bluuebunny/crossref_metadata_2025 huggingface dataset:
EPCT-24 THE REMIND TRIAL: MULTI-ANTIGEN TARGETED T CELLS FOR PEDIATRIC CNS TUMORS
Authors: Grant Melanie , Fortiz Maria , Wang Lu , Lang Haili , Datar Anushree , Reynolds Emily , Terpilowski Madeleine , Geiger Ashley , Lazarski Chris , Tanna Jay , Pitino Adriana , Zhang Nan , Hoq Fahmida , Hanley Patrick , Cruz C Russell , Kilburn Lindsay , Packer Roger , Rood Brian , Bollard Catherine
Published: June 2021

Background

Patients with relapsed CNS malignancies or DIPG face terrible prognoses. We hypothesized that T cells specific for 3 tumor-associated antigens (TAA), WT1, PRAME and survivin, would be safe and elicit anti-tumor immunity.

Methods

Patients (n=18) received autologous tumor antigen-associated T cells (TAAT) (up to 8x107/m2) for newly diagnosed DIPG (Group A) or recurrent CNS malignancies (Group B) on a Phase I dose-escalation study (NCT03652545) and were monitored for safety and response.

Results/Discussion

16/18 patients who received TAAT completed the 45-day safety monitoring phase with no dose-limiting toxicities. Adverse events were minimal despite multiple pretreatments in Group B. Infused cells were predominantly CD3+ T cells (median 96%; range: 87–99%), with CD4+ and CD8+ comprising 16% (range: 5–87%) and 40% (range: 4–67%) respectively. Specificity for 1–3 TAAs was demonstrated in 11/18 TAAT by a-IFN-γ ELISPOT. Dose escalation is complete, and clinical and immunologic response assessments are ongoing. Plasma cytokine and proteomic analyses demonstrated dynamic post-infusion immune cytokine and protein responses. Consistent with an infusion-mediated immune response all patients in Grp A showed increased T cell effector, inflammatory and immune-stimulatory cytokines IFN-γ, TNF-α, IL-2, IL-5, IL-7, IL-1β, IL-6, IL-8, IL-12p70, IL-17A and GM-CSF at Weeks 1 and 2 post-infusion (n = 6). Of 9 patients who have been tested, 29/92 plasma proteins showed significant differences between dose levels 1 and 2, including increased IL-7 (p <0.0004) and CD40L (p <0.046) and reduced IL-4 (p <0.0004). T cell receptor sequencing showed expansion and persistence of clones detected in infusion products. In summary, TAAT have thus far been safe and elicit immune responses in vivo. Clinical and immunologic response assessments are ongoing.
Phase II trial of proton therapy versus photon IMRT for GBM: secondary analysis comparison of progression-free survival between RANO versus clinical assessment
Authors: Al Feghali Karine A , Randall James W , Liu Diane D , Wefel Jeffrey S , Brown Paul D , Grosshans David R , McAvoy Sarah A , Farhat Maguy A , Li Jing , McGovern Susan L , McAleer Mary F , Ghia Amol J , Paulino Arnold C , Sulman Erik P , Penas-Prado Marta , Wang Jihong , de Groot John , Heimberger Amy B , Armstrong Terri S , Gilbert Mark R , Mahajan Anita , Guha-Thakurta Nandita , Chung Caroline
Published: June 2021

Background

This secondary image analysis of a randomized trial of proton radiotherapy (PT) versus photon intensity-modulated radiotherapy (IMRT) compares tumor progression based on clinical radiological assessment versus Response Assessment in Neuro-Oncology (RANO).

Methods

Eligible patients were enrolled in the randomized trial and had MR imaging at baseline and follow-up beyond 12 weeks from completion of radiotherapy. “Clinical progression” was based on a clinical radiology report of progression and/or change in treatment for progression.

Results

Of 90 enrolled patients, 66 were evaluable. Median clinical progression-free survival (PFS) was 10.8 (range: 9.4–14.7) months; 10.8 months IMRT versus 11.2 months PT (P = .14). Median RANO-PFS was 8.2 (range: 6.9, 12): 8.9 months IMRT versus 6.6 months PT (P = .24). RANO-PFS was significantly shorter than clinical PFS overall (P = .001) and for both the IMRT (P = .01) and PT (P = .04) groups. There were 31 (46.3%) discrepant cases of which 17 had RANO progression more than a month prior to clinical progression, and 14 had progression by RANO but not clinical criteria.

Conclusions

Based on this secondary analysis of a trial of PT versus IMRT for glioblastoma, while no difference in PFS was noted relative to treatment technique, RANO criteria identified progression more often and earlier than clinical assessment. This highlights the disconnect between measures of tumor response in clinical trials versus clinical practice. With growing efforts to utilize real-world data and personalized treatment with timely adaptation, there is a growing need to improve the consistency of determining tumor progression within clinical trials and clinical practice.
Closure relations during the plateau emission of Swift GRBs and the fundamental plane
Authors: Dainotti Maria Giovanna , Lenart Aleksander Ł , Fraija Nissim , Nagataki Shigehiro , Warren Donald C , De Simone Biagio , Srinivasaragavan Gokul , Mata Aurora
Published: June 2021

The Neil Gehrels Swift observatory observes gamma-ray burst (GRB) plateaus in X-rays. We test the reliability of the closure relations through the fireball model when dealing with GRB plateau emissions. We analyze 455 X-ray light curves collected by Swift from 2005 January until 2019 August for which the redshifts are either known or unknown using the phenomenological Willingale 2007 model. Using these fits, we analyze the emission mechanisms and astrophysical environments of these GRBs through the closure relations within the time interval of the plateau emission. Finally, we test the three-dimensional fundamental plane relation (Dainotti relation) which connects the prompt peak luminosity, the time at the end of the plateau (rest frame), and the luminosity at that time, for the GRBs with redshift, concerning groups determined by the closure relations. This allows us to check if the intrinsic scatter σint of any of these groups is reduced compared to previous literature. The most fulfilled environments for the electron spectral distribution, p > 2, are wind slow cooling (SC) and interstellar material (ISM) slow cooling for cases in which the parameter q, which indicates the flatness of the plateau emission and accounts for the energy injection, is 0 and 0.5, respectively, in cases with both known and unknown redshifts. We also find that for short GRBs all ISM environments with q = 0 have the smallest σint = 0.04 ± 0.15 in terms of the fundamental plane relation holding a probability of occurring by chance of p = 0.005. We have shown that the majority of GRBs presenting plateau emission fulfill the closure relations, including the energy injection, with a particular preference for the wind SC environment. The subsample of GRBs that fulfill the given relations can be used as possible standard candles and can suggest a way to reduce the intrinsic scatter of these studied relationships.
Covid-19 and the future of charitable foundations—renewal in crisis?
Authors: Strasser Claudia
Published: June 2021

The effects of Covid-19 are tangible around the globe with emerging and third world countries being particularly affected by the economic and social consequences of the pandemic. The author explains the impact of Covid-19 on the work of foundations and the role of the latter in addressing global challenges. Foundations that are set up in perpetuity are often deemed slow and dilatory when it comes to taking decisions. Covid-19, however, demands fast, not to say unbureaucratic action. This is often contrary to the character of foundations and the way in which many of them pursue their programmatic goals. Foundations, therefore, risk falling short of their social mission and even missing the opportunity to offer society pioneering solutions. Yet, the current crisis has also underlined the importance of strategic partnerships between foundations and other players and of involving local people in bringing about social change. This being said, by their very nature, foundations are eminently predisposed to provide sustainable relief in crises such as Covid-19 and to mitigate long-term societal impact.
New Approach Methodology for Assessing Inhalation Risks of a Contact Respiratory Cytotoxicant: Computational Fluid Dynamics-Based Aerosol Dosimetry Modeling for Cross-Species and In Vitro Comparisons
Authors: Corley Richard A , Kuprat Andrew P , Suffield Sarah R , Kabilan Senthil , Hinderliter Paul M , Yugulis Kevin , Ramanarayanan Tharacad S
Published: June 2021

Regulatory agencies are considering alternative approaches to assessing inhalation toxicity that utilizes in vitro studies with human cells and in silico modeling in lieu of additional animal studies. In support of this goal, computational fluid-particle dynamics models were developed to estimate site-specific deposition of inhaled aerosols containing the fungicide, chlorothalonil, in the rat and human for comparisons to prior rat inhalation studies and new human in vitro studies. Under bioassay conditions, the deposition was predicted to be greatest at the front of the rat nose followed by the anterior transitional epithelium and larynx corresponding to regions most sensitive to local contact irritation and cytotoxicity. For humans, simulations of aerosol deposition covering potential occupational or residential exposures (1–50 µm diameter) were conducted using nasal and oral breathing. Aerosols in the 1–5 µm range readily penetrated the deep region of the human lung following both oral and nasal breathing. Under actual use conditions (aerosol formulations >10 µm), the majority of deposited doses were in the upper conducting airways. Beyond the nose or mouth, the greatest deposition in the pharynx, larynx, trachea, and bronchi was predicted for aerosols in the 10–20 µm size range. Only small amounts of aerosols >20 µm penetrated past the pharyngeal region. Using the ICRP clearance model, local retained tissue dose metrics including maximal concentrations and areas under the curve were calculated for each airway region following repeated occupational exposures. These results are directly comparable with benchmark doses from in vitro toxicity studies in human cells leading to estimated human equivalent concentrations that reduce the reliance on animals for risk assessments.
Characterizing Heterogeneity and Determining Sample Sizes for Accurately Estimating Wheat Fusarium Head Blight Index in Research Plots
Authors: Moraes Wanderson Bucker , Madden Laurence V. , Paul Pierce A.
Published: June 2021

Because Fusarium head blight (FHB) intensity is usually highly variable within a plot, the number of spikes rated for FHB index (IND) quantification must be considered when designing experiments. In addition, quantification of sources of IND heterogeneity is crucial for defining sampling protocols. Field experiments were conducted to quantify the variability of IND (“field severity”) at different spatial scales and to investigate the effects of sample size on estimated plot-level mean IND and its accuracy. A total of 216 7-row × 6-m-long plots of a moderately resistant and a susceptible cultivar were spray-inoculated with different Fusarium graminearum spore concentrations at anthesis to generate a range of IND levels. A one-stage cluster sampling approach was used to estimate IND, with an average of 32 spikes rated at each of 10 equally spaced points per plot. Plot-level mean IND ranged from 0.9 to 37.9%. Heterogeneity of IND, quantified by fitting unconditional hierarchical linear models, was higher among spikes within clusters than among clusters within plots or among plots. The projected relative error of mean IND increased as mean IND decreased, and as sample size decreased to <100 spikes per plot. Simple random samples were drawn with replacement 50,000 times from the original dataset for each plot and used to estimate the effects of sample sizes on mean IND. Samples of 100 or more spikes resulted in more precise estimates of mean IND than smaller samples. Poor sampling may result in inaccurate estimates of IND and poor interpretation of results.
Nurse-Led Model of Care That Helps a Community Heal
Authors: Murphy Maureen , Serowoky Mary L. , Grant Susan M.
Published: June 2021

The COVID-19 pandemic has overwhelmed communities. Physical, emotional, and financial struggles have heightened, especially with our vulnerable populations. People have been afraid to return to their provider's office. For children, there has been an interruption of well-visits and immunizations. As the nation saw a decline in immunization uptake, a pilot nurse-led program was designed to increase vaccinations and address the social determinant needs during a global pandemic. The purpose of this article is to describe the planning and implementation of a curbside immunization event. The Logic model was used as a framework to ensure an efficient and replicable process. Initial observations showed an overall increase in immunization uptake and 97% of participants current with recommended vaccinations. Most parents (93%) would attend again and recommend it to others. They also felt that infection control precautions helped make the care delivered safe and efficient. Social determinants of health were assessed and addressed. This method of vaccine delivery is a viable model going into the future. Others may replicate this model, and it may also serve as a platform regarding flu or COVID-19 vaccine distribution.
The Impact of Nurse-Led Innovations and Tactics During a Pandemic
Authors: Phillips Joan , Carr Andrea , Guesman Kim , Foreman-Lovell Melissa , Levesque Paula , Lukas Brad , Parent Kelly , Snyder Dana , Grant Susan
Published: June 2021

The COVID-19 pandemic hit southeast Michigan hard and a rapid influx of patients forced Beaumont Health to shift rapidly into an emergency management model with a laser focus on transforming clinical care and administrative processes to meet complex patient care needs. Navigating this landscape required agility, surge planning, strong interprofessional teams, transformational leadership, nurse-led innovations, support, and transparency to manage the ever-changing environment. This article explains nursing's response and nurse-led innovations that were implemented to meet the needs of the community, patients, and staff, as well as lessons learned to ensure preparedness for any potential future surge.
Double mutations in the H9N2 avian influenza virus PB2 gene act cooperatively to increase viral host adaptation and replication for human infections
Authors: Elgendy Emad Mohamed , Arai Yasuha , Kawashita Norihito , Isobe Ayana , Daidoji Tomo , Ibrahim Madiha Salah , Ono Takao , Takagi Tatsuya , Nakaya Takaaki , Matsumoto Kazuhiko , Watanabe Yohei
Published: June 2021

Avian H9N2 influenza viruses in East Asia are genetically diversified and multiple genotypes (A-W) have been established in poultry. Genotype S strains are currently the most prevalent strains, have caused many human infections and pose a public health threat. In this study, human adaptation mutations in the PB2 polymerase in genotype S strains were identified by database screening. Several PB2 double mutations were identified that acted cooperatively to produce higher genotype S virus polymerase activity and replication in human cells than in avian cells and to increase viral growth and virulence in mice. These mutations were chronologically and phylogenetically clustered in a new group within genotype S viruses. Most of the relevant human virus isolates carry the PB2-A588V mutation together with another PB2 mutation (i.e. K526R, E627V or E627K), indicating a host adaptation advantage for these double mutations. The prevalence of PB2 double mutations in human H9N2 virus isolates has also been found in genetically related human H7N9 and H10N8 viruses. These results suggested that PB2 double mutations in viruses in the field acted cooperatively to increase human adaptation of the currently prevalent H9N2 genotype S strains. This may have contributed to the recent surge of H9N2 infections and may be applicable to the human adaptation of several other avian influenza viruses. Our study provides a better understanding of the human adaptation pathways of genetically related H9N2, H7N9 and H10N8 viruses in nature.
Reporting and Misreporting of Sex Differences in the Biological Sciences
Authors: Garcia-Sifuentes Yesenia , Maney Donna L.
Published: June 2021

As part of an initiative to improve rigor and reproducibility in biomedical research, the U. S. National Institutes of Health now requires the consideration of sex as a biological variable in preclinical studies. This new policy has been interpreted by some as a call to compare males and females with each other. Researchers testing for sex differences may not be trained to do so, however, increasing risk for misinterpretation of results. Using a list of recently published articles curated by Woitowich et al. (eLife, 2020; 9:e56344), we examined reports of sex differences and non-differences across nine biological disciplines. Sex differences were claimed in the majority of the 147 articles we analyzed; however, statistical evidence supporting those differences was often missing. For example, when a sex-specific effect of a manipulation was claimed, authors usually had not tested statistically whether females and males responded differently. Thus, sex-specific effects may be over-reported. In contrast, we also encountered practices that could mask sex differences, such as pooling the sexes without first testing for a difference. Our findings support the need for continuing efforts to train researchers how to test for and report sex differences in order to promote rigor and reproducibility in biomedical research.
Development and operationalization of an electronic palliative care registry in a large integrated health system
Authors: Sudat Sylvia EK , Blanton Kathy
Published: June 2021

Background

Palliative care teams generally lack prospective tools to identify individuals who could benefit from specialty palliative care, which hinders their ability to find and treat patients early in their illness trajectories. Health systems are also limited in their ability to assess how well their palliative care services reach the population in need, which in turn makes it much more difficult to determine the quality, value, and effectiveness of those services. This study describes the creation, validation, and operationalization of an electronic registry of patients potentially eligible for palliative care at Sutter Health, a large integrated health system in northern California, US.

Results

The electronic palliative care eligibility algorithm performed well within the chart review validation sample, with an area under the receiver operating characteristic curve (AUROC) of 0.903 and area under the precision-recall curve (AUPRC) of 0.545. Within the 2.4 million individuals who contacted the SH electronic health record (EHR) during 2017, the final algorithm identified 1.1%-1.8% of patients (26,773-42,847) as potentially eligible for palliative care services. This included approximately 12.9%-17.7% of inpatients (16,392-22,507 out of 126,916), and 1.2%-1.9% of ambulatory care patients (20,140-32,212 out of 1.7 million).

Conclusions

A palliative care electronic patient registry was successfully created and operationalized. Performance based on an extensive chart review sample of Sutter Health patients indicated good capture of the palliative care-appropriate population, and this is further supported by successful identification of a majority of enrollees in Sutter Health’s palliative care programs during 2017.
Forecasting COVID-19 Number of Cases by Implementing ARIMA and SARIMA with Grid Search in United States
Authors: Abolmaali Saina , Shirzaei Samira
Published: June 2021

COVID-19 has surged in the United States since January 2020. Since then, social distancing and lockdown have helped many people to avoid infectious diseases. However, this did not help the upswing of the number of cases after the lockdown was finished. Modeling the infectious disease can help the health care providers and governors to plan ahead for obtain the needed resources. In this manner, precise short-term determining of the number of cases can be imperative to the healthcare system. Many models have been used since the pandemic has started. In this paper we will compare couple of time series models like Simple Moving Average, Exponentially Weighted Moving Average, Holt-Winters Double Exponential Smoothing Additive, ARIMA, and SARIMA. Two models that have been used to predict the number of cases are ARIMA and SARIMA. A grid search has been implemented to select the best combination of the parameters for both models. Results show that in the case of modeling, the Holt-Winters Double Exponential model outperforms Exponentially Weighted Moving Average and Simple Moving Average while forecasting ARIMA outperforms SARIMA.
Covid-19: Comparisons by Country and Implications for Future Pandemics
Authors: Lewis Mehl-Madrona Bangor , Orono Maine , Bricaire François , Cuyugan Adrian , Barac Jovan , Parvaiz Asadullah , Jamil Ali Bin , Iqbal Sajid , Vally Ryan , Koliali Meryem , Sellier Mohamed Karim
Published: June 2021

Background

We set out in this paper to compare Covid-19 results by country to better understand the factors leading to the differing results found internationally.

Methods

We used publicly available large datasets to explore differences by country for Covid-19 mortality statistics. We continuously challenged our projections with reality and numbers from countries around the world, allowing us to refine our models and better understand the progression of the epidemic. All our predictions and findings were discussed and validated from a clinical viewpoint.

Results

While no lockdown resulted in higher mortality, the difference between strict lockdown and lax lockdown was not terribly different and favored lax lockdown. Only one of the top 44 countries had long and strict restrictions. Strict restrictions were more common in the worst performing countries in terms of Covid mortality. The United States had both the largest economic growth coupled with the largest rate of mortality. Those who did well economically, had lower mortality and less pressure on their population. Yet they had less mortality than average and less than their neighbors.

Conclusions

Countries with the least restrictions fared best economically. Some of them fared well in terms of mortality, even better than neighboring countries with similar social structures and more severe restrictions. The mortality rates in the USA, however, appeared to suffer from very high obesity rates. Norway and the northern European countries have less strict restrictions from the rest of Europe and had lower mortality rates. COVID-19 mortality was associated with vitamin D status.
Admission criteria in critically ill COVID-19 patients: a physiology-based approach
Authors: Ceruti Samuele , Glotta Andrea , Biggiogero Maira , Maida Pier Andrea , Marzano Martino , Urso Patrizia , Bona Giovanni , Garzoni Christian
Published: June 2021

Introduction

The COVID-19 pandemic required a careful management of intensive care unit (ICU) admissions, to reduce ICU overload while facing resources’ limitations. We implemented standardized, physiology-based, ICU admission criteria and analyzed the mortality rate of patients refused from the ICU.

Materials and Methods

COVID-19 patients proposed for ICU admission were consecutively analyzed; Do-not-resuscitate patients were excluded. Patients presenting a SpO2 lower than 85% and/or dyspnea and/or mental confusion resulted eligible for ICU admission; patients not presenting these criteria remained in the ward with an intensive monitoring protocol. Primary outcome was both groups’ survival rate. Secondary outcome was a sub analysis correlating SpO2 cutoff with ICU admission.

Results

From March 2020 to January 2021, 1623 patients were admitted to our Center; 208 DNR patients were excluded; 97 patients underwent intensivist evaluation. The ICU-admitted group mortality rate resulted 15.9% at 28 days and 27% at 40 days; the ICU-refused group mortality rate resulted 0% at both intervals (p < 0.001). With a SpO2 cut-off of 92%, the hypoxia rate distribution did not correlate with ICU admission (p = 0.26); with a SpO2 cut-off of 85%, a correlation was found (p = 0.009). A similar correlation was also found with dyspnea (p =0.0002).

Conclusion

In COVID-19 patients, standardized ICU admission criteria appeared to reduce safely ICU overload. In the absence of dyspnea and/or confusion, a SpO2 cutoff up to 85% for ICU admission was not burdened by negative outcomes. In a pandemic context, the SpO2 cutoff of 92%, as a threshold for ICU admission, needs critical re-evaluation.
Evaluation of a clinical decision support tool for matching cancer patients to clinical trials using simulation-based research
Authors: Gardner Clarissa , Halligan Jack , Fontana Gianluca , Fernandez Crespo Roberto , Prime Matthew , Guo Chaohui , Ekinci Okan , Ghafur Saira , Darzi Ara
Published: June 2021

Simulation-based research (SBR) methods have been proposed as an alternative methodology for evaluating digital health solutions; however, applicability remains to be established. This study used SBR to evaluate a clinical decision support (CDS) tool used for matching cancer patients to clinical trials. 25 clinicians and research staff were recruited to match 10 synthetic patient cases to clinical trials using both the CDS tool and publicly available online trial databases. Participants were significantly more likely to report having sufficient time (p = 0.020) and to require less mental effort (p = 0.001) to complete trial matching with the CDS tool. Participants required less time for trial matching using the CDS tool, but the difference was not significant (p = 0.093). Most participants reported that they had sufficient guidance to participate in the simulations (96%). This study demonstrates the use of SBR methods is a feasible approach to evaluating digital health solutions.
Contributions of PTSD polygenic risk and environmental stress to suicidality in preadolescents
Authors: Daskalakis Nikolaos P , Schultz Laura M , Visoki Elina , Moore Tyler M , Argabright Stirling T , Harnett Nathaniel G , DiDomenico Grace E , Warrier Varun , Almasy Laura , Barzilay Ran
Published: June 2021

Suicidal ideation and attempts (i.e., suicidality) are complex behaviors driven by environmental stress, genetic susceptibility, and their interaction. Preadolescent suicidality is a major health problem with rising rates, yet its underlying biology is understudied. Here we studied effects of genetic stress susceptibility, estimated by polygenic risk score (PRS) for post-traumatic-stress-disorder (PTSD), on preadolescent suicidality in participants from the Adolescent Brain Cognitive Development (ABCD) Study®. We further evaluated PTSD-PRS effects on suicidality in the presence of environmental stressors that are established suicide risk factors. Analyses included both European and African ancestry participants using PRS calculated based on summary statistics from ancestry-specific genome-wide association studies. In European ancestry participants (N=4,619, n=378 suicidal), PTSD-PRS was associated with preadolescent suicidality (odds ratio [OR]=1.12, 95%CI 1-1.25, p=0.038). Results in African ancestry participants (N=1,334, n=130 suicidal) showed a similar direction but were not statistically significant (OR=1.21, 95%CI 0.93-1.57, p=0.153). Sensitivity analyses using non-psychiatric polygenic score for height and using cross-ancestry PTSD-PRS did not reveal any association with suicidality, supporting the specificity of the association of ancestry-specific PTSD-PRS with suicidality. Environmental stressors were robustly associated with suicidality across ancestries with moderate effect size for negative life events and family conflict (OR 1.27-1.6); and with large effect size (OR ∼ 4) for sexual-orientation discrimination. When combined with environmental factors, PTSD-PRS showed marginal additive effects in explaining variability in suicidality, with no evidence for G X E interaction. Results support use of cross-phenotype PRS, specifically stress-susceptibility, as a robust genetic marker for suicidality risk early in the lifespan.
A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions
Authors: Chaintoutis Serafeim C. , Chassalevris Taxiarchis , Tsiolas George , Balaska Sofia , Vlatakis Ioannis , Mouchtaropoulou Evangelia , Siarkou Victoria I. , Tychala Areti , Koutsioulis Dimitris , Skoura Lemonia , Argiriou Anagnostis , Dovas Chrysostomos I.
Published: June 2021

The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94% and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
Quantifying the role of naturally- and vaccine-derived neutralizing antibodies as a correlate of protection against COVID-19 variants
Authors: Cohen Jamie A. , Stuart Robyn M. , Rosenfeld Katherine , Lyons Hil , White Michael , Kerr Cliff C. , Klein Daniel J. , Famulare Michael
Published: June 2021

The functional relationship between neutralizing antibodies (NAbs) and protection against SARS-CoV-2 infection and disease remains unclear. We jointly estimated protection against infection and disease progression following natural infection and vaccination from meta-study data. We find that NAbs are strongly correlated with prevention of infection and that any history of NAbs will stimulate immune memory to moderate disease progression. We also find that natural infection provides stronger protection than vaccination for the same level of NAbs, noting that infection itself, unlike vaccination, carries risk of morbidity and mortality, and that our most potent vaccines induce much higher NAb levels than natural infection. These results suggest that while sterilizing immunity may decay, we expect protection against severe disease to be robust over time and in the face of immune-evading variants.
A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia
Authors: Reisman Benjamin J. , Guo Hui , Ramsey Haley E. , Wright Madison T. , Reinfeld Bradley I. , Ferrell P. Brent , Sulikowski Gary A. , Rathmell W. Kimryn , Savona Michael R. , Plate Lars , Rubinstein John L. , Bachmann Brian O.
Published: June 2021

Cancer cells have long been recognized to exhibit unique bioenergetic requirements. The apoptolidin family of glycomacrolides are distinguished by their selective cytotoxicity towards oncogene transformed cells, yet their molecular mechanism remains uncertain. We used photoaffinity analogs of the apoptolidins to identify the F1 subcomplex of mitochondrial ATP synthase as the target of apoptolidin A. CryoEM of apoptolidin and ammocidin-ATP synthase complexes revealed a novel shared mode of inhibition that was confirmed by deep mutational scanning of the binding interface to reveal resistance mutations which were confirmed using CRISPR-Cas9. Ammocidin A was found to suppress leukemia progression in vivo at doses that were tolerated with minimal toxicity. The combination of cellular, structural, mutagenesis, and in vivo evidence define the mechanism of action of apoptolidin family glycomacrolides and establish a path to address OXPHOS-dependent cancers.
Scaling principles of white matter brain connectivity
Authors: Ardesch Dirk Jan , Scholtens Lianne H. , de Lange Siemon C. , Roumazeilles Lea , Khrapitchev Alexandre A. , Preuss Todd M. , Rilling James K. , Mars Rogier B. , van den Heuvel Martijn P.
Published: June 2021

Brains come in many shapes and sizes. Nature has endowed big-brained primate species like humans with a proportionally large cerebral cortex. White matter connectivity – the brain’s infrastructure for long-range communication – might not always scale at the same pace as the cortex. We investigated the consequences of this allometric scaling for white matter brain network connectivity. Structural T1 and diffusion MRI data were collated across fourteen primate species, describing a comprehensive 350-fold range in brain volume. We report volumetric scaling relationships that point towards a restriction in macroscale connectivity in larger brains. Building on previous findings, we show cortical surface to outpace white matter volume and the corpus callosum, suggesting the emergence of a white matter ‘bottleneck’ of lower levels of connectedness through the corpus callosum in larger brains. At the network level, we find a potential consequence of this bottleneck in shaping connectivity patterns, with homologous regions in the left and right hemisphere showing more divergent connectivity in larger brains. Our findings show conserved scaling relationships of major brain components and their consequence for macroscale brain circuitry, providing a comparative framework for expected connectivity architecture in larger brains such as the human brain.
3D atlas of the pituitary gland of the model fish medaka
Authors: Royan Muhammad Rahmad , Siddique Khadeeja , Csucs Gergely , Puchades Maja A. , Nourizadeh-Lillabadi Rasoul , Bjaalie Jan G. , Henkel Christiaan V. , Weltzien Finn-Arne , Fontaine Romain
Published: June 2021

In vertebrates, the anterior pituitary plays a crucial role in regulating several essential physiological processes via the secretion of at least seven peptide hormones by different endocrine cell types. Comparative and comprehensive knowledge of the spatial distribution of those endocrine cell types is required to better understand their role during the animal life. Using medaka as the model and several combinations of multi-color fluorescence in situ hybridization, we present the first 3D atlas revealing the gland-wide distribution of seven endocrine cell populations: lactotropes, thyrotropes, Lh and Fsh gonadotropes, somatotropes, and pomca-expressing cells (corticotropes and melanotropes) in the anterior pituitary of a teleost fish. By combining in situ hybridization and immunofluorescence techniques, we deciphered the location of corticotropes and melanotropes within the pomca-expressing cell population. The 3D localization approach reveals sexual dimorphism of tshba- and pomca-expressing cells in the adult medaka pituitary. Finally, we show the existence of bi-hormonal cells co-expressing lhb-fshb, fshb-tshba and lhb-sl using single-cell transcriptomics analysis and in situ hybridization. This study offers a solid basis for future comparative studies of the teleost pituitary and its developmental plasticity.

Highlights

- We offer the first 3D atlas of a teleost pituitary, which presents a valuable resource to the endocrinology and model fish community.

- The atlas reveals the 3D spatial distribution of the seven endocrine cell types and blood vessels in the juvenile/adult male and female pituitary.

- Gene expression for tshba and pomca, as well as the population size of cells expressing these genes, displays obvious sexual dimorphism in the adult medaka pituitary.

- Multi-color in situ hybridization and single cell RNA-seq reveal the existence of bi-hormonal cells, co-expressing lhb-fshb, fshb-tshba, lhb-sl, and a few multi-hormonal cells.

- An online version of the atlas is available at https://www.nmbu.no/go/mpg-atlas.
Accelerated Antibody Discovery Targeting the SARS-CoV-2 Spike Protein for COVID-19 Therapeutic Potential
Authors: Mullen Tracey E. , Abdullah Rashed , Boucher Jacqueline , Brousseau Anna Susi , Dasuri Narayan K. , Ditto Noah T. , Doucette Andrew M. , Emery Chloe , Gabriel Justin , Greamo Brendan , Patil Ketan S. , Rothenberger Kelly , Stolte Justin , Souders Colby A.
Published: June 2021

Rapid deployment of technologies capable of high-throughput and high-resolution screening is imperative for timely response to viral outbreaks. Risk mitigation in the form of leveraging multiple advanced technologies further increases the likelihood of identifying efficacious treatments in an aggressive timeline. In this study, we describe two parallel, yet distinct, in vivo approaches for accelerated discovery of antibodies targeting the SARS-CoV-2 spike protein. Working with human transgenic Alloy-GK mice, we detail a single B-cell discovery workflow to directly interrogate antibodies secreted from plasma cells for binding specificity and ACE2 receptor blocking activity. Additionally, we describe a concurrent accelerated hybridoma-based workflow utilizing a DiversimAb™ mouse model for increased diversity. The panel of antibodies isolated from both workflows revealed binding to distinct epitopes with both blocking and non-blocking profiles. Sequence analysis of the resulting lead candidates uncovered additional diversity with the opportunity for straightforward engineering and affinity maturation. By combining in vivo models with advanced integration of screening and selection platforms, lead antibody candidates can be sequenced and fully characterized within one to three months.
Neuromodulators generate multiple context-relevant behaviors in a recurrent neural network by shifting activity flows in hyperchannels
Authors: Tsuda Ben , Pate Stefan C. , Tye Kay M. , Siegelmann Hava T. , Sejnowski Terrence J.
Published: June 2021

Neuromodulators are critical controllers of neural states, with dysfunctions linked to various neuropsychiatric disorders. Although many biological aspects of neuromodulation have been studied, the computational principles underlying how neuromodulation of distributed neural populations controls brain states remain unclear. Compared with specific contextual inputs, neuromodulation is a single scalar signal that is broadcast broadly to many neurons. We model the modulation of synaptic weight in a recurrent neural network model and show that neuromodulators can dramatically alter the function of a network, even when highly simplified. We find that under structural constraints like those in brains, this provides a fundamental mechanism that can increase the computational capability and flexibility of a neural network. Diffuse synaptic weight modulation enables storage of multiple memories using a common set of synapses that are able to generate diverse, even diametrically opposed, behaviors. Our findings help explain how neuromodulators “unlock” specific behaviors by creating task-specific hyperchannels in the space of neural activities and motivate more flexible, compact and capable machine learning architectures.

Significance

Neuromodulation through the release of molecules like serotonin and dopamine provides a control mechanism that allows brains to shift into distinct behavioral modes. We use an artificial neural network model to show how the action of neuromodulatory molecules acting as a broadcast signal on synaptic connections enables flexible and smooth behavioral shifting. We find that individual networks exhibit idiosyncratic sensitivities to neuromodulation under identical training conditions, highlighting a principle underlying behavioral variability. Network sensitivity is tied to the geometry of network activity dynamics, which provides an explanation for why different types of neuromodulation (molecular vs direct current modulation) have different behavioral effects. Our work suggests experiments to test biological hypotheses and paths forward in the development of flexible artificial intelligence systems.
More than a stick in the mud: Eelgrass leaf and root bacterial communities are distinct from those on physical mimics
Authors: Kardish Melissa R. , Stachowicz John. J.
Published: June 2021

We examine the role of physical structure vs. biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulfur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea.

Originality-Significance Statement

We show that eelgrass establishes a distinct microbial community from a physical mimic on both its leaves and roots. This is, to our knowledge, the first comparison of seagrass to a mimicked physical environment. Insights from our study establish bacterial targets for future functional studies of seagrass-microbiome interactions.
CamelliA-based simultaneous imaging of Ca2+ dynamics in subcellular compartments
Authors: Guo Jingzhe , He Jiangman , Dehesh Katayoon , Yang Zhenbiao
Published: June 2021

As a universal second messenger, calcium (Ca2+) transmits specific cellular signals via a spatiotemporal signature generated from its extracellular source and internal stores. Our knowledge of the mechanisms underlying generation of a Ca2+ signature is hampered by limited tools enabling simultaneous monitoring of the dynamics of Ca2+ levels in multiple subcellular compartments. To overcome the limitation and to further improve spatiotemporal resolutions, here we have assembled a molecular toolset (the CamelliA lines) in Arabidopsis that enables simultaneous and high-resolution monitoring of Ca2+ dynamics in multiple subcellular compartments through imaging analyses of different single-colored GECIs (Genetically Encoded Calcium Indicators). Indeed, the uncovering of the previously unrecognized Ca2+ signatures in three types of Arabidopsis cells in response to internal and external cues is a testimony to the wide applicability of the newly generated toolset for elucidating the subcellular sources contributing to the Ca2+signatures in plants.

One sentence summary

A toolset for simultaneous imaging of Ca2+ dynamics in subcellular compartments has uncovered unrecognized Ca2+ signatures in Arabidopsis cells in response to developmental and external cues.
Decoding continuous variables from event-related potential (ERP) data with linear support vector regression (SVR) using the Decision Decoding Toolbox (DDTBOX)
Authors: Bode Stefan , Schubert Elektra , Hogendoorn Hinze , Feuerriegel Daniel
Published: June 2021

Background

Multivariate classification analysis for event-related potential (ERP) data is a powerful tool for predicting cognitive variables. However, classification is often restricted to categorical variables and under-utilises continuous data, such as response times, response force, or subjective ratings. An alternative approach is Support Vector Regression (SVR), which uses single-trial data to predict continuous variables of interest.

New Method

In this tutorial-style paper, we demonstrate how SVR is implemented in the Decision Decoding Toolbox (DDTBOX). To illustrate in more detail how results depend on specific toolbox settings and data features, we report results from two simulation studies resembling real EEG data, and one real ERP-data set, in which we predicted continuous variables across a range of analysis parameters.

Results

Across all studies, we demonstrate that SVR is effective for analysis windows ranging from 2 ms – 100 ms, and relatively unaffected by temporal averaging. Prediction is still successful when only a small number of channels encode true information, and the analysis is robust to temporal jittering of the relevant information in the signal.

Comparison with existing Methods

Our result show that SVR as implemented in DDTBOX can reliably predict continuous, more nuanced variables, which may not be well-captured by classification analysis.

Conclusions

In sum, we demonstrate that linear SVR is a powerful tool for the investigation of single-trial EEG data in relation to continuous variables, and we provide practical guidance for users.
Genetic and chemotherapeutic causes of germline hypermutation
Authors: Kaplanis Joanna , Ide Benjamin , Sanghvi Rashesh , Neville Matthew , Danecek Petr , Coorens Tim , Prigmore Elena , Short Patrick , Gallone Giuseppe , McRae Jeremy , Odhams Chris , Moutsianas Loukas ,   Genomics England Research Consortium, Carmichael Jenny , Barnicoat Angela , Firth Helen , O’Brien Patrick , Rahbari Raheleh , Hurles Matthew
Published: June 2021

Mutation in the germline is the source of all evolutionary genetic variation and a cause of genetic disease. Previous studies have shown parental age to be the primary determinant of the number of new germline mutations seen in an individual’s genome. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 hypermutated individuals with between two and seven times more de novo single nucleotide variants (dnSNVs) than expected. In most of these families (8/12) the excess mutations could be attributed to the father. We determined that two of these families had genetic drivers of germline hypermutation, with the fathers carrying damaging genetic variation in known DNA repair genes, causing distinctive mutational signatures. For five families, by analysing clinical records and mutational signatures, we determined that paternal exposure to chemotherapeutic agents prior to conception was a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare and relatively modest in degree and that most hypermutated individuals will not have a genetic disease.
Gene Expression Associated with Individual Variability in Intrinsic Functional Connectivity
Authors: Li Liangfang , Wei Yongbin , Zhang Jinbo , Ma Junji , Yi Yangyang , Gu Yue , Li Liman Man Wai , Lin Ying , Dai Zhengjia
Published: June 2021

It has been revealed that intersubject variability (ISV) in intrinsic functional connectivity (FC) is associated with a wide variety of cognitive and behavioral performances. However, the underlying organizational principle of ISV in FC and its related gene transcriptional profiles remain unclear. Using resting-state fMRI data from the Human Connectome Project (299 participants) and microarray gene expression data from the Allen Human Brain Atlas, we conducted a transcription-neuroimaging association study to investigate the spatial configurations of ISV in intrinsic FC and their associations with gene transcriptional profiles. We found that the multimodal association cortices showed the greatest ISV in FC, while the unimodal cortices and subcortical areas showed the least ISV. Importantly, partial least squares regression analysis revealed that the transcriptional profiles of genes associated with human accelerated regions (HARs) could explain 31.29% of the variation in the spatial distribution of ISV in FC. The top-related genes in the transcriptional profiles were enriched for the development of the central nervous system, neurogenesis and the cellular components of synapse. Moreover, we observed that the effect of gene expression profile on the heterogeneous distribution of ISV in FC was significantly mediated by the cerebral blood flow configuration. These findings highlighted the spatial arrangement of ISV in FC and their coupling with variations in transcriptional profiles and cerebral blood flow supply.