bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Y Chromosome Haplogroups in Parkinson’s Disease
Authors: Grenn Francis P. , Makarious Mary B , Bandres-Ciga Sara , Iwaki Hirotaka , Singleton Andrew , Nalls Mike , Blauwendraat Cornelis ,   The International Parkinson Disease Genomics Consortium
Published: March 2022

Parkinson’s disease is a complex neurodegenerative disorder that is about 1.5 times more prevalent in males than females. Extensive work has been done to identify the genetic risk factors behind Parkinson’s disease on autosomes and more recently on chromosome X, but work remains to be done on the male specific Y chromosome. In an effort to explore the role of the Y chromosome in Parkinson’s disease we analyzed whole genome sequencing data from the Accelerating Medicines Partnership - Parkinson’s disease initiative (1,466 cases and 1,664 controls), genotype data from NeuroX (3,491 cases and 3,232 controls) and genotype data from UKBiobank (182,517 controls, 1,892 cases, and 3,783 proxy cases) all consisting of male European ancestry samples. We classified sample Y chromosomes by haplogroup using three different tools for comparison (Snappy, Yhaplo, Y-LineageTracker), and meta-analyzed this data to identify haplogroups associated with Parkinson’s disease. This was followed up with a Y chromosome association study to identify specific variants associated with disease. We also analyzed blood based RNASeq data obtained from the Accelerating Medicines Partnership - Parkinson’s disease initiative (1,020 samples) and RNASeq data obtained from the North American Brain Expression Consortium (171 samples) to identify Y chromosome genes differentially expressed in cases, controls, specific haplogroups, and specific tissues. RNASeq analyses suggest Y chromosome gene expression differs between brain and blood tissues but does not differ significantly in cases, controls or specific haplogroups. Overall, we did not find any strong associations between Y chromosome genetics and Parkinson’s disease, suggesting the explanation for increased prevalence in males may lie elsewhere.
Characteristics and healthcare use of patients attending virtual walk-in clinics: a cross-sectional analysis
Authors: Lapointe-Shaw Lauren , Salahub Christine , Bhatia R. Sacha , Desveaux Laura , Glazier Richard H. , Hedden Lindsay , Ivers Noah M. , Martin Danielle , Spithoff Sheryl , Na Yingbo , Tadrous Mina , Kiran Tara
Published: March 2022

Importance

Virtual walk-in clinics have proliferated since the onset of COVID-19. Yet, little is known about those who participate in this care model, and how virtual walk-in clinics contribute to care continuity and patient healthcare utilization.

Objectives

To describe the characteristics and healthcare use of patients using virtual walk-in clinics compared to the general population, and a subset that received any virtual family physician visit.

Design

This was a retrospective, population-based, cross-sectional study.

Setting

Ontario, Canada’s most populous province.

Participants

Patients who had received at least one family physician visit at one of 13 virtual walk-in clinics from April 1st to December 31st, 2020. They were compared to Ontario residents who had any virtual family physician visit in the same time period.

Main Outcome(s) and Measure(s)

Patient characteristics and 30-day post-visit healthcare utilization.

Results

Virtual walk-in patients (N=132,168) had fewer comorbidities and lower previous healthcare utilization than Ontarians with any virtual visit. Less than 0.1% of virtual walk-in visits were with a patient’s own family physician. Compared to Ontarians having any virtual family physician visit, virtual walk-in patients were significantly less likely to have a subsequent in-person visit with the same physician (0.2% vs. 11.0%, SMD = 0.48), more likely to have a subsequent virtual visit (30.3% vs. 21.9%, SMD = 0.19), and twice as likely to have an emergency department visit within 30 days (8.3% vs. 4.1%, SMD = 0.18), an effect that persisted after adjustment and across rurality groups: large urban (aOR 2.26; 95% CI 2.08-2.45), small urban (aOR 2.08; 95% CI 1.99-2.18), and rural (aOR 1.87; 95% CI 1.69-2.07).

Conclusions and Relevance

Compared to Ontarians attending any family physician virtual visit, virtual walk-in patients were less likely to have a subsequent in-person physician visit, but were more likely to visit the emergency department. Low continuity and the lack of physical examination may be contributing to increased emergency department utilization for virtual walk-in clinic patients.
Cost-effectiveness of implementing HIV and HIV/syphilis dual testing among key populations in Viet Nam: a modeling analysis
Authors: Coomes David , Green Dylan , Barnabas Ruanne , Sharma Monisha , Barr-DiChiara Magdalena , Jamil Muhammad S. , Baggaley Rachel , Owiredu Morkor Newman , Macdonald Virginia , Nguyen Van , Hai Son Vo , Taylor Melanie M. , Wi Teodora E , Johnson Cheryl , Drake Alison L.
Published: March 2022

Objectives

Key populations, including sex workers, men who have sex with men, and people who inject drugs, have a high risk of HIV and sexually transmitted infections (STIs). We assessed the health and economic impacts of different HIV and syphilis testing strategies among three key populations in Viet Nam using a dual HIV/syphilis rapid diagnostic test (RDT).

Setting

We used the Spectrum AIDS Impact Model to simulate the HIV epidemic in key populations in Viet Nam and evaluated five testing scenarios. We used a 15-year time horizon and all costs are from the provider’s perspective.

Participants

We include the entire population of Viet Nam in the model.

Interventions

We model five testing scenarios among key populations: 1) annual testing with an HIV rapid diagnostic test (RDT), 2) annual testing with a dual RDT, 3) biannual testing using dual RDT and HIV RDT, 4) biannual testing using HIV RDT, and 5) biannual testing using dual RDTs.

Primary and secondary outcome measures

The primary outcome is incremental cost-effectiveness ratios (ICERS). Secondary outcomes include HIV and syphilis cases and costs for each proposed intervention.

Results

Annual testing using a dual HIV/syphilis RDT was cost saving and averted 3,206 HIV cases and treated 7,719 syphilis cases compared to baseline over 15 years. Biannual testing using one dual test and one HIV RDT, or two dual tests both averted an additional 875 HIV cases and were cost-effective ($1,024 and $2,518 per DALY averted, respectively). Annual or biannual HIV testing using HIV RDTs and separate syphilis tests were more costly and less effective than using one or two dual RDTs.

Conclusions

Annual or biannual HIV and syphilis testing using dual RDTs among key populations can be cost-effective and support countries in reaching global reduction goals for HIV and syphilis.

STRENGTHS AND LIMITATIONS OF THIS STUDY

Strength: Our model presents novel cost-effectiveness estimates for the use of dual HIV/syphilis testing in key populations that can inform health planners

Strength: We include five testing scale up scenarios using both HIV RDT and dual HIV/syphilis RDT

Strength: Our model is informed by demographic, behavioral, and biological data from government sources, surveys, surveillance, publicly available reports, databases, and peer-reviewed literature

Limitation: We made some assumptions regarding the timing and uptake of HIV and syphilis testing among key populations that may be inaccurate.

Limitation: Our model assumes that increased syphilis testing and treatment will not impact syphilis prevalence, however, it is unknown whether increased testing will reduce or increase syphilis prevalence.
STING activation promotes robust immune response and NK cell-mediated tumor regression in glioblastoma models
Authors: Berger Gilles , Knelson Erik H. , Jimenez-Macias Jorge L. , Nowicki Michal O. , Han Saemi , Panagioti Eleni , Lizotte Patrick H. , Adu-Berchie Kwasi , Stafford Alexander , Dimitrakakis Nikolaos , Zhou Lanlan , Chiocca E. Antonio , Mooney David J. , Barbie David A. , Lawler Sean E.
Published: March 2022

Immunotherapy has had a tremendous impact on cancer treatment in the past decade, with hitherto unseen responses at advanced and metastatic stages of the disease. However, the aggressive brain tumor glioblastoma (GBM) is highly immunosuppressive and remains largely refractory to current immunotherapeutic approaches. The cGAS-STING cytoplasmic double stranded DNA (dsDNA) sensing pathway has emerged as a next-generation immunotherapy target with potent local immune stimulatory properties.

Here, we investigated the status of the STING pathway in GBM and the modulation of the brain tumor microenvironment (TME) with the STING agonist ADU-S100. Our data reveal the presence of STING in human GBM specimens, where it stains strongly in the tumor vasculature. We show that human GBM explants can respond to STING agonist treatment by secretion of inflammatory cytokines. In murine GBM models, we show a profound shift in the tumor immune landscape after STING agonist treatment, with massive infiltration of the tumor-bearing hemisphere with innate immune cells including inflammatory macrophages, neutrophils and NK populations. Treatment of established murine intracranial GL261 and CT-2A tumors by biodegradable ADU-S100-loaded intracranial implants demonstrated a significant increase in survival in both models and long-term survival with immune memory in GL261. Responses to treatment were abolished by NK cell depletion. This study reveals therapeutic potential and deep remodeling of the TME by STING activation in GBM and warrants the further examination of STING agonists alone or in combination with other immunotherapies such as cancer vaccines, CAR T cells, NK therapies or immune checkpoint blockade.

Significance statement

Modulation of the immune microenvironment is critical for immunosuppressive and therapy refractory tumors like glioblastoma. Activation of the STING pathway deeply remodels the brain tumor environment and attracts innate immune cells and natural killer cell populations, producing a robust antitumor effect with long-term immune memory. We further show that human glioblastoma tissue can respond to the therapy and lay the foundations for combined intracranial immunotherapies by using crosslinked biodegradable brain implants.
Heterogeneity of Inflammation-associated Synovial Fibroblasts in Rheumatoid Arthritis and Its Drivers
Authors: Smith Melanie H , Gao Vianne R , Schizas Michail , Kochen Alejandro , DiCarlo Edward F , Goodman Susan M , Norman Thomas M , Donlin Laura T , Leslie Christina S , Rudensky Alexander Y
Published: March 2022

Inflammation of non-barrier immunologically quiescent tissues is associated with a massive influx of blood-borne innate and adaptive immune cells. Cues from the latter are likely to alter and expand the spectrum of states observed in cells that are constitutively resident. However, local communications between immigrant and resident cell types in human inflammatory disease remain poorly understood. Here, we explored heterogeneity of synovial fibroblasts (FLS) in inflamed joints of rheumatoid arthritis (RA) patients using paired single cell RNA and ATAC sequencing (scRNA/ATAC-seq), multiplexed imaging, and spatial transcriptomics along within vitromodeling of cell extrinsic factor signaling. These analyses suggest that local exposures to myeloid and T cell derived cytokines, TNFα, IFNγ, IL-1β, or lack thereof, drive six distinct FLS states some of which closely resemble fibroblast states in other disease-affected tissues including skin and colon. Our results highlight a role for concurrent, spatially distributed cytokine signaling within the inflamed synovium.
4D Cell-Condensate Bioprinting
Authors: Ding Aixiang , Tang Rui , He Felicia , Lee Sang Jin , Gasvoda Kaelyn , Alsberg Eben
Published: March 2022

4D bioprinting techniques that facilitate formation of shape-changing scaffold-free cell condensates with prescribed geometries have yet been demonstrated. Here, a simple yet novel 4D bioprinting approach is presented that enables formation of a shape-morphing cell condensate-laden bilayer system comprised of an actuation layer and a cell condensate-supporting microgel (MG) layer. The strategy produces scaffold-free cell condensates which morph over time into predefined complex shapes. With a sequential printing (i.e., MG printing first onto the preformed actuation hydrogel layer and cell-only printing inside the pre-printed MG construct second), cell condensate-laden bilayers with specific geometries are readily fabricated and can be further UV-crosslinked to form strong interlayer adhesion. Since the bilayers have tunable deformability and MG degradation can be tailored, this enables controllable morphological transformations and on-demand liberation of cell condensates. With this system, large cell condensate-laden constructs with various complex shapes were obtained through predefined conformational conversions. As a proof-of-concept study, the formation of the letter “C” and helix-shaped robust cartilage-like tissues differentiated from human mesenchymal stem cells (hMSCs) was demonstrated. This new system brings about a new versatile 4D bioprinting platform idea that is anticipated to broaden and facilitate the applications of cell condensation-based 4D bioprinting.
Tactile Stimulation Improves Cognition, Motor, and Anxiety-Like Behaviours and Attenuates the AD Pathology in Adult APP NL-G-F/NL-G-F mice
Authors: Hossain Shakhawat R. , Karem Hadil , Jafari Zahra , Kolb Bryan E. , Mohajerani Majid H.
Published: March 2022

Alzheimer’s Disease (AD) is one of the largest health crises in the world. There are, however, limited but expensive pharmaceutical interventions to treat AD and most of the treatment options are not for cure or prevention, but to slow down the progression of the disease. The aim of this study was to examine the effect of tactile stimulation on AD-like symptoms and pathology in APP NL-G-F/NL-G-F mice, a mouse model of AD. The results show that tactile stimulation improves the AD-like symptoms on tests of cognition, motor, and anxiety-like behaviours and these improvements are associated with reduced AD pathology in APP mice.
Transmembrane protein KIRREL1 regulates Hippo signaling via a feedback loop and represents a potential therapeutic target in YAP/TAZ-active cancers
Authors: Gu Yuan , Wang Yu , Sha Zhao , Li Jian , He Chenxi , Lan Fei , Yu Fa-Xing
Published: March 2022

Dysregulation of the Hippo tumor suppressor pathway and hyperactivation of YAP/TAZ are frequently observed in human cancers and represent promising therapeutic targets. However, strategies targeting the mammalian Hippo pathway are limited due to the lack of a well-established cell surface regulator. By combining protein interactome data and clinical data, we have identified transmembrane protein KIRREL1 as an upstream regulator of the Hippo pathway. KIRREL1 interacts with Hippo pathway components SAV1 and LATS1/2 via its intracellular C-terminal domain and promotes LATS1/2 activation by MST1/2 (Hippo kinases), in turn inhibiting YAP/TAZ activity and target gene expression. Conversely, YAP/TAZ directly induce the expression of KIRREL1 in a TEAD1-4–dependent manner. In mouse liver tumors driven by YAP activation, KIRREL1 protein is robustly induced. Moreover, KIRREL1 expression positively correlates with canonical YAP/TAZ target gene expression in clinical tumor specimens and predicts poor prognosis. Finally, transgenic expression of KIRREL1 effectively blocked tumorigenesis in a mouse intrahepatic cholangiocarcinoma model, suggesting an important role of KIRREL1 in inhibiting cancer development. Together, these findings indicate that KIRREL1 constitutes a negative feedback mechanism regulating the Hippo pathway, and serves as a cell surface marker and potential drug target in cancers with YAP/TAZ dependency.
Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens
Authors: Vinceti Alessandro , Perron Umberto , Trastulla Lucia , Iorio Francesco
Published: March 2022

Pooled genome-wide CRISPR-Cas9 screens are furthering our mechanistic understanding of human biology and have allowed us to identify new oncology therapeutic targets. Scale-limited CRISPR-Cas9 screens – typically employing guide RNA libraries targeting subsets of functionally related genes, individual biological pathways, or portions of the druggable genome – constitute an optimal setting for investigating narrow hypotheses and they are easier to execute on complex models, such as organoids and in vivo models. Different supervised methods are used for the computational analysis of genome-wide CRISPR-Cas9 screens; most are not well suited for scale-limited screens as they require large sets of positive/negative control genes (gene templates) to be included among the screened ones. We have developed a computational framework identifying optimal subsets of known essential and nonessential genes (at different subsampling percentages) that can be used as templates for supervised analyses of scale-limited CRISPR-Cas9 screens, while having a reduced impact on the size of the employed library.

Highlights

Scale-limited CRISPR-Cas9 screens are experimentally easier than genome-wide screens

Reference gene templates are used for supervised analyses of genome-wide screens

Reduced templates allow supervised analyses of scale-limited CRISPR-Cas9 screens

We present optimal reduced templates and a computational method to assemble them

Graphical abstract
Mutation patterns in SARS-COV-2 Alpha and Beta variants indicate non-neutral evolution
Authors: Kurpas Monika , Kimmel Marek
Published: March 2022

Due to the emergence of new variants of the SARS-CoV-2 coronavirus, the question of how the viral genomes evolved, leading to the formation of highly infectious strains, becomes particularly important. Two early emergent strains, Alpha and Beta, characterized by a significant number of missense mutations, provide natural testing samples.

In this study we are exploring the history of each of the segregating sites present in Alpha and Beta variants of concern, to address the question whether defining mutations were accumulating gradually leading to the formation of sequence characteristic of these variants.

Our analysis exposes data features that suggest other than neutral evolution of SARS-CoV-2 genomes, leading to emergence of variants of concern. We observe only small number of possible combinations of mutations indicating rapid evolution of genomes. In addtion, mutation patterns observed in whole genome samples of Alpha and Beta variants also indicate presence of stronger selection than in remaining genome samples.
Evolutionary analysis of genomes of SARS-CoV-2-related bat viruses suggests old roots, constant effective population size, and possible increase of fitness
Authors: Kurpas Monika , Jaksik Roman , Kimmel Marek
Published: March 2022

It is of vital practical interest to understand the co-evolution of bat β-coronaviruses with their hosts, since a number of these most likely crossed the species boundaries and infected humans. Complete sequences of 47 consensus genomes are available for bat β-coronaviruses related to the SARS-CoV-2 human virus. We carried out several types of evolutionary analyses using these data. First, using the publicly available BEAST 2 software, we generated phylogenetic trees and skyline plots. The roots of the trees, both for the entire sequences and subsequences coding for the E and S proteins as well as the 5’ and 3’ UTR regions, are estimated to be located from several decades to more than a thousand years ago, while the effective population sizes remained largely constant. Motivated by this, we developed a simple estimator of the effective population size in a Moran model with constant population, which, under the model is equal to the expected age of the MRCA measured in generations. Comparisons of these estimates to those produced by BEAST 2 shows qualitative agreement. We also compared the site frequency spectra (SFS) of the bat genomes to those provided by the Moran Tug-of-War model. Comparison does not exclude the possibility that overall fitness of the bat β-coronaviruses was increasing over time as a result of directional selection. Stability of interactions of bats and their viruses was considered likely on the basis of specific manner in which bat immunity is tuned, and it seems consistent with our analysis.
Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature
Authors: Boppana Avinash , Lee Sujin , Malhotra Rajeev , Halushka Marc , Quardokus Ellen M , Herr Bruce W. , Börner Katy , Weber Griffin M
Published: March 2022

More than 150 scientists from 17 consortia are collaborating on an international project to build a Human Reference Atlas, which maps all 37 trillion cells in the healthy adult human body. The initial release of this atlas provided hierarchical lists of the anatomical structures, cell types, and biomarkers in 11 organs. Here, we describe the methods we used as part of this initiative to build the first open, computer-readable, and comprehensive database of the adult human blood vasculature, called the Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF). It includes 961 vessels and their branching connections, 10 cell types, and 10 biomarkers. With this paper we are releasing additional details on vessel types and subtypes, branching sequence, anastomoses, portal systems, microvasculature, functional tissue units, mappings to regions vessels supply or drain, and links to 3D reference objects. Future versions will add variants, geometric properties of vessels, and connections to the lymph vasculature; and, it will iteratively expand and improve the database as additional experimental data become available through the participating consortia.
High Viral Specific Antibody Convalescent Plasma Effectively Neutralizes SARS-CoV-2 Variants of Concern
Authors: Li Maggie , Beck Evan J. , Laeyendecker Oliver , Eby Yolanda , Tobian Aaron AR , Caturegli Patrizio , Wouters Camille , Chiklis Gregory R. , Block William , McKie Robert , Joyner Michael , Wiltshire Timothy D. , Dietz Allan B. , Gniadek Thomas J. , Shapiro Arell , Yarava Anusha , Lane Karen , Hanley Daniel , Bloch Evan M. , Shoham Shmuel , Cachay Edward R. , Meisenberg Barry R. , Huaman Moises A. , Fukuta Yuriko , Patel Bela , Heath Sonya L. , Levine Adam C. , Paxton James H. , Anjan Shweta , Gerber Jonathan M. , Gebo Kelly A. , Casadevall Arturo , Pekosz Andrew , Sullivan David J. ,   the CSSC group
Published: March 2022

The ongoing evolution of SARS-Co-V2 variants to omicron severely limits available effective monoclonal antibody therapies. Effective drugs are also supply limited. Covid-19 convalescent plasma (CCP) qualified for high antibody levels effectively reduces immunocompetent outpatient hospitalization. The FDA currently allows outpatient CCP for the immunosuppressed. Viral specific antibody levels in CCP can range ten-to hundred-fold between donors unlike the uniform viral specific monoclonal antibody dosing. Limited data are available on the efficacy of polyclonal CCP to neutralize variants. We examined 108 pre-delta/pre-omicron donor units obtained before March 2021, 20 post-delta COVID-19/post-vaccination units and one pre-delta/pre-omicron hyperimmunoglobulin preparation for variant specific virus (vaccine-related isolate (WA-1), delta and omicron) neutralization correlated to Euroimmun S1 IgG antibody levels. We observed a 2-to 4-fold and 20-to 40-fold drop in virus neutralization from SARS-CoV-2 WA-1 to delta or omicron, respectively. CCP antibody levels in the upper 10% of the 108 donations as well as 100% of the post-delta COVID-19/post-vaccination units and the hyperimmunoglobulin effectively neutralized all three variants. High-titer CCP neutralizes SARS-CoV-2 variants despite no previous donor exposure to the variants.

Key points

All of the post-delta COVID-19/post vaccination convalescent plasma effectively neutralizes the omicron and delta variants.

High-titer CCP and hyperimmunoglobulin neutralizes SARS-CoV-2 variants despite no previous donor exposure to the variants.
Descriptive epidemiology of cardiorespiratory fitness in UK adults: The Fenland Study
Authors: Gonzales Tomas I. , Westgate Kate , Hollidge Stefanie , Lindsay Tim , Wijndaele Katrien , Forouhi Nita G. , Griffin Simon , Wareham Nick , Brage Soren
Published: March 2022

Background

Cardiorespiratory fitness is rarely measured in population studies. Most studies of fitness do not examine differences by population subgroups or seasonal trends.

Methods

We used a validated submaximal exercise test to measure fitness in 5976 women and 5316 men, residing in England. We expressed fitness as maximal oxygen consumption per kilogram total body mass (VO2maxtbm) and fat free mass (VO2maxffm). Descriptive statistics were computed across anthropometric and sociodemographic characteristics, as well as across the year. Progressive multivariable analyses were performed to examine mediation by physical activity energy expenditure (PAEE) and BMI.

Results

Mean±SD VO2maxtbm was lower in women (35.4±7.6 ml·min-1·kg-1) than men (42.1±7.4 ml·min-1·kg-1) but VO2maxffm was similar (women: 59.7±11.8 ml·min-1·kg-1; men: 62.5±10.4 ml·min-1·kg-1). Fitness was inversely associated with age but not after adjustment for PAEE. People in more physically demanding jobs were fitter compared to those in sedentary jobs but this association was attenuated in women and reversed in men following adjustment for total PAEE. PAEE and BMI and were positively associated with fitness at all levels of adjustment when fitness was expressed relative to fat-free mass. Fitness during summer was 4% higher than the winter among women, but did not differ by season among men.

Conclusions

Fitness was inversely associated with age but less steeply than anticipated, suggesting older generations are comparatively fitter than younger generations. PAEE and BMI were stronger determinants of the variance in fitness than any other characteristic including age. This emphasizes the importance of modifiable physical activity behaviours in public health interventions.

KEY MESSAGES

Fitness was inversely associated with age but less steeply than anticipated, suggesting older generations are comparatively fitter than younger generations

Relationships between cardiorespiratory fitness and sociodemographic characteristics were primarily mediated by physical activity.

A one standard deviation difference in physical activity had the same impact on cardiorespiratory fitness as being 25 years younger
Patients with CLL have similar high risk of death upon the omicron variant of COVID-19 as previously during the pandemic
Authors: Niemann Carsten U , Cunha-Bang Caspar da , Helleberg Marie , Ostrowski Sisse Rye , Brieghel Christian
Published: March 2022

Previous studies have shown that patients with chronic lymphocytic leukemia (CLL) and coronavirus disease 2019 (COVID-19) have high mortality rates. The omicron variant has been reported to give milder disease in the general population, but outcomes of infections with the omicron variant among immunocompromised patients have not previously been reported. In a population-based cohort we assessed rates of hospitalizations, ICU-admissions, and 30-day all-cause mortality among all patients with CLL from Eastern Denmark testing positive for severe adult respiratory syndrome coronavirus 2 (SARS-CoV-2) in time periods before and after dominance of the omicron variant. Rates of hospitalizations and ICU-admissions declined significantly, whereas 30-day mortality remained as high as 23% in the period with dominance of the omicron sublineage BA.2 variant. Thus, patients with CLL in general and in particular those above 70 years of age with one or more comorbidities should be considered for closer monitoring and pre-emptive antiviral therapy upon a positive SARS-CoV-2 test.

Key points

The omicron variant of COVID-19 leads to high fatality rates in CLL, despite milder disease in the background population

Patients with CLL who test positive for SARS-CoV-2 in the era of the omicron variant should be considered for pre-emptive antiviral therapy

Explanation of novelty

The omicron variant has been reported to give milder disease in the general population, but outcomes of infections with the omicron variant among immunocompromised patients have not previously been reported. These population-based data on outcome for patients with CLL upon infection with the omicron variant of SARS-CoV-2 warrants closer monitoring and pre-emptive antiviral therapy upon a positive SARS-CoV-2 test for patients with CLL.
Childhood meningitis in rural Gambia: 10 years of population-based surveillance
Authors: Ikumapayi Usman N , Hill Philip C , Hossain Ilias , Olatunji Yekini , Ndiaye Malick , Badji Henry , Manjang Ahmed , Salaudeen Rasheed , Ceesay Lamin , Adegbola Richard A , Greenwood Brian M , Mackenzie Grant A
Published: March 2022

Background

The introduction in many countries of conjugate vaccines against Haemophilus influenzae type-b, Streptococcus pneumoniae, and Neisseria meningitidis has led to significant reductions in acute bacterial meningitis (ABM) in children. However, recent population-based data on ABM in sub-Saharan Africa are limited.

Methods

Population-based surveillance for meningitis was carried out in a rural area of The Gambia under demographic surveillance from 2008 to 2017, using standardised criteria for referral, diagnosis and investigation. We calculated incidence using population denominators.

Results

We diagnosed 1,599 patients with suspected meningitis and collected cerebrospinal fluid (n=1,121) and/or blood (n=1,070) from 1,427 (88%) of cases. We detected 169 cases of ABM, 209 cases of non-bacterial meningitis and 1,049 cases of clinically suspected meningitis. The estimated average annual incidence of ABM was high at 145 per 100,000 population in the <2-month age group, 56 per 100,000 in the 2–23-month age group, but lower at 5 per 100,000 in the 5–14-year age group. The most common causes of ABM were Streptococcus pneumoniae (n=44), Neisseria meningitidis (n=42), and Gram-negative coliform bacteria (n=26). Eighteen of 22 cases caused by pneumococcal serotypes included in PCV13 occurred prior to vaccine introduction and four afterwards. The overall case fatality ratio for ABM was 29% (49/169) and highest in the <2-month age group 37% (10/27). The fatality rate was 8.6% (18/209) for non-bacterial meningitis cases.

Conclusions

Gambian children continue to experience substantial morbidity and mortality associated with suspected meningitis, especially acute bacterial meningitis. Such severely ill children in sub-Saharan Africa require improved diagnostics and clinical care.

Summary of the articles main point

Population-based surveillance in a health demographic surveillance area in Gambia showed a high incidence and mortality in clinically suspected, acute-bacterial, and non-bacterial meningitis among children 14-years of age. Findings revealed potential gaps in the diagnosis of meningitis in The Gambia requiring urgent attention.
Describing a complex primary health care population in a learning health system to support future decision support and artificial intelligence initiatives
Authors: Kueper Jacqueline K. , Rayner Jennifer , Zwarenstein Merrick , Lizotte Daniel J.
Published: March 2022

Introduction

Learning health systems (LHS) use data to improve care. Descriptive epidemiology to reveal health states and needs of the LHS population is essential for informing LHS initiatives, including development of decision support tools. To properly characterize complex populations, both simple statistical and artificial intelligence techniques can be useful. We present the first large-scale description of the population served by one of the first primary care LHS in North America.

Objectives

Our objective is to describe sociodemographic, clinical, and health care use characteristics of adult primary care clients served by the Alliance for Healthier Communities, which provides team-based primary health care through Community Health Centres (CHCs) across Ontario, Canada.

Methods

Using electronic health record data from 2009-2019 for all CHCs, we perform table-based summaries for each characteristic; and apply unsupervised leaning techniques to explore patterns of common condition co-occurrence, care provider teams, and care frequency.

Results

Of the 221,047 eligible clients, those at CHCs that primarily serve those most at risk (homeless, mental health, addictions) tend to have more chronic conditions and social determinants of health, which are also prominent in clients with multimorbidity. Most care is provided by physician and nursing providers, with heterogeneous combinations of other provider types. A subset of clients have many issues addressed within single-visits and there is within- and between-client variability in care frequency. Example methodological considerations learned for future LHS initiatives include the need to carefully consider the level of analysis and associated implications for data quality and target population, heterogeneity in conditions and care characteristics, and non-uniform risk profiles across the care history.

Conclusions

We demonstrate the use of methods from statistics and artificial intelligence, applied with an epidemiological lens, to provide an overview of a complex primary care population. In addition to substantive findings, we discuss implications for future LHS initiatives.
Omicron-specific mRNA vaccine elicits potent immune responses in mice, hamsters, and nonhuman primates
Authors: Wu Yi , Shen Yanqiong , Wu Namei , Zhang Xinghai , Chen Shaohong , Yang Chang , Zhou Junhui , Wu Yan , Chen Da , Wang Li , Wang Yuye , Xu Jiejie , Liu Ke , Wang Chao , Zhang Huajun , Xia Ninuo , Chiu Sandra , Wang Yucai
Published: March 2022

SARS-CoV-2 has infected more than 400 million people around the globe and caused millions of deaths. Since its identification in November 2021, Omicron, a highly transmissible variant, has become the dominant variant in most countries. Omicron’s highly mutated spike protein, the main target of vaccine development, significantly compromises the immune protection from current vaccination. We develop an mRNA vaccine (SOmicron-6P) based on an Omicron-specific sequence. In mice, SOmicron-6P shows superior neutralizing antibodies inducing abilities to a clinically approved inactivated virus vaccine, a clinically approved protein subunit vaccine, and an mRNA vaccine (SWT-2P) with the same sequence of BNT162b2 RNA. Significantly, SOmicron-6P induces a 14.4∼27.7-fold and a 28.3∼50.3-fold increase of neutralizing activity against the pseudovirus of Omicron and authentic Omicron compared to SWT-2P, respectively. In addition, two doses SOmicron-6P significantly protects Syrian hamsters against challenge with SARS-CoV-2 Omicron variant and elicits high titers of nAbs in a dose-dependent manner in macaques. Our results suggest that SOmicron-6P offers advantages over current vaccines, and it will be helpful for those with weak immunity.
Structure of cyanobacterial photosystem I complexed with Cytochrome c6 and Ferredoxin at 1.97 Å resolution
Authors: Li Jiannan , Hamaoka Noriyuki , Makino Fumiaki , Kawamoto Akihiro , Lin Yuxi , Rögner Matthias , Nowaczyk Marc M. , Lee Young-Ho , Namba Keiichi , Gerle Christoph , Kurisu Genji
Published: March 2022

Photosystem I (PSI) is a light driven electron pump transferring electrons from Cytochrome c6 (Cyt c6) to Ferredoxin (Fd). An understanding of this electron transfer process is hampered by a paucity of structural detail concerning the binding of Fd and the bound Cyt c6. Here we describe the high resolution cryo-EM structure of Thermosynechococcus elongatus BP-1 PSI in complex with Fd and Cyt c6. In our structure Cyt c6 is loosely bound in a non-productive site on the periphery of the complex. Side chain interactions at the PSI:Fd interface are visualized in detail. The structure explains the properties of mutants of PsaE and PsaC and suggests a molecular switch for the dissociation of Fd upon reduction. Calorimetry-based thermodynamic analyses confirms a single binding site for Fd and demonstrates that PSI:Fd complexation is purely driven by entropy. A reaction cycle for the efficient transfer of electrons from Cyt c6 to Fd via PSI is proposed.
Tween-20 induces the structural remodelling of single lipid vesicles
Authors: Dresser Lara , Graham Sarah P. , Miller Lisa M. , Schaefer Charley , Conteduca Donato , Johnson Steven , Leake Mark C. , Quinn Steven D.
Published: March 2022

The interaction of Tween-20 with lipid membranes is crucial for a number of biotechnological applications including viral inactivation and membrane protein extraction, but the underlying mechanistic details have remained elusive. Evidence from ensemble assays supports a global model of Tween-20 induced membrane disruption that broadly encompasses association of the surfactant with the membrane surface, membrane fragmentation and the release of mixed micelles to solution, but whether this process involves intermediate and dynamic transitions between regimes is an open question. In search of the mechanistic origins of membrane disruption, increasing focus is put on identifying Tween-20 interactions with highly controllable model membranes. In light of this, and to unveil quantitative mechanistic details, we employed highly interdisciplinary biophysical approaches, including quartz-crystal microbalance with dissipation monitoring, steady-state and time-resolved fluorescence and FRET spectroscopy, dynamic light scattering, fluorescence correlation spectroscopy, wide-field single-vesicle imaging and scanning electron microscopy, to interrogate the interactions between Tween-20 and both freely-diffusing and surface-immobilized model-membrane vesicles. Using ultrasensitive sensing approaches, we discovered that Tween-20 leads to a stepwise and phase-dependent structural remodelling of sub-micron sized vesicles that includes permeabilization and swelling, even at detergent concentrations below the critical micellar concentration. These insights into the structural perturbation of lipid vesicles upon Tween-20 interaction highlight the impact on vesicle conformation prior to complete solubilization, and the tools presented may have general relevance for probing the interaction between lipid vesicles and a wide variety of disruptive agents.
Redundant PLETHORA activity promotes development of early embryonic cell lineages in Arabidopsis
Authors: Kerstens Merijn , Galinha Carla , Hofhuis Hugo , Nodine Michael , Scheres Ben , Willemsen Viola
Published: March 2022

The BABY BOOM/PLETHORA4 (BBM/PLT4) transcription factor has received much attention due to its ability to induce somatic and zygotic embryogenesis, two processes of pivotal importance in plant breeding. Loss of additional AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) genes, encoding members of the APETALA2 transcription factor family, causes embryo arrest and abortion, but whether BBM/PLT4 provides specific information for embryo development has remained unknown. Here, we reveal that AIL/PLT members are expressed in partially overlapping domains from their first appearance in the apical cell daughter of the zygote. Redundant early embryonic activity of BABY BOOM/PLT4 and PLT2 triggers development of the apical cell lineage and is required to initiate embryonic primordia. Furthermore, promoter swap experiments show that PLT1 and PLT3 expression in the expression domains of PLT2 and BABY BOOM/PLT4 is sufficient to rescue plt2 bbm double mutants. Our data indicate that generic AIL/PLT factors, involved in maintenance of stem cells, promotion of cell division and suppression of cell differentiation, provide the necessary information to initiate embryogenesis in Arabidopsis.
Chaperones facilitate heterologous expression of naturally evolved putative de novo proteins
Authors: Eicholt Lars A. , Aubel Margaux , Berk Katrin , Bornberg-Bauer Erich , Lange Andreas
Published: March 2022

Over the past decade, evidence has accumulated that new protein coding genes can emerge de novo from previously non-coding DNA. Most studies have focused on large scale computational predictions of de novo protein coding genes across a wide range of organisms. In contrast, experimental data concerning the folding and function of de novo proteins is scarce. This might be due to difficulties in handling de novo proteins in vitro, as most are predicted to be short and disordered. Here we propose a guideline for the effective expression of eukaryotic de novo proteins in Escherichia coli.

We used 11 sequences from Drosophila melanogaster and 10 from Homo sapiens, that are predicted de novo proteins from former studies, for heterologous expression. The candidate de novo proteins have varying secondary structure and disorder content. Using multiple combinations of purification tags, E. coli expression strains and chaperone systems, we were able to increase the number of solubly expressed putative de novo proteins from 30 % to 62 %. Our findings indicate that the best combination for expressing putative de novo proteins in E.coli is a GST-tag with T7 Express cells and co-expressed chaperones. We found that, overall, proteins with higher predicted disorder were easier to express.
The mitochondrion of Plasmodium falciparum generates essential acetyl-CoA for protein acetylation
Authors: Nair Sethu C. , Munro Justin T. , Mann Alexis , Llinás Manuel , Prigge Sean T.
Published: March 2022

Coenzyme A (CoA) biosynthesis is an excellent target for antimalarial intervention. While most studies have focused on the use of CoA to produce acetyl-CoA in the apicoplast and the cytosol of malaria parasites, mitochondrial acetyl-CoA production is less well understood. In the current study, we performed metabolite labeling experiments to measure endogenous metabolites in Plasmodium falciparum lines with genetic deletions affecting mitochondrial dehydrogenase activity. Our results show that mitochondrial acetyl-CoA biosynthesis is essential for parasite growth and identify a catalytic redundancy between the two main ketoacid dehydrogenase enzymes, both of which are able to produce acetyl-CoA. The activity of these enzymes is dependent on the lipoate attachment enzyme LipL2, which is essential for parasite survival solely based on its role in supporting acetyl-CoA metabolism. We also find that acetyl-CoA produced in the mitochondrion is essential for the acetylation of histones and other proteins outside of the mitochondrion. Taken together, our results demonstrate that the mitochondrion is an essential de novo source of acetyl-CoA and is required for P. falciparum protein acetylation critical to parasite survival.
TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1
Authors: Zhou Jianwen , Rasmussen Nikoline Lander , Olsvik Hallvard Lauritz , Akimov Vyacheslav , Hu Zehan , Evjen Gry , Blagoev Blagoy , Lamark Trond , Johansen Terje , Dengjel Jörn
Published: March 2022

Limitation of excessive inflammation due to selective degradation of pro-inflammatory proteins is one of the cytoprotective functions attributed to autophagy. In the current study, we highlight that selective autophagy also plays a vital role in promoting the establishment of a robust inflammatory response. Under inflammatory conditions, here TLR3-activation by poly(I:C) treatment, the inflammation repressor TNIP1 (TNFAIP3 interacting protein 1) is phosphorylated by TBK1 (Tank-binding kinase 1) activating a LIR motif that leads to the selective autophagy-dependent degradation of TNIP1, supporting expression of pro-inflammatory genes and proteins. Thus, similarly as in cancer, autophagy may play a dual role in controlling inflammation depending on the exact state and timing of the inflammatory response.

Autophagy is well known for its anti-inflammatory effects. Here, we highlight that selective, autophagy-dependent degradation of the inflammation repressor TNIP1 supports pro-inflammatory gene and protein expression. Similarly as in cancer, autophagy appears to play a dual role in controlling inflammation.
Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli
Authors: Shibai Atsushi , Kotani Hazuki , Sakata Natsue , Furusawa Chikara , Tsuru Saburo
Published: March 2022

The evolutionary speed of a protein sequence is constrained by its expression level, with highly expressed proteins evolving relatively slowly. This negative correlation between expression levels and evolutionary rates (known as the E–R anticorrelation) has already been widely observed in past macroevolution between species from bacteria to animals. However, it remains unclear whether this seemingly general law also governs recent evolution, including past and de novo, within a species. However, the advent of genomic sequencing and high-throughput phenotyping, particularly for bacteria, has revealed fundamental gaps between the two evolutionary processes and has provided empirical data opposing the possible underlying mechanisms which are widely believed. These conflicts raise questions about the generalization of the E–R anticorrelation and the relevance of plausible mechanisms. To explore the ubiquitous impact of expression level on molecular evolution, and to test the relevance of the possible underlying mechanisms, we analyzed the genome sequences of 99 strains of Escherichia coli for microevolution in nature. We also analyzed genomic mutations accumulated under laboratory conditions as a model of de novo microevolution. Here, we show that the E–R anticorrelation is significant in both past and de novo microevolution in E. coli. Our data also confirmed ongoing purifying selection acting on highly expressed genes. Ongoing selection included codon-level purifying selection, supporting the relevance of the underlying mechanisms. However, their contributions to the constraints in recent evolution might be smaller than previously expected from past macroevolution.
Ligand-mediated structural dynamics of a mammalian pancreatic KATP channel
Authors: Sung Min Woo , Driggers Camden M. , Mostofian Barmak , Russo John D. , Patton Bruce L. , Zuckerman Daniel M. , Shyng Show-Ling
Published: March 2022

Regulation of pancreatic KATP channels involves orchestrated interactions of channel subunits, Kir6.2 and SUR1, and their ligands. How ligand interactions affect channel conformations and activity is not well understood. To elucidate the structural correlates pertinent to ligand interactions and channel gating, we compared cryo-EM structures of channels in the presence and absence of pharmacological inhibitors and ATP, focusing on channel conformational dynamics. We found pharmacological inhibitors and ATP enrich a channel conformation in which the Kir6.2 cytoplasmic domain is closely associated with the transmembrane domain relative to one where the Kir6.2 cytoplasmic domain is extended away into the cytoplasm. This conformation change remodels a network of intra and inter-subunit interactions as well as both the ATP and PIP2 binding pockets. The structures resolved key contacts between the distal N-terminus of Kir6.2 and SUR1’s ABC module involving residues implicated in channel function. A SUR1 residue, K134, is identified to directly contribute to the PIP2 binding pocket. Molecular dynamics simulations revealed two Kir6.2 residues, K39 and R54, that mediate both ATP and PIP2 binding, suggesting a mechanism for competitive gating by ATP and PIP2.