bluuebunny/crossref_metadata_2025 huggingface dataset:
Liver stiffness and fibrosis-4 alone better predict liver events compared with aspartate aminotransferase to platelet ratio index in a cohort of human immunodeficiency virus and hepatitis C virus co-infected patients from ANRS CO13 HEPAVIH cohort
Authors: Chalouni Mathieu , Sogni Philippe , Miailhes Patrick , Lacombe Karine , Poizot-Martin Isabelle , Chas Julie , Vittecoq Daniel , Neau Didier , Aumaitre Hugues , Alric Laurent , Piroth Lionel , Bouchaud Olivier , Katlama Christine , Morlat Philippe , Lascoux-Combe Caroline , Gervais Anne , Naqvi Alissa , Rosenthal Eric , Garipuy Daniel , Barange Karl , Esterle Laure , Salmon Dominique , Wittkop Linda
Published: April 2019

Objectives

HIV/hepatitis C virus (HCV) co-infection leads to major complications, and noninvasive markers developed to stage liver fibrosis could be used as prognostic markers. We aimed to compare the performances of liver stiffness (LS), fibrosis-4 (FIB-4), and aspartate aminotransferase to platelet ratio index (APRI) to predict liver-related events in HIV/HCV co-infected patients.

Patients and methods

HIV/HCV co-infected patients from the ANRS CO13 HEPAVIH cohort were included if they had LS, FIB-4, and APRI measurements done in a window of 3 months. Primary outcome was the time between inclusion and occurrence of a liver-related event. Univariable and multivariable Fine and Gray models were performed. Predictive performances were compared by the area under the receiver operating characteristic (AUROC) differences after correction of optimistic by bootstrap samples. Best cutoffs to predict liver-related events were estimated by sensitivity and specificity maximization.

Results

A total of 998 patients were included. Overall, 70.7% were men. Their median age was 46.8 years. According to LS value, 204 (20.4%) patients had cirrhosis. Overall, 39 patients experienced at least one liver-related event. In univariable analysis, LS AUROC curve was significantly superior to FIB-4 and APRI AUROC curves, being 87.9, 78.2, and 75.0%, respectively. After adjustment on age, CD4 levels, and insulin resistance, no differences were observed. The best cutoffs to identify patients at low or high risk of liver-related events were below 8.5, 1.00, and 0.35 and above 16.5, 4.00, and 1.75 for LS, FIB-4, and APRI, respectively.

Conclusion

To predict HCV-related events, APRI had lower performance than LS and FIB-4. FIB-4 is as good as LS to predict HCV-related events, suggesting that it can be used for the management of HIV/HCV co-infected patients and replace LS.
Hepatocellular carcinoma macroscopic gross appearance on imaging: predictor of outcome after transarterial chemoembolization in a real-life multicenter French cohort
Authors: Adhoute Xavier , Pénaranda Guillaume , Raoul Jean-Luc , Pietri Olivia , Bronowicki Jean-Pierre , Castellani Paul , Perrier Hervé , Monnet Olivier , Bayle Olivier , Oules Valérie , Pol Bernard , Beaurain Patrick , Muller Cyrille , Cassagneau Pierre , Bourlière Marc
Published: April 2019

Background

Conventional transarterial chemoembolization (cTACE) with lipiodol is widely performed in patients with hepatocellular carcinoma (HCC) unsuitable for curative treatment. Additional tumor parameters such as HCC macroscopic appearance based on imaging might be helpful for transarterial chemoembolization prognostication and management.

Patients and methods

A total of 405 patients with HCC who underwent cTACE between 2008 and 2016 from a real-life multicenter French cohort were retrospectively reviewed. Tumors were classified into two macroscopic types according to HCC gross appearance on imaging: nodular versus non-nodular. The study population was stratified into two groups: derivation and validation cohorts. Independent prognostic factors of survival based on multivariate cox regression models were determined and then assessed in the validation set. Thereafter, time to progression (TTP) and radiological response rate were investigated for each prognostic factors of survival.

Results

Median overall survival (OS) was 35 months for Barcelona Clinic Liver Cancer (BCLC) stage A, 22 months for BCLC stage B and 12 months for BCLC stage C patients (P < 0.0001). The corresponding TTP for these patients was 12 (7–17) months, 5 (3–6) months and 1.2 (1.2–3) months (P < 0.0001). Multivariate analysis revealed that tumors size and number, non-nodular type, alpha-fetoprotein, aspartate aminotransferase serum levels and impairment of performance status-1 were independent predictors of survival among the study groups. Non-nodular type was the most powerful factor that influences OS, TTP and radiological response rate for the recommended transarterial chemoembolization candidates. TTP was consistent with OS within each stage.

Conclusion

HCC macroscopic appearance on imaging is a determinant predictor of outcome after cTACE in a real-life multicenter cohort.
Ex-vivo lung perfusion and ventilation: where to from here?
Authors: Ali Aadil , Cypel Marcelo
Published: April 2019

Purpose of review

Within the last decade, ex-vivo lung perfusion (EVLP) has become a widespread technology used for organ assessment and reconditioning within clinical transplantation. This review aims to offer insights toward future applications and developments in regards to its utility.

Recent findings

The intervention of EVLP is a well-tolerated method to effectively allow for extended preservation periods. The thoughtful usage of EVLP can therefore be used to optimize operating room logistics and progress lung transplantation toward becoming a more elective procedure. EVLP has also demonstrated itself as an excellent platform for targeted therapies. Prolonged perfusion achieved through further platform stability will allow for time-dependent molecular therapies. Lastly, EVLP allows for the opportunity to perform advanced diagnostics within an isolated setting. Sophistication of point-of-care technologies will allow for accurate predictive measures of transplant outcomes within the platform.

The future of EVLP involves usage of the system as a preservation modality, utilizing advanced diagnostics to predict transplant outcome, and performing therapeutic interventions to optimize organ quality. The generation of clinical data to facilitate and validate these approaches should be performed by transplant centers, which have acquired significant experience using EVLP within their clinical activity.
Characteristics and Survival Outcomes of Children With Hodgkin Lymphoma Treated Primarily With Chemotherapy
Authors: Ashraf Muhammad S. , Naz Fozia , Yakoob Mohammad Y.
Published: April 2019

Background:

Hodgkin disease is a malignant tumor of the lymphatic system that comprises ∼6% of childhood cancers. In developing countries, efforts are made to ensure adherence to standard protocol/regimens, study patients’ outcomes, and compare with that in developed world.

Materials and Methods:

We conducted a retrospective medical records’ review of 212 children younger than 20 years presenting to The Indus Hospital in Pakistan with previously untreated Hodgkin lymphoma between August 2000 and December 2012. We collected demographic and other epidemiologic variables such as age, sex, stage, subtype of disease, and survival outcomes.

Results:

The mean±SD age of patients at time of diagnosis was 9.0±3.8 years with a male to female ratio of ∼4.7:1. In total, 44 (20.8%) patients were 5 years of age or above at presentation. Overall, 131 (61.8%) patients presented with B-symptoms and mixed cellularity was the most frequently diagnosed subtype in 65.1% of cases. In total, 170 (80.2%) achieved full remission after completion of chemotherapy. Patients were treated with alternating cycles of ABVD (Adriamycin, Bleomycin, Vincristine, and Dacarbazine) and COPDAC (Cyclophosphamide, Vincristine, Prednisolone, and Dacarbazine). The majority (n=114, 59.1%) received 6 cycles of chemotherapy, 44 (22.8%) received ≤4 cycles followed by 24 (12.4%) receiving 8 cycles. Radiotherapy was administered only to those patients with significant residual disease at the end of chemotherapy (n=20, 10%). The 5-year overall survival and event-free survival in our cohort was 89.6% and 82.1%, respectively.

Conclusion:

Our findings suggest that treatment with 4 to 8 alternating cycles of ABVD/COPDAC has an excellent outcome in childhood Hodgkin disease.
Antibiotic Susceptibility of Bloodstream Isolates in a Pediatric Oncology Population: The Case for Ongoing Unit-specific Surveillance
Authors: Knight Tristan , Glaser Darryl W. , Ching Natascha , Melish Marian
Published: April 2019

Fever in a neutropenic oncology patient requires rapid initiation of effective empiric antibiotics to prevent mortality. We evaluated the appropriateness of our current empiric antibiotic regimen by assessing local antibiotic-susceptibility patterns in our pediatric oncology patients, and comparing them to the general pediatric patterns in our hospital. All blood culture isolates from pediatric oncology patients were reviewed over a 3-year period. Gram-negative and Gram-positive organisms were reviewed separately, with antibiotic susceptibilities for all unique isolates evaluated, and antibiograms generated and compared with general pediatric patients via the Fisher exact test. A total of 84% of Gram negatives were susceptible to meropenem; all resistant organisms were Pseudomonas aeruginosa, with 50% meropenem susceptibility. A total of 91% of Gram negatives were susceptible to cefepime, including 90% of P. aeruginosa and 80% of Escherichia coli. In total, 96% of Gram positives were vancomycin-susceptible; the only resistant organism was a single enterococcal isolate. In comparison with the general pediatric population, significantly fewer pseudomonal isolates were sensitive to meropenem among the oncology population (50% vs. 89%, P=0.0034). As such, in our population, meropenem does not provide adequate monotherapy against Pseudomonas. Ongoing surveillance of antibiotic resistance in this high-risk population is warranted, to ensure appropriate empiric antibiotic usage.
Simple and choice reaction times of healthy adults and patients after stroke during simulated driving
Authors: Debeljak Mojca , Vidmar Gaj , Oberstar Ksaver , Zupan Anton
Published: April 2019

We examined whether driving-related reaction times differ between 26 healthy adults (university students) and 26 patients after stroke, and how distractors and leg-dominance affect reaction time and correctness of reactions of healthy adults. Reaction times were measured with the Fiat Mediatester driving simulator using 18-lamps reaction test (simple reaction time measurement) and choice reaction test (scored as reaction time and number of correct reactions). There was no statistically significant difference between the groups in simple reaction time. As expected, choice reaction times of the healthy adults were shorter on average and their reactions more accurate than those of the patients. Under the influence of distractors, healthy adults had statistically significantly longer choice and simple reaction times and made fewer correct choices compared to normal conditions. Leg dominance statistically significantly affected choice reaction times and correctness of reactions, but not simple reaction times. Our results confirm validity and usefulness of the Fiat Mediatester driving simulator for research purposes.
Feasibility of Assessing Sodium-Associated Body Fluid Composition in End-Stage Renal Disease
Authors: Clark-Cutaia Maya N. , Reisinger Nathaniel , Anache Maria Rita , Ramos Kara , Sommers Marilyn S. , Townsend Raymond R. , Yu Gary , Fargo Jamison
Published: April 2019

Background

Cardiovascular disease accounts for more than half of all deaths in the hemodialysis (HD) population. Although much of this mortality is associated with fluid overload (FO), FO is difficult to measure, and many HD patients have significant pulmonary congestion despite the absence of clinical presentation. Cohort studies have observed that FO, as measured by bioimpedance spectroscopy (BIS), correlates with mortality. Other studies have observed that lower sodium intake is associated with less fluid-related weight gain, improved hypertension, and survival. Whether sodium intake influences FO in HD patients as measured by BIS is not known.

Objective

The aims of the study were to determine the feasibility of assessing the impact of sodium restriction on body fluid composition as measured by BIS among patients with three levels of sodium intake and to determine if there are statistical and/or clinical differences in BIS measures across sodium intake groups.

Methods

We used a double-blinded randomized controlled trial design with three levels of sodium restriction, 2,400 mg per day, 1,500 mg per day, and unrestricted (control group), to test our aims. Forty-two HD patients from a tertiary acute care academic institution associated with three urban DaVita dialysis centers were enrolled. Participants remained in the inpatient center for 5 days and 4 nights and were randomly assigned to sodium intake groups. Body fluid composition was measured with BIS.

Results

Recruitment, enrollment, and retention statistics supported the feasibility of the study design. Regression analyses showed that there were no statistically significant differences among sodium intake groups on any of the outcomes.

Discussion

Our data suggest the need for additional research into the effects of sodium restriction on body fluid composition.
Overcoming Challenges in Multisite Trials
Authors: Smith Laureen , Tan Alai , Stephens Janna D. , Hibler David , Duffy Sonia A.
Published: April 2019

Background

Conducting multisite studies has many challenges, including determining the geographic distance between sites, ensuring effective communication, monitoring intervention and data integrity, handling institutional policy variations, seeking institutional review board approval with unique site needs or complex subcontracts, and planning for additional costs.

Objectives

This article discusses common challenges in conducting multisite studies and identifies strategies to overcome these challenges using real-world examples from the literature, the authors’ research studies, and their personal experiences.

Methods

A summary of articles on multisite trials conducted within the past 10 years was explored to uncover common challenges in conducting multisite trials. To enrich the context, exemplars from authors’ works are included. Based on literature and experience, strategies to combat challenges are summarized.

Results

Unique issues related to multisite studies include site selection, use of epicenters/coordinating centers, hiring/managing staff, fidelity monitoring, institutional review board approval, statistical considerations, and approaches to authorship.

Conclusion

Addressing challenges a priori can improve scientific rigor, reproducibility, and evidence from multisite studies. Given the benefits to scientific rigor, reproducibility, and design, findings from multisite studies are more likely to provide evidence to transform clinical practice and influence policy.
Predictive Performance of Cardiovascular Disease Risk Prediction Algorithms in People Living With HIV
Authors: van Zoest Rosan A. , Law Matthew , Sabin Caroline A. , Vaartjes Ilonca , van der Valk Marc , Arends Joop E. , Reiss Peter , Wit Ferdinand W. ,   on behalf of the ATHENA National Observational HIV Cohort
Published: April 2019

Background:

People living with HIV (PLWH) experience a higher cardiovascular disease (CVD) risk. Yet, traditional algorithms are often used to estimate CVD risk. We evaluated the performance of 4 commonly used algorithms.

Setting:

The Netherlands.

Methods:

We used data from 16,070 PLWH aged ≥18 years, who were in care between 2000 and 2016, had no pre-existing CVD, had initiated first combination antiretroviral therapy >1 year ago, and had available data on CD4 count, smoking status, cholesterol, and blood pressure. Predictive performance of 4 algorithms [Data Collection on Adverse Effects of Anti-HIV Drugs Study (D:A:D); Systematic COronary Risk Evaluation adjusted for national data (SCORE-NL); Framingham CVD Risk Score (FRS); and American College of Cardiology and American Heart Association Pooled Cohort Equations (PCE)] was evaluated using a Kaplan–Meier approach. Model discrimination was assessed using Harrell's C-statistic. Calibration was assessed using observed-versus-expected ratios, calibration plots, and Greenwood-Nam-D'Agostino goodness-of-fit tests.

Results:

All algorithms showed acceptable discrimination (Harrell's C-statistic 0.73–0.79). On a population level, D:A:D, SCORE-NL, and PCE slightly underestimated, whereas FRS slightly overestimated CVD risk (observed-versus-expected ratios 1.35, 1.38, 1.14, and 0.92, respectively). D:A:D, FRS, and PCE best fitted our data but still yielded a statistically significant lack of fit (Greenwood-Nam-D'Agostino χ2 ranged from 24.57 to 34.22, P < 0.05). Underestimation of CVD risk was particularly observed in low-predicted CVD risk groups.

Conclusions:

All algorithms perform reasonably well in PLWH, with SCORE-NL performing poorest. Prediction algorithms are useful for clinical practice, but clinicians should be aware of their limitations (ie, lack of fit and slight underestimation of CVD risk in low-risk groups).
Comprehensive Treatment of Facial Deformity Due to Radiotherapy in Rhabdomyosarcoma Patients: Distraction Osteogenesis and Free Flaps Surgical Technique
Authors: Bianchi Alberto , Crimi Salvatore , Cipriani Riccardo , De Ponte Francesco Saverio , Cicciù Marco , Marchetti Claudio
Published: April 2019

Radiotherapy is essential for achieving and maintaining local control in head and neck rhabdomyosarcoma patients. However, radiotherapy may cause outgrowth disturbances of facial bone and soft tissue, resulting in facial asymmetry.

Several studies have shown that the management of irradiated bones still remains challenging. The possibility of obtaining functional and aesthetic results when managing facial deformities due to radiation therapy with distraction osteogenesis combined with free flaps reconstruction is not common and not well documented in recent literature.

In this report, we present the long-term results of distraction osteogenesis and soft tissue reconstruction via microvascular free flap to correct the facial hypoplasia of a young patient who underwent radiation therapy for rhabdomyosarcoma.

This is the first presentation of 26 years long-term results in a patient who also underwent free flaps reconstruction as ancillary surgery for esthetic good results.
National Stop the Bleed Day: The impact of a social media campaign on the Stop the Bleed program
Authors: Fisher Andrew D. , Carius Brandon M. , Lacroix John , Dodge P. Max , Dodd Jimm , Soderlund Eric , Thompson Dominic , Loos Paul , Fannin Jacob , Montgomery Harold R. , Gestring Mark L.
Published: April 2019

BACKGROUND

National Stop the Bleed Day (NSTBD) was created to increase public awareness of the official Stop-the-Bleed initiative and the Bleeding Control Basic course. The goal was to develop and employ an effective national social media strategy that would encourage and support efforts already in place to train the public in basic bleeding control techniques.

METHODS

March 31, 2018, was designated as NSTBD. Analysis focused on a 2-week window centered on NSTBD. The number of courses offered, number of instructors registered and total number of students trained overall during this period was derived from the American College of Surgeons (ACS) website bleedingcontrol.org. Courses not registered with the ACS were not included. Data on overall website activity were also included for analysis.

RESULTS

Forty-three states and 18 countries participated in NSTBD. During the study period, there were 1884 courses registered on bleedingcontrol.org. Comparatively, over a 4-month period from August to November 2017, the mean number of registered courses per month was 834. There were 34,699 students trained during the two-week study period as opposed to August to November 2017, the mean number of people trained per month was 9,626. In addition, 576 new B-Con instructors were certified during this time window. Additionally, the international coordinators reported 1500 students were trained during the study period. During this time, the ACS reported a significant increase in website activity. This included 10,530 new visitors, 12,772 visitors overall and 35,342 page views recorded during the study period.

CONCLUSION

The NSTBD effort was successful in generating widespread interest for the Stop-the-Bleed initiative. The use of a targeted social media campaign in this context was successful in driving people to available training opportunities while also increasing awareness of the overall effort. While only in its early stages, the NSTBD concept is a good one and should be developed further in coming years.

LEVEL OF EVIDENCE

Retrospective, Level V.
Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections
Authors: Verbeke Eric J. , Zhou Yi , Horton Andrew P. , Mallam Anna L. , Taylor David W. , Marcotte Edward M.
Published: April 2019

Cryo-electron microscopy is traditionally applied to samples purified to near homogeneity as current reconstruction algorithms are unable to handle heterogeneous mixtures of structures from many macromolecular complexes. We extend on long established methods and demonstrate that relating two-dimensional projection images by their common lines in a graphical framework is sufficient for partitioning distinct protein and multiprotein complexes within the same data set. Using this approach, we first group a large set of synthetic reprojections from 35 unique macromolecular structures ranging from ∼30 – 3000 kDa into individual homogenous classes. We then apply our algorithm on cryo-EM data collected from a mixture of five protein complexes and use existing reconstruction methods to solve multiple three-dimensional structuresab initio. Incorporating methods to sort cryo-EM data from heterogeneous mixtures will alleviate the need for stringent purification and pave the way toward investigation of samples containing many unique structures.
Modeling the effects of EMT-immune dynamics on epithelial cancer progression
Authors: Bergman Daniel R. , Karikomi Matthew K. , Yu Min , Nie Qing , MacLean Adam L.
Published: April 2019

During progression from carcinoma in situ to an invasive tumor, the immune system is engaged in complex sets of interactions with various tumor cells. Tumor cell plasticity also alters disease trajectories via epithelial-to-mesenchymal transition (EMT). Several of the same pathways that regulate EMT are involved in tumor-immune interactions, yet little is known about the mechanisms and consequences of crosstalk between these regulatory processes. Here we introduce a multiscale evolutionary model to describe tumor-immune-EMT interactions and their impact on epithelial cancer progression from in situ to invasive disease. Through in silico analyses of large patient cohorts, we find controllable regions that maximize invasion-free survival. We identify that delaying tumor progression depends crucially on properties of the mesenchymal tumor cell phenotype: its growth rate and its immune-evasiveness. Through analysis of EMT-inflammation-associated data from The Cancer Genome Atlas, we find that association with EMT significantly worsens invasion-free survival probabilities in support of our model, and we predict new genes influencing outcomes in bladder and uterine cancer, including FGF pathway members. These results offer novel means to delay disease progression by regulating properties of EMT through specific gene interactions, and demonstrate the importance of studying cancer-immune interactions in light of EMT.
Quantitative Structural Assessment of Graded Receptor Agonism
Authors: Shang Jinsai , Brust Richard , Griffin Patrick R. , Kamenecka Theodore M. , Kojetin Douglas J.
Published: April 2019

Ligand-receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded-efficacy receptor conformations predicted by receptor theory has been limited, but is critical to fully validate theoretical models. We applied quantitative structure-function approaches to characterize the effects of structurally similar and structurally diverse agonists on the conformational ensemble of nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). For all ligands, agonist efficacy is correlated to a shift in the conformational ensemble equilibrium from a ground state towards an active state, which is detected by NMR spectroscopy but not observed in crystal structures. For the structurally similar ligands, ligand potency is also correlated to efficacy and conformation, indicating ligand residence times among related analogs can influence receptor conformation and function. Our results derived from quantitative graded activity-conformation correlations provide new experimental evidence and a platform with which to extend and test theoretical models of receptor pharmacology to more accurately describe and predict ligand-dependent receptor activity.
Polyubiquitin-dependent recruitment of NEMO/IKKγ into T cell receptor signaling microclusters
Authors: DeRiso Elizabeth A. , Szymczak-Workman Andrea L. , Montecalvo Angela , Murphy Joanne M. , Seminario Maria-Cristina , Kane Lawrence P. , Bunnell Stephen C.
Published: April 2019

The NF-κB essential modulator protein (NEMO) is required for activation of canonical NF-κB by the T cell antigen receptor (TCR). However, the subcellular localization of NEMO during this process is not well understood. By dynamically imaging fluorescent NEMO chimeras in live human T cells, we demonstrate that NEMO is rapidly recruited into TCR microclusters via domains previously implicated in the recognition of linear and K63-linked polyubiquitin. The recruitment of NEMO into TCR microclusters requires the activities of the tyrosine kinases Lck and ZAP-70, but not the adaptor proteins LAT or SLP-76. Thus, our findings reveal that the pathways leading from TCR to NF-κB bifurcate downstream of ZAP-70 to independently control the recruitment and activation of NEMO.
Fitness barriers limit reversion of a proofreading-deficient coronavirus
Authors: Graepel Kevin W. , Agostini Maria L. , Lu Xiaotao , Sexton Nicole R. , Denison Mark R.
Published: April 2019

The 3′-to-5′ exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), III (D). Alanine substitution of the motif I residues (AA-E-D, four nucleotide substitutions) in murine hepatitis virus (MHV) and SARS-CoV yields viable mutants with impaired replication and fitness, increased mutation rates, and attenuated virulencein vivo. Despite these impairments, MHV- and SARS-CoV ExoN motif I AA mutants (ExoN-AA) have not reverted at motif I in diversein vitroandin vivoenvironments, suggesting that profound fitness barriers prevent motif I reversion. To test this hypothesis, we engineered MHV-ExoN-AA with 1, 2 or 3 nucleotide mutations along genetic pathways to AA-to-DE reversion. We show that engineered intermediate revertants were viable but had no increased replication or competitive fitness compared to MHV-ExoN-AA. In contrast, a low passage (P10) MHV-ExoN-AA showed increased replication and competitive fitness without reversion of ExoN-AA. Finally, engineered reversion of ExoN-AA to ExoN-DE in the presence of ExoN-AA passage-adaptive mutations resulted in significant fitness loss. These results demonstrate that while reversion is possible, at least one alternative adaptive pathway is more rapidly advantageous than intermediate revertants and may alter the genetic background to render reversion detrimental to fitness. Our results provide an evolutionary rationale for lack of ExoN-AA reversion, illuminate potential multi-protein replicase interactions and coevolution, and support future studies aimed at stabilizing attenuated CoV ExoN-AA mutants.

IMPORTANCE

Coronaviruses encode an exoribonuclease (ExoN) that is important for viral replication, fitness, and virulence, yet coronaviruses with a defective ExoN (ExoN-AA) have not reverted under diverse experimental conditions. In this study, we identify multiple impediments to MHV-ExoN-AA reversion. We show that ExoN-AA reversion is possible but evolutionarily unfavorable. Instead, compensatory mutations outside of ExoN-AA motif I are more accessible and beneficial than partial reversion. We also show that coevolution between replicase proteins over long-term passage partially compensates for ExoN-AA motif I but renders the virus inhospitable to a reverted ExoN. Our results reveal the evolutionary basis for the genetic stability of ExoN-inactivating mutations, illuminate complex functional and evolutionary relationships between coronavirus replicase proteins, and identify potential mechanisms for stabilization of ExoN-AA coronavirus mutants.
Longitudinal analysis of blood markers reveals progressive loss of resilience and predicts ultimate human lifespan limit
Authors: Pyrkov Timothy V. , Avchaciov Konstantin , Tarkhov Andrei E. , Menshikov Leonid I. , Gudkov Andrei V. , Fedichev Peter O.
Published: April 2019

We investigated the dynamic properties of the organism state fluctuations along individual aging trajectories in a large longitudinal database of CBC measurements from a consumer diagnostics laboratory. To simplify the analysis, we used a log-linear mortality estimate from the CBC variables as a single quantitative measure of aging process, henceforth referred to as dynamic organism state index (DOSI). We observed, that the age-dependent population DOSI distribution broadening could be explained by a progressive loss of physiological resilience measured by the DOSI auto-correlation time. Extrapolation of this trend suggested that DOSI recovery time and variance would simultaneously diverge at a critical point of 120 − 150 years of age corresponding to a complete loss of resilience. The observation was immediately confirmed by the independent analysis of correlation properties of intraday physical activity levels fluctuations collected by wearable devices. We conclude that the criticality resulting in the end of life is an intrinsic biological property of an organism that is independent of stress factors and signifies a fundamental or absolute limit of human lifespan.
A Framework for Integrating Directed and Undirected Annotations to Build Explanatory Models of cis-eQTL Data
Authors: Lamparter David , Bhatnagar Rajat , Hebestreit Katja , Belgard T. Grant , Hanson-Smith Victor
Published: April 2019

1

A longstanding goal of regulatory genetics is to understand how variants in genome sequences lead to changes in gene expression. Here we present a method named Bayesian Annotation Guided eQTL Analysis (BAGEA), a variational Bayes framework to model cis-eQTLs using directed and undirected genomic annotations. In a use case, we integrated directed genomic annotations with eQTL summary statistics from tissues of various origins. This analysis revealed epigenetic marks that are relevant for gene expression in different tissues and cell types. We estimated the predictive power of the models that were fitted based on directed genomic annotations. This analysis showed that, depending on the underlying eQTL data used, the directed genomic annotations could predict up to 1.5% of the variance observed in the expression of genes with top nominal eQTL association p-values < 10−7. For genes with estimated effect sizes in the top 25% quantile, up to 5% of the expression variance could be predicted. Based on our results, we recommend the use of BAGEA for the analysis of cis-eQTL data to reveal annotations relevant to expression biology.
Selective Influence and Sequential Operations: A Research Strategy for Visual Search
Authors: Lowe Kaleb A. , Reppert Thomas R. , Schall Jeffrey D
Published: April 2019

We introduce conceptually and empirically a powerful but underutilized experimental approach to dissect the cognitive processes supporting performance of a visual search task with factorial manipulations of singleton-distractor identifiability and stimulus-response cue discriminability. We show that systems factorial technology can distinguish processing architectures from the performance of macaque monkeys. This demonstration offers new opportunities to distinguish neural mechanisms through selective manipulation of visual encoding, search selection, rule encoding, and stimulus-response mapping.
Irrational risk aversion in ants is driven by perceptual mechanisms
Authors: De Agrò Massimo , Grimwade Daniel , Czaczkes Tomer J.
Published: April 2019

Animals must often decide between exploiting safe options or risky options with a chance for large gains. While traditional optimal foraging theories assume rational energy maximisation, they fail to fully describe animal behaviour. A logarithmic rather than linear perception of stimuli may shape preference, causing animals to make suboptimal choices. Budget-based rules have also been used to explain risk-preference, and the relative importance of these theories is debated. Eusocial insects represent a special case of risk sensitivity, as they must often make collective decisions based on resource evaluations from many individuals. Previously, colonies of the antLasius nigerwere found to be risk-neutral, but the risk preference of individual foragers was unknown. Here, we tested individualL. nigerin a risk sensitivity paradigm. Ants were trained to associate a scent with 0.55M sucrose solution and another scent with an equal chance of either 0.1 and 1.0M sucrose. Preference was tested in a Y-maze. Ants were extremely risk averse, with 91% choosing the safe option. Even when the risky option offered on average more sucrose (0.8M) than the fixed option, 75% preferred the latter. Based on the psychophysical Weber-Fechner law, we predicted that logarithmically balanced alternatives (0.3M vs 0.1M/0.9M) would be perceived as having equal value. Our prediction was supported, with ants having no preference for either feeder (53% chose the fixed option). Our results thus strongly support perceptual mechanisms driving risk-aversion in ants, and demonstrate that the behaviour of individual foragers can be a very poor predictor of colony-level behaviour.
The Drosophila metallopeptidase superdeath decouples apoptosis from the activation of the ER stress response
Authors: Palu Rebecca A.S. , Chow Clement Y.
Published: April 2019

Endoplasmic reticulum (ER) stress-induced apoptosis is a primary cause and modifier of degeneration in a number of genetic disorders. Understanding how genetic variation between individuals influences the ER stress response and subsequent activation of apoptosis could improve individualized therapies and predictions of outcomes for patients. In this study, we find that the uncharacterized, membrane-bound metallopeptidase CG14516 in Drosophila melanogaster, which we rename as SUPpressor of ER stress-induced DEATH (superdeath), plays a role in modifying ER stress-induced apoptosis. We demonstrate that loss of superdeath reduces apoptosis and degeneration in the Rh1G69D model of ER stress through the JNK signaling cascade. This effect on apoptosis occurs without altering the activation of the unfolded protein response (IRE1 and PERK), suggesting that the beneficial pro-survival effects of this response are intact. Furthermore, we show that superdeath functions epistatically upstream of CDK5, a known JNK-activated pro-apoptotic factor in this model of ER stress. We demonstrate that superdeath is not only a modifier of this particular model, but functions as a general modifier of ER stress-induced apoptosis across different tissues and ER stresses. Finally, we present evidence of Superdeath localization to the endoplasmic reticulum membrane. While similar in sequence to a number of human metallopeptidases found in the plasma membrane and ER membrane, its localization suggests that superdeath is orthologous to ERAP1/2 in humans. Together, this study provides evidence that superdeath is a link between stress in the ER and activation of cytosolic apoptotic pathways.

SIGNIFICANCE STATEMENT

Genetic diseases display a great deal of variability in presentation, progression, and overall outcomes. Much of this variability is caused by differences in genetic background among patients. One process that commonly modifies degenerative disease is the endoplasmic reticulum (ER) stress response. Understanding the genetic sources of variation in the ER stress response could improve individual diagnosis and treatment decisions. In this study, we characterized one such modifier in Drosophila melanogaster, the membrane-bound metallopeptidase CG14516 (superdeath). Loss of this enzyme suppresses a model of ER stress-induced degeneration by reducing cell death without altering the beneficial activation of the unfolded protein response. Our findings make superdeath and its orthologues attractive therapeutic targets in degenerative disease.
Deconvolute individual genomes from metagenome sequences through read clustering
Authors: Li Kexue , Wang Lili , Shi Lizhen , Deng Li , Wang Zhong
Published: April 2019

Motivation

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems.

Results

Based on a previously developed scalable read clustering method on Apache Spark, SpaRC, that has very low false positives, here we extended its capability by adding a new method to further cluster small clusters. This method exploits statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using a synthetic dataset from mouse gut microbiomes we show that this method has the potential to cluster almost all of the reads from genomes with sufficient sequencing coverage. We also explored several clustering parameters that deferentially affect genomes with various sequencing coverage.

Availability

https://bitbucket.org/berkeleylab/jgi-sparc/.

Contact

zhongwang@lbl.gov
Neuronal avalanches in input and associative layers of auditory cortex
Authors: Bowen Zac , Winkowski Daniel E. , Seshadri Saurav , Plenz Dietmar , Kanold Patrick O.
Published: April 2019

The primary auditory cortex processes acoustic sequences for the perception of behaviorally meaningful sounds such as speech. Sound information arrives at its input layer 4 from where activity propagates to associative layer 2/3. It is currently not known whether there is a particular organization of neuronal population activity that is stable across layers and sound levels during sound processing. We used in vivo 2-photon imaging of pyramidal neurons in cortical layers L4 and L2/3 of mouse A1 to characterize the populations of neurons that were active spontaneously, i.e. in the absence of a sound stimulus, and those recruited by single-frequency tonal stimuli at different sound levels. Single-frequency sounds recruited neurons of widely ranging frequency selectivity in both layers. We defined neural ensembles as neurons being active within or during successive temporal windows at the temporal resolution of our imaging. For both layers, neuronal ensembles were highly variable in size during spontaneous activity as well as during sound presentation. Ensemble sizes distributed according to power laws, the hallmark of neuronal avalanches, and were similar across sound levels. Avalanches activated by sound were composed of neurons with diverse tuning preference, yet with selectivity independent of avalanche size. Thus, spontaneous and evoked activity in both L4 and L2/3 of A1 are composed of neuronal avalanches with similar power law relationships. Our results demonstrate network principles linked to maximal dynamic range, optimal information transfer and matching complexity between L4 and L2/3 to shape population activity in auditory cortex.
Bacteriophage can promote the emergence of physiologically sub-optimal host phenotypes
Authors: Schenk Hanna , Sieber Michael
Published: April 2019

Reproduction of bacteria-specific viruses, or bacteriophage, requires the replication and translation machinery of the host cell. As a consequence, phage fitness depends intimately on the physiological state, i.e. growth rate, of the host. We include this dependence of critical phage traits on host growth rate in a mathematical model of a bacteria-phage interaction. This leads to a feedback loop between phage success, host population size, nutrient availability and host growth rate. We find that this feedback allows slow growing bacteria to have a competitive advantage in the presence of phage. Under certain conditions a slow growing host mutant can even drive the phage to extinction. Since in a phage-free environment slow growth is deleterious, the mutant subsequentely dies out as well, constituting a kind of altruistic scenario similar to abortive infections.
Consistent trade-offs in ecosystem services between land covers with different production intensities
Authors: Gómez-Creutzberg Carla , Lagisz Malgorzata , Nakagawa Shinichi , Brockerhoff Eckehard G. , Tylianakis Jason M.
Published: April 2019

Sustaining multiple ecosystem services across a landscape requires an understanding of how consistently services are shaped by different categories of land uses. Yet, this understanding is generally constrained by the availability of fine-resolution data for multiple services across large areas and the spatial variability of land-use effects on services. We systematically surveyed published literature for New Zealand (1970 – 2015) to quantify the supply of 17 services across 25 land covers (as a proxy for land use). We found a consistent trade-off in the services supplied by anthropogenic land covers with a high production intensity (e.g., cropping) versus those with extensive or no production. In contrast, forest cover was not associated with any distinct patterns of service supply. By drawing on existing research findings we reveal complementarity and redundancy (potentially influencing resilience) in service supply from different land covers. This can guide practitioners in shaping land systems that sustainably support human well-being.
Intron-targeted mutagenesis reveals roles forDscam1RNA pairing-mediated splicing bias in neuronal wiring
Authors: Hong Weiling , Dong Haiyang , Zhang Jian , Zhou Fengyan , Wu Yandan , Shi Yang , Chen Shuo , Xu Bingbing , You Wendong , Shi Feng , Yang Xiaofeng , Gong Zhefeng , Huang Jianhua , Jin Yongfeng
Published: April 2019

Drosophila melanogasterDown syndrome cell adhesion molecule (Dscam1) can potentially generate 38,016 different isoforms through stochastic, yet highly biased, alternative splicing. Genetic studies demonstrated that stochastic expression of multiple Dscam1 isoforms provides each neuron with a unique identity for self/non-self-discrimination. However, due to technical obstacles, the functional significance of the highly specific bias in isoform expression remains entirely unknown. Here, we provide conclusive evidence thatDscam1splicing bias is required for precise mushroom body (MB) axonal wiring in flies in a variable exon-specific manner. We showed that targeted deletion of the intronic docking site perturbed base pairing-mediated regulation of inclusion of variable exons. Unexpectedly, we generated mutant flies with normal overall Dscam1 protein levels and an identical number but global changes in exon 4 and exon 9 isoform bias (DscamΔ4D−/−and DscamΔ9D−/−), respectively. DscamΔ9D−/−mutant exhibited remarkable mushroom body defects, which were correlated with the extent of the disrupted isoform bias. By contrast, the DscamΔ4D−/−animals exhibited a much less severe defective phenotype than DscamΔ9D−/−animals, suggestive of a variable domain-specific requirement for isoform bias. Importantly, mosaic analysis revealed that changes in isoform bias caused axonal defects but did not influence the self-avoidance of axonal branches. We concluded that, in contrast to the Dscam1 isoform number that provides the molecular basis for neurite self-avoidance, isoform bias may play a non-repulsive role in mushroom body axonal wiring.
Myelination of major white matter tracts continues beyond childhood—combining tractography and myelin water imaging
Authors: Meissner Tobias W. , Genç Erhan , Mädler Burkhard , Weigelt Sarah
Published: April 2019

Axonal myelination is a key white matter maturation process as it increases conduction velocity, synchrony, and reliability. While diffusion tensor imaging (DTI) is sensitive to myelination, it is also sensitive to unrelated microstructural properties, thus hindering straightforward interpretations. Myelin water imaging (MWI) provides a more reliable and direct in vivo measure of myelination. Although early histological studies show protracted myelination from childhood to adulthood, reliable tract-specific in vivo evidence from MWI is still lacking. Here, we combine MWI and DTI tractography to investigate myelination in middle childhood, late childhood, and adulthood in 18 major white matter tracts. In the vast majority of major white matter tracts, myelin water fraction continued to increase beyond late childhood. Our study provides first in vivo evidence for protracted myelination beyond late childhood.
Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome
Authors: Abildgaard Amanda B. , Stein Amelie , Nielsen Sofie V. , Schultz-Knudsen Katrine , Papaleo Elena , Shrikhande Amruta , Hoffmann Eva R. , Bernstein Inge , Gerdes Anne-Marie , Takahashi Masanobu , Ishioka Chikashi , Lindorff-Larsen Kresten , Hartmann-Petersen Rasmus
Published: April 2019

Defective mismatch repair leads to increased mutation rates, and germline loss-of-function variants in the repair component MLH1 cause the hereditary cancer predisposition disorder known as Lynch syndrome. Early diagnosis is important, but complicated by many variants being of unknown significance. Here we show that a majority of the disease-linked MLH1 variants we studied are present at reduced cellular levels. We show that destabilized MLH1 variants are targeted for chaperone-assisted proteasomal degradation, resulting also in degradation of co-factors PMS1 and PMS2.In silicosaturation mutagenesis and computational predictions of thermodynamic stability of MLH1 missense variants revealed a correlation between structural destabilization, reduced steady-state levels and loss-of-function. Thus, we suggest that loss of stability and cellular degradation is an important mechanism underlying manyMLH1variants in Lynch syndrome. Combined with analyses of conservation, the thermodynamic stability predictions separate disease-linked from benignMLH1variants, and therefore hold potential for Lynch syndrome diagnostics.
Identifying Novel Candidates for Re-Purposing as Potential Therapeutic Agents for Alzheimer’s disease
Authors: Ballard C , Creese B , Gatt A , Doherty P , Francis PT , Whitfield D , Corbett A , Corcoran J , Hanger D , Thuret S , Killick R , Williams G
Published: April 2019

The current paper describes the identification of novel candidate compounds for repositioning as treatments for Alzheimer’s disease (AD) from the CMAP library. Candidate compounds were identified based on inverse correlation with transcriptome signatures developed from meta-analyses of Alzheimer RNA expression studies using the SPIED platform. The 78 compounds with a significant inverse correlation were taken forward into an in vitro programme using 6 well validated screening assays relevant to potential treatment targets in AD. Nineteen pf the compounds were hits in at least 2 of these assays. A description of each of these compounds is presented.