bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanopore Translocation of Topologically Linked DNA Catenanes
Authors: Rheaume Sierra N. , Klotz Alexander R.
Published: August 2022

The electrical signal associated with a biopolymer translocating through a nanoscale pore depends depends on the size, topology, and configuration of each molecule. Building upon recent interest in using solid-state nanopores for studying the topology of knotted and supercoiled DNA, we present the first experimental observations of topologically linked catenanes translocating through a solid-state nanopore. Using restriction enzymes, linked circular molecules were isolated from the mitochondrial DNA of Crithidia fasciculata, a structure known as a kinetoplast that is comprised of thousands of topologically interlocked minicircles. Digested kinetoplasts produce a spectrum of catenane topologies, which are identified from their nanopore translocation signals by spikes in the blockade current associated with the topological linkages. We identify the translocation signatures of 2-catenanes, linear and triangular 3-catenanes, and several types of 4- and 5-catenanes as well as more complex structures. Measurements of the translocation time of 2- and 3-catenanes suggest that topological friction between the linkages and the pore slows the translocation time of these structures, as predicted in recent simulations.
Group B streptococcal membrane vesicles induce proinflammatory cytokine production and are sensed in an NLRP3 inflammasome-dependent mechanism in human macrophages
Authors: McCutcheon Cole R. , Gaddy Jennifer A. , Aronoff David M. , Manning Shannon D. , Petroff Margaret G.
Published: August 2022

Group BStreptococcus(GBS) is a major cause of fetal and neonatal mortality worldwide. Many of the adverse effects associated with invasive GBS are associated with inflammation that leads to chorioamnionitis, preterm birth, sepsis, and meningitis; therefore, understanding bacterial factors that promote inflammation is of critical importance. Membrane vesicles (MVs), which are produced by many pathogenic and non-pathogenic bacteria, may modulate host inflammatory responses. In mice, GBS MVs injected intra-amniotically can induce preterm birth and fetal death. Although it is known that GBS MVs induce large-scale leukocyte recruitment into infected tissues, the immune effectors driving these responses are unclear. Here, we hypothesized that macrophages respond to GBS-derived MVs by producing proinflammatory cytokines and are recognized through one or more pattern recognition receptors. We show that THP-1 macrophage-like cells produce high levels of neutrophil- and monocyte-specific chemokines in response to MVs derived from different clinical isolates of GBS. Interleukin (IL)-1β was significantly upregulated in response to MVs, which was independent of NF-kB signaling but dependent on both caspase-1 and NLRP3. These data indicate that MVs contain one or more pathogen-associated molecular patterns that can be sensed by the immune system. Furthermore, this study identifies the NLRP3 inflammasome as a novel sensor of GBS MVs. Our data additionally indicate that MVs may serve as immune effectors that can be targeted for immunotherapeutics, particularly given that similar responses were observed across this subset of GBS isolates.
Characteristics of People with Type I or Type II Diabetes with and without a History of Homelessness: A Population-based Cohort Study
Authors: Wiens Kathryn , Bai Li , Austin Peter C , Ronksley Paul E , Hwang Stephen W , Spackman Eldon , Booth Gillian L , Campbell David JT
Published: August 2022

Introduction

Homelessness poses unique barriers to diabetes management. Population-level data on the risks of diabetes outcomes among people experiencing homelessness are needed to inform resource investment. The aim of this study was to create a population cohort of people with diabetes with a history of homelessness to understand their unique demographic and clinical characteristics and improve long-term health outcomes.

Methods

Ontario residents with diabetes were identified in administrative hospital databases between 2006 and 2020. A history of homelessness was identified using a validated algorithm. Demographic and clinical characteristics were compared between people with and without a history of homelessness. Propensity score matching was used to create a cohort of people with diabetes experiencing homelessness matched to comparable non-homeless controls.

Results

Of the 1,455,567 patients with diabetes who used hospital services, 0.7% (n=8,599) had a history of homelessness. Patients with a history of homelessness were younger (mean: 54 vs 66 years), more likely to be male (66% vs 51%) and more likely to live in a large urban centre (25% vs 7%). Notably, they were also more likely to be diagnosed with mental illness (49% vs 2%) and be admitted to a designated inpatient mental health bed (37% versus 1%). A suitable match was found for 5219 (75%) people with documented homelessness. The derived matched cohort was balanced on important demographic and clinical characteristics.

Conclusion

People with diabetes experiencing homelessness have unique characteristics that may require additional supports. Population-level comparisons can inform the delivery of tailored diabetes care and self-management resources.
Risk factors, temporal dependence, and seasonality of human ESBL-producing E. coli and K. pneumoniae colonisation in Malawi: a longitudinal model-based approach
Authors: Sammarro Melodie , Rowlingson Barry , Cocker Derek , Chidziwisano Kondwani , Jacob Shevin T. , Kajumbula Henry , Mugisha Lawrence , Musoke David , Lester Rebecca , Morse Tracy , Feasey Nicholas , Jewell Chris
Published: August 2022

Background

Antimicrobial resistance (AMR) represents an important threat to achieving the sustainable development goals in Sub-Saharan Africa (sSA). sSA is reported to have the highest estimated death rate attributable to AMR, with Extended-Spectrum Beta-Lactamase-producing Enterobacterales, such as Klebsiella pneumoniae and Escherichia coli, representing the greatest challenge. However, the dynamics of human colonisation with such bacteria in the sSA community setting are not well known. Inadequate water, sanitation and hygiene (WASH) infrastructure and associated behaviours are thought to play an important role in transmission of AMR-bacteria, and an improved understanding of the temporal dynamics of within-household transmission could help inform the design of public health policies that interrupt transmission of AMR-bacteria.

Methods and Findings

In this 18-month study, individuals from households in diverse areas of Southern Malawi were recruited and human stool samples were longitudinally collected. Using microbiological data and household surveys, we built a multivariable hierarchical harmonic logistic regression model to identify risk factors for colonisation with ESBL-producing E. coli and K. pneumoniae, reflecting household structure and temporal correlation of colonisation status between timepoints.

Important risk factors were identified, with men having a lower risk of becoming colonised with ESBL-producing E. coli (OR 0.786 CrI[0.678-0.910]) and the use of a tube well or a borehole as a water drinking source highly increasing the risk of becoming colonised (OR 1.550 CrI[1.003-2.394]). Coming into contact with standing water also appeared to be negatively associated with colonisation status (OR 0.749 CrI[0.574-0.978]). For ESBL-producing K. pneumoniae, having recently taken a course of antibiotics increased the risk of being colonised (OR 1.281 CrI[1.049-1.565]). We also found a negative association between eating from shared plates and colonisation with ESBL-producing K. pneumoniae (OR 0.672 CrI[0.460-0.980]). Finally, we detected a temporal correlation range of eight to eleven weeks, providing evidence that within-household transmission occurs within this time frame.

Conclusions

We suggest that interventions aimed at preventing transmission might have the best impact when targeted at the household-level and focused on a combination of improving WASH infrastructure and modifying associated behaviours. Additionally, we showed that antibiotic use is important when looking at colonisation with ESBL-producing K. pneumoniae and therefore infection prevention and control measures and antibiotic use and stewardship training could help in reducing transmission.
ADuLT: An efficient and robust time-to-event GWAS
Authors: Pedersen Emil M. , Agerbo Esben , Plana-Ripoll Oleguer , Steinbach Jette , Krebs Morten Dybdahl , Hougaard David M. , Werge Thomas , Nordentoft Merete , Børglum Anders D. , Musliner Katherine L. , Ganna Andrea , Schork Andrew J. , Mortensen Preben B. , McGrath John J. , Privé Florian , Vilhjálmsson Bjarni J.
Published: August 2022

Proportional hazards models have previously been proposed to analyse time-to-event phenotypes in genome-wide association studies(GWAS). While proportional hazards models have many useful applications, their ability to identify genetic associations under different generative models where ascertainment is present in the analysed data is poorly understood. This includes widely used study designs such as case-control and case-cohort designs (e.g. the iPSYCH study design) where cases are commonly ascertained.

Here we examine how recently proposed and computationally efficient Cox regression for GWAS perform under different generative models with and without ascertainment. We also propose the age-dependent liability threshold model (ADuLT), first introduced as the underlying model for the LT-FH++ method, as an alternative approach for time-to-event GWAS. We then benchmark ADuLT with SPACox and standard case-control GWAS using simulated data with varying degrees of ascertainment. We find Cox regression GWAS to underperform when cases are strongly ascertained (cases are oversampled by a factor larger than 5), regardless of the generative model used. In contrast, we found ADuLT to be robust to case-control ascertainment, while being much faster to run. We then used the methods to conduct GWAS for four psychiatric disorders, ADHD, Autism, Depression, and Schizophrenia in the iPSYCH case-cohort sample, which has a strong case-ascertainment. Summarising across all four mental disorders, ADuLT found 20 independent genome-wide significant associations, while case-control GWAS found 17 and SPACox found 8, consistent with our simulation results.

As more genetic data are being linked to electronic health records, robust GWAS methods that can make use of age-of-onset information have the opportunity to increase power in analyses. We find that ADuLT to be a robust time-to-event GWAS method that performs on par with or better than Cox-regression GWAS, both in simulations and real data analyses of four psychiatric disorders. ADuLT has been implemented in an R package called LTFHPlus, and is available on GitHub.
NRX-101 (D-cycloserine plus lurasidone) vs. lurasidone for the maintenance of initial stabilization after ketamine in patients with severe bipolar depression with acute suicidal ideation and behavior: A randomized prospective phase 2 trial
Authors: Nierenberg Andrew , Lavin Philip , Javitt Daniel C. , Shelton Richard , Matthew Sanjay , Besthof Robert A , Javitt Jonathan C.
Published: August 2022

Objectives

We tested the hypothesis that after initial improvement with intravenous ketamine in patients with bipolar disorder (BD) with severe depression and acute suicidal thinking or behavior, a fixed-dose combination of oral D-cycloserine (DCS) and lurasidone (NRX-101) can maintain improvement more effectively lurasidone alone.

Methods

This was a multi-center, double-blind, two-stage, parallel randomized trial. Adult BD patients with depression and suicidal ideation or behavior were infused with ketamine or saline (Stage 1); those who improved were randomized to a fixed dose combination of DCS and lurasidone vs. lurasidone alone (Stage 2) to maintain the improvement achieved in Stage 1. Depression was measured by the Montgomery Åsberg Depression Rating Scale (MADRS) and suicidal thinking and behavior was measured by the Columbia Suicide Severity Rating Scale (C-SSRS); global improvement was measured by the clinical global severity scale (CGI-S).

Results

Thirty-seven patients were screened and 22 were enrolled, randomized, and treated. All 22 patients treated in Stage 1 (17 with ketamine and 5 with saline) were enrolled into Stage 2 and 11 completed the study. The fixed dose combination of DCS and lurasidone was significantly more effective than lurasidone alone in maintaining improvement in depression (MADRS LMS Δ-7.7; p=.03) and reducing suicidal ideation, as measured by C-SSRS (Δ-1.5; p=0.02) and by CGI-SS (Δ-2.9; p=0.03), and with a non-statistically significant decrease in depressive relapse (0% vs. 40%; p=0.07). This sequential treatment regimen did not cause any significant safety events and demonstrated improvements in patient reported side effects.

Conclusions

Sequential treatment of a single infusion of ketamine followed by NRX-101 maintenance is a promising therapeutic approach for reducing depression and suicidal ideation in patients with bipolar depression who require hospitalization due to acute suicidal ideation and behavior. On the basis of these findings, Breakthrough Therapy Designation was awarded and a Special Protocol Agreement was granted by the FDA for a registrational trial.
Triple network model of brain connectivity changes related to adverse mood effects in an oral contraceptive placebo-controlled trial
Authors: Hidalgo-Lopez Esmeralda , Engman Jonas , Sundström Poromaa Inger , Gingnell Malin , Pletzer Belinda
Published: August 2022

Combined oral contraceptives (COC) are among the most commonly used contraceptive methods worldwide, and mood side effects are the major reason for discontinuation of treatment. We here investigate the directed connectivity patterns associated with the mood side effects of an androgenic COC in a double-blind randomized, placebo-controlled trial in women with a history of affective COC side effects (n=34). We used spectral dynamic causal modeling on a triple network model consisting of the default mode network (DMN), salience network (SN) and executive central network (ECN). Within this framework, we assessed the treatment-related changes in directed connectivity associated with adverse mood side effects. Overall, during COC use, we found a pattern of enhanced connectivity within the DMN and decreased connectivity within the ECN. The dorsal anterior cingulate cortex mediates an increased recruitment of the DMN by the ECN during treatment. Mood lability was the most prominent COC-induced symptom and also arose as the side effect most consistently related to connectivity changes. Connections that were related to increased mood lability showed increased connectivity during COC treatment, while connections that were related to decreased mood lability showed decreased connectivity during COC treatment. Among these, the connections with the highest effect size could also predict the participants’ treatment group above chance.

Significance Statement

Mood side effects are the major reason for discontinuation of oral contraceptive (OC) use. However, the neural substrate underlying these adverse mood effects is still unknown. Here, we investigate the connectivity changes during OC use in women with a history of OC-related mood side effects. We show that mood lability experienced during OC use relates to connectivity patterns previously reported across different mood disorders. The dorsal anterior cingulate cortex, crucial for emotional and cognitive regulation, arose as a mediator area between networks. These neural dynamics during OC treatment may affect cognitive processes underlying mood stability. These findings have important implications for women’s mental health and well-being.
The Effect of Novel Exogenous Ketone Supplements on Blood Beta-Hydroxybutyrate and Glucose
Authors: Falkenhain Kaja , Daraei Ali , Little Jonathan P
Published: August 2022

Background

Recently developed exogenous ketone monoester supplements can acutely raise blood β-OHB and lower blood glucose without the need for other nutritional modifications or invasive procedures. However, unpleasant taste and the potential for gastrointestinal discomfort may make adherence to a supplement regimen challenging. Two novel ketone supplements have been developed that promise an improved consumer experience but differ in their chemical properties; it is currently unknown how these affect blood β-OHB and blood glucose compared to the original ketone monoester supplement.

Methods

In a double-blind randomized cross-over pilot study, N = 12 healthy individuals (29 ± 5 years, BMI = 25 ± 4 kg/m2, 42% female) participated in three experimental trials with a different ketone supplement providing 10 grams of active ingredient in each trial; (i) the monoester (R)-3-hydroxybutyl (R)-3-hydroxybutyrate, (ii) D-β-hydroxybutyric acid with R-1,3-butanediol, and (iii) R-1,3-butanediol. Blood β-OHB and glucose were measured via finger prick capillary blood samples at baseline and across 240 minutes post-supplementation. Supplement acceptability, hunger, and gastrointestinal distress were assessed via questionnaires.

Results

β-OHB was elevated compared to baseline in all conditions. Total and incremental area under the curve (bothp< 0.05) and peak β-OHB (p< 0.001) differed between conditions with the highest values seen in the ketone monoester condition. Blood glucose concentration was reduced after consumption of each supplement, with no differences in total and incremental area under the curve across supplements. Supplement acceptability was greatest for D-β-hydroxybutyric acid with R-1,3-butanediol, with no effect on hunger or evidence of gastrointestinal distress across all supplements.

Conclusions

Despite differences in composition, all ketone supplements tested raised β-OHB with the highest values seen after ketone monoester ingestion. Blood glucose was lowered to a similar extent across the assessed time frame with all three supplements.
Clustering of adverse health and educational outcomes in adolescence following early childhood poverty: implications for UK’s ‘levelling up’ agenda
Authors: Villadsen Aase , Asaria Miqdad , Skarda Ieva , Ploubidis George B. , Williams Mark Mon , Brunner Eric John , Cookson Richard
Published: August 2022

Background

Early childhood poverty is associated with poorer health and educational outcomes in adolescence. However, there is limited evidence about the clustering of these adverse outcomes by income group.

Methods

We analysed five outcomes at age 17 known to limit life chances – psychological distress, self-assessed ill health, smoking, obesity, and poor educational achievement – using data from the longitudinal UK Millennium Cohort Study (N=15,245). We compared how single and multiple outcomes were distributed across quintiles of household income in early childhood (0-5 years) and modelled the maximum potential benefit of tackling the income gradient in these outcomes.

Findings

Children from the poorest households were 12.7(95% CI 6.4-25.1) times more likely than those from the richest to experience four or five adverse adolescent outcomes, with poor educational achievement and smoking showing the largest single risk ratios–4.6(95% CI: 4.2-5.0) and 3.6(95% CI 3.0-4.2), respectively. We modelled hypothetical absolute and relative poverty elimination scenarios, as well as an income inequality elimination scenario, and found these would yield maximum reductions in multiple adolescent adversity of 5%, 30%, and 80% respectively.

Interpretation

Early childhood poverty is more strongly correlated with multiple adolescent adversity than any single adverse outcome. Reducing absolute poverty alone is not sufficient to eliminate the life-long burden of multiple adversity, which disproportionately impacts children across the bottom three-fifths of the income distribution. An ambitious levelling up agenda needs co-ordinated multi-agency action to tackle the complex interacting factors generating the steep social gradient in multiple adolescent adversity.
Mislabeled learning for psychiatric disorder detection
Authors: Li Dongdong , Liu Wenbin , Han Henry
Published: August 2022

Mislabeled learning for high-dimensional data is essentially important in AI health and relevant fields but rarely investigated in machine learning. In this study, we address the challenge by proposing a novel mislabeled learning algorithm for high-dimensional data: psychiatric map diagnosis and applying it to solve a long-time bipolar disorder and schizophrenia misdiagnosis in psychiatry. The proposed algorithm converts each input high-dimensional SNP sample into a corresponding 2D characteristic image called a psychiatric map through feature self-organizing learning. It can automatically detect mislabeled observations and relabel them with the most likely ground truth before reproducible machine learning besides providing informative visualization for mislabeling detection. Our method attains more accurate and reproducible psychiatry diagnoses, besides discovering latent psychiatry subtypes not reported before. It works well for those datasets with a limited number of samples and achieves leading advantages over the deep learning peers. This study also presents new insight into the pathology of psychiatric disorders by constructing the devolution path of psychiatric states via relative entropy analysis that discloses latent internal transfer and devolution road maps between different psychiatric states. To the best of our knowledge, it is the first study to solve mislabeled learning for high-dimensional data and will inspire more future work in this field.
Common Genetic Variation Important in Early Subcortical Brain Development
Authors: Cullen Harriet , Dimitrakopoulou Konstantina , Patel Hamel , Curtis Charles , Batalle Dafnis , Gale-Grant Oliver , Cordero-Grande Lucilio , Price Anthony , Hajnal Joseph , Edwards A David
Published: August 2022

1.

Recent genome-wide association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with subcortical brain volumes. These studies have been undertaken in largely adult cohorts. To better understand the role of genetic variability in foetal and perinatal brain development, we investigate how common genetic variation affects subcortical brain development in a cohort of 208 term-born infants from the Developing Human Connectome Project.

We examine six SNPs, that have shown robust associations with subcortical brain volumes in adult studies and ask if these associations exist at birth. We then investigate whether genome-wide polygenic scores (GPSs) for adult subcortical brain volumes are predictive of the corresponding neonatal brain volume. Finally, we explore the relationship between GPSs for psychiatric disorders and subcortical brain volume at birth.

We find the association between SNP rs945270 and putamen volume, seen in adults, is present at birth (p=3.67×10-3, β=0.13, SE=0.04). The associations between SNP rs61921502 and hippocampal volume and SNP rs11111090 and brainstem volume are also nominally present in our neonatal cohort. We show that neonatal hippocampal, brainstem, putamen and thalamic volume are all significantly associated with the GPSs for their corresponding volume in adults. Finally, we find that GPSs for five psychiatric disorders and a cross-disorder score are not significantly predictive of subcortical brain volumes or total brain volume at birth. Our results indicate that SNPs important in shaping adult subcortical brain volume are also significant in foetal and perinatal brain development.

Key Points

We show that the association between the single nucleotide polymorphism, rs945270 and putamen volume, seen in adults, is present in neonates.

We show that neonatal hippocampal, putamen, brainstem and thalamic volumes are all significantly predicted by the genome-wide polygenic scores for corresponding adult brain volumes.

We do not find any robust association between genome-wide polygenic scores for psychiatric disorders and neonatal brain volume although we observe several nominal associations.
Screening Avian Pathogens in Eggs from Commercial Hatcheries in Nepal- an Effective Poultry Disease Surveillance Tool
Authors: Sharma Shreeya , Dhital Kavya , Puri Dhiraj , Pradhan Saman , Rajbhandari Udaya , Basnet Amit , Ghaju Sajani , Manandhar Prajwol , Ghimire Nabin U , Shahi Manoj K , Poudel Ajit , Napit Rajindra , Karmacharya Dibesh
Published: August 2022

Background

Commercial hatcheries play an important role in the overall poultry value chain-providing small to large poultry farmers with day old chicks. Any outbreak in such hatcheries can spread diseases to other farms. Regular screening of major avian pathogens, along with strict bio-security measures, can prevent spread of diseases in hatcheries. Newcastle Disease Virus (NDV), Infectious Bronchitis Virus (IBV), Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), Infectious Bursal Disease Virus (IBDV) and Influenza A Virus (IAV) are among the most prevalent poultry diseases which can be detected in egg albumin.

Method

We retrospectively (August 2020-August 2021, except October 2020) analyzed diagnostic results for six selected avian pathogens (NDV, IBV, MS, MG, IBDV and IAV) on eggs (n=4343) received from eleven major commercial poultry hatcheries located in the five adjoining districts of Kathmandu, Nepal. Albumin from 10% randomly selected eggs from each hatchery were tested for the six avian pathogens using multiplex PCR.

Result

Majority (7/11, 64%) of the poultry hatcheries had at least one of the six pathogens present. We detected at least one avian pathogen in nine out of eleven months (82%) of screening. Except for IBDV, we found one or more of the other major avian pathogens-Influenza A (IAV) (n=4 times) and Mycoplasma gallisepticum (MG) (n=4 times) were detected the most, followed by Newcastle Virus (NDV) (n=3 times). Infectious bronchitis virus (IBV) were detected twice, and Mycoplasma synoviae (MS) was detected once.

Conclusion

In a resource strapped country like Nepal, poultry disease outbreak investigation in particular and surveillance in general are challenging. Meanwhile, poultry production is highly impacted by disease outbreaks often triggered by poor bio-security and lack of pathogen screening practices. Our molecular screening tests have picked up major poultry pathogens present throughout the year in eggs collected from hatcheries. Influenza A was detected at 4 different incidences throughout the year, which is of concern to both human and animal health. Quick systematic screening of eggs at key distribution points (hatcheries) for major avian pathogens is an effective surveillance tool for early disease detection and containment of outbreaks.
Phenotypic Plasticity of Symbiotic Organ Highlight Deep-sea Mussel as Model Species in Monitoring Exploitation of Deep-sea Methane Hydrate
Authors: Li Mengna , Chen Hao , Wang Minxiao , Zhong Zhaoshan , Lian Chao , Zhou Li , Zhang Huan , Wang Hao , Cao Lei , Li Chaolun
Published: August 2022

The rapid progress of deep-sea methane hydrate exploration and exploitation calls for a thorough evaluation of its potential impact on local chemosynthetic ecosystems, particularly on endemic species. As one dominant megafauna in cold seeps, the deep-sea mussels mainly rely on methanotrophic endosymbionts for nutrition and therefore could serve as a promising model in monitoring the exploitation of methane hydrate. However, knowledge on the long-term responses of deep-sea mussels to environmental stresses induced by methane hydrate exploitation, especially to methane reduction and deprivation, is still lacking. Here, we set up a laboratory system and cultivated methanotrophic deep-sea musselGigantidas platifronswithout methane supply to survey the phenotypic changes after methane deprivation. While the mussels managed to survive for more than 10 months after the methane deprivation, drastic changes in the metabolism, function, and development of gill tissue, and in the association with methanotrophic symbionts were observed. In detail, the mussel digested all methanotrophic endosymbionts shortly after methane deprivation for nutrition and remodeled the global metabolism of gill to conserve energy. As the methane deprivation continued, the mussel replaced its bacteriocytes with ciliated cells to support filter-feeding, which is an atavistic trait in non-symbiotic mussels. During the long-term methane deprivation assay, the mussel also retained the generation of new cells to support the phenotypic changes of gill and even promoted the activity after being transplanted back to deep-sea, showing the potential resilience after long-term methane deprivation. Evidences further highlighted the participation of symbiont sterol metabolism in regulating these processes, which might be one direct cue for the mussels to respond to methane deprivation. These results collectively show the phenotypic plasticity of deep-sea mussels and their dynamic responses to methane deprivation, providing essential information in assessing the long-term influence of methane hydrate exploitation.
Is cold-induced nuclear import of CBF4 regulating freezing tolerance?
Authors: Shi Wenjing , Riemann Michael , Rieger Sophie-Marie , Nick Peter
Published: August 2022

C-repeat binding factors (CBFs) are crucial transcriptional activators in plant responses to low temperature. CBF4 differs by a slower, but more persistent regulation and its role in cold acclimation. Cold acclimation is of accentuated relevance for the tolerance to late spring frosts as they become progressively common as consequence of blurred seasonality in the context of global climate change. In the current study, we explore the functions of CBF4 from grapevine, VvCBF4. Overexpression of VvCBF4 fused to GFP in tobacco BY-2 cells confers cold tolerance. Furthermore, this protein shuttles from the cytoplasm to the nucleus in response to cold stress, associated with accumulation of transcripts for other CBFs and the cold responsive gene ERD10d. This response differs for chilling as compared to freezing and is regulated differently by upstream signalling involving oxidative burst, proteasome activity and jasmonate synthesis. This difference between chilling and freezing is also seen in the regulation of CBF4 transcripts in leaves from different grapevines differing in their cold tolerance. We propose the quality of cold stress is transduced by different upstream signals inducing nuclear import to regulate other CBF factor and activate COR genes.
Post-phagocytosis activation of NLRP3 inflammasome by two novel T6SS effectors
Authors: Cohen Hadar , Baram Noam , Fridman Chaya M. , Edry-Botzer Liat , Salomon Dor , Gerlic Motti
Published: August 2022

The type VI secretion system (T6SS) is used by bacteria to deliver toxic effectors directly into target cells. Most T6SSs mediate antibacterial activities, whereas the potential anti-eukaryotic role of T6SS remains understudied. Here, we found a Vibrio T6SS that delivers two novel effectors into mammalian host immune cells. We showed that these effectors induce a pyroptotic cell death in a phagocytosis-dependent manner; we identified the NLRP3 inflammasome as being the underlying mechanism leading to the T6SS-induced pyroptosis. Moreover, we identified a compensatory T6SS-induced pathway that is activated upon inhibition of the canonical pyroptosis pathway. Genetic analyses revealed possible horizontal spread of this T6SS and its anti-eukaryotic effectors into emerging pathogens in the marine environment. Our findings reveal novel T6SS effectors that activate the host inflammasome and possibly contribute to virulence and to the emergence of bacterial pathogens.
Intratumoral heterogeneity and clonal evolution induced by HPV integration
Authors: Akagi Keiko , Symer David E. , Mahmoud Medhat , Jiang Bo , Goodwin Sarah , Wangsa Darawalee , Li Zhengke , Xiao Weihong , Dunn Joe Dan , Ried Thomas , Coombes Kevin R. , Sedlazeck Fritz J. , Gillison Maura L.
Published: August 2022

The human papillomavirus (HPV) genome is integrated into host DNA in most HPV-positive cancers, but the consequences for chromosomal integrity are unknown. Continuous long-read sequencing of oropharyngeal cancers and cancer cell lines revealed a unique form of structural variation, i.e., heterocateny, characterized by diverse, interrelated, and repetitive patterns of concatemerized virus and host DNA segments within a cancer. Unique breakpoint sequences shared across structural variants facilitated stepwise reconstruction of their evolution from a common molecular ancestor. This analysis revealed that virus and virus-host concatemers are unstable and, upon insertion into and excision from chromosomes, facilitate capture, amplification, and recombination of host DNA and chromosomal rearrangements. Evidence of heterocateny was detected in extrachromosomal and intrachromosomal DNA. The data indicate that heterocateny is driven by the dynamic, aberrant replication and recombination of an oncogenic DNA virus, thereby extending known consequences of HPV integration to include promotion of intratumoral heterogeneity and clonal evolution.
Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)–G(syn) pair
Authors: Kiliszek Agnieszka , Pluta Martyna , Bejger Magdalena , Rypniewski Wojciech
Published: August 2022

The self-complementary triplet 5’UGG3’/5’UGG3’ is a particular structural motif containing noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.
Generation of Recombinant Rotaviruses Expressing Human Norovirus Capsid Proteins
Authors: Philip Asha A. , Patton John T.
Published: August 2022

Rotaviruses, segmented dsRNA viruses of the Reoviridae family, are a primary cause of acute gastroenteritis in young children. In countries where rotavirus vaccines are widely used, norovirus (NoV) has emerged as the major cause of acute gastroenteritis. Towards the goal of creating a combined rotavirus-NoV vaccine, we explored the possibility of generating recombinant rotaviruses (rRVs) expressing all or portions of NoV GII.4 VP1 capsid proteins. This was accomplished by replacing the segment 7 NSP3 ORF with a cassette encoding sequentially NSP3, a 2A stop-restart translation element, and all or portions (P, P2) of NoV VP1. In addition to successfully recovering SA11 rRVs with modified SA11 segment 7 RNAs encoding NoV capsid proteins, analogous rRVs were recovered through modification of the RIX4414 segment 7 RNA. Immunoblot assay confirmed that rRVs expressed NoV capsid proteins as independent products. Moreover, VP1 expressed by rRVs underwent dimerization and was recognized by conformational-dependent anti-VP1 antibodies. Serially passaged rRVs that expressed the NoV P and P2 were genetically stable, retaining sequences up to 1.1 kbp without change. However, serially passaged rRVs containing the longer 1.5 kb VP1 sequence were less stable and gave rise to virus populations with segment 7 RNAs lacking VP1 coding sequences. Together, these studies suggest that it may be possible to develop combined rotavirus-NoV vaccines using modified segment 7 RNA to express NoV P or P2. In contrast, development of potential rotavirus-NoV vaccines expressing NoV VP1 will need additional efforts to improve genetic stability.

Importance

Rotavirus (RV) and norovirus (NoV) are the two most important causes of viral acute gastroenteritis (AGE) in young children. While the incidence of RV AGE has been brought under control in many countries through the introduction of live attenuated RV vaccines, similar highly effective NoV vaccines are not available. To pursue the development of a combined RV-NoV vaccine, we examined the potential usefulness of RV as an expression vector of all or portions of the NoV capsid protein VP1. Our results showed that by replacing the NSP3 open reading frame in RV genome segment 7 RNA with a coding cassette for NSP3, a 2A stop-restart translation element, and VP1, recombinant RVs can be generated that express NoV capsid proteins as separate products. These findings raise the possibility of developing a new generation of RV-based combination vaccines that can provide protection against a second enteric pathogen, such as the NoV.
Machine learning with validation to detect diabetic microvascular complications using clinical and metabolomics data
Authors: He Feng , Ling Clarissa Ng Yin , Nusinovici Simon , Cheng Ching-Yu , Wong Tien Y. , Li Jialiang , Sabanayagam Charumathi
Published: August 2022

AIMS

Using machine learning integrated with clinical and metabolomic data to identify biomarkers associated with diabetic kidney disease (DKD) and diabetic retinopathy (DR), and to improve the performance of DKD/DR detection models beyond traditional risk factors.

METHODS

We examined a population-based cross-sectional sample of 2,772 adults with type 1 or type 2 diabetes from Singapore Epidemiology of Eye Diseases study (SEED, 2004-2011). LASSO logistic regression (LASSO) and gradient boosting decision tree (GBDT) were used to select markers of prevalent DKD (defined as an eGFR < 60ml/min/1.73m2) and prevalent DR (defined as an ETDRS severity level ≥ 20) from an expanded set of 19 established risk factors and 220 NMR-quantified circulating metabolites. Risk assessment models were developed based on the variable selection results and externally validated in UK Biobank (n=5,843, 2007-2010). Model performance (AUC with 95% CI, sensitivity, and specificity) of machine learning was compared to that of traditional logistic regression adjusted for age, gender, diabetes duration, HbA1c%, systolic BP, and BMI.

RESULTS

SEED participants had a median age of 61.7 years, with 49.1% female, 20.2% having DKD, and 25.4% having DR. UK Biobank participants had a median age of 61.0 years, with 39.2% female, 6.4% having DKD, and 5.7% having DR. Both algorithms identified diabetes duration, insulin usage, age, and tyrosine as the most important factors of both DKD and DR. DKD was additionally associated with CVD, hypertension medication, and three metabolites (lactate, citrate, and cholesterol esters to total lipids ratio in intermediate-density-lipoprotein); While DR was additionally associated with HbA1c, blood glucose, pulse pressure, and alanine. Machine-learned models for DKD and DR detection outperformed traditional logistic regression in both internal (AUC: 0.832-0.838 vs. 0.743 for DKD, and 0.779-0.790 vs. 0.764 for DR) and external validation (AUC: 0.737-0.790 vs. 0.692 for DKD, and 0.778 vs. 0.760 for DR).

CONCLUSIONS

Machine-learned biomarkers suggested insulin resistance to be a primary factor associated with diabetic microvascular complications. Integrating machine learning with biomedical big data enabled biomarker discovery from a wide range of correlated variables, which may facilitate our understanding of the disease mechanisms and improve disease screening.
Informing antimicrobial stewardship with explainable AI
Authors: Cavallaro Massimo , Moran Ed , Collyer Benjamin , McCarthy Noel D. , Green Christopher , Keeling Matt J.
Published: August 2022

The accuracy and flexibility of artificial intelligence (AI) systems often comes at the cost of a decreased ability to offer an intuitive explanation of their predictions. This hinders trust and discourage adoption of AI in healthcare, exacerbated by concerns over liabilities and risks to patients’ health in case of misdiagnosis. Providing an explanation for a model’s prediction is possible due to recent advances in the field of interpretable machine learning. We considered a data set of hospital admissions linked to records of antibiotic prescriptions and susceptibilities of bacterial isolates. An appropriately trained gradient boosted decision tree algorithm, supplemented by a Shapley explanation model, predicts the likely antimicrobial drug resistance, with the odds of resistance informed by characteristics of the patient, admission data, and historical drug treatments and culture test results. Applying this AI-based system, we found that it substantially reduces the risk of mismatched treatment compared with the observed prescriptions. The Shapley values provide an intuitive association between observations/data and outcomes; the associations identified are broadly consistent with expectations based on prior knowledge from health specialists. The results, and the ability to attribute confidence and explanations, support the wider adoption of AI in healthcare.
Exploring structural connectomes in children with unilateral cerebral palsy using graph theory
Authors: Radwan Ahmed , Decraene Lisa , Dupont Patrick , Leenaerts Nicolas , Simon-Martinez Cristina , Klingels Katrijn , Ortibus Els , Feys Hilde , Sunaert Stefan , Blommaert Jeroen , Mailleux Lisa
Published: August 2022

Background and objectives

Brain damage during early development impacts the brain structural network and its coinciding functions. Here, we explored structural brain connectomes in children with unilateral cerebral palsy and its relation to sensory-motor function using a novel semi-automated graph theory analysis, investigating both hemispheres.

Methods

In 46 children with spastic unilateral cerebral palsy (mean age 10y7m±2y9m, 27 boys, 25 right-sided hemiplegia; Manual Ability Classification System I=15, II=16, III=15) we assessed upper limb somatosensory (two-point discrimination and stereognosis) and motor function (grip force, Assisting Hand Assessment and Jebsen-Taylor Hand Function Test). We collected multi-shell diffusion-weighted, T1-weighted and T2-FLAIR MRI and performed transcranial magnetic stimulation to identify the corticospinal tract (CST) wiring pattern. Structural connectomes were constructed using Desikan-Killiany parcellations with Virtual Brain Grafting and FreeSurfer, and Multi-Shell Multi-Tissue Constrained Spherical Deconvolution diffusion modelling with anatomically constrained tractography. Graph metrics (characteristic path length, global/local efficiency and clustering coefficient) were calculated for the whole brain, the ipsilesional/contralesional hemisphere, and the full/ipsilesional/contralesional sensory-motor network, and were compared between lesion types (periventricular white matter (PWM)=28, cortical and deep grey matter (CDGM)=18) and CST-wiring patterns (ipsilateral=14, bilateral=14, contralateral=12, unknown=6) using ANCOVA with age as covariate. We used elastic-net regularized regression to investigate how graph metrics, lesion volume, lesion type, CST-wiring pattern and age predicted sensory-motor function.

Results

In both the whole brain and subnetworks, we observed a hyperconnectivity pattern in children with CDGM-lesions compared to PWM-lesions, with higher clustering coefficient (p=[<0.001-0.047], ), characteristic path length (p=0.003, ) and local efficiency (p=[0.001-0.02], ), as well as a faster decrease in global efficiency with age (p=[0.01-0.04], ). No differences were found between CST-wiring groups. In general, good predictions of sensory-motor function were obtained with elastic-net regression (R2=0.40-0.87). For motor function, the CST-wiring pattern was identified as the strongest predictor. For somatosensory function all independent variables contributed equally to the model.

Discussion

With this study, we demonstrated the feasibility and potential of structural connectomes using graph theory analysis in understanding disease severity and brain development in children with unilateral cerebral palsy. Hence, this exploratory study could support and direct future research.
Longitudinal analysis of serum neutralization of SARS-CoV-2 Omicron BA.2, BA.4 and BA.5 in patients receiving monoclonal antibodies
Authors: Bruel Timothée , Stéfic Karl , Nguyen Yann , Toniutti Donatella , Staropoli Isabelle , Porrot Françoise , Guivel-Benhassine Florence , Bolland William-Henry , Planas Delphine , Hadjadj Jérôme , Handala Lynda , Planchais Cyril , Prot Matthieu , Simon-Lorière Etienne , André Emmanuel , Baele Guy , Cuypers Lize , Mouthon Luc , Mouquet Hugo , Buchrieser Julian , Sève Aymeric , Prazuck Thierry , Maes Piet , Terrier Benjamin , Hocqueloux Laurent , Schwartz Olivier
Published: August 2022

The emergence of novel Omicron lineages, such as BA.5, may impact the therapeutic efficacy of anti-SARS-CoV-2 neutralizing monoclonal antibodies (mAbs). Here, we evaluated the neutralization and ADCC activity of 6 therapeutic mAbs against Delta, BA.2, BA.4 and BA.5 isolates. The Omicron sub-variants escaped most of the antibodies but remained sensitive to Bebtelovimab and Cilgavimab. Consistent with their shared spike sequence, BA.4 and BA.5 displayed identical neutralization profiles. Sotrovimab was the most efficient at eliciting ADCC. We also analyzed 121 sera from 40 immunocompromised individuals up to 6 months after infusion of 1200 mg of Ronapreve (Imdevimab + Casirivimab), and 300 or 600 mg of Evusheld (Cilgavimab + Tixagevimab). Sera from Ronapreve-treated individuals did not neutralize Omicron subvariants. Evusheld-treated individuals neutralized BA.2 and BA.5, but titers were reduced by 41- and 130-fold, respectively, compared to Delta. A longitudinal evaluation of sera from Evusheld-treated patients revealed a slow decay of mAb levels and neutralization. The decline was more rapid against BA.5. Our data shed light on the antiviral activities of therapeutic mAbs and the duration of effectiveness of Evusheld pre-exposure prophylaxis.
Epidemiological profile and effectiveness of immediate postpartum contraception in Brazilian women
Authors: Steiner Marcelo Luis , Mendes Júlia Lorenzini , Giovanelli Silvana Aparecida , Carneiro Mônica , Strufaldi Rodolfo , da Silva Mariliza Henrique
Published: August 2022

We analyzed the epidemiological profile of women who inserted copper intrauterine device (Cu-IUD), subdermal etonogestrel implant (ENG), tubal ligation (TL), depot medroxyprogesterone acetate (DMPA) or did not choose a contraceptive method (NCM) in the immediate postpartum. Also, we compared the contraceptive effectiveness of Cu-IUD and DPMA with non-MAC. Data from 20896 women were collected, of which 8183 (39%) opted for Cu-IUD, 559 (2.5%) DPMA, and 10989 (52.5%) for any method. When comparing these groups, women in the DPMA were younger (26.5±7.3, p<0.05), and NCM showed women with a lower number of pregnancies (2.2±1.3, p<0.05). Subjects in the TL group (4,6%) had the higher number of pregnancies (3,8±1.2, p<0.05), and ENG group, the highest number of miscarriages (1.6±1.3, p<0.05). Of those women who returned pregnant, 5.5% belonged to the DPMA group, 6% to the NCM group, and 2.3% to the Cu-IUD. Women who opted for Cu-IUD insertion were younger, had more pregnancies and vaginal delivery when compared to those who did not choose a method. Of those women who returned, the minority opted for Cu-IUD compared to those that opted for DPMA or no method.