpretation

We constructed a promising model to predict VACs 1 hour prior to occurrence with 36 hours of ICU patient data. The model provides early warnings of VACs, which may allow actionable therapies to prevent or mitigate ventilator associated complications.

Funding

N/A
Neutrophil Extracellular Trap Biomarker Titers and Delayed Cerebral Ischemia in Patients With Aneurysmal Subarachnoid Hemorrhage
Authors: Witsch Jens , Spalart Valérie , Martinod Kimberly , Schneider Hauke , Oertel Joachim , Geisel Jürgen , Hendrix Philipp , Hemmer Sina
Published: February 2022

Background

Myeloperoxidase (MPO)-DNA complexes, biomarkers of neutrophil extracellular traps, have been associated with arterial and venous thrombosis. Their role in patients with aneurysmal subarachnoid hemorrhage (aSAH) is unknown. Here, we sought to explore whether serum MPO-DNA-complexes are present in patients with aSAH, and whether these levels are associated with delayed cerebral ischemia (DCI).

Methods

We performed a post-hoc analysis of a prospective, blinded, observational single-center biomarker study that enrolled consecutive patients with spontaneous SAH between July 2018 and September 2020. Serum samples obtained on admission and on hospital day 4 were analyzed for concentrations of MPO-DNA complexes. The primary outcome was the occurrence of DCI defined as new infarction on brain CT-scan. The secondary outcome was clinical vasospasm, a composite of clinical and transcranial doppler parameters. We used Wilcoxon’s signed-rank-test to assess for differences between paired measures.

Results

Among 100 patients with spontaneous SAH, mean age 59 (SD+13) years, 55% women, 78 patients had an aneurysmal SAH and complete DCI information. Among these, 29 (37%) developed DCI. MPO-DNA complexes were detected in all samples. The median MPO-DNA level was 33 ng/ml (IQR, 18-43 ng/ml) on admission, and 22 ng/ml (IQR, 11-31 ng/ml) on day 4 (Mann-Whitney test: p=0.015). In the primary outcome analysis, we found a significant reduction in MPO-DNA levels from admission to day 4 in patients with DCI (paired test, p=0.036) but not in those without DCI (p=0.171). The secondary analysis showed a similar reduction in MPO-DNA levels between admission and day 4 in patients with (p=0.006), but not in those without clinical vasospasm (p=0.473).

Conclusions

MPO-DNA-complexes are detectable in peripheral serum samples of patients with aSAH. A pronounced reduction in MPO-DNA levels over the first days after aSAH might herald DCI. The potential of MPO-DNA levels to serve as a biomarker of DCI requires further exploration.