bluuebunny/crossref_metadata_2025 huggingface dataset:
Juvenile idiopathic arthritis, marriage and parenthood: a nationwide matched cohort study
Authors: Bruze Gustaf , Askling Johan , Horne AnnaCarin , Neovius Martin
Published: July 2021

Objectives

To compare trajectories of marriage and parenthood in individuals with JIA vs the general population.

Methods

Patients with JIA (n = 4399) were identified in the Swedish National Patient Register (2001–2016) and individually matched to up to five general population comparators on birthyear, sex and residence county (n = 21 981). Marriage and parenthood data were retrieved from the Total Population Register from age 18 y, and parenthood from the Multigeneration Register from age 15 y, respectively. Hazard ratios (HRs) were estimated using Cox regression adjusted for parental education, parental marital status and number of siblings.

Results

During a median of 6.3 years of follow-up, 362 patients with JIA and 1744 comparators got married (12.9 vs. 12.5 per 1000 person-years; HR 1.03, 95%CI 0.93-1.15). During a median of 8.8 years of follow-up, 680 patients with JIA and 3477 matched comparators became parents (17.1 vs 17.8 per 1000 person-years; HR 0.94, 95%CI 0.87-1.01). In the subgroup of patients with systemic onset JIA (SJIA), the adjusted hazard ratios for marriage and parenthood were 0.79 (95%CI 0.53-1.17) and 0.73 (95%CI 0.55-0.97), respectively.

Conclusion

The times to first marriage and first parenthood are similar for patients with JIA and the general population, suggesting that adolescents with JIA transition into family life along a trajectory resembling their community peers. One exception is the subgroup of patients with systemic onset JIA, who become parents for the first time at a lower rate than general population comparators.
A 7-Tesla MRI study of the periaqueductal gray: resting state and task activation under threat
Authors: Weis Carissa N , Bennett Kenneth P , Huggins Ashley A , Parisi Elizabeth A , Gorka Stephanie M , Larson Christine
Published: July 2021

The periaqueductal gray (PAG) is a region of the midbrain implicated in a variety of behaviors including defensive responses to threat. Despite the wealth of knowledge pertaining to the differential functional roles of the PAG columns in nonhuman and human research, the basic functional connectivity of the PAG at rest has not been well characterized. Therefore, the current study utilized 7-Tesla magnetic resonance imaging (MRI) to characterize PAG functional connectivity at rest and task activation under uncertain threat. A sample of 53 neurologically healthy undergraduate participants (Mage = 22.2, s.d.age = 3.62) underwent structural and resting state functional MRI scans. Supporting previous work, voxel-wise analyses showed that the PAG is functionally connected to emotion regulation and fear networks. The comparison of functional connectivity of PAG columns did not reveal any significant differences. Thirty-five participants from the same sample also completed an uncertain threat task with blocks of three conditions—no shock, predictable shock and unpredictable shock. There were no robust activity differences within the PAG columns or the whole PAG across conditions although there was differential activity at the voxel level in the PAG and in other regions theoretically relevant to uncertain threat. Results of this study elucidate PAG connectivity at rest and activation in response to uncertain threat.
Mothers’ Parenting in an Era ofProactive Policing
Authors: Turney Kristin
Published: July 2021

A family systems perspective suggests the repercussions of adolescent police contact likely extend beyond the adolescent to proliferate to the broader family unit, but little research investigates these relationships. I used data from the Fragile Families and Child Wellbeing Study, a longitudinal survey of children who became adolescents during an era of proactive policing, to examine the relationship between adolescent police contact and four aspects of family life: mothers’ parenting stress, mothers’ monitoring, mothers’ discipline, and the mother-adolescent relationship. Adolescent police contact, especially invasive police contact, is associated with increased parenting stress, increased discipline, and decreased engagement, net of adolescent and family characteristics that increase the risk of police contact. There is also evidence that suggests adolescent police contact is more consequential for family life when mothers themselves had experienced recent police contact. These findings suggest the repercussions of police contact extend beyond the individual and proliferate to restructure family relationships.
How trees thrive in a dry climate: diurnal and seasonal hydrology and water relations in a riparian cottonwood grove
Authors: Phelan Colleen A , Pearce David W , Franks Carmen G , Zimmerman Oscar , Tyree Melvin T , Rood Stewart B
Published: July 2021

In semi-arid ecoregions, trees are restricted to river valley floodplains where river water supplements the limited precipitation. To characterize the associated diurnal and seasonal dynamics in hydrology and water relations, we studied narrowleaf cottonwoods (Populus angustifolia) along a prairie river in Canada. From June through August, the shallow soil moisture was depleted but moisture remained higher above the alluvial groundwater table, which dropped to 2.3 m along with river recession. Throughout the summer, with the daily rise in temperature and insolation, foliar stomatal conductance (gs) and transpiration (E) increased to midday and then fell, thus maintaining the midday leaf water potential (Ψmd) above ~−1.7 MPa. This Ψmd approximated the water potential associated with 12% loss of xylem conductivity due to cavitation for branches (P12); the Ψmd and P12 varied independently across eight trees, providing differences in relative hydraulic risk. Sap flux density (Fd) was measured with thermal dissipation probes, and revealed diurnal patterns similar to foliar E. In contrast to our expectation, the daily Fd maxima were consistent through the summer despite the seasonal recession in water supply. Canopy conductances (GS), derived from Fd, sapwood area and canopy area, declined with vapor pressure deficit (D) and fell slightly in late summer along with stomatal sensitivity, which reflects the magnitude of decrease in GS with increasing D. For spatial up-scaling, satellite-derived near-infrared reflectance of vegetation revealed the woodland phenology, with leaf expansion from May through June and gradual decline in photosynthetic productivity through the summer. Thus, the phreatophytic cottonwoods: (i) sustained substantial water use and productivity through the warm and dry summer, by (ii) accessing shallow soil moisture and then deeper alluvial groundwater, and (iii) providing diurnal stomatal regulation, to (iv) avoid xylem cavitation and (v) maintain fairly constant hydraulic conductance.
Development of Recombinase Polymerase Amplification Combined with Lateral Flow Detection Assay for Rapid and Visual Detection of Ralstonia solanacearum in Tobacco
Authors: Li Changfeng , Ju Yuliang , Shen Pengfei , Wu Xun , Cao Le , Zhou Benguo , Yan Xiaoming , Pan Yuemin
Published: July 2021

Bacterial wilt caused by Ralstonia solanacearum is a serious soilborne disease that results in severe losses to tobacco (Nicotiana tabacum) production in China. In this study, a novel RPA-LFD assay for the rapid visual detection of R. solanacearum was established using recombinase polymerase amplification (RPA) and lateral-flow dipstick (LFD). The RPA-LFD assay was performed at 37°C in 30 min without complex equipment. Targeting the sequence of the RipTALI-9 gene, we designed RPA primers (Rs-rpa-F/R) and an LF probe (Rs-LF-probe) that showed high specificity to R. solanacearum. The sensitivity of RPA-LFD assay to R. solanacearum was the same as that in conventional PCR at 1 pg genomic DNA, 103 CFU/g artificially inoculated tobacco stems, and 104 CFU/g artificially inoculated soil. The RPA-LFD assay could also detect R. solanacearum from plant and soil samples collected from naturally infested tobacco fields. These results suggest that the RPA-LFD assay developed in this study is a rapid, accurate molecular diagnostic tool with high sensitivity for the detection of R. solanacearum.
Human bocavirus 1 respiratory tract reactivations or reinfections in two adults, contributing to neurological deficits and death
Authors: Rayamajhi Thapa Rajita , Plentz Annelie , Edinger Matthias , Wolff Daniel , Angstwurm Klemens , Söderlund-Venermo Maria
Published: July 2021

Human bocavirus 1 (HBoV1) of the family Parvoviridae causes mild to life-threatening respiratory tract infections in young children, but, due to widespread immunity, it is uncommon in adults. HBoV1 reinfections or reactivations leading to casualties are rare, but might be underdiagnosed. We report two young adults, one previously healthy and one immunosuppressed, with rare diagnostic patterns of HBoV1 respiratory tract infection. Both patients exhibited very high loads of HBoV1 DNA in respiratory samples. The immunosuppressed patient was also HBoV1 DNA-positive in blood, stool and a colon biopsy, but exhibited prior HBoV1-specific high-avidity IgG and weak IgM positivity 9 months before the respiratory symptoms. Likewise, the previously healthy patient exhibited HBoV1 IgG of high avidity and very weak IgM in serum, pointing to prior immunity, but with a seroconversion in cerebrospinal fluid. This patient also showed strong HBoV2 cross-reactivity. The molecular and serological results, together with their ages, suggest that both patients exhibited unusual reinfection or reactivation of HBoV1, contributing to neurological deficits and death.
Discovering Monogenic Patients with a Confirmed Molecular Diagnosis in Millions of Clinical Notes with MonoMiner
Authors: Wu David Wei , Bernstein Jonathan A. , Bejerano Gill
Published: July 2021

Purpose

Cohort building is a powerful foundation for improving clinical care, performing research, clinical trial recruitment, and many other applications. We set out to build a cohort of all patients with monogenic conditions who have received a definitive causal gene diagnosis in a 3 million patient hospital system.

Methods

We define a subset of half (4,461) of OMIM curated diseases for which at least one monogenic causal gene is definitively known. We then introduce MonoMiner, a natural language processing framework to identify molecularly confirmed monogenic patients from free-text clinical notes.

Results

We show that ICD-10-CM codes cover only a fraction of known monogenic diseases, and even where available, code-based patient retrieval offers 0.12 precision. Searching by causal gene symbol offers great recall but an even worse 0.09 precision. MonoMiner achieves 7-9 times higher precision (0.82), with 0.88 precision on disease diagnosis alone, tagging 4,259 patients with 560 monogenic diseases and 534 causal genes, at 0.48 recall.

Conclusion

MonoMiner enables the discovery of a large, high-precision cohort of monogenic disease patients with an established molecular diagnosis, empowering numerous downstream uses. Because it relies only on clinical notes, MonoMiner is highly portable, and its approach is adaptable to other domains and languages.
Sustaining effective COVID-19 control in Malaysia through large-scale vaccination
Authors: Jayasundara Pavithra , Peariasamy Kalaiarasu M. , Law Kian Boon , Abd Rahim Ku Nurhasni Ku , Lee Sit Wai , Ghazali Izzuna Mudla M. , Abayawardana Milinda , Le Linh-Vi , K.S.Khalaf Rukun , Razali Karina , Le Xuan , Chong Zhuo Lin , McBryde Emma S , Meehan Michael T , Caldwell Jamie M. , Ragonnet Romain , Trauer James M
Published: July 2021

Introduction

As of 3rdJune 2021, Malaysia is experiencing a resurgence of COVID-19 cases. In response, the federal government has implemented various non-pharmaceutical interventions (NPIs) under a series of Movement Control Orders and, more recently, a vaccination campaign to regain epidemic control. In this study, we assessed the potential for the vaccination campaign to control the epidemic in Malaysia and four high-burden regions of interest, under various public health response scenarios.

Methods

A modified susceptible-exposed-infectious-recovered compartmental model was developed that included two sequential incubation and infectious periods, with stratification by clinical state. The model was further stratified by age and incorporated population mobility to capture NPIs and micro-distancing (behaviour changes not captured through population mobility). Emerging variants of concern (VoC) were included as an additional strain competing with the existing wild-type strain. Several scenarios that included different vaccination strategies (i.e. vaccines that reduce disease severity and/or prevent infection, vaccination coverage) and mobility restrictions were implemented.

Results

The national model and the regional models all fit well to notification data but underestimated ICU occupancy and deaths in recent weeks, which may be attributable to increased severity of VoC or saturation of case detection. However, the true case detection proportion showed wide credible intervals, highlighting incomplete understanding of the true epidemic size. The scenario projections suggested that under current vaccination rates complete relaxation of all NPIs would trigger a major epidemic. The results emphasise the importance of micro-distancing, maintaining mobility restrictions during vaccination roll-out and accelerating the pace of vaccination for future control. Malaysia is particularly susceptible to a major COVID-19 resurgence resulting from its limited population immunity due to the country’s historical success in maintaining control throughout much of 2020.
Associations between cardiovascular risk factors, stroke severity, and post-stroke cognition: a moderated mediation analysis
Authors: Hua Jianian , Zhou Yixiu , Chen Licong , Diao Shanshan , Fang Qi
Published: July 2021

Introduction

Cognitive impairment may affect one third of the stroke survivors. Cardiovascular risk factors have been described to be risk factors for lower cognition after stroke. However, most previous studies only used multivariate regression models to learn the association. The aim of our study was to investigate whether the effect of cardiovascular risk factors on cognition after stroke was mediated by stroke severity, the estimated effect of direct and indirect pathways, and the moderated association.

Method

In this incident cross-sectional study, 300 stroke patients received cognitive test within seven days after stroke. Cognitive tested was performed by the Chinese version of Mini-Mental State Examination (MMSE). A second stage dual moderated mediation model was used the select moderation variables. Finally, we constructed a structural equation model to test the indirect effects of cardiovascular and demographic factors on cognition stroke severity, the direct effects of predictors on cognition, and the moderated effects of hypertension.

Results

Age (estimate, -0.114; 95% bias-corrected CI, -0.205, -0.032; P<0.001), female (estimate, -2.196; 95% bias-corrected CI, -4.359, -0.204; P=0.009), lower education (estimate, -0.893; 95% bias-corrected CI, -1.662, --0.160; P<0.001), stroke severity (estimate, -1.531; 95% bias-corrected CI, -3.015, -0.095), hypertension (estimate, -2.242; 95% bias-corrected CI, -4.436, -0.242; P=0.003) and atrial fibrillation (estimate, -4.930; 95% bias-corrected CI, -12.864, -0.126; P=0.048) were directly associated with lower cognitive function after stroke. We found no evidence that cardiovascular risk factors indirectly correlated cognitive function through stroke severity. The combination of hypertension could alleviate the negative effect of atrial fibrillation on cognition (estimate, -3.928; 95% bias-corrected CI, -7.954, 0.029; P=0.009).

Conclusions

We explored the complex relationship between cardiovascular risk factors, stroke severity, and cognitive function after stroke. Using our method, researchers using other dataset could repeat the analysis and achieve a better understanding of the relationship. Future researchers are needed to find whether the moderated associations were casual or modifiable.
Epidemic preparedness -Leishmania tarentolaeas an easy-to-handle tool to produce antigens for viral diagnosis: application to COVID-19
Authors: Varotto-Boccazzi Ilaria , Manenti Alessandro , Dapporto Francesca , Gourlay Louise J. , Bisaglia Beatrice , Gabrieli Paolo , Forneris Federico , Faravelli Silvia , Bollati Valentina , Zuccotti Gian Vincenzo , Montomoli Emanuele , Epis Sara , Bandi Claudio
Published: July 2021

To control future epidemics, discovery platforms are urgently needed, for the rapid development of diagnostic assays. Molecular diagnostic tests for COVID-19 emerged shortly after the isolation of SARS-CoV-2, however, serological tests based on antiviral antibody detection, revealing previous exposure to the virus, required longer developmental phases, due to the need for correctly folded and glycosylated antigens. The delay between the identification of a new virus and the development of reliable serodiagnostic tools limits our readiness for the control of a future epidemic. In this context, we propose the protozoanLeishmania tarentolaeas an easy-to-handle micro-factory for the rapid production of viral antigens, to be used at the forefront of emerging epidemics. As a study model, we engineeredL. tarentolaeto express the SARS-CoV-2 Receptor Binding Domain (RBD) and report the ability of the purified RBD antigen to detect SARS-CoV-2 infection, with a sensitivity and reproducibility comparable to that of a reference antigen produced in human cells. This is the first application of an antigen produced inL. tarentolaefor the serodiagnosis of a Coronaviridae infection. Based on our results, we proposeL. tarentolaeas an effective system for viral antigen production, even in countries that lack high-tech cell factories.
Better Antimicrobial Resistance Data Analysis & Reporting in Less Time
Authors: Luz Christian F. , Berends Matthijs S. , Zhou Xuewei , Lokate Mariëtte , Friedrich Alex W. , Sinha Bhanu , Glasner Corinna
Published: July 2021

Introduction

The global challenge of antimicrobial resistances (AMR) requires the rational and responsible use of antimicrobials. Insights and knowledge about the local AMR levels and epidemiology are essential to guide optimal decision-making processes in antimicrobial use. However, dedicated tools for reliable and reproducible AMR data analysis and reporting are often lacking. Previously, we have developed a novel approach to AMR data analysis and reporting using open-source software tools. In this study, we aimed at comparing the effectiveness and efficiency of traditional analysis and reporting versus this new approach for reliable and reproducible AMR data analysis in a clinical setting.

Methods

Ten professionals in the field of AMR that routinely work with AMR data were recruited to participate and provided with one year’s blood culture test results from a tertiary care hospital results including antimicrobial susceptibility test results. Participants were asked to perform a detailed AMR data analysis in a two-step process: first (round 1) using their analysis software of choice and next (round 2) using the previously developed open-source software tools. Accuracy of the results and time spent were compared between the two rounds. Paired student’s t-tests were used to test for statistical significance. Finally, participants rated the usability of the tools using the systems usability scale.

Results

The mean time spent on creating a comprehensive AMR report reduced from 93.7 (SD ±21.6) minutes to 22.4 (SD ±13.7) minutes (p < 0.001). Average task completion per round changed from 56% (SD: ±23%) to 96% (SD: ±5.5%) (p<0.05). The proportion of correct answers in the available results increased from 37.9% in the first round to 97.9% in the second round (p < 0.001). The usability of the new AMR reporting tool was rated with a median of 83.8 (out of 100) on the system usability scale.

Conclusion

This study demonstrated the significant improvement in efficiency and accuracy in standard AMR data analysis and reporting workflows through the use of open-source software tools in a clinical setting. Integrating these tools in clinical settings can democratise the access to fast and reliable insights about local microbial epidemiology and associated AMR levels. Thereby, our approach can support evidence-based decision-making processes in the use of antimicrobials.
Socio-economic Transition in an Indian Rural Setting and Its Impact on Health: Pune Maternal Nutrition Study
Authors: Shukla S R. , Kumaran K , Radkar A , Bhalerao A J. , Solat V A. , Chougule S D. , Deokar T M. , Yajnik P C. , Fall C HD. , Yajnik C S.
Published: July 2021

Background

There is scant scientific information on socioeconomic transition and its effects on health parameters in India. The prospective data collection in the Pune Maternal Nutrition Study (PMNS) birth cohort provided an opportunity to examine the changes in socio-economic status (SES) and 1) its comparison against state and district indicators, 2) association with body size and cardio-metabolic risk factors.

Method

We followed up ∼700 families for biomedical information in the PMNS. SES data was collected in the index pregnancy (1993-96) and serially every six years (∼2001, ∼2007, ∼2013). Comparisons with rural Maharashtra and Pune were made using data from the National Family Health Survey 1999 and 2006 (NFHS II and III).

Results

There was an increase in the proportion of those in the high Standard of Living Index (SLI, NFHS) from 64% to 90% between 2001 and 2013. The increase in SES in our study area was faster and greater compared to the state and district. Higher SLI was associated with higher weight, height, body fat percent and total cholesterol concentrations at each followup. However, there were no associations between transition and health parameters.

Conclusion

Our data suggest a rapid socio-economic transition in the study area which is faster than the state and district.
Modeling of leptospirosis outbreaks in relation to hydroclimatic variables in the northeast of Argentina
Authors: Gómez Andrea A. , López María Soledad , Müller Gabriela V. , López Leonardo , Sione Walter , Giovanini Leonardo
Published: July 2021

The transmission of leptospirosis is conditioned by climatic variables. In northeastern Argentina leptospirosis outbreaks occur mainly in coincidence with periods of abundant precipitation and high hydrometric level. A Susceptible-Infectious-Recovered Epidemiological Model (SIR) is proposed, which incorporates hydroclimatic variables for the three most populated cities in the area (Santa Fe, Paraná and Rosario), during the 2009 – 2018 period. Results obtained by solving the proposed SIR model for the 2010 outbreaks are in good agreement with the actual data, capturing the dynamics of the leptospirosis outbreak wave. However, the model does not perform very well when isolated cases appear outside the outbreak periods, probably due to non-climatic factors not explicitly considered in the present version of the model. Nevertheless, the dynamic modeling of infectious diseases considering hydroclimatic variables constitutes a climatic service for the public health system, not yet available in Argentina.
Wireless endovascular nerve stimulation with a millimeter-sized magnetoelectric implant
Authors: Chen Joshua C. , Kan Peter , Yu Zhanghao , Alrashdan Fatima , Garcia Roberto , Singer Amanda , Lai C.S. Edwin , Avants Ben , Crosby Scott , Felicella Michelle M. , Robledo Ariadna , Hartgerink Jeffrey D. , Sheth Sunil A. , Yang Kaiyuan , Robinson Jacob T.
Published: July 2021

Implanted bioelectronic devices have the potential to treat disorders that are resistant to traditional pharmacological therapies; however, reaching many therapeutic nerve targets requires invasive surgeries and implantation of centimeter-sized devices. Here we show that it is possible to stimulate peripheral nerves from within blood vessels using a millimeter-sized wireless implant. By directing the stimulating leads through the blood vessels we can target specific nerves that are difficult to reach with traditional surgeries. Furthermore, we demonstrate this endovascular nerve stimulation (EVNS) with a millimeter sized wireless stimulator that can be delivered minimally invasively through a percutaneous catheter which would significantly lower the barrier to entry for neuromodulatory treatment approaches because of the reduced risk. This miniaturization is achieved by using magnetoelectric materials to efficiently deliver data and power through tissue to a digitally-programmable 0.8 mm2 CMOS system-on-a-chip. As a proof-of-principle we show wireless stimulation of peripheral nerve targets both directly and from within the blood vessels in rodent and porcine models. The wireless EVNS concept described here provides a path toward minimally invasive bioelectronics where mm-sized implants combined with endovascular stimulation enable access to a number of nerve targets without open surgery or implantation of battery-powered pulse generators.
Efficient gradient boosting for prognostic biomarker discovery
Authors: Li Kaiqiao , Yao Sijie , Zhang Zhenyu , Cao Biwei , Wilson Christopher M. , Kuan Pei Fen , Zhu Ruoqing , Wang Xuefeng
Published: July 2021

Motivation

Gradient boosting decision tree (GBDT) is a powerful ensemble machine learning method that has the potential to accelerate biomarker discovery from high-dimensional molecular data. Recent algorithmic advances, such as Extreme Gradient Boosting (XGB) and Light Gradient Boosting (LGB), have rendered the GBDT training more efficient, scalable and accurate. These modern techniques, however, have not yet been widely adopted in biomarkers discovery based on patient survival data, which are key clinical outcomes or endpoints in cancer studies.

Results

In this paper, we present a new R packageXsurvas an integrated solution which applies two modern GBDT training framework namely, XGB and LGB, for the modeling of censored survival outcomes. Based on a comprehensive set of simulations, we benchmark the new approaches against traditional methods including the stepwise Cox regression model and the original gradient boosting function implemented in the packagegbm. We also demonstrate the application ofXsurvin analyzing a melanoma methylation dataset. Together, these results suggest thatXsurvis a useful and computationally viable tool for screening a large number of prognostic candidate biomarkers, which may facilitate cancer translational and clinical research.

Availability

Xsurvis freely available as an R package at:https://github.com/topycyao/Xsurv

Contact

xuefeng.wang@moffitt.org

Supplementary information

Supplementary data are available atBioinformaticsonline.
SAFA facilitates chromatin opening of immune genes through interacting with nascent antiviral RNAs
Authors: Cao Lili , Li Yunfei , Luo Yujie , Guo Xuefei , Liu Shengde , Li Siji , Li Junhong , Zhang Zeming , Zhao Yingchi , Zhang Qiao , Gao Feng , Ji Xiong , Wang Yiguang , Gao Xiang , You Fuping
Published: July 2021

Regulation of chromatin accessibility determines the transcription activities of genes, which endow the host with function-specific gene expression patterns. It remains unclear how chromatin accessibility is specifically directed, particularly, during host defense against viral infection. We previously reported that the nuclear matrix protein SAFA surveils viral RNA and regulates antiviral immune genes expression. However, how SAFA regulates the expression and what determines the specificity of antiviral immune genes remains unknown. Here, we identified that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes in a genome-wide scale after VSV infection. SAFA exclusively bound with antiviral related RNAs, which mediated the specific opening of the according chromatin and robust transcription of these genes. Knockdown of these associated RNAs dampened the accessibility of corresponding genes in an extranuclear signaling pathway dependent manner. Moreover, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products during viral infection collaborate and remodel chromatin accessibility to facilitate antiviral innate immune response.
In silico analysis and molecular investigation of the nuclear shuttle protein-interacting kinase 1 (NIK1) in six Solanaceous species
Authors: Safaeizadeh Mehdi , Malpica Nachelli
Published: July 2021

The first layer of innate immunity in plants is initiated through the perception of microbe-associated molecular patterns (MAMPs) or damage-associated molecular patterns (DAMPs) by pattern recognition receptors (PRRs). MAMP/DAMP perception initiates downstream defense responses, a process which ultimately leads to pattern triggered immunity (PTI). In Arabidopsis, the nuclear shuttle protein-interacting kinase 1 (NIK1), among other PRRs, is one of the most important central components of PTI signaling and kinase signaling cascade, since it is involved in the plant antiviral response against geminiviruses. Despite the characterization of the structure and function of the NIK1 receptors made by some groups, studies related to NIK1 importance in the current gene-editing era are missing. By simple in silico analysis, in this study we investigated the NIK1 homologues from six Solanaceous plant species including: tomato (Solanum lycopersicum), potato (Solanum tuberosum), Solanum pennellii, eggplant (Solanum melongena), pepper (Capsicum annum), and Nicotiana benthamiana. The phylogenetic analyses of different NIK1 proteins from Arabidopsis and six Solanaceous plants revealed nine different clades. As expected, we found that these NIK1 orthologs have similar genomic structures suggesting a similar function. We could identify that SotubNIK1, SolyNIK1, SopenNIK1, CANIK1, NibenNIK1, SmeNIK1 have the highest sequence homology with AtNIK1. Additionally, the conserved protein kinase domain (PKD) that is present in NIK1 from Arabidopsis thaliana was bioinformatically analyzed and found in other species. As this highly conserved NIK1 region is present in several crops of economic importance, its potential is highlighted as a possible target site for gene editing, to develop crops tolerant to geminiviral infections.
Optimization of the TeraTox assay for preclinical teratogenicity assessment
Authors: Manuela Jaklin , David Zhang Jitao , Nicole Schäfer , Nicole Clemann , Paul Barrow , Erich Küng , Lisa Sach-Peltason , Claudia McGinnis , Marcel Leist , Stefan Kustermann
Published: July 2021

Current animal-free methods to assess teratogenicity of drugs under development still deliver high numbers of false negatives, and more sensitive approaches of toxicity prediction are required. To address this issue, we characterized the TeraTox test, a newly developed multi-lineage differentiation assay for human teratogenicity prediction using 3D human induced pluripotent stem cells. TeraTox produces as primary output concentration-dependent data sets for each test compound on cytotoxicity and altered gene expression. These data are then fed into a prediction model based on an interpretable machine-learning approach. The final information obtained relates to the concentration-dependent human teratogenicity potential of drug candidates. We applied TeraTox to profile 33 approved pharmaceuticals and 12 proprietary drug candidates with known in vivo data. This way, it was possible to relate the test predictions to known human or animal toxicity. The TeraTox had an accuracy of 69% (specificity: 53%, sensitivity: 79%). It clearly performed better than two quantitative structure-activity relationship (QSAR) models and it had a higher sensitivity than the murine embryonic stem cell test (mEST) run in the same laboratory. By combining TeraTox and mEST data, the overall prediction accuracy was further improved. The knowledge on the pattern of altered gene expression may provide additional value in grouping toxicologically similar compounds and possibly deducing common modes of action. The assay will thus be a helpful additional tool in drug discovery, and the dataset provided here will be a valuable resource for the field of stem cell-based drug profiling.
A single-cell transcriptomic atlas characterizes liver non-parenchymal cells in healthy and diseased mice
Authors: Wang Zheng , Qian Jingyang , Lu Xiaoyan , Zhang Ping , Guo Rongfang , Lou He , Zhang Shuying , Yang Jihong , Fan Xiaohui
Published: July 2021

The heterogeneity of liver non-parenchymal cells (NPCs) is essential for liver structure and function. However, the current understanding of liver NPCs, especially in different liver diseases, remains incompletely elucidated. Here, a single-cell transcriptome atlas of 171,814 NPCs from healthy and 5 typical liver disease mouse models, including alcoholic liver disease, nonalcoholic steatohepatitis (NASH), drug-induced liver injury, cholestatic, and ischemia-reperfusion liver injury is constructed. The inter- and intra-group heterogeneity of 12 types (and numerous subtypes) of NPCs involving endothelial cells, hepatic stellate cells (HSCs), neutrophils, T cells, and mononuclear phagocytes (MPs) are summarized. A protective subtype of neutrophils characterized by Chil3high is validated and found significantly increasing only in drug-induced and cholestatic liver injury models. Transcriptional regulatory network analysis reveals disease-specific transcriptional reprogramming. Metabolic activity analysis indicates that fibrosis is accompanied by increases in glycolysis and retinol metabolism in activated HSCs and MPs. Moreover, we found that cell-cell interactions between cholangiocytes and immune cells contribute more to cholestatic liver fibrosis compared with NASH, while HSCs are more important for NASH fibrosis. Our atlas, together with an interactive website provides a systematic view of highly heterogeneous NPCs and a valuable resource to better understand pathological mechanisms underlying liver diseases.
Defining the Immune Responses for SARS-CoV-2-Human Macrophage Interactions
Authors: Abdelmoaty Mai M. , Yeapuri Pravin , Machhi Jatin , Olson Katherine E. , Shahjin Farah , Zhou You , Jingjing Liang , Pandey Kabita , Acharya Arpan , Byrareddy Siddappa N. , Lee Mosley R. , Gendelman Howard E.
Published: July 2021

Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end organ malfunctions. All follow an abortive viral infection. To elucidate SARS-CoV-2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the SARS-CoV-2 receptor, the angiotensin-converting enzyme 2, paralleled monocyte-macrophage differentiation it failed to affect productive viral infection. In contrast, simple macrophage viral exposure led to robust pro-inflammatory cytokine and chemokine expression but attenuated type I interferon (IFN) activity. Both paralleled dysregulation of innate immune signaling pathways specifically those linked to IFN. We conclude that the SARS-CoV-2-infected host mounts a robust innate immune response characterized by a pro-inflammatory storm heralding consequent end-organ tissue damage.
High-throughput functional analysis of CFTR and other apically localized channels in iPSC derived intestinal organoids
Authors: Xia Sunny , Bozóky Zoltán , Laselva Onofrio , Di Paola Michelle , Ahmadi Saumel , Jiang Jia Xin , Pitstick Amy , Jiang Chong , Rotin Daniela , Mayhew Christopher N. , Jones Nicola L. , Bear Christine E.
Published: July 2021

Induced Pluripotent Stem Cells (iPSCs) can be differentiated into epithelial organoids that recapitulate the relevant context for CFTR and enable testing of therapies targeting Cystic Fibrosis (CF)-causing mutant proteins. However, to date, CF-iPSC-derived organoids have only been used to study pharmacological modulation of mutant CFTR channel activity and not the activity of other disease relevant membrane protein constituents. In the current work, we describe a high-throughput, fluorescence-based assay of CFTR channel activity in iPSC-derived intestinal organoids and describe how this method can be adapted to study other apical membrane proteins. In these proof-of-concept studies, we show how this fluorescence-based assay of apical membrane potential can be employed to study CFTR and ENaC channels and an electrogenic acid transporter in the same iPSC-derived intestinal tissue. This multiparameter phenotypic platform promises to expand CF therapy discovery to include strategies to target multiple determinants of epithelial fluid transport.
CAT, AGTR2, L-SIGN and DC-SIGN are potential receptors for the entry of SARS-CoV-2 into human cells
Authors: Guo Dongjie , Guo Ruifang , Li Zhaoyang , Zhang Yuyang , Zheng Wei , Huang Xiaoqiang , Aziz Tursunjan , Zhang Yang , Liu Lijun
Published: July 2021

Since December 2019, the COVID-19 caused by SARS-CoV-2 has been widely spread all over the world. It is reported that SARS-CoV-2 infection affects a series of human tissues, including lung, gastrointestinal tract, kidney, etc. ACE2 has been identified as the primary receptor of the SARS-CoV-2 Spike (S) protein. The relatively low expression level of this known receptor in the lungs, which is the predominantly infected organ in COVID-19, indicates that there may be some other co-receptors or alternative receptors of SARS-CoV-2 to work in coordination with ACE2. Here, we identified twenty-one candidate receptors of SARS-CoV-2, including ACE2-interactor proteins and SARS-CoV receptors. Then we investigated the protein expression levels of these twenty-one candidate receptors in different human tissues and found that five of which CAT, MME, L-SIGN, DC-SIGN, and AGTR2 were specifically expressed in SARS-CoV-2 affected tissues. Next, we performed molecular simulations of the above five candidate receptors with SARS-CoV-2 S protein, and found that the binding affinities of CAT, AGTR2, L-SIGN and DC-SIGN to S protein were even higher than ACE2. Interestingly, we also observed that CAT and AGTR2 bound to S protein in different regions with ACE2 conformationally, suggesting that these two proteins are likely capable of the co-receptors of ACE2. Conclusively, we considered that CAT, AGTR2, L-SIGN and DC-SIGN were the potential receptors of SARS-CoV-2. Moreover, AGTR2 and DC-SIGN tend to be highly expressed in the lungs of smokers, which is consistent with clinical phenomena of COVID-19, and further confirmed our conclusion. Besides, we also predicted the binding hot spots for these putative protein-protein interactions, which would help develop drugs against SARS-CoV-2.
UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
Authors: Wallmeroth Damaris , Boehm Volker , Lackmann Jan-Wilm , Altmüller Janine , Dieterich Christoph , Gehring Niels H.
Published: July 2021

The paralogous human proteins UPF3A and UPF3B are involved in recognizing mRNAs targeted by nonsense-mediated mRNA decay (NMD). While UPF3B has been demonstrated to support NMD, contradicting reports describe UPF3A either as an NMD activator or inhibitor. Here, we present a comprehensive functional analysis of UPF3A and UPF3B in human cells using combinatory experimental approaches. Overexpression or knockout of UPF3A as well as knockout of UPF3B did not detectably change global NMD activity. In contrast, the co-depletion of UPF3A and UPF3B resulted in a marked NMD inhibition and a transcriptome-wide upregulation of NMD substrates, demonstrating a functional redundancy between both NMD factors. Although current models assume that UPF3 bridges NMD-activating exon-junction complexes (EJC) to the NMD factor UPF2, UPF3B exhibited only slightly impaired NMD activity in rescue experiments when UPF2 or EJC binding was impaired. Further rescue experiments revealed partially redundant functions of UPF3B domains in supporting NMD, involving both UPF2 and EJC interaction sites and the central region of UPF3. Collectively, UPF3A and UPF3B serve as fault-tolerant NMD activators in human cells.
Oncogenic RABL6A promotes NF1-associated MPNST progression in vivo
Authors: Kohlmeyer Jordan L , Kaemmer Courtney A , Lingo Joshua J , Leidinger Mariah R , Meyerholz David K , Tanas Munir R , Dodd Rebecca D , Quelle Dawn E
Published: July 2021

Background

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that display complex molecular and genetic alterations. Powerful tumor suppressors CDKN2A and TP53 are commonly disrupted in these lesions along with NF1, a gene that encodes a negative regulator of Ras. Many additional factors have been implicated in MPNST pathogenesis. A greater understanding of critical drivers of the disease is needed to guide more informed targeted therapies for patients. RABL6A is a newly identified driver of MPNST cell survival and proliferation whose in vivo role in the disease is unknown.

Methods

Using CRISPR-Cas9 targeting of Nf1+Cdkn2a or Nf1+Tp53 in the sciatic nerve to form de novo MPNSTs, we investigated the biological significance of RABL6A in MPNST development. Molecular evaluation of terminal tumors (western blot, qRT-PCR, immunohistochemistry) yielded several insights.

Results

Mice lacking Rabl6 displayed slower tumor growth and extended survival relative to wildtype animals in both genetic contexts. YAP oncogenic activity was selectively downregulated in RABL6A-null, Nf1+Cdkn2a lesions but not in RABL6A-null, Nf1+Tp53 tumors. Regardless of genetic context, loss of RABL6A caused upregulation of the CDK inhibitor, p27 in tumors. Paradoxically, both models displayed elevated Myc protein expression and Ki67 staining in terminal tumors lacking RABL6A.

Conclusions

These findings demonstrate RABL6A is required for optimal tumor progression of NF1 mutant MPNSTs in vivo in both Cdkn2a and p53 inactivated settings. However, sustained RABL6A loss may provide selective pressure for molecular alterations, such as Myc upregulation, that ultimately promote an unwanted, hyper-proliferative tumor phenotype akin to drug resistant lesions.

Importance of the Study

MPNSTs are aggressive, deadly, and challenging to treat tumors due to location around nerves and high mutational burden. Many factors implicated in MPNST genesis have yet to be fully tested for biological significance in disease formation. We establish a critical physiological role for a new oncoprotein, RABL6A, in promoting NF1-associated MPNST progression. We identify novel RABL6A-regulated pathways that likely contribute to tumor growth, specifically YAP and Myc signaling, and found that sustained RABL6A loss eventually yields more proliferative tumors. We liken RABL6A deficient tumors to those being treated with therapies targeting RABL6A effectors, such as CDKs. Therefore, those lesions should provide a powerful platform to uncover key mediators of drug resistance. Our data suggest oncogenic YAP and Myc could be such mediators of resistance. This study provides a novel system to examine one of the most pressing clinical challenges, drug resistant tumor growth and relapse, in cancer therapy.
Immunogenicity of low dose prime-boost vaccination of mRNA vaccine CV07050101 in non-human primates
Authors: van Doremalen Neeltje , Fischer Robert J. , Schulz Jonathan E. , Holbrook Myndi G. , Smith Brian J. , Lovaglio Jamie , Petsch Benjamin , Munster Vincent J.
Published: July 2021

Many different vaccine candidates against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of COVID-19, are currently approved and under development. Vaccine platforms vary from mRNA vaccines to viral-vectored vaccines, and several candidates have been shown to produce humoral and cellular responses in small animal models, non-human primates and human volunteers. In this study, six non-human primates received a prime-boost intramuscular vaccination with 4 µg of mRNA vaccine candidate CV07050101, which encodes a pre-fusion stabilized spike (S) protein of SARS-CoV-2. Boost vaccination was performed 28 days post prime vaccination. As a control, six animals were similarly injected with PBS. Humoral and cellular immune responses were investigated at time of vaccination, and two weeks afterwards. No antibodies could be detected two and four weeks after prime vaccination. Two weeks after boost vaccination, binding but no neutralizing antibodies were detected in 4 out of 6 non-human primates. SARS-CoV-2 S protein specific T cell responses were detected in these 4 animals. In conclusion, prime-boost vaccination with 4 µg of vaccine candidate CV07050101 resulted in limited immune responses in 4 out of 6 non-human primates.
The E. coli helicase does not use ATP during replication
Authors: Spenkelink Lisanne M. , Spinks Richard R. , Jergic Slobodan , Lewis Jacob S. , Dixon Nicholas E. , van Oijen Antoine M.
Published: July 2021

The replisome is responsible for replication of DNA in all domains of life, with several of its individual enzyme components relying on hydrolysis of nucleoside triphosphates to provide energy for replisome function. Half a century of biochemical studies have demonstrated a dependence on ATP as an energy source for helicases to unwind duplex DNA during replication. Through single-molecule visualization of DNA replication by the Escherichia coli replisome, we demonstrate that the DnaB helicase does not rely on hydrolysis of ATP (or any ribo-NTPs) in the context of the elongating replisome. We establish that nucleotide incorporation by the leading-strand polymerase is the main motor driving the replication process.

One Sentence Summary

Polymerases provide the energy for helicase-mediated DNA unwinding during E. coli DNA replication.
Performance and characterization of the FinEstBeAMS beamline at the MAX IV Laboratory
Authors: Chernenko Kirill , Kivimäki Antti , Pärna Rainer , Wang Weimin , Sankari Rami , Leandersson Mats , Tarawneh Hamed , Pankratov Vladimir , Kook Mati , Kukk Edwin , Reisberg Liis , Urpelainen Samuli , Käämbre Tanel , Siewert Frank , Gwalt Grzegorz , Sokolov Andrey , Lemke Stephanie , Alimov Svyatoslav , Knedel Jeniffa , Kutz Oliver , Seliger Tino , Valden Mika , Hirsimäki Mika , Kirm Marco , Huttula Marko
Published: July 2021

FinEstBeAMS (Finnish–Estonian Beamline for Atmospheric and Materials Sciences) is a multidisciplinary beamline constructed at the 1.5 GeV storage ring of the MAX IV synchrotron facility in Lund, Sweden. The beamline covers an extremely wide photon energy range, 4.5–1300 eV, by utilizing a single elliptically polarizing undulator as a radiation source and a single grazing-incidence plane grating monochromator to disperse the radiation. At photon energies below 70 eV the beamline operation relies on the use of optical and thin-film filters to remove higher-order components from the monochromated radiation. This paper discusses the performance of the beamline, examining such characteristics as the quality of the gratings, photon energy calibration, photon energy resolution, available photon flux, polarization quality and focal spot size.