bluuebunny/crossref_metadata_2025 huggingface dataset:
A Ralstonia solanacearum effector targets TGA transcription factors to subvert salicylic acid signaling
Authors: Qi Peipei , Huang Mengling , Hu Xuehan , Zhang Ying , Wang Ying , Li Pengyue , Chen Shiyun , Zhang Dan , Cao Sen , Zhu Wanting , Xie Jiatao , Cheng Jiasen , Fu Yanping , Jiang Daohong , Yu Xiao , Li Bo
Published: January 2022

The bacterial pathogen Ralstonia solanacearum causes wilt disease on Arabidopsis thaliana and tomato (Solanum lycopersicum). This pathogen uses type III effectors to inhibit the plant immune system; however, how individual effectors interfere with plant immune responses, including transcriptional reprograming, remain elusive. Here, we show that the type III effector RipAB targets Arabidopsis TGACG SEQUENCE-SPECIFIC BINDING PROTEIN (TGA) transcription factors, the central regulators of plant immune gene regulation, via physical interaction in the nucleus to dampen immune responses. RipAB was required for R. solanacearum virulence on wild-type tomato and Arabidopsis but not Arabidopsis tga1 tga4 and tga2 tga5 tga6 mutants. Stable expression of RipAB in Arabidopsis suppressed the pathogen-associated molecular pattern-triggered reactive oxygen species (ROS) burst and immune gene induction as well as salicylic acid (SA) regulons including RBOHD and RBOHF, responsible for ROS production, all of which were phenocopied by the tga1 tga4 and tga2 tga5 tga6 mutants. We found that TGAs directly activate RBOHD and RBOHF expression and that RipAB inhibits this through interfering with the recruitment of RNA polymerase II. These results suggest that TGAs are the bona fide and major virulence targets of RipAB, which disrupts SA signaling by inhibiting TGA activity to achieve successful infection.
Clinical features and immune-related protein patterns of anti-MDA5 positive clinically amyopathic dermatomyositis Dutch patients
Authors: Hensgens Marjolein P M , Delemarre Eveline M , Drylewicz Julia , Voortman Mareye , Krol Roline M , Dalm Virgil A S H , Miedema Jelle R , Wiertz Ivo , Grutters Jan , Limper Maarten , Nierkens Stefan , Leavis Helen L
Published: January 2022

Objectives

The presence of melanoma differentiation-associated protein 5 (MDA5) antibodies in patients with DM is associated with the development of a rapidly progressive interstitial lung disease (RPILD), unresponsive to conventional treatment. We characterize patients and provide more insight into potential biomarkers to identify patients with RPILD.

Methods

Patients diagnosed with anti-MDA5 positive DM between December 2015 and November 2017 were included in this study. Clinical data were retrospectively retrieved from medical records. A total of 180 immune-related markers were measured in sera of 16 patients and 15 healthy controls using proximity extension assay-based technology.

Results

Twenty patients were included, with a median time from symptoms till diagnosis of 4 months. All patients had clinically amyopathic DM. Interstitial lung disease (ILD) was present at diagnosis in 94% of the patients, 45% presented with RPILD. The mortality rate was 35% within 4 months after diagnosis and respiratory failure was the main cause of death in these patients. Furthermore, unsupervised analysis revealed that patients with RPILD show clearly different inflammatory serum profiles than healthy controls. In addition, in comparison to healthy controls, the IFN, IL1, IL10 and IL18 signalling pathways are different regulated in anti-MDA5 positive patients.

Conclusion

In this Dutch anti-MDA5 positive clinically amyopathic DM (CADM) cohort, one-third of the patients died due to RPILD soon after diagnosis, which underlines the severity of this disease. In addition, we have found several possible pathways that are differentially regulated in RPILD vs no RPILD DM and healthy controls. These markers await further validation before clinical use.
Sleep and circadian informatics data harmonization: a workshop report from the Sleep Research Society and Sleep Research Network
Authors: Mazzotti Diego R , Haendel Melissa A , McMurry Julie A , Smith Connor J , Buysse Daniel J , Roenneberg Till , Penzel Thomas , Purcell Shaun , Redline Susan , Zhang Ying , Merikangas Kathleen R , Menetski Joseph P , Mullington Janet , Boudreau Eilis
Published: January 2022

The increasing availability and complexity of sleep and circadian data are equally exciting and challenging. The field is in constant technological development, generating better high-resolution physiological and molecular data than ever before. Yet, the promise of large-scale studies leveraging millions of patients is limited by suboptimal approaches for data sharing and interoperability. As a result, integration of valuable clinical and basic resources is problematic, preventing knowledge discovery and rapid translation of findings into clinical care. To understand the current data landscape in the sleep and circadian domains, the Sleep Research Society (SRS) and the Sleep Research Network (now a task force of the SRS) organized a workshop on informatics and data harmonization, presented at the World Sleep Congress 2019, in Vancouver, Canada. Experts in translational informatics gathered with sleep research experts to discuss opportunities and challenges in defining strategies for data harmonization. The goal of this workshop was to fuel discussion and foster innovative approaches for data integration and development of informatics infrastructure supporting multi-site collaboration. Key recommendations included collecting and storing findable, accessible, interoperable, and reusable data; identifying existing international cohorts and resources supporting research in sleep and circadian biology; and defining the most relevant sleep data elements and associated metadata that could be supported by early integration initiatives. This report introduces foundational concepts with the goal of facilitating engagement between the sleep/circadian and informatics communities and is a call to action for the implementation and adoption of data harmonization strategies in this domain.
High-cited favorable studies for COVID-19 treatments ineffective in large trials
Authors: Ioannidis John P.A.
Published: January 2022

Importance

COVID-19 has resulted in massive production, publication and wide dissemination of clinical studies trying to identify effective treatments. However, several widely touted treatments failed to show effectiveness in large well-done randomized controlled trials (RCTs).

Objective

To evaluate for COVID-19 treatments that showed no benefits in subsequent large RCTs how many of their most-cited clinical studies had declared favorable results for these interventions.

Methods

Scopus (last update December 23, 2021) identified articles on lopinavir-ritonavir, hydroxycholoroquine/azithromycin, remdesivir, convalescent plasma, colchicine or interferon (index interventions) that represented clinical trials and that had received >150 citations. Their conclusions were assessed and correlated with study design features. The ten most recent citations for the most-cited article on each index intervention were examined on whether they were critical to the highly-cited study. Altmetric scores were also obtained.

Findings

40 articles of clinical studies on these index interventions had received >150 citations (7 exceeded 1,000 citations). 20/40 (50%) had favorable conclusions and 4 were equivocal. Highly-cited articles with favorable conclusions were rarely RCTs while those without favorable conclusions were mostly RCTs (3/20 vs 15/20, p=0.0003). Only 1 RCT with favorable conclusions had sample size >160. Citation counts correlated strongly with Altmetric scores, in particular news items. Only 9 (15%) of 60 recent citations to the most highly-cited studies with favorable or equivocal conclusions were critical to the highly-cited study.

Conclusion

Many clinical studies with favorable conclusions for largely ineffective COVID-19 treatments are uncritically heavily cited and disseminated. Early observational studies and small randomized trials may cause spurious claims of effectiveness that get perpetuated.
MS1Connect: a mass spectrometry run similarity measure
Authors: Lin Andy , Kaiser Brooke L. Deatherage , Hutchison Janine R. , Bilmes Jeffrey A. , Noble William Stafford
Published: January 2022

Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols. We propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though this data is not used by MS1Connect. The MS1Connect software will be made available upon acceptance at https://github.com/bmx8177/MS1Connect.
Harmonized-Multinational qEEG Norms (HarMNqEEG)
Authors: Li Min , Wang Ying , Lopez-Naranjo Carlos , Abd Hamid Aini Ismafairus , Evans Alan C. , Savostyanov Alexander N. , Calzada-Reyes Ana , Areces-Gonzalez Ariosky , Villringer Arno , Tobon-Quintero Carlos A. , Garcia-Agustin Daysi , Paz-Linares Deirel , Yao Dezhong , Dong Li , Aubert-Vazquez Eduardo , Reza Faruque , Omar Hazim , Abdullah Jafri Malin , Galler Janina R. , Ochoa-Gomez John F. , Prichep Leslie S. , Galan-Garcia Lidice , Morales-Chacon Lilia , Valdes-Sosa Mitchell J. , Tröndle Marius , Mohd Zulkifly Mohd Faizal Bin , Abdul Rahman Muhammad Riddha Bin , Milakhina Natalya S. , Langer Nicolas , Rudych Pavel , Hu Shiang , Koenig Thomas , Virues-Alba Trinidad A. , Lei Xu , Bringas-Vega Maria L. , Bosch-Bayard Jorge F. , Valdes-Sosa Pedro Antonio
Published: January 2022

This paper extends our frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. i) Create lifespan Hermitian Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross-spectral tensors were shared. After visual and automatic quality control developmental equations for the mean and standard deviation of qEEG traditional and Hermitian Riemannian descriptive parameters were calculated using additive mixed-effects models. We demonstrate qEEG “batch effects” and provide methods to calculate harmonized z-scores. ii) We also show that the multinational harmonized Hermitian Riemannian norms produce z-scores with increased diagnostic accuracy to predict brain dysfunction at school-age produced by malnutrition only in the first year of life. We provide data and software for constructing norms. iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.

Highlights

We create lifespan Hermitian Riemannian qEEG norms for cross-spectral tensors.

The norms are based on 9 countries, 12 devices, and 14 studies, with 1564 subjects.

We demonstrate qEEG “batch effects”, providing harmonization methods to remove them.

Multinational harmonized z-scores increase diagnostic accuracy of brain dysfunction.

Data and software are available for norm and individual z-scores calculation.
The blowflyChrysomya latifronsinhabits fragmented rainforests, but lacks genetic diversity and population structure
Authors: Butterworth Nathan J. , Wallman James F. , Johnston Nikolas P. , Dawson Blake M. , McGaughran Angela
Published: January 2022

Climate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. It is not currently feasible to assess the population structure of every invertebrate species, so there is a compelling need to identify ‘indicator species’ that are broadly indicative of habitat-level patterns and processes. Blowflies are an ideal candidate, because they are widespread, abundant, and can be easily collected within rainforests.

Here, we present the first study of the blowflyChrysomya latifrons, which is endemic to the rainforests of New South Wales, Australia. We genotyped 188 flies from 15 isolated rainforests and found low overall genetic diversity and a complete lack of genetic structure between populations – suggesting the presence of a single large panmictic population along ~1,000 km of the Australian east coast. This highlights that: (1)Ch. latifronsinhabits every rainforest in NSW and undoubtedly plays an important role in these ecosystems, but low genetic diversity may cause it to struggle to adapt to a changing climate; (2) strongly dispersing insects have the capacity to migrate between isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens with them to form crucial trophic networks; and (3) there is an urgent need for similar studies on poorly dispersing rainforest insects, as these may be the most fragmented and at highest risk of local extinction.
A digital self-care intervention for Ugandan patients with heart failure and their clinicians: User-centred design and usability study
Authors: Hearn Jason , Wali Sahr , Birungi Patience , Cafazzo Joseph A. , Ssinabulya Isaac , Akiteng Ann R. , Ross Heather J. , Seto Emily , Schwartz Jeremy I.
Published: January 2022

Background

The prevalence of heart failure (HF) is increasing in Uganda. Ugandan patients with HF report receiving limited information about their illness, disease management, or empowerment to engage in self-care behaviors. Interventions targeted at improving HF self-care have been shown to improve patient quality of life and to reduce hospitalizations in high-income countries. However, such interventions remain underutilized in resource-limited settings like Uganda.

Objective

To develop a digital health intervention that enables improved self-care amongst HF patients in Uganda.

Methods

We implemented a user-centred design process to develop a self-care intervention entitled Medly Uganda. The ideation phase comprised a systematic scoping review and preliminary data collection amongst HF patients and clinicians in Uganda. An iterative design process was then used to advance an initial prototype into a fully-functional digital health intervention. The evaluation phase involved usability testing of the developed intervention amongst Ugandan patients with HF and their clinicians.

Results

Medly Uganda is a digital health intervention that is fully integrated within a government-operated mobile health platform. The system allows patients to report daily HF symptoms, receive tailored treatment advice, and connect with a clinician when showing signs of decompensation. Medly Uganda harnesses Unstructured Supplementary Service Data technology that is already widely used in Uganda for mobile phone-based financial transactions. Usability testing showed the system to be accepted by patients, caregivers, and clinicians.

Conclusions

Medly Uganda is a fully-functional and well-accepted digital health intervention that enables Ugandan HF patients to better care for themselves. Moving forward, we expect the system to help decongest cardiac clinics and improve self-care efficacy amongst HF patients in Uganda.
Associations between multiple long-term conditions and mortality in diverse ethnic groups
Authors: Stafford Mai , Knight Hannah , Hughes Jay , Alarilla Anne , Mondor Luke , Kone Anna Pefoyo , Wodchis Walter , Deeny Sarah R
Published: January 2022

Background

Multiple conditions are more prevalent in some minoritised ethnic groups and are associated with higher mortality rate but studies examining differential mortality once conditions are established is US-based. Our study tested whether the association between multiple conditions and mortality varies across ethnic groups in England.

Methods and Findings

A random sample of primary care patients from Clinical Practice Research Datalink (CPRD) was followed from 1st January 2015 until 31st December 2019. Ethnicity, usually self-ascribed, was obtained from primary care records if present or from hospital records. Cox regression models were used to estimate mortality by number of long-term conditions, ethnicity and their interaction, with adjustment for age and sex for 532,059 patients with complete data.

During five years of follow-up, 5.9% of patients died. Each additional long-term condition at baseline was associated with increased mortality. This association differed across ethnic groups. Compared with 50-year-olds of white ethnicity with no conditions, the mortality rate was higher for white 50-year-olds with two conditions (HR 1.77) or four conditions (HR 3.13). Corresponding figures were higher for 50-year-olds of Black Caribbean ethnicity with two conditions (HR=2.22) or four conditions (HR 4.54). The direction of the interaction of number of conditions with ethnicity showed higher mortality associated with long-term conditions in nine out of ten minoritised ethnic groups, attaining statistical significance in four (Pakistani, Black African, Black Caribbean and Black other ethnic groups).

Conclusions

The raised mortality rate associated with having multiple conditions is greater in minoritised ethnic groups compared with white people. Research is now needed to identify factors that contribute to these inequalities. Within the health care setting, there may be opportunities to target clinical and self-management support for people with multiple conditions from minoritised ethnic groups.
SARS-CoV-2 Omicron Neutralization After Heterologous Vaccine Boosting
Authors: Lyke Kirsten E. , Atmar Robert L. , Islas Clara Dominguez , Posavad Christine M. , Szydlo Daniel , PaulChourdhury Rahul , Deming Meagan E. , Eaton Amanda , Jackson Lisa A. , Branche Angela R. , Sahly Hana M. El , Rostad Christina A. , Martin Judith M. , Johnston Christine , Rupp Richard E. , Mulligan Mark J. , Brady Rebecca C. , Frenck Robert W. , Bäcker Martín , Kottkamp Angelica C. , Babu Tara M. , Rajakumar Kumaravel , Edupuganti Srilatha , Dobrzynski David , Coler Rhea N. , Archer Janet I. , Crandon Sonja , Zemanek Jillian A. , Brown Elizabeth R. , Neuzil Kathleen M. , Stephens David S. , Post Diane J. , Nayak Seema U. , Roberts Paul C. , Beigel John H. , Montefiori David ,   the DMID 21-0012 Study Group
Published: January 2022

As part of an ongoing study assessing homologous and heterologous booster vaccines, following primary EUA series, we assessed neutralization of D614G and Omicron variants prior to and 28 days after boost. Subset analysis was done in six combinations (N = 10/group): four homologous primary-booster combinations included mRNA-1273 two-dose priming followed by boosting with 100-μg or 50-μg mRNA-1273, Ad26.COV2.S single-dose priming followed by Ad26.COV2.S booster and BNT162b2 two-dose priming followed by BNT162b2 boosting; and two heterologous primary-booster combinations: BNT162b2 followed by Ad26.COV2.S and Ad26.COV2.S followed by BNT162b2. Neutralizing antibody (Nab) titers to D614G on the day of boost (baseline) were detected in 85-100% of participants, with geometric mean titers (GMT) of 71-343 in participants who received an mRNA vaccine series versus GMTs of 35-41 in participants primed with Ad26.OV2.S. Baseline NAb titers to Omicron were detected in 50-90% of participants who received an mRNA vaccine series (GMT range 12.8-24.5) versus 20-25% among participants primed with Ad26.COV2.S. The booster dose increased the neutralizing GMT in most combinations to above 1000 for D614G and above 250 for Omicron by Day 29. Homologous prime-boost Ad26.COV2.S had the lowest NAb on Day 29 (D614G GMT 128 and Omicron GMT 45). Results were similar between age groups. Most homologous and heterologous boost combinations examined will increase humoral immunity to the Omicron variant.
A national survey of early treatment seeking behavior among those with incident SARS-CoV-2 infection
Authors: Kojima Noah , Brobeck Matthew , Slepnev Vladimir , Klausner Jeffrey D.
Published: January 2022

Background

Despite effective means to treat SARS-CoV-2 infection, the early treatment seeking behavior of those newly diagnosed with infection is not clear.

Methods

We surveyed users of a national SARS-CoV-2 testing company to assess the frequency and correlates of early treatment seeking behavior for a positive test result. We recruited adults (18 years or older) who had tested positive for SARS-CoV-2 by PCR at a large clinical laboratory. To be eligible, individuals had to have a positive test result within 7 days of enrollment. Surveys were anonymous and voluntary. We collected data on demographic characteristics, general health care access and utilization, awareness of treatment for COVID-19, treatment seeking behavior, and treatments received. Descriptive statistics and odds ratios (OR) with 95% confidence intervals (95% CI) were calculated on StataSE.

Results

Participants were surveyed from 3-7 January 2022: among the 15,991 who viewed a survey request, 7,647 individuals were eligible and provided responses. The median age of a respondent was 42 years (interquartile range: 32 to 54), 68.9% of respondents were women, and respondents represented 33 different states, districts, and territories. Among respondents, 23.1% reported they had sought treatment or medical advice for their current COVID-19 diagnosis. Of those who were very aware of treatment for COVID-19, 31.0% sought treatment versus 16.7% who were unaware (p-value< 0.001). The odds of treatment seeking behavior were higher for those that were contacted by a medical professional after their diagnosis (OR: 4.57 [95% CI: 3.89 to 5.37]), those with a primary doctor (OR: 2.94 [95% CI: 2.52 to 3.43]), those who self-measured their oxygen saturation (OR: 2.53 [95% CI: 2.25 to 2.84]), and those over 65 years of age (OR: 2.36 [95% CI: 2.02 to 2.76]). There was no difference in those seeking treatment based on heritage, ethnicity, prior COVID-19 diagnosis, state political affiliation, or vaccination status. The odds of seeking treatment were lower among men (OR: 0.88 [95% CI: 0.78 to 0.99]) and those without insurance (OR: 0.62 [95% CI: 0.52 to 0.72]). The most common treatment locations were clinics and most common treatments were Vitamin C, Vitamin D, Zinc, Tylenol, and NSAIDs.

Conclusion

More public outreach is needed to raise awareness of the benefits of treatment for COVID-19. We found that people who were more aware about treatment for COVID-19 were more likely to seek medical advice or therapy. Efforts to increase awareness might increase early treatment for SARS-CoV-2 infection. Increased outreach with treatment facilitation from medical professionals and/or public health staff to those with newly detected SARS-CoV-2 infections, particularly among those at higher-risk of complications, might also be helpful.
Cost of tuberculosis-related aeromedical retrievals in the Torres Strait, Australia
Authors: Foster J’Belle , Judge Daniel , Mendez Diana , Marais Ben J. , Peniyamina Dunstan , McBryde Emma S.
Published: January 2022

Tuberculosis (TB) remains a disease of public health significance at the Australia / Papua New Guinea (PNG) international border. In the remote Torres Strait Islands, aeromedical evacuation is a necessary but costly component of TB management and patients with critical care needs require support to prevent onward TB transmission. A detailed costing of an exemplar TB patient from PNG who presented to a Queensland Health facility in the Torres Strait and required urgent aeromedical evacuation was performed. Data were drawn from patient charts, financial and clinical information systems used within Queensland Health and the Torres and Cape Hospital and Health Service. The total cost of aeromedical evacuation was AUD 124,280; 54% of the cost was attributed to travel. Between 2016 and 2019, 19 patients diagnosed with TB were medically evacuated from an outer Torres Strait Island with a median length of hospital stay of 57 days. Aeromedical evacuation and medical management costs require adequate budget allocation.
Rapid detection of single nucleotide polymorphisms using the MinION nanopore sequencer: a feasibility study for perioperative precision medicine
Authors: Tabata Yoshiteru , Matsuo Yoshiyuki , Fujii Yosuke , Ohta Atsufumi , Hirota Kiichi
Published: January 2022

Introduction

Precision medicine is a phrase used to describe personalized medical care tailored to specific patients based on their clinical presentation and genetic makeup. However, despite the fact that several single nucleotide polymorphisms (SNPs) have been reported to be associated with increased susceptibility to particular anesthetic agents and the occurrence of perioperative complications, genomic profiling and thus precision medicine has not been widely applied in perioperative management.

Methods

We validated six SNP loci known to affect perioperative outcomes in Japanese patients using genomic DNA from saliva specimens and nanopore sequencing of each SNP loci to facilitate allele frequency calculations and then compared the nanopore results to those produced using the conventional dideoxy sequencing method.

Results

Nanopore sequencing reads clustered into the expected genotypes in both homozygous and heterozygous cases. In addition, the nanopore sequencing results were consistent with those obtained using conventional dideoxy sequencing and the workflow provided reliable allele frequency estimation, with a total analysis time of less than 4 h.

Conclusion

Thus, our results suggest that nanopore sequencing may be a promising and versatile tool for SNP genotyping, allowing for rapid and feasible risk prediction of perioperative outcomes.
Human Leukocyte Antigen Homozygosity Contributes to Sensitization in Kidney Transplant Candidates
Authors: Rushakoff Joshua A. , Gragert Loren , Pando Marcelo J , Stewart Darren , Huang Edmund , Kim Irene , Jordan Stanley , Lindblad Kelsi , Zhang Xiaohai , Lalli Peter , Patel Jignesh K. , Kobashigawa Jon A. , Kransdorf Evan P.
Published: January 2022

Background

Homozygosity for human leukocyte antigens (HLA) has been associated with adverse outcomes after viral infection as well as pregnancy-induced HLA sensitization. We sought to assess the relationship between HLA locus homozygosity and the level of HLA antibody sensitization.

Methods

We measured sensitization using the calculated panel reactive antibody (CPRA) value for a large cohort of 147,461 patients added to the US OPTN/UNOS kidney transplant waitlist between December 2014 and December 2019. We used multinomial logistic modeling to compare 62,510 sensitized patients to 84,955 unsensitized controls.

Results

We found that the number of homozygous HLA loci was strongly associated with the level of sensitization. Within highly- or extremely-sensitized candidates, women displayed a higher relative abundance of HLA homozygosity at multiple HLA loci as compared to men, with attenuation of this effect in Black candidates. In multinomial logistic modeling, the number of homozygous HLA loci was an independent predictor of sensitization and interacted with female sex but not with other factors associated with sensitization.

Conclusions

This study shows that HLA homozygosity is an innate genetic factor that contributes to HLA sensitization, and enhances the effect of pregnancy-related sensitization.
The interactome of Cryptococcus neoformans Rmt5 reveals multiple regulatory points in fungal cell biology and pathogenesis
Authors: Kalem Murat C. , Subbiah Harini , Shen Shichen , Chen Runpu , Terry Luke , Sun Yijun , Qu Jun , Panepinto John C.
Published: January 2022

Protein arginine methylation is a key post-translational modification in eukaryotes that modulates core cellular processes, including translation, morphology, transcription, and RNA fate. However, this has not been explored in Cryptococcus neoformans, a human-pathogenic basidiomycetous encapsulated fungus. We characterized the five protein arginine methyltransferases in C. neoformans and highlight Rmt5 as critical regulator of cryptococcal morphology and virulence. An rmt5Δ mutant was defective in thermotolerance, had a remodeled cell wall, and exhibited enhanced growth in an elevated carbon dioxide atmosphere and in chemically induced hypoxia. We revealed that Rmt5 interacts with post-transcriptional gene regulators, such as RNA-binding proteins and translation factors. Further investigation of the rmt5Δ mutant showed that Rmt5 is critical for the homeostasis of eIF2α and its phosphorylation state following 3-amino-1,2,4-triazole-induced ribosome stalling. RNA sequencing of one rmt5Δ clone revealed stable chromosome 9 aneuploidy that was ameliorated by complementation but did not impact the rmt5Δ phenotype. As a result of these diverse interactions and functions, loss of RMT5 enhanced phagocytosis by murine macrophages and attenuated disease progression in mice. Taken together, our findings link arginine methylation to critical cryptococcal cellular processes that impact pathogenesis, including post-transcriptional gene regulation by RNA-binding proteins.

Significance

The fungal pathogen Cryptococcus neoformans is a huge threat for people living with immune deficits, especially HIV/AIDS. Its virulence potential is dependent on virulence factors, stress adaptation, and thermotolerance. Post-transcriptional gene regulation is important for these pathogenic processes, but the mechanisms that govern post-transcriptional regulator function are unexplored. Protein arginine methylation is a major modification of post-transcriptional regulators that has not been investigated in pathogenic fungi. Here we investigated the role of arginine methylation by arginine methyltransferases on the biology and virulence of C. neoformans. Phenotypic characterization of deletion mutants revealed pleiotropic functions for RMTs in this pathogen. Further investigation of the Rmt5 interactome using proximity-dependent biotinylation revealed interactions with RNA binding proteins and translation factors, thereby impacting virulence-associated processes.
Automated bioprocess feedback operation in a high throughput facility via the integration of a mobile robotic lab assistant
Authors: Kaspersetz Lucas , Waldburger Saskia , Schermeyer M.-Therese , Riedel Sebastian L. , Groß Sebastian , Neubauer Peter , Cruz-Bournazou M.-Nicolas
Published: January 2022

Biotechnological processes development is challenging due to the sheer variety of process parameters. For efficient upstream development parallel cultivation systems have proven to reduce costs and associated timelines successfully, while offering excellent process control. However, the degree of automation of such small scale systems is comparably low and necessary sample analysis requires manual steps. Although the subsequent analysis can be performed in a high-throughput manner, the integration of analytic devices remains challenging. Especially, when cultivation and analysis laboratories are spatially separated. Mobile robots offer a potential solution, but the implementation in research laboratories is not widely adopted. Our approach demonstrates the integration of a small scale cultivation system into a liquid handling station for an automated sample procedure. The samples are transferred via a mobile robotic lab assistant and subsequently analysed by a high-throughput analyzer. The process data is stored in a centralized database. The mobile robotic workflow guarantees a flexible solution for device integration and facilitates automation. Restrictions regarding spatial separation of devices are circumvented, enabling a modular platform throughout different laboratories. The presented cultivation platform is evaluated based on industrial relevant E. coli BW25113 high cell density fed-batch cultivation. Here its suitability for accelerating bioprocess development is proven. The necessary magnesium addition for reaching high cell densities in mineral salt medium is automated via a feedback operation loop. The feedback operation loop demonstrates the possibility for advanced control options. This study sets the foundation for a fully integrated facility with different cultivation scales sharing the same data infrastructure, where the mobile robotic lab assistant physically connects the devices.
Increased insula activity precedes the formation of subjective Gestalt
Authors: Wilding Marilena , Körner Christof , Ischebeck Anja , Zaretskaya Natalia
Published: January 2022

The constructive nature of human perception sometimes leads us to perceiving rather complex impressions from simple sensory input. Bistable stimuli give us a rare opportunity to study the neural mechanisms behind this process. Such stimuli can be visually interpreted as simple or as more complex on the basis of the same sensory input. Previous studies demonstrated increased activity in the superior parietal cortex when participants perceived an illusory Gestalt impression compared to a simpler interpretation of individual elements. Here we tested whether activity related to the illusory Gestalt can be detected not only during, but also prior to it, by examining the slow fluctuations of resting-state-fMRI activity before the stimulus onset. We presented 31 participants with a bistable motion stimulus, which can be perceived either as four moving dot pairs (local) or two moving illusory squares (global). This allowed us to isolate the specific neural mechanisms that accompany the experience of an illusion under matched sensory input. fMRI was used to measure brain activity in a sparse event-related design. We observed stronger IPS and putamen responses to the stimulus when participants perceived the global interpretation compared to local, confirming the previously reported role of these areas in perceptual grouping. Most importantly, we also observed that the global stimulus interpretation was preceded by an increased activity of the bilateral dorsal insula, which is known to process saliency and gate information for conscious access. Our data suggest an important role of the dorsal insula in shaping an internally generated illusory Gestalt percept.
Enhancement of RecET-mediated in vivo linear DNA assembly by a xonA mutation
Authors: Sawitzke James A. , Costantino Nina , Hutchinson Ellen , Thomason Lynn C. , Court Donald L.
Published: January 2022

Assembly of intact, replicating plasmids from linear DNA fragments introduced into bacterial cells, i.e. in vivo cloning, is a facile genetic engineering technology that avoids many of the problems associated with standard in vitro cloning. Here we report characterization of various parameters of in vivo linear DNA assembly mediated by either the RecET recombination system or the bacteriophage λ Red recombination system. As previously observed, RecET is superior to Red for this reaction when the terminal homology is 50 bases. Deletion of the E. coli xonA gene, encoding Exonuclease I, a 3’→5’ single-strand DNA exonuclease, substantially improves the efficiency of in vivo linear DNA assembly for both systems. Deletion of ExoI function allowed robust RecET assembly of six DNA segments to create a functional plasmid. The linear DNAs are joined accurately with very few errors. This discovery provides a significant improvement to previously reported in vivo linear DNA assembly technologies.
Expressing the pro-apoptotic Reaper protein via insertion into the structural open reading frame of Sindbis virus reduces the ability to infect Aedes aegypti mosquitoes
Authors: Carpenter Alexis , Clem Rollie J.
Published: January 2022

Arboviruses continue to threaten a significant portion of the human population, and a better understanding is needed of the determinants of successful arbovirus infection of arthropod vectors. Avoiding apoptosis has been shown to be one such determinant. Previous work showed that a Sindbis virus (SINV) construct called MRE/rpr that expresses the pro-apoptotic protein Reaper via a duplicated subgenomic promoter had a reduced ability to orally infect Aedes aegypti mosquitoes at 3 days post-blood meal (PBM), but this difference diminished over time as virus variants containing deletions in the inserted reaper gene rapidly predominated. The goal of this study was to generate a SINV construct that more stably expressed Reaper, in order to further clarify the effect of midgut apoptosis on disseminated infection in Ae. aegypti. We did this by inserting reaper as an in-frame fusion into the structural open reading frame (ORF) of SINV. This construct, MRE/rprORF, successfully expressed Reaper, replicated similarly to MRE/rpr in cell lines, and induced apoptosis in cultured cells and in mosquito midgut tissue. Mosquitoes that fed on blood containing MRE/rprORF developed less midgut and disseminated infection when compared to MRE/rpr or a control virus up to at least 7 days PBM, when less than 50% of mosquitoes that ingested MRE/rprORF had detectable disseminated infection, compared with around 80% or more of mosquitoes fed with MRE/rpr or control virus. However, virus titer in mosquitoes infected with MRE/rprORF was not significantly different from control virus, suggesting that induction of apoptosis by expression of Reaper by this method can reduce infection prevalence, but if infection is established then apoptosis induced by this method has limited ability to continue to suppress replication.
National-scale surveillance of emerging SARS-CoV-2 variants in wastewater
Authors: Amman Fabian , Markt Rudolf , Endler Lukas , Hupfauf Sebastian , Agerer Benedikt , Schedl Anna , Richter Lukas , Zechmeister Melanie , Bicher Martin , Heiler Georg , Triska Petr , Thornton Matthew , Penz Thomas , Senekowitsch Martin , Laine Jan , Keszei Zsofia , Daleiden Beatrice , Steinlechner Martin , Niederstätter Harald , Scheffknecht Christoph , Vogl Gunther , Weichlinger Günther , Wagner Andreas , Slipko Katarzyna , Masseron Amandine , Radu Elena , Allerberger Franz , Popper Niki , Bock Christoph , Schmid Daniela , Oberacher Herbert , Kreuzinger Norbert , Insam Heribert , Bergthaler Andreas
Published: January 2022

SARS-CoV-2 surveillance is crucial to identify variants with altered epidemiological properties. Wastewater-based epidemiology (WBE) provides an unbiased and complementary approach to sequencing individual cases. Yet, national WBE surveillance programs have not been widely implemented and data analyses remain challenging.

We deep-sequenced 2,093 wastewater samples representing 95 municipal catchments, covering >57% of Austria’s population, from December 2020 to September 2021. Our Variant Quantification in Sewage pipeline designed for Robustness (VaQuERo) enabled us to deduce variant abundance from complex wastewater samples and delineate the spatiotemporal dynamics of the dominant Alpha and Delta variants as well as regional clusters of other variants of concern. These results were cross validated by epidemiological records of >130,000 individual cases. Finally, we provide a framework to predict emerging variants de novo and infer variant-specific reproduction numbers from wastewater.

This study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without dense individual monitoring.

Graphical Abstract
Novel Application of a Force Sensor during Sit-to-Stands to Measure Dynamic Cerebral Autoregulation Onset
Authors: Whitaker Alicen A. , Vidoni Eric D. , Aaron Stacey E. , Rouse Adam G. , Billinger Sandra A.
Published: January 2022

Purpose

Current sit-to-stand methods measuring dynamic cerebral autoregulation (dCA) do not capture the precise onset of the time delay (TD) response. Reduced sit-to-stand reactions in older adults and individuals post-stroke could inadvertently introduce variability, error, and imprecise timing. We applied a force sensor during a sit-to-stand task to more accurately determine how TD before dCA onset may be altered.

Methods

Middle cerebral artery blood velocity (MCAv) and mean arterial pressure (MAP) were measured during two sit-to-stands separated by 15 minutes. Recordings started with participants sitting on a force-sensitive resistor for 60 seconds, then asked to stand for two minutes. Upon standing, the force sensor voltage immediately dropped and marked the exact moment of arise- and-off (AO). Time from AO until an increase in cerebrovascular conductance (CVC = MCAv/MAP) was calculated as TD.

Results

We tested the sensor in 4 healthy young adults, 2 older adults, and 2 individuals post-stroke. Healthy young adults stood quickly and the force sensor detected a small change in TD compared to classically estimated AO, from verbal command to stand. When compared to the estimated AO, older adults had a delayed measured AO and TD decreased up to ~53% while individuals post-stroke had an early AO and TD increased up to ~14%.

Conclusion

The transition reaction speed during the sit to stand has the potential to influence dCA metrics. As observed in the older adults and participants with stroke, this response may drastically vary and influence TD.

New & Noteworthy

We developed a force sensor and are the first to apply it during sit-to-stands measuring the dynamic cerebral autoregulation (dCA) response. Current methodologies estimate the transition reaction speed of the sit-to-stand, which influences the dCA metrics. Compared to estimating the kinetic moment of arise-and-off (AO), our force sensor can detect early or delayed AO in individuals who may present with lower extremity weakness such as older adults and clinical populations such as stroke.
A Mixed-Methods Feasibility Study of a Novel AI-Enabled, Web-Based, Clinical Decision Support System for the Treatment of Major Depression in Adults
Authors: Qassim Sabrina , Golden Grace , Slowey Dominique , Sarfas Mary , Whitmore Kate , Perez Tamara , Strong Elizabeth , Lundrigan Eryn , Fradette Marie-Jeanne , Baxter Jacob , Desormeau Bennet , Tanguay-Sela Myriam , Popescu Christina , Israel Sonia , Perlman Kelly , Armstrong Caitrin , Fratila Robert , Mehltretter Joseph , Looper Karl , Steiner Warren , Rej Soham , Karp Jordan F. , Heller Katherine , Parikh Sagar V. , McGuire-Snieckus Rebecca , Ferrari Manuela , Margolese Howard , Benrimoh David
Published: January 2022

The objective of this paper is to discuss perceived clinical utility and impact on physician-patient relationship of a novel, artificial-intelligence (AI) enabled clinical decision support system (CDSS) for use in the treatment of adults with major depression. Patients had a baseline appointment, followed by a minimum of two appointments with the CDSS. For both physicians and patients, study exit questionnaires and interviews were conducted to assess perceived clinical utility, impact on patient-physician relationship, and understanding and trust in the CDSS. 17 patients consented to participate in the study, of which 14 completed. 86% of physicians (6/7) felt the information provided by the CDSS provided a more comprehensive understanding of patient situations and 71% (5/7) felt the information was helpful. 86% of physicians (6/7) reported the AI/predictive model was useful when making treatment decisions. 62% of patients (8/13) reported improvement in their care as a result of the tool. 46% of patients (6/13) felt the app significantly or somewhat improved their relationship with their physicians; 54% felt it did not change. 71% of physicians (5/7) and 62% of patients (8/13) rated they trusted the tool. Qualitative results are analyzed and presented. Findings suggest physicians perceived the tool as useful in conducting appointments and used it while making treatment decisions. Physicians and patients generally found the tool trustworthy, and it may have positive effects on physician-patient relationships.
Pramipexole Enhances Reward Learning by Preserving Value Estimates
Authors: Halahakoon Don Chamith , Kaltenboeck Alexander , Martens Marieke , Geddes John G. , Harmer Catherine J. , Cowen Philip , Browning Michael
Published: January 2022

Background

Dopamine D2-like receptor agonists show promise as treatments for depression. They are thought to act by altering how individuals learn from rewarding experiences. However, the nature of these reward learning alterations, and the mechanisms by which they are produced is not clear. Reinforcement learning accounts describe three distinct processes that may produce similar changes in reward learning behaviour; increased reward sensitivity, increased inverse decision temperature and decreased value decay. As these processes produce equivalent effects on behaviour, arbitrating between them requires measurement of how expectations and prediction errors are altered. In the present study, we characterised the behavioural effects of a sustained 2-week course of the D2/3/4 receptor agonist pramipexole on reward learning and used fMRI measures of expectation and prediction error to assess which of these three mechanistic processes were responsible for the behavioural effects.

Methods

40 healthy volunteers (Age: 18-43, 50% female) were randomly allocated to receive either two weeks of pramipexole (titrated to 1mg/day) or placebo in a double-blind, between subject design. Participants completed a probabilistic instrumental learning task, in which stimuli were associated with either rewards or losses, before the pharmacological intervention and twice between days 12-15 of the intervention (once with and once without fMRI). Both asymptotic choice accuracy, and a reinforcement learning model, were used to assess reward learning.

Results

Behaviourally, pramipexole specifically increased choice accuracy in the reward condition, with no effect in the loss condition. Pramipexole increased the BOLD response in the orbital frontal cortex during the expectation of win trials but decreased the BOLD response to reward prediction errors in the ventromedial prefrontal cortex. This pattern of results indicates that pramipexole enhances choice accuracy by reducing the decay of estimated values during reward learning.

Conclusions

The D2-like receptor agonist pramipexole enhances reward learning by preserving learned values. This is a plausible candidate mechanism for pramipexole’s observed anti-depressant effect.