bluuebunny/crossref_metadata_2025 huggingface dataset:
STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale
Authors: Zheng Jingyang , Jackson Thomas Wyse , Fortier Lisa A. , Bonassar Lawrence J. , Delco Michelle L. , Cohen Itai
Published: June 2022

Cellular response to stimulation governs tissue scale processes ranging from growth and development to maintaining tissue health and initiating disease. To determine how cells coordinate their response to such stimuli, it is necessary to simultaneously track and measure the spatiotemporal distribution of their behaviors throughout the tissue. Here, we report on a novel SpatioTemporal Response AnalysisIN Situ(STRAINS) tool that uses fluorescent micrographs, cell tracking, and machine learning to measure such behavioral distributions. STRAINS is broadly applicable to any tissue where fluorescence can be used to indicate changes in cell behavior. For illustration, we use STRAINS to simultaneously analyze the mechanotransduction response of 5000 chondrocytes—over 20 million data points—in cartilage during the 50 ms to 4 hours after the tissue was subjected to local mechanical injury, known to initiate osteoarthritis. We find that chondrocytes exhibit a range of mechanobiological responses indicating activation of distinct biochemical pathways with clear spatial patterns related to the induced local strains during impact. These results illustrate the power of this approach.
Accurate Estimation of Molecular Counts from Amplicon Sequence Data with Unique Molecular Identifiers
Authors: Peng Xiyu , Dorman Karin S
Published: June 2022

Motivation

Amplicon sequencing is widely applied to explore heterogeneity and rare variants in genetic populations. Resolving true biological variants and quantifying their abundance is crucial for downstream analyses, but measured abundances are distorted by stochasticity and bias in amplification, plus errors during Polymerase Chain Reaction (PCR) and sequencing. One solution attaches Unique Molecular Identifiers (UMIs) to sample sequences before amplification eliminating amplification bias by clustering reads on UMI and counting clusters to quantify abundance. While modern methods improve over naïve clustering by UMI identity, most do not account for UMI reuse, or collision, and they do not adequately model PCR and sequencing errors in the UMIs and sample sequences.

Results

We introduce Deduplication and accurate Abundance estimation with UMIs (DAUMI), a probabilistic framework to detect true biological sequences and accurately estimate their deduplicated abundance from amplicon sequence data. DAUMI recognizes UMI collision, even on highly similar sequences, and detects and corrects most PCR and sequencing errors in the UMI and sampled sequences. DAUMI performs better on simulated and real data compared to other UMI-aware clustering methods.

Availability

Source code is available at https://github.com/xiyupeng/AmpliCI-UMI.
Multi-task learning for activity detection in neovascular age-related macular degeneration
Authors: Ayhan Murat Seçkin , Faber Hanna , Kühlewein Laura , Inhoffen Werner , Aliyeva Gulnar , Ziemssen Focke , Berens Philipp
Published: June 2022

Purpose

Comparison of performance and explainability of a multi-task convolutional deep neuronal network to single-task networks for activity detection in neovascular age-dependent macular degeneration.

Methods

From n = 70 patients (46 female, 24 male) who attended the University Eye Hospital Tübingen 3762 optical coherence tomography B-scans (right eye: 2011, left eye: 1751) were acquired with Heidelberg Spectralis, Heidelberg, Germany. B-scans were graded by a retina specialist and an ophthalmology resident, and then used to develop a multi-task deep learning model to predict disease activity in neovascular age-related macular degeneration along with the presence of sub- and intraretinal fluid. We used performance metrics for comparison to single-task networks and visualized the DNN-based decision with t-distributed stochastic neighbor embedding and clinically validated saliency mapping techniques.

Results

The multi-task model surpassed single-task networks in accuracy for activity detection (94.2). Further-more, compared to single-task networks, visualizations via t-distributed stochastic neighbor embedding and saliency maps highlighted that multi-task networks’ decisions for activity detection in neovascular age-related macular degeneration were highly consistent with the presence of both sub- and intraretinal fluid.

Conclusions

Multi-task learning increases the performance of neuronal networks for predicting disease activity, while providing clinicians with an easily accessible decision control, which resembles human reasoning.

Translational Relevance

By improving nAMD activity detection performance and transparency of automated decisions, multi-task DNNs can support the translation of machine learning research into clinical decision support systems for nAMD activity detection.
Cycle threshold values in symptomatic COVID-19 cases in England
Authors: Funk Sebastian , Abbott Sam
Published: June 2022

Introduction

Since the start of the pandemic SARS-CoV-2 infection has most commonly been confirmed using reverse transcriptase polymerase chain reaction (RT-PCR), with results translated into a binary positive/negative outcomes. Previous studies have found that there is additional useful information in the level of the Cycle threshold (Ct value) of positive cases. Here we characterise variation in Ct values as a proxy for viral loads in more than 3 million test-positive COVID-19 cases in England with the aim of better quantifying the utility of such data.

Methods

We used individual N gene Ct values from symptomatic PCR positive (with Ct value less than 30) Pillar 2 cases in England who self-reported the date of symptom onset, and for whom age, reinfection status, variant status, and the number of vaccines received was available. Those with a positive test result more than 6 days after their reported symptom onset were excluded to mitigate the potential impact of recall bias. We used a generalised additive model, to estimate Ct values empirical mean Ct values for each strata of interest independently as well as to predict Ct values using a model that adjusted for a range of demographic and epidemiological covariates jointly. We present empirical Ct values and compare them to predicted mean Ct values.

Results

We found that mean Ct values varied by vaccine status, and reinfection status with the number of vaccine doses having little apparent effect. Modelling Ct values as a smooth function of time since onset and other variables struggled to reproduce the individual variation in the data but did match the population-level variation over time relatively well with this being apparently dominated by large differences between variants. Other variation over time was also captured to some degree though their remained several periods where the model could not capture the empirical means with a potential explanation being epidemic phase bias.

Conclusions

Analysing a large dataset of routine Ct values from symptomatic COVID-19 cases in England we found variation based on time since symptom onset, vaccine status, age, and variant. Ct values were highest 1-3 days after symptom onset and differed most due to variant status. We found no clear correlation between previously estimated differences in intrinsic transmissibility and Ct values indicating that this is potentially mediated at least partly by factors other than viral load as estimated using Ct values. We found evidence that a model adjusting for a range of covariates could explain some of the population-level variation over time but systematically underestimated Ct values when incidence was increasing, and overestimated them when incidence was decreasing. This indicates the utility of Ct values from this data source as a tool for surveillance, potentially avoiding some of the biases of aggregated positive counts.
Massively Parallel Dissection of RNA in RNA-protein interactions in vivo
Authors: Hass Evan P. , Lee Yu Hsuan , Campodonico Will , Lee Yong Kyu , Lasda Erika , Shah Jaynish S , Rinn John L. , Hwang Taeyoung
Published: June 2022

Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to molecular biology. Here, we present MPRNA-immunoprecipitation (MPRNA-IP), an adaptation of the previously developed massively parallel RNA assay (MPRNA), and a new avenue for in vivo high-throughput dissection of RNA-protein interactions. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, we are able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest including NORAD, MS2, and human telomerase RNA, and we describe statistical models for identifying RNA domains and parsing the structural contributions of RNA in these interactions. By blending modern and classical approaches, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions.
CaV1.2 channelopathic mutations evoke diverse pathophysiological mechanisms
Authors: Bamgboye Moradeke A. , Herold Kevin G. , Vieira Daiana C.O. , Traficante Maria K. , Rogers Philippa J. , Ben-Johny Manu , Dick Ivy E.
Published: June 2022

The first pathogenic mutation in CaV1.2 was identified in 2004 and was shown to cause a severe multisystem disorder known as Timothy syndrome (TS). The mutation was localized to the distal S6 region of the channel, a region known to play a major role in channel activation. TS patients suffer from life-threatening cardiac symptoms as well as significant neurodevelopmental deficits including autism spectrum disorder (ASD). Since this discovery, the number and variety of mutations identified in CaV1.2 has grown tremendously, and the distal S6 regions remains a frequent locus for many of these mutations. While the majority of patients harboring these mutations exhibit cardiac symptoms which can be well explained by known pathogenic mechanisms, the same cannot be said for the ASD or neurodevelopmental phenotypes seen in some patients, indicating a gap in our understanding of the pathogenesis of CaV1.2 channelopathies. Here, we use of whole cell patch clamp, quantitative Ca2+ imaging, and single channel recordings to expand the known mechanisms underlying the pathogenesis of CaV1.2 channelopathies. Specifically, we find that mutations within the S6 region can exert independent and separable effects on activation, voltage-dependent inactivation (VDI) and Ca2+-dependent inactivation (CDI). Moreover, the mechanisms underlying the CDI effects of these mutations are varied and include altered channel opening and possible disruption of CDI transduction. Overall, these results provide a structure-function framework to conceptualize the role of S6 mutations in pathophysiology and offer insight into the biophysical defects associated with distinct clinical manifestations.
Overt and occult hypoxemia in patients hospitalized with novel coronavirus disease 2019
Authors: Gadrey Shrirang M. , Mohanty Piyus , Haughey Sean P. , Jacobsen Beck A. , Dubester Kira J. , Webb Katherine M. , Kowalski Rebecca L. , Dreicer Jessica J. , Andris Robert T. , Clark Matthew T. , Moore Christopher C. , Holder Andre , Kamaleswaran Rishi , Ratcliffe Sarah J. , Moorman J. Randall
Published: June 2022

Background

Progressive hypoxemia is the predominant mode of deterioration in COVID-19. Among hypoxemia measures, the ratio of the partial pressure of arterial oxygen to the fraction of inspired oxygen (P/F ratio) has optimal construct validity but poor availability because it requires arterial blood sampling. Pulse oximetry reports oxygenation continuously, but occult hypoxemia can occur in Black patients because the technique is affected by skin color. Oxygen dissociation curves allow non-invasive estimation of P/F ratios (ePFR) but this approach remains unproven.

Research Question

Can ePFRs measure overt and occult hypoxemia?

Study Design and methods

We retrospectively studied COVID-19 hospital encounters (n=5319) at two academic centers (University of Virginia [UVA] and Emory University). We measured primary outcomes (death or ICU transfer within 24 hours), ePFR, conventional hypoxemia measures, baseline predictors (age, sex, race, comorbidity), and acute predictors (National Early Warning Score (NEWS) and Sepsis-3). We updated predictors every 15 minutes. We assessed predictive validity using adjusted odds ratios (AOR) and area under receiver operating characteristics curves (AUROC). We quantified disparities (Black vs non-Black) in empirical cumulative distributions using the Kolmogorov-Smirnov (K-S) two-sample test.

Results

Overt hypoxemia (low ePFR) predicted bad outcomes (AOR for a 100-point ePFR drop: 2.7 [UVA]; 1.7 [Emory]; p<0.01) with better discrimination (AUROC: 0.76 [UVA]; 0.71 [Emory]) than NEWS (AUROC: 0.70 [UVA]; 0.70 [Emory]) or Sepsis-3 (AUROC: 0.68 [UVA]; 0.65 [Emory]). We found racial differences consistent with occult hypoxemia. Black patients had better apparent oxygenation (K-S distance: 0.17 [both sites]; p<0.01) but, for comparable ePFRs, worse outcomes than other patients (AOR: 2.2 [UVA]; 1.2 [Emory], p<0.01).

Interpretation

The ePFR was a valid measure of overt hypoxemia. In COVID-19, it may outperform multi-organ dysfunction models like NEWS and Sepsis-3. By accounting for biased oximetry as well as clinicians’ real-time responses to it (supplemental oxygen adjustment), ePFRs may enable statistical modelling of racial disparities in outcomes attributable to occult hypoxemia.
Health System Resilience-enhancing Strategies for Managing Public Health Emergencies of International Concerns (PHEIC): Success and Challenges A Systematic Review Protocol
Authors: Rajapaksha R. M. Nayani Umesha , Khatri Resham , Abeysena Chrishantha , Wijesinghe Millawage Supun Dilara , Thomas Toms K. , Endalamaw Aklilu , Perera Nadeeka , Fernando Mekala , De Silva Gayani , Rambukwella Roshan , Assefa Yibeltal
Published: June 2022

Introduction

Health system resilience is the ability to prepare, manage, and learn from a sudden and unpredictable extreme change which impacts health systems. Health systems globally have recently been affected by a number of catastrophic events, including natural disasters, and infectious disease epidemics. Understanding health system resilience has never been more essential until emerging global pandemics. Therefore, the application of resilience-enhancing strategies with existing frameworks needs to be assessed to identify the management gaps and give valuable recommendations from the lessons learnt from the global pandemic.

Methods

The systematic review will be reported using the Preferred reporting items for systematic review and meta-analysis protocols guideline (PRISMA-P). Reporting data on health system building blocks and systematic searches on resilience enhancing strategies for the management of Public Health Emergencies of International Concerns (PHEIC) after the establishment of International Health Regulations (IHR) since managing PHEIC after the establishment of IHR in 2007 will be included. The search will be conducted in PubMed, Scopus, Web of Science, and Google Scholar.

Discussion

Health system resilience is key to coping with catastrophic events, such as the economic crisis and COVID-19 pandemic. The mapping of available literature towards the application of resilience-enhancing strategies with existing frameworks needs to be assessed to identify the management gaps and give valuable recommendations from the lessons learnt from the global pandemic to improve the level of preparedness and response to similar public health emergencies in the future.

Conclusion

A protocol for a global review of health system resilience for pandemic management is described. This review will add to the body of knowledge about health systems enhancing research and policy formulation.

Strengths and limitations of this study Strengths

Assessing success and challenges of resilience-enhancing strategies to identify the management gaps and give valuable recommendations from the lessons learnt from the global pandemic in future disasters

The systematic review will be reported using the Preferred reporting items for systematic review and meta-analysis protocols guideline (PRISMA-P).

Collaboration between Asia-Pacific researchers with different background

Limitation

Unable to do meta-analysis due to nature of the selected scope of the research
Nirmatrelvir plus ritonavir for early COVID-19 and hospitalization in a large US health system
Authors: Dryden-Peterson Scott , Kim Andy , Kim Arthur Y. , Caniglia Ellen C. , Lennes Inga , Patel Rajesh , Gainer Lindsay , Dutton Lisa , Donahue Elizabeth , Gandhi Rajesh T. , Baden Lindsey R. , Woolley Ann E.
Published: June 2022

Background

In the EPIC-HR trial, nirmatrelvir plus ritonavir led to an 88% reduction in hospitalization or death among unvaccinated outpatients with early COVID-19. Clinical impact of nirmatrelvir plus ritonavir among vaccinated populations is uncertain.

Objective

To assess whether nirmatrelvir plus ritonavir reduces risk of hospitalization among outpatients with early COVID-19 in the setting of prevalent SARS-CoV-2 immunity and immune evasive SARS-CoV-2 lineages.

Design

Population-based cohort study analyzed to emulate a clinical trial utilizing two-stage, inverse-probability weighted models to account for anticipated bias in testing and treatment.

Setting

A large healthcare system providing care for 1.5 million patients in Massachusetts and New Hampshire during Omicron wave (January 1 to May 15, 2022) with staged access and capacity to prescribe nirmatrelvir plus ritonavir.

Patients

30,322 non-hospitalized adults (87.2% vaccinated) aged 50 and older with COVID-19 and without contraindications to nirmatrelvir plus ritonavir.

Measurement

Primary outcome was hospitalization within 14 days of COVID-19 diagnosis.

Results

During the study period, 6036 (19.9%) patients were prescribed nirmatrelvir plus ritonavir and 24,286 (80.1%) patients were not. Patients prescribed nirmatrelvir were more likely to be older, have more comorbidities, and be unvaccinated. Hospitalization occurred in 40 (0.66%) and 232 (0.96%) patients prescribed and not prescribed nirmatrelvir plus ritonavir, respectively. The adjusted risk ratio was 0.55 (95% confidence interval 0.38 to 0.80, p = 0.002). Observed risk reduction was greater among unvaccinated patients and obese patients.

Limitations

Potential for residual confounding due to differential access and uptake of COVID-19 vaccines, diagnostics, and treatment.

Conclusions

The overall risk of hospitalization was already low (<1%) following an outpatient diagnosis of COVID-19, but this risk was 45% lower among patients prescribed nirmatrelvir plus ritonavir.

Funding

National Institutes of Health (P30 AI060354 and R01 CA236546).
Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae
Authors: Swank Zoe , Senussi Yasmeen , Alter Galit , Walt David R.
Published: June 2022

The diagnosis and management of post-acute sequelae of COVID-19 (PASC) poses an ongoing medical challenge. Identifying biomarkers associated with PASC would immensely improve the classification of PASC patients and provide the means to evaluate treatment strategies. We analyzed plasma samples collected from a cohort of PASC and COVID-19 patients (n = 63) to quantify circulating viral antigens and inflammatory markers. Strikingly, we detect SARS-CoV-2 spike antigen in a majority of PASC patients up to 12 months post-diagnosis, suggesting the presence of an active persistent SARS-CoV-2 viral reservoir. Furthermore, temporal antigen profiles for many patients show the presence of spike at multiple time points over several months, highlighting the potential utility of the SARS-CoV-2 full spike protein as a biomarker for PASC.
Conformational rearrangements in 2nd voltage sensor domain switch PIP2- and voltage-gating modes in two-pore channels
Authors: Shimomura Takushi , Hirazawa Kiichi , Kubo Yoshihiro
Published: June 2022

Two-pore channels (TPCs) are activated by PIP2 binding to domain I and/or by voltage-sensing in domain II (DII). Little is known about how these two stimuli are integrated and how each TPC subtype achieves its unique preference. Here, we show that the distinct conformations of DII-S4 in the voltage-sensor domain determine the two gating modes. DII-S4 takes an intermediate conformation, and forced stabilization in this conformation was found to give or maintain a high PIP2-dependence in primarily voltage- dependent TPC3 or in PIP2-gated and non-voltage-dependent TPC2, respectively. We also found in TPC2 that a tricyclic antidepressant desipramine induces the DII-S4 based voltage-dependence and that a flavonoid naringenin biases the mode preference from PIP2-gating to desipramine-induced voltage-gating. Taken together, our study on TPCs revealed an unprecedented mode-switching mechanism involving conformational changes in DII-S4. This will pave the way for drug development by targeting specific gating modes of TPCs.

Significance statement

Membrane voltage and PIP2 are different types of signals on endosomal and lysosomal membranes. The two signals are integrated into two-pore channels (TPCs) whose two repeating domains, DI and DII, play roles in PIP2 binding and voltage sensing, respectively. We showed that the conformation of the S4 helix in DII determines the voltage-dependent or PIP2-dependent gating mode, which explains the different preferences of the two signals between TPC subtypes. The preference for these two gating modes can be changed by a flavonoid, naringenin. Our findings on the molecular mechanism of the two gating modes in TPCs provide a clue to the understanding and pharmacological manipulation of the signaling by PIP2 and voltage in intracellular organelles.
Epidemiological Mapping of Onchocerciasis Hypoendemic Area of North Achefer District, Amhara Regional State, Ethiopia
Authors: Mekonnin Wuletaw Tadesse , Kebede Tadesse , Mekasha Sindew
Published: June 2022

Background

Onchocerciasis (river blindness) is caused by a filarial nematode worm called Onchocerca volvulus encapsulated in nodules under skin. The adult worm logged itself in nodules of cutaneous skin producing thousands of microfilariae per-day those migrating under the dermis of the skin causing cutaneous and eye disease. Ethiopia is one of countries with a high disease burden of onchocerciasis in Africa. Epidemiological mapping of onchocerciasis in hypoendemic area is a first step in elimination programme and to identify intervention eligible areas. Many districts are uncertain about onchocerciasis transmission; in identifying intervention eligible areas especially North Achefer is located adjacent to onchocerciasis endemic district (Alefa) which receiving semi-annual MDA, and its transmission status of the district is not well studied.

Objective

The purpose of this study was to assess the epidemiological status of onchocerciasis in the hypoendemic area of the North Achefer district of the Amhara Regional State.

Methodology

community-based cross-sectional study design conducted from July to August 2021. Parasitological, immunological and serological (ELISA and RDT) data were collected from the field and for central laboratory. Statistical analysis was conducted using Epi-info software version 7, transported to SPSS software version 26. Descriptive analysis was conducted and presented with frequencies and percentages. The association between dependent and independent variables was analyzed using bivariate logistic regression and variables those with a P-value <0.05% was considered statistically significant.

Result

a total of 264 participants enrolled in the study out of which 56.4% were male, with mean age of 28 years. The microscopic examination of skin snip was no microfilariae positive cases, whereas, 3% and 9.1% positive were recorded for Ov16 RDT and Ov16 ELISA test, respectively. Onchocerciasis morbidity indicators were 6 (2.3%), 12 (4.5%), and 9 (3.4%) palpable nodule, skin discoloration, and skin depigmentation respectively. Age, gender, village type, and distance from the river were independent variables that had a significant association with positivity for Ov16 ELISA test.

Conclusion

a high prevalence of onchocerciasis exposure which is above the WHO recommended threshold (5%) by Ov16 ELISA assay was observed. Distance from the river, village type, age, and gender had significantly associated with Ov16 ELISA test. Therefore, onchocerciasis elimination intervention in North Achefer is recommended to be implemented. Increasing the sample size and including molecular (i.e. PCR) and entomological technique best recommended to maximize the positivity of the disease and to insure the exact status of the disease in the district respectively.
Efficacy and Safety of Nebulized Ethanol Inhalation in COVID-19 Treatment. A Randomized, Clinical Trial
Authors: Amoushahi Ali , Moazam Elham , Reza Tabatabaei Amin , Ghasimi Golnaz , Salvatori Pietro , Grant-Whyte Ian , Ragab Ezz Ahmed
Published: June 2022

Background

Considering anti coronavirus effects of ethanol, the efficacy of its administration was evaluated in this research. Because of respiratory tract entrance of virus in COVID-19, this study was done by inhalation of nebulized ethanol.

Methods

Ninety-nine positive SARS-CoV-2-PCR patients who had been admitted at a respiratory clinic were included in this study. Patients were randomly assigned to the control (distilled water spray) and intervention (35% ethanol spray) group. Both groups were instructed to inhale 3 puffs of spray and inhale it, every six hours for a week. Global symptomatic score (GSS), clinical status scale,0020Blood Oxygenation, and C-Reactive Protein (CRP) at the first visit and days 3, 7, 14 were measured and compared between groups.

Results

The GSS decreased more and faster in the intervention group (ethanol) (1.4+1.4 vs 2.3+1.7, P=0.035) two weeks after starting intervention. On day 14, the odds of intervention group to have better clinical status was 5.715 times (95% CI, 2.47 to 13.19) than of control group a statistically significant effect, Wald χ2 (1) =16.67, P =0.001. Blood oxygen saturation also improved earlier in the ethanol group but without statistical significance difference. The readmission rate was lower in the intervention group (zero vs 10.9%, P=0.02).

Conclusion

Inhaled ethanol seems to be effective in improvement, mitigating clinical symptoms and reducing the need to repeat treatment. Considering the low cost, availability and no significant adverse events of ethanol, research and additional efforts are recommended to evaluate its curative effects in the early stages of COVID-19.
Accuracy of a Risk Alert Threshold for ICU Hypoglycemia: Retrospective Analysis of Alert Performance and Association with Clinical Deterioration Events
Authors: Horton William B. , Hannah Elaine E. , Morales Frances L. , Chaney Cherie R. , Krahn Katy N. , Chernyavskiy Pavel , Clark Matthew T. , Moorman J. Randall
Published: June 2022

Objective

To quantify the accuracy of and clinical events associated with a risk alert threshold for impending hypoglycemia during ICU admissions.

Design

Retrospective electronic health record review of clinical events occurring ≥1 and ≤12 hours after the hypoglycemia risk alert threshold was met.

Setting

Adult ICU admissions from June 2020 through April 2021 at the University of Virginia Medical Center.

Patients

342 critically-ill adults that were 63.5% male with median age 60.8 years, median weight 79.1 kg, and median body mass index of 27.5 kg/m2.

Interventions

Real-world testing of our validated predictive model as a clinical decision support tool for ICU hypoglycemia.

Measurements and Main Results

We retrospectively reviewed 350 hypothetical alerts that met inclusion criteria for analysis. The alerts correctly predicted 48 cases of Level 1 hypoglycemia that occurred ≥1 and ≤12 hours after the alert threshold was met (positive predictive value= 13.7%). Twenty-one of these 48 cases (43.8%) involved Level 2 hypoglycemia. Notably, three myocardial infarctions, one medical emergency team call, two initiations of cardiopulmonary resuscitation, 6 unplanned surgeries, 19 deaths, 20 arrhythmias, and 38 blood or urine cultures were identified or obtained ≥1 and ≤12 hours after an alert threshold was met. Alerts identified 102 total events of hypoglycemia and/or clinical deterioration, yielding a positive predictive value for any event of 29.1%.

Conclusions

Alerts generated by a validated ICU hypoglycemia prediction model had positive predictive value of 29.1% for hypoglycemia and other associated adverse clinical events.

Key Points

Question

What are the accuracy of and clinical events associated with a risk alert threshold for ICU hypoglycemia?

Findings

We retrospectively reviewed 350 hypothetical alerts that correctly predicted 48 cases of Level 1 hypoglycemia occurring ≥1 and ≤12 hours after the alert threshold was met (positive predictive value= 13.7%). Notably, three myocardial infarctions, one medical emergency team call, two initiations of cardiopulmonary resuscitation, 6 unplanned surgeries, 19 deaths, 20 arrhythmias, and 38 blood or urine cultures were identified or obtained ≥1 and ≤12 hours after an alert threshold was met.

Meaning

Alerts generated by a validated ICU hypoglycemia prediction model had positive predictive value of 29.1% for hypoglycemia and other associated adverse clinical events.
Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron
Authors: van Dorp Christiaan , Goldberg Emma , Ke Ruian , Hengartner Nick , Romero-Severson Ethan
Published: June 2022

New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness both over time and space. In this paper we extend a previously published model for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to globally estimate selection effects at different spatial levels while controlling for complex patterns of transmission and jointly inferring the effects of unit-level covariates in the spatial heterogeneity of SARS-CoV-2 selection effects. Applying this model to the spread of Omicron in 40 counties finding evidence for very strong (64%) but very heterogeneous selection effects at the country level. We further considered different measures of vaccination levels and measures of recent population-level infection as possible explanations. However, none of those variables were found to explain a significant proportion of the heterogeneity in country-level selection effects. We did find a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard commercial-grade computing resources, and should be straightforward to apply to future variants.
Effectiveness of mRNA COVID-19 vaccine boosters against infection, hospitalization and death: a target trial emulation in the omicron (B.1.1.529) variant era
Authors: Ioannou George N. , Bohnert Amy SB , O’Hare Ann M. , Boyko Edward J. , Maciejewski Matthew L. , Smith Valerie A. , Bowling C. Barrett , Viglianti Elizabeth , Iwashyna Theodore J. , Hynes Denise M. , Berry Kristin ,   the COVID-19 Observational Research Collaboratory (CORC)
Published: June 2022

Background

The effectiveness of a 3rd mRNA COVID-19 vaccine (“booster”) dose against the omicron (B.1.1.529) variant is uncertain especially in older, high-risk populations.

Objective

To determine mRNA booster vaccine effectiveness (VE) against SARS-CoV-2 infection, hospitalization and death in the omicron era by type of booster, type of primary vaccine, time since primary vaccine, age and comorbidity burden.

Design

Target trial emulation study comparing booster vaccination versus no booster.

Setting

U.S. Department of Veterans Affairs (VA) healthcare system

Participants and Intervention

Among persons who had received two mRNA COVID-19 vaccine doses at least 5 months earlier, we designed this retrospective matched cohort study to emulate a target trial of booster mRNA vaccination (BNT162b2 or mRNA-1273) versus no booster, conducted from 12/01/2021 to 03/31/2022.

Measurements

Booster VE.

Results

Each group included 490,838 well-matched persons, predominantly male (88%), mean age 63.0±14.0 years, followed for up to 121 days (mean 79.8 days). Booster VE >10 days after booster was 42.3% (95% CI 40.6-43.9) against SARS-CoV-2 infection, 53.3% (48.1-58.0) against SARS-CoV-2-related hospitalization and 79.1% (71.2-84.9) against SARS-CoV-2-related death. Booster VE was similar for different booster types (BNT162b2 or mRNA-1273), age groups or primary vaccination regimens, but was significantly higher with longer time since primary vaccination and with higher comorbidity burden.

Limitations

Predominantly male population.

Conclusions

Booster mRNA vaccination was highly effective in preventing death and moderately effective in preventing infection and hospitalization for up to 4 months after administration in the omicron era. Increased uptake of booster vaccination, which is currently suboptimal, should be pursued to limit the morbidity and mortality of SARS-CoV-2 infection, especially in persons with high comorbidity burden.

Primary Funding Source: Department of Veterans Affairs
Insights for disease modeling from single cell transcriptomics of iPSC-derived Ngn2-induced neurons and astrocytes across differentiation time and co-culture
Authors: Das D , Sonthalia S , Stein-O’Brien G , Wahbeh MH , Feuer K , Goff L , Colantuoni C , Mahairaki V , Avramopoulos D
Published: June 2022

Trans-differentiation of human induced pluripotent stem cells into neurons via Ngn2-induction (hiPSC-N) has become an efficient system to quickly generate neurons for disease modeling andin vitroassay development, a significant advance from previously used neoplastic and other cell lines. Recent single-cell interrogation of Ngn2-induced neurons however, has revealed some similarities to unexpected neuronal lineages. Similarly, a straightforward method to generate hiPSC derived astrocytes (hiPSC-A) for the study of neuropsychiatric disorders has also been described. Here we examine the homogeneity and similarity of hiPSC-N and hiPSC-A to theirin vivocounterparts, the impact of different lengths of time post Ngn2 induction on hiPSC-N (15 or 21 days) and of hiPSC-N / hiPSC-A co-culture. Leveraging the wealth of existing public single-cell RNA-seq (scRNA-seq) data in Ngn2-induced neurons andin vivodata from the developing brain, we provide perspectives on the lineage origins and maturation of hiPSC-N and hiPSC-A. While induction protocols in different labs produce consistent cell type profiles, both hiPSC-N and hiPSC-A show significant heterogeneity and similarity to multiplein vivocell fates, and both more precisely approximate theirin vivocounterparts when co-cultured. Gene expression data from the hiPSC-N show enrichment of genes linked to schizophrenia (SZ) and autism spectrum disorders (ASD) as has been previously shown for neural stem cells and neurons. These overrepresentations of disease genes are strongest in our system at early times (day 15) in Ngn2-induction/maturation of neurons, when we also observe the greatest similarity to earlyin vivoexcitatory neurons. We have assembled this new scRNA-seq data along with the public data explored here as an integrated biologist-friendly web-resource for researchers seeking to understand this system more deeply: nemoanalytics.org/p?l=DasEtAlNGN2&g=PRPH.
DHCR7 as a novel regulator of ferroptosis in hepatocytes
Authors: Yamada Naoya , Karasawa Tadayoshi , Komada Takanori , Matsumura Takayoshi , Baatarjav Chintogtokh , Ito Junya , Nakagawa Kiyotaka , Yamamuro Daisuke , Ishibashi Shun , Miura Kouichi , Sata Naohiro , Takahashi Masafumi
Published: June 2022

Recent evidence indicates that ferroptosis is implicated in the pathophysiology of various liver diseases; however, the mechanism of ferroptosis regulation in the liver is poorly understood. Here, using the whole-genome screening approach, we identified 7-dehydrocholesterol reductase (DHCR7), the terminal enzyme of cholesterol biosynthesis, as a novel regulator of ferroptosis in hepatocytes. Genetic and pharmacological inhibition (with AY9944) of DHCR7 suppressed lipid peroxidation and ferroptosis in human hepatocellular carcinoma Huh-7 cells. DHCR7 inhibition increased its substrate, 7-dehydrocholesterol (7-DHC), and extrinsic 7-DHC supplementation in turn suppressed ferroptosis. On the other hand, cholesterol deprivation had no effect on ferroptosis. A 7-DHC-derived oxysterol metabolite, 3β,5α-dihydroxycholest-7-en-6-one (DHCEO), was increased by a ferroptosis inducer RSL-3 in DHCR7-deficient cells, suggesting that the ferroptosis-suppressive effect of DHCR7 inhibition was driven by intracellular 7-DHC as a radical scavenger. While extrinsic 7-DHC supplementation suppressed ferroptosis in various cancer cells, pharmacological DHCR7 inhibition by AY9944 showed cell-type specific effects, which could be explained by high DHCR7 expression in Huh-7 cells. We further showed that AY9944 suppressed ferroptosis in murine primary hepatocytes in vitro and systemic administration of AY9944 inhibited hepatic ischemia-reperfusion injury in vivo. These findings provide new insights into the regulatory mechanism of liver ferroptosis and suggest that DHCR7 inhibition is a potential therapeutic option for ferroptosis-related liver diseases.
The essential role of disulfide bonds for the hierarchical self-assembly and wet-adhesion of CP20-derived peptides
Authors: Li Baoshan , Song Junyi , Mao Ting , Zeng Ling , Ye Zonghuang , Hu Biru
Published: June 2022

Barnacles are typical fouling organisms which strongly adhere to immersed solid substrates by secreting proteinaceous adhesives called cement proteins (CPs). The self-assembly of the cement proteins forms a permanently bounded layer that binds barnacle to foreign surfaces. However, due to the abundance of cysteines in whole-length CP20, it is difficult to determine its natural structure and to properly describe its self-assembly properties. In this study, a putative functional motif of Balanus albicostatus CP20 (BalCP20) is identified and found to present distinctive self-assembly and wet-adhesion characteristics. The atomic force microscopy (AFM) and transmission electron microscope (TEM) investigations show that wildtype BalCP20-P3 forms grain-like spindles, which further assembly into fractal-like structures looks like ears of wheat. SDS-PAGE, AFM and LSCM show that DTT treatment opens up disulfide bonds between cysteines and disrupts the fractal-like structures (eras of wheat). Additionally, these morphologies are abolished when one of the BalCP20-P3 four cysteines is mutated by alanine. Circular dichroism (CD) results further suggest that the morphological diversity among BalCP20-P3 and its mutations lays on the proportion of α-helix. The above results demonstrate that cysteines and disulfide bonds play a crucial role in the self-assembly of BalCP20-P3. This study provides new insights into BalCP20 underwater adhesion, and brings in new inspirations for the development of novel bionic underwater adhesive.
An engineered xCas12i with high activity, high specificity and broad PAM range
Authors: Zhang Hainan , Kong Xiangfeng , Xue Mingxing , Wang Zikang , Wei Yinghui , Wang Haoqiang , Zhou Jingxing , Zhang Weihong , Xu Mengqiu , Shen Xiaowen , Li Jinhui , Hu Jing , Zhong Na , Zhou Yingsi , Yang Hui
Published: June 2022

The type-V CRISPR effector Cas12i, with its smaller size, short crRNA guiding, and self-processing features, is a potentially versatile genome editing tool. By screening Cas12i proteins from a metagenomic database, we identified a natural variant with high activity in mammalian cells, named as xCas12i. We further engineered the PAM-interacting, REC, and RuvC domains for enhanced cleavage activity and specificity. This variant, named as high-fidelity Cas12Max, exhibited robust genome editing activity and minimal off-target activity with a broad 5’-TN recognition profile. With the fusion of deaminase TadA8e and further optimization of xCas12i, the base editor dCas12i-Tad8e also showed the high editing efficiency. This study provides highly efficient and specific tools for gene therapy.
Phenotypic selection analysis and confounding environmental variables
Authors: Morrissey Michael B. , Henshaw Jonathan M.
Published: June 2022

When environmental variation contributes to relationships between traits and fitness, it can confound analyses of phenotypic selection and, ultimately, bias predictions of adaptive evolution. To date, discussions of how to combat this problem emphasise complex statistical analyses aimed at estimating the genetic basis of the relationship between traits and fitness (e.g., the secondary theorem of selection). This article presents a path analysisbased description of the environmental confounding problem, which clarifies the issue and motivates simpler analyses as potential solutions. We show how standard selection analyses can be expanded to explicitly include environmental variables that may confound trait-fitness relationships, potentially leading to dramatically improved predictions of the evolutionary response to selection relative to classical phenotype-based estimates. We provide both univariate and multivariate treatments of the decomposition of the selection differential into components that may cause evolution via direct and indirect selection and components representing evolutionarily inert, environmentally-induced covariance. The multivariate treatment also yields expressions for the decomposition of the selection differential based on extended selection gradients, which may be of wide general interest beyond the environmental problem. Our approach to the environmental confounding problem makes more plausible demands on data than previous, more involved, quantitative genetic approaches, and addresses the issue of environmental confounding in a more biologically informative way.
Kiss and spit metabolomics highlights the role of the host cN-II enzyme on purine metabolism during pathogen infection
Authors: Gallego-Lopez Gina M. , Olson William J. , Tibabuzo-Perdomo Andres M. , Stevenson David , Amador-Noguez Daniel , Knoll Laura J.
Published: June 2022

Intracellular pathogens are auxotrophic for many metabolites and must rely on the host. While this reliance is well established, how pathogens manipulate host metabolism to their benefit is not understood. For intracellular pathogens, distinguishing the origin of the metabolite as host- or pathogen-derived is challenging. The obligate intracellular parasite Toxoplasma gondii alters the host cell by a pre-invasion process known as “kiss and spit”, where the contents of the parasite rhoptry organelles are secreted into the host cytoplasm before invasion occurs. This separation of microbe from the host offers a rare opportunity to demonstrate pathogen manipulation of the host. Using mass spectrometry-based metabolomics, we determined that kiss and spit changed host metabolites in nucleotide synthesis, the pentose phosphate pathway, glycolysis, and amino acid synthesis. An increase in 2,3-bisphosphoglycerate (2,3-BPG) abundance led us to hypothesize that high levels of host 2,3-BPG contribute to the activation of host cytosolic nucleosidase II (cN-II) to alter purine availability. Treatment with the cN-II inhibitor fludarabine and a cell line with a cN-II genetic knockout reduced T. gondii growth. Our results demonstrate that T. gondii rhoptry contents discharged during kiss and spit remodel host metabolism. They also suggest that T. gondii manipulates the host cN-II enzyme to acquire its necessary purine metabolites.
Mechanotransductive feedback control of endothelial cell motility and vascular morphogenesis
Authors: Mason Devon E. , Camacho Paula , Goeckel Megan E. , Tobin Brendan R. , Vega Sebastián L. , Wu Pei-Hsun , Johnson Dymonn , Heo Su-Jin , Wirtz Denis , Burdick Jason A. , Wood Levi , Chow Brian Y. , Stratman Amber N. , Boerckel Joel D.
Published: June 2022

Vascular morphogenesis requires persistent endothelial cell motility that is responsive to diverse and dynamic mechanical stimuli. Here, we interrogated the mechanotransductive feedback dynamics that govern endothelial cell motility and vascular morphogenesis. We show that the transcriptional regulators, YAP and TAZ, are activated by mechanical cues to transcriptionally limit cytoskeletal and focal adhesion maturation, forming a conserved mechanotransductive feedback loop that mediates human endothelial cell motilityin vitroand zebrafish intersegmental vessel (ISV) morphogenesisin vivo. This feedback loop closes in 4 hours, achieving cytoskeletal equilibrium in 8 hours. Feedback loop inhibition arrested endothelial cell migrationin vitroand ISV morphogenesisin vivo. Inhibitor washout at 3 hrs, prior to feedback loop closure, restored vessel growth, but washout at 8 hours, longer than the feedback timescale, did not, establishing lower and upper bounds for feedback kineticsin vivo. Mechanistically, YAP and TAZ induced transcriptional suppression of RhoA signaling to maintain dynamic cytoskeletal equilibria. Together, these data establish the mechanoresponsive dynamics of a transcriptional feedback loop necessary for persistent endothelial cell migration and vascular morphogenesis.
Cytoplasmic divisions without nuclei
Authors: Bakshi Anand , Iturra Fabio Echegaray , Alamban Andrew , Rosas-Salvans Miquel , Dumont Sophie , Aydogan Mustafa G.
Published: June 2022

Cytoplasmic divisions have been commonly considered a sequel to nuclear divisions, even in the absence of DNA replication. Here we found in fruit fly embryos that the cytoplasm can compartmentalize and divide without nuclei. Our targeted screen for potential necessary and sufficient conditions revealed that, although the cytoplasmic compartments are tightly associated with centrosomes, they can form without astral microtubules and divide without centrioles. Although a focal pool of microtubules is necessary for maintaining cytoplasmic compartments, this is not sufficient for their initial formation. Actin filaments are similarly an essential component of cytoplasmic compartments; however, their myosin II-based contractility is unexpectedly dispensable for divisions. We show that the myosin II-based contractility is instead involved in regulating the pace of these divisions. Importantly, our results revealed that the cytoplasmic divisions without nuclei can occur in a periodic manner autonomously of the Cdk-Cyclin oscillator that normally drives the cell cycle. We demonstrate that such autonomy of cytoplasmic divisions is preserved even in normal development, where it is leveraged to extrude mitotically delayed nuclei from the blastoderm, protecting the synchrony of rapid nuclear divisions against local delays in mitotic entry. We propose that an active coordination between otherwise autonomous cycles of cytoplasmic and nuclear divisions acts as a quality control mechanism for genome integrity and partitioning in development.