bluuebunny/crossref_metadata_2025 huggingface dataset:
Profiling COVID-19 pneumonia progressing into the cytokine storm syndrome: results from a single Italian Centre study on tocilizumab versus standard of care
Authors: Quartuccio Luca , Sonaglia Arianna , McGonagle Dennis , Fabris Martina , Peghin Maddalena , Pecori Davide , Monte Amato De , Bove Tiziana , Curcio Francesco , Bassi Flavio , De Vita Salvatore , Tascini Carlo
Published: May 2020

Objective

Approximately 5% of patients with coronavirus disease 2019 (COVID-19) develop a life-threatening pneumonia that often occurs in the setting of increased inflammation or “cytokine storm”. Anti-cytokine treatments are being evaluated but optimal patient selection remains unclear, and the aim of our study is to address this point.

Methods

Between February 29 to April 6, 2020, 111 consecutive hospitalized patients with COVID-19 pneumonia were evaluated in a single centre retrospective study. Patients were divided in two groups: 42 severe cases (TOCI) with adverse prognostic features including raised CRP and IL-6 levels, who underwent anti-cytokine treatments, mostly tocilizumab, and 69 standard of care patients (SOC).

Results

In the TOCI group, all received anti-viral therapy and 40% also received glucocorticoids. In TOCI, 62% of cases were ventilated and there were 3 deaths (17.8±10.6 days, mean follow up) with 7/26 cases remaining on ventilators, without improvement, and 17/26 developed bacterial superinfection. One fatality occurred in the 15 TOCI cases treated on noninvasive ventilation and 1 serious bacterial superinfection. Of the 69 cases in SOC, there was no fatalities and no bacterial complications. The TOCI group had higher baseline CRP and IL-6 elevations (p<0.0001 for both) and higher neutrophils and lower lymphocyte levels (p= 0.04 and p=0.001, respectively) with the TOCI ventilated patients having higher markers than non-ventilated TOCI patients.

Conclusion

Higher inflammatory markers, more infections and worse outcomes characterized ventilated TOCI cases compared to ward based TOCI. Despite the confounding factors, this suggests that therapy time in anti-cytokine randomized trials will be key.

Funding

This research received no external funding.

Conflicts of Interest

“The authors declare no conflict of interest.”

Highlights

There is an urgent need for markers of prognosis in COVID-19.

Higher inflammatory markers best select tocilizumab treatment.

The ward based tocilizumab group showed better responses and less infections than ICU tocilizumab group.

The former group may be the best for evaluating the impact of anti-cytokine therapy in COVID-19.

The known poor risk factors for COVID-19 infection were present in the TOCI treated rather than in the good prognosis standard of care group.
TRACKING AND PREDICTING COVID-19 RADIOLOGICAL TRAJECTORY USING DEEP LEARNING ON CHEST X-RAYS: INITIAL ACCURACY TESTING
Authors: Duchesne S. , Gourdeau D. , Archambault P. , Chartrand-Lefebvre C. , Dieumegarde L. , Forghani R. , Gagné C. , Hains A. , Hornstein D. , Le H. , Lemieux S. , Lévesque M.H. , Martin D. , Rosenbloom L. , Tang A. , Vecchio F. , Potvin O. , Duchesne N.
Published: May 2020

Background

Decision scores and ethically mindful algorithms are being established to adjudicate mechanical ventilation in the context of potential resources shortage due to the current onslaught of COVID-19 cases. There is a need for a reproducible and objective method to provide quantitative information for those scores.

Purpose

Towards this goal, we present a retrospective study testing the ability of a deep learning algorithm at extracting features from chest x-rays (CXR) to track and predict radiological evolution.

Materials and Methods

We trained a repurposed deep learning algorithm on the CheXnet open dataset (224,316 chest X-ray images of 65,240 unique patients) to extract features that mapped to radiological labels. We collected CXRs of COVID-19-positive patients from two open-source datasets (last accessed on April 9, 2020)(Italian Society for Medical and Interventional Radiology and MILA). Data collected form 60 pairs of sequential CXRs from 40 COVID patients (mean age ± standard deviation: 56 ± 13 years; 23 men, 10 women, seven not reported) and were categorized in three categories: “Worse”, “Stable”, or “Improved” on the basis of radiological evolution ascertained from images and reports. Receiver operating characteristic analyses, Mann-Whitney tests were performed.

Results

On patients from the CheXnet dataset, the area under ROC curves ranged from 0.71 to 0.93 for seven imaging features and one diagnosis. Deep learning features between “Worse” and “Improved” outcome categories were significantly different for three radiological signs and one diagnostic (“Consolidation”, “Lung Lesion”, “Pleural effusion” and “Pneumonia”; all P < 0.05). Features from the first CXR of each pair could correctly predict the outcome category between “Worse” and “Improved” cases with 82.7% accuracy.

Conclusion

CXR deep learning features show promise for classifying the disease trajectory. Once validated in studies incorporating clinical data and with larger sample sizes, this information may be considered to inform triage decisions.
Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease
Authors: Günther Sebastian , Reinke Patrick Y. A. , Oberthuer Dominik , Yefanov Oleksandr , Ginn Helen , Meier Susanne , Lane Thomas J. , Lorenzen Kristina , Gelisio Luca , Brehm Wolfgang , Dunkel Illona , Domaracky Martin , Saouane Sofiane , Lieske Julia , Ehrt Christiane , Koua Faisal , Tolstikova Alexandra , White Thomas A. , Groessler Michael , Fleckenstein Holger , Trost Fabian , Galchenkova Marina , Gevorkov Yaroslav , Li Chufeng , Awel Salah , Peck Ariana , Xavier P. Lourdu , Barthelmess Miriam , Schlünzen Frank , Werner Nadine , Andaleeb Hina , Ullah Najeeb , Falke Sven , Franca Bruno Alves , Schwinzer Martin , Brognaro Hévila , Seychell Brandon , Gieseler Henry , Melo Diogo , Zaitseva-Kinneberg Joanna I. , Norton-Baker Brenna , Knoska Juraj , Esperanza Gisel , Mashhour Aida Rahmani , Guicking Filip , Hennicke Vincent , Fischer Pontus , Rogers Cromarte , Monteiro Diana C. F. , Hakanpää Johanna , Meyer Jan , Noei Heshmat , Gribbon Phil , Ellinger Bernhard , Kuzikov Maria , Wolf Markus , Zhang Linlin , Sun Xinyuanyuan , Pletzer-Zelgert Jonathan , Wollenhaupt Jan , Feiler Christian , Weiss Manfred , Schulz Eike-Christian , Mehrabi Pedram , Schmidt Christina , Schubert Robin , Han Huijong , Krichel Boris , Fernández-García Yaiza , Escudero-Pérez Beatriz , Günther Stephan , Turk Dusan , Uetrecht Charlotte , Beck Tobias , Tidow Henning , Chari Ashwin , Zaliani Andrea , Rarey Matthias , Cox Russell , Hilgenfeld Rolf , Chapman Henry N. , Pearson Arwen R. , Betzel Christian , Meents Alke
Published: May 2020

Here we present the crystal structure of SARS-CoV-2 main protease (Mpro) covalently bound to 2-methyl-1-tetralone. This complex was obtained by co-crystallization of Mprowith HEAT (2-(((4-hydroxyphenethyl)amino)methyl)-3,4-dihydronaphthalen-1(2H)-one) in the framework of a large X-ray crystallographic screening project of Mproagainst a drug repurposing library, consisting of 5632 approved drugs or compounds in clinical phase trials. Further investigations showed that HEAT is cleaved by Mproin an E1cB-like reaction mechanism into 2-methylene-1-tetralone and tyramine. The catalytic Cys145 subsequently binds covalently in a Michael addition to the methylene carbon atom of 2-methylene-1-tetralone. According to this postulated model HEAT is acting in a pro-drug-like fashion. It is metabolized by Mpro, followed by covalent binding of one metabolite to the active site. The structure of the covalent adduct elucidated in this study opens up a new path for developing non-peptidic inhibitors.
Group Testing Performance Evaluation for SARS-COV-2 Massive Scale Screening and Testing
Authors: Nalbantoglu Ozkan Ufuk
Published: May 2020

The capacity of current molecular testing convention does not allow high-throughput and community level scans of COVID-19 infections. The diameter in current paradigm of shallow tracing is unlikely to reach the silent clusters that might be as important as the symptomatic cases in the spread of the disease. Group testing is a feasible and promising approach when the resources are scarce and when a relatively low prevalence regime is observed on the population. We employed group testing with a sparse random pooling scheme and conventional group test decoding algorithms both for exact and inexact recovery. Our simulations showed that significant reduction in per case test numbers (or expansion in total test numbers preserving the number of actual tests conducted) for very sparse prevalence regimes is available. Currently proposed COVID-19 group testing schemes offer a gain up to 10X scale-up. There is a good probability that the required scale up to achieve massive scale testing might be greater in certain scenarios. We investigated if further improvement is available, especially in sparse prevalence occurrence where outbreaks are needed to be avoided by population scans. Our simulations show that sparse random pooling can provide improved efficiency gains compared to row-column group testing or Reed-Solomon error correcting codes. Therefore, we propose that special designs for different scenarios could be available and it is possible to scale up testing capabilities significantly.
The interplay between Bag-1, Hsp70, and Hsp90 reveals that inhibiting Hsp70 rebinding is essential for Glucocorticoid Receptor activity
Authors: Kirschke Elaine , Roe-Zurz Zygy , Noddings Chari , Agard David
Published: May 2020

The glucocorticoid receptor (GR), like many signaling proteins requires Hsp90 for sustained activity. Previous biochemical studies revealed that the requirement for Hsp90 is explained by its ability to reverse Hsp70-mediated inactivation of GR through a complex process requiring both cochaperones and Hsp90 ATP hydrolysis. How ATP hydrolysis on Hsp90 enables GR reactivation is unknown. The canonical mechanism of client release from Hsp70 requires ADP:ATP exchange, which is normally rate limiting. Here we show that independent of ATP hydrolysis, Hsp90 acts as an Hsp70 nucleotide exchange factor (NEF) to accelerate ADP dissociation, likely coordinating GR transfer from Hsp70 to Hsp90. As Bag-1 is a canonical Hsp70 NEF that can also reactivate Hsp70:GR, the impact of these two NEFs was compared. Simple acceleration of Hsp70:GR release was insufficient for GR reactivation as Hsp70 rapidly re-binds and re-inactivates GR. Instead, inhibition of GR re-inactivation by Hsp70 is critical. This can be accomplished by high non-physiological Bag-1 concentrations, which also inhibit Hsp70:ATP binding. In contrast, in an ATP-hydrolysis dependent process, Hsp90 plays a unique role by kinetically partitioning GR into a state that can bind ligand, but is protected from Hsp70 inactivation, thus allowing GR to be activated by its ligand but still able to re-enter the chaperone cycle. At physiologic concentrations, Bag-1 works synergistically with Hsp90 to accelerate the first rate-limiting step in GR reactivation. The net effect is that the chaperone machinery cyclically dictates the on and off rates for GR ligand, providing a timer controlling the persistence of activated GR.

Significance Statement

The glucocorticoid receptor (GR) is an essential transcription regulatory factor. Like many signaling proteins, GR activity is regulated by two essential molecular chaperones: Hsp90 and Hsp70. Functioning like a toggle switch, Hsp70 first inactivates GR, and then Hsp90 reactivates GR in an Hsp90 ATP hydrolysis dependent manner. Here, an intricate set of biochemistry experiments uncover fundamental principles governing how these chaperone systems collaboratively regulate GR activity. While Hsp90 promotes GR release from Hsp70 by modulating Hsp70’s nucleotide state, this occurs independently of Hsp90 ATP hydrolysis. Instead, ATP hydrolysis on Hsp90 facilitates a second essential reactivation step resulting in an Hsp90-bound GR state that protects GR from Hsp70 re-inactivation. A kinetic partitioning model best describes chaperone modulation of GR’s activity.
Bacterial load slopes as biomarkers of tuberculosis therapy success, failure, and relapse
Authors: Magombedze Gesham , Pasipanodya Jotam G. , Gumbo Tawanda
Published: May 2020

Background

Tuberculosis is expensive to treat, especially since therapy duration is at least six-months, and patients must be followed for up to two years in order to document relapse. There is an urgent need to discover biomarkers that are predictive of long-term treatment outcomes. Currently, tuberculosis programs use two-months sputum conversion for clinical decision making, while phase I clinical trials use extended [14 day] early bactericidal activity [EBA] to triage regimens. Our objective was to develop early treatment stage biomarkers that are predictive of long-term outcomes.

Methods and Findings

Data from 1,924 patients in the REMoxTB study was divided into [1] a derivation data-set of 318 patients on six-months standard therapy, [2] two sets of validation datasets comprised of 319 patients on six-months standard therapy, and 1,287 patients randomized to four-months experimental therapy. Sputum time-to-positivity [TTP] data was modeled using a system of ordinary differential equations that identified bacillary kill rates [termed γ-slopes], for fast-replicating bacteria [γf] and for semi-dormant/non-replicating persistent bacteria [γs], and to estimate time-to-extinction for all bacteria sub-populations in each patient. Time-to-extinction is used to predict the minimum therapy duration required to achieve cure. Using the derivation dataset, machine learning identified the γs slope, calculated using first 8 weeks of therapy TTP data, as the highest ranked predictor for treatment outcomes. We then computed γs slope thresholds that would reliably predict relapse-free cure for 2, 3, 4, and 6 months therapy duration regimens, and used these to create a diagnostic rule. In the first-validation dataset for six-months therapy duration, the γs-derived decision rule demonstrated a sensitivity of 92% and a specificity of 89%; among patients with positive biomarker the relative risk [RR] of failure was 20.40 [95% confidence interval (CI): 7.17-58.08]. In comparison, two-month sputum culture conversion had a sensitivity of 33% and specificity of 71% [RR=1.20 (95% CI: 0.60-2.34)], while for extended-EBA sensitivity was 14% and specificity was 92% [RR=1.71 [95% CI: 0.73-3.48]. In the second validation dataset for four-months therapy duration, the γs-derived diagnostic rule sensitivity was 81% while specificity was 87% for picking failure versus cure [RR=14.51 (95% CI: 8.33-25.41)]

Conclusions

The ability to predict treatment outcomes during the first eight-weeks of therapy could accelerate evaluation of novel regimens, development of new clinical trial designs, as well as allow personalization of therapy duration in routine treatment programs. Future research applying these diagnostic rules to different clinical trials data are required.
Mechanical dysfunction induced by a hypertrophic cardiomyopathy mutation is the primary driver of cellular adaptation
Authors: Clippinger Sarah R. , Cloonan Paige E. , Wang Wei , Greenberg Lina , Stump W. Tom , Angsutararux Paweorn , Nerbonne Jeanne M. , Greenberg Michael J.
Published: May 2020

Familial hypertrophic cardiomyopathy (HCM), a leading cause of sudden cardiac death, is primarily caused by mutations in sarcomeric proteins. The pathogenesis of HCM is complex, with functional changes that span scales from molecules to tissues. This makes it challenging to deconvolve the biophysical molecular defect that drives the disease pathogenesis from downstream changes in cellular function. Here, we examined a HCM mutation in troponin T, R92Q. We demonstrate that the primary molecular insult driving the disease pathogenesis is mutation-induced alterations in tropomyosin positioning, which causes increased molecular and cellular force generation during calcium-based activation. We demonstrate computationally that these increases in force are direct consequences of the initial molecular insult. This altered cellular contractility causes downstream alterations in gene expression, calcium handling, and electrophysiology. Taken together, our results demonstrate that molecularly driven changes in mechanical tension drive the early disease pathogenesis, leading to activation of adaptive mechanobiological signaling pathways.
A GRAB sensor reveals activity-dependent non-vesicular somatodendritic adenosine release
Authors: Wu Zhaofa , Cui Yuting , Wang Huan , Song Kun , Yuan Zhengwei , Dong Ao , Wu Hao , Wan Yi , Pan Sunlei , Peng Wanling , Jing Miao , Xu Min , Luo Minmin , Li Yulong
Published: May 2020

The purinergic signaling molecule adenosine (Ado) modulates many physiological and pathological brain functions,but its spatiotemporal release dynamics in the brain remains largely unknown. We developed a genetically encodedGPCR-Activation–BasedAdosensor (GRABAdo) in which Ado-induced changes in the human A2Areceptor are reflected by fluorescence increases. This GRABAdorevealed that neuronal activity-induced extracellular Ado elevation was due to direct Ado release from somatodendritic regions of the neuron, requiring calcium influx through L-type calcium channels, rather than the degradation of extracellular ATP. The Ado release was slow (∼30 s) and depended on equilibrative nucleoside transporters (ENTs) rather than conventional vesicular release mechanisms. Thus, GRABAdoreveals an activity-dependent slow Ado release from somatodendritic region of the neuron, potentially serving modulating functions as a retrograde signal.
Validity of natural isotope abundance correction for metabolic flux analysis
Authors: Nilsson Roland
Published: May 2020

A pervasive issue in stable isotope tracing and metabolic flux analysis is the presence of naturally occurring isotopes such as13C. For mass isotopomer distributions (MIDs) measured by mass spectrometry, it is common practice to correct for natural isotopes within metabolites of interest using a particular linear transform based on binomial distributions. However, the origin and mathematical derivation of this transform is rather obscure, and it may be difficult for nonexperts to understand precisely how to interpret the resulting corrected MIDs. Moreover, corrected MIDs are often used to fit metabolic network models and infer metabolic fluxes, which implicitly assumes that corrected MIDs will yield the same flux solution as the actual observed MIDs. Yet, there seems to be no published proof of this important property. Here, we provide a detailed derivation of the MID-correcting linear transform, reflecting its historical development, and describe some interesting properties. We also provide a proof that for metabolic flux analysis on noise-free MID data at steady state, observed and corrected MIDs indeed yield the same flux solution. On the other hand, for noisy MID data, the flux solution will generally differ between the two representations.
PHOSPHO1, a novel skeletal regulator of insulin resistance and obesity
Authors: Suchacki KJ , Morton NM , Vary C , Huesa C , Yadav MC , Thomas BJ , Rajoanah S , Bunger L , Ball D , Barrios-Llerena M , Guntur AR , Khavandgar Z , Cawthorn WP , Ferron M , Karsenty G , Murshed M , Rosen CJ , MacRae VE , Millán JL , Farquharson C
Published: May 2020

The skeleton is recognised as a key endocrine regulator of metabolism. Here we show that mice lacking the bone mineralization enzyme PHOSPHO1 (Phospho1-/-) exhibited improved basal glucose homeostasis and resisted high-fat-diet induced weight gain and diabetes. The metabolic protection inPhospho1-/-mice was manifested in the absence of altered levels of osteocalcin. Osteoblasts isolated fromPhospho1-/-mice were enriched for genes associated with energy metabolism and diabetes;Phospho1both directly and indirectly interacted with genes associated with glucose transport and insulin receptor signalling. Canonical thermogenesis via brown adipose tissue did not underlie the metabolic protection observed in adultPhospho1-/-mice. However, the decreased serum choline levels inPhospho1-/-mice were normalized by feeding a 2% choline rich diet resulting in a normalization in insulin sensitivity and fat mass. This study identifies PHOSPHO1 as a potential therapeutic target for the treatment of obesity and diabetes.
Removal of the extracellular matrix biases auditory cortical layer dynamics towards supragranular frequency integration
Authors: El-Tabbal M , Niekisch H , Henschke JU , Budinger E , Frischknecht R , Deliano M , Happel MFK
Published: May 2020

In the adult vertebrate brain, enzymatic removal of the extracellular matrix (ECM) is increasingly recognized to promote learning, memory recall, and restorative plasticity. However, the underlying impact of local removal of the ECM on cortical circuit processing is still not understood. Here, we removed the ECM in the primary auditory cortex (ACx) of adult Mongolian gerbils using local injections of hyaluronidase (HYase). Using laminar current-source density (CSD) analysis, we found layer-specific changes of the spatiotemporal synaptic activity patterns. Applying multitaper spectral analysis and time-domain conditional Granger causality (GC) measures, we found increased stimulus-evoked oscillatory power in the beta band (25-36 Hz) selectively within infragranular layers Vb and enhanced supragranular synaptic activity. Our findings reveal new insights on how ECM modulation affects the sensory integration via altered translaminar cortical network dynamics with a supragranular lead of the columnar response profile.
Machine learning prediction of particle-size distribution from infrared spectra, methodologies and soil features
Authors: Parent Elizabeth J. , Parent Serge-É. , Parent Léon E.
Published: May 2020

Accuracy of infrared (IR) models to measure soil particle-size distribution (PSD) depends on soil preparation, methodology (sedimentation, laser), settling times and relevant soil features. Compositional soil data may require log ratio (ilr) transformation to avoid numerical biases. Machine learning can relate numerous independent variables that may impact on NIR spectra to assess particle-size distribution. Our objective was to reach high IRS prediction accuracy across a large range of PSD methods and soil properties. A total of 1298 soil samples from eastern Canada were IR-scanned. Spectra were processed by Stochastic Gradient Boosting (SGB) to predict sand, silt, clay and carbon. Slope and intercept of the log-log relationships between settling time and suspension density function (SDF) (R2= 0.84-0.92) performed similarly to NIR spectra using eitherilr-transformed (R2= 0.81-0.93) or raw percentages (R2= 0.76-0.94). Settling times of 0.67-min and 2-h were the most accurate for NIR predictions (R2= 0.49-0.79). The NIR prediction of sand sieving method (R2= 0.66) was more accurate than Bouyoucos (R2= 0.53). The NIR 2X gain was less accurate (R2= 0.69-0.92) than 4X (R2= 0.87-0.95). The MIR (R2= 0.45-0.80) performed better than NIR (R2= 0.40-0.71) spectra. Adding soil carbon, reconstituted bulk density, pH, red-green-blue color, oxalate and Mehlich3 extracts returned R2value of 0.86-0.91 for texture prediction. In addition to slope and intercept of the SDF, 4X gain, method and pre-treatment classes, soil carbon and color appeared to be promising features for routine SGB-processed NIR particle-size analysis.

Soil Classification(Soil Taxonomy): Inceptisols, Spodosols
Potential Impact of Climate Change on One-Horned Rhinoceros (Rhinoceros unicornis) in Nepal
Authors: Adhikari Ayush , Shah Deep Narayan
Published: May 2020

Abrupt change in climate or simply termed as climate change is considered to be one of the major challenges in biodiversity. Change in climate has impacted many species around the world, particularly threatened species like One-Horned Rhinoceros (Rhinoceros unicornis).Rhinoceros unicornisis placed as an endangered species by International Union for Conservation of Nature (IUCN). Being an endangered species, studies regarding the impact of climate on the distribution ofRhinoceros unicornisis very rare in Nepal. Thus, the present study focuses on identifying the potential impact of climate change on the suitable habitat ofRhinoceros unicornisin Nepal using Species Distribution Modelling (SDM). For this, we used the present climatic scenarios and two greenhouse concentration trajectories (RCP 4.5 and RCP 8.5) for two different time periods (2050 and 2070) using different bioclimatic variables. Our model demonstrated the loose of the suitable habitat ofRhincoeros unicornisby 51.87% and 56.54% in RCP 4.5 for year 2050 and 2070 respectively. Under RCP 8.5 for year 2050 and 2070, the model demonstrated the loose of present suitable habitat by 54.25% and 49.51% respectively. Likewise, our result also predicted elevation as an important bioclimatic variable. This study would provide an information to the policy makers, conservationist and government officer of Nepal for the management and protection of habitat ofRhinoceros unicornisin present and future climatic context.
Bioengineered model of the human motor unit with physiologically functional neuromuscular junctions
Authors: Rimington Rowan P. , Fleming Jacob W. , Capel Andrew J. , Wheeler Patrick C. , Lewis Mark P.
Published: May 2020

Investigations of the human neuromuscular junction (NMJ) have predominately utilised experimental animals and model organisms. Consequently, there remains a paucity of data regarding the development of the human NMJ and a lack of systems that enable temporal investigation of the motor unit. This work addresses this need, providing the methodologies to bioengineer 3D models of the human motor unit. Separate maturation of primary human skeletal muscle and iPSC derived motor neurons seeks to accurately represent neuromuscular development via controlled addition of motor axons following primary myogenesis. Spheroid cultures of motor neuron progenitors augmented the transcription of OLIG2, ISLET1 and SMI32 motor neuron mRNAs ∼400, ∼150 and ∼200-fold respectively. Axon projections of adhered motor neuron spheroids exceeded 1000μm in monolayer, with transcription of SMI32 and VACHT mRNAs further enhanced in a concentration dependent manner within optimised 3D type I collagen extracellular matrices. Bioengineered skeletal muscles produce functional forces, demonstrate increased acetylcholine receptor (AChR) clustering, and transcription of MUSK and LRP4 mRNAs indicating enhanced organisation of the post-synaptic membrane. Dosed integration of motor neuron spheroids outlined the motor pool required to functionally innervate muscle tissues in 3D, generating physiologically functional human NMJs that evidence pre- and post-synaptic membrane and motor nerve terminal co-localisation. Spontaneous firing was significantly elevated in 3D motor units, confirmed to be driven by the motor nerve via antagonistic inhibition of the AChR. Finally, functional analyses outlined decreased time to peak twitch and half relaxation times, indicating enhanced physiology of excitation contraction coupling of NMJs within innervated motor units.
Ustilago maydisserves as a novel production host for the synthesis of plant and fungal sesquiterpenoids
Authors: Lee Jungho , Hilgers Fabienne , Loeschke Anita , Jaeger Karl-Erich , Feldbrügge Michael
Published: May 2020

Abtract

Sesquiterpenoids are important secondary metabolites with various pharma- and nutraceutical properties. In particular, higher basidiomycetes possess a versatile biosynthetic repertoire for these bioactive compounds. To date, only a few microbial production systems for fungal sesquiterpenoids have been established. Here, we introduceUstilago maydisas a novel production host. This model fungus is a close relative of higher basidiomycetes. It offers the advantage of metabolic compatibility and potential tolerance for substances toxic to other microorganisms. We successfully implemented a heterologous pathway to produce the carotenoid lycopene that served as a straightforward read-out for precursor pathway engineering. Overexpressing genes encoding enzymes of the mevalonate pathway resulted in increased lycopene levels. Verifying the subcellular localisation of the relevant enzymes revealed that initial metabolic reactions might take place in peroxisomes: despite the absence of a canonical peroxisomal targeting sequence, acetyl-CoA C-acetyltransferase Aat1 localised to peroxisomes. By expressing the plant (+)-valencene synthase CnVS and the basidiomycete sesquiterpenoid synthase Cop6, we succeeded in producing (+)-valencene and α-cuprenene, respectively. Importantly, the fungal compound yielded about tenfold higher titres in comparison to the plant substance. This proof of principle demonstrates thatU. maydiscan serve as promising novel chassis for the production of terpenoids.
Cooperative foraging during larval stage affects fitness inDrosophila
Authors: Dombrovski Mark , Kuhar Rives , Mitchell Alexandra , Shelton Hunter , Condron Barry
Published: May 2020

Cooperative behavior can confer advantages to animals. This is especially true for cooperative foraging which provides fitness benefits through more efficient acquisition and consumption of food. While examples of group foraging have been widely described, the principles governing formation of such aggregations and rules that determine group membership remain poorly understood. Here we take advantage of an experimental model system featuring cooperative foraging behavior inDrosophila. Under crowded conditions, fly larvae form coordinated digging groups (clusters), where individuals are linked together by sensory cues and group membership requires prior experience. However, fitness benefits ofDrosophilalarval clustering remain unknown. We demonstrate that animals raised in crowded conditions on food partially processed by other larvae experience a developmental delay presumably due to the decreased nutritional value of the substrate. Intriguingly, same conditions promote formation of cooperative foraging clusters which further extends larval stage compared to non-clustering animals. Remarkably, this developmental retardation also results in a relative increase in wing size, serving an indicator of adult fitness. Thus, we find that the clustering-induced developmental delay is accompanied by fitness benefits. Therefore, cooperative foraging, while delaying development, may have evolved to giveDrosophilalarvae benefits when presented with competition for limited food resources.
Fenchel duality of Cox partial likelihood and its application in survival kernel learning
Authors: Wilson Christopher M. , Li Kaiqiao , Sun Qiang , Kuan Pei Fen , Wang Xuefeng
Published: May 2020

The Cox proportional hazard model is the most widely used method in modeling time-to-event data in the health sciences. A common form of the loss function in machine learning for survival data is also mainly based on Cox partial likelihood function, due to its simplicity. However, the optimization problem becomes intractable when more complicated regularization is employed with the Cox loss function. In this paper, we show that a convex conjugate function of Cox loss function based on Fenchel Duality exists, and this provides an alternative framework to optimization based on the primal form. Furthermore, the dual form suggests an efficient algorithm for solving the kernel learning problem with censored survival outcomes. We illustrate the application of the derived duality form of Cox partial likelihood loss in the multiple kernel learning setting
Regulation of light harvesting in multimeric and monomeric photosystem II supercomplexes
Authors: Kim Eunchul , Watanabe Akimasa , Duffy Christopher D. P. , Ruban Alexander V. , Minagawa Jun
Published: May 2020

An intriguing architecture called ‘semi-crystalline photosystem II (PSII) array’ has been observed in the thylakoid membranes in vascular plants. It is an array of PSII–light harvesting complex II (LHCII) supercomplexes only appears in the low-light, whose functional role has not been clarified. We identified PSII–LHCII supercomplexes in their monomeric and multimeric forms in the low-light acclimated spinach leaves and prepared them using sucrose density gradient-ultracentrifugation in the presence of amphipol A8-35. When the leaves were acclimated to high-light, however, only monomeric forms were present. Single particle electron microscopy identified that the multimeric PSII–LHCII supercomplexes were composed of two (‘megacomplex’) or three (‘arraycomplex’) units of PSII–LHCII supercomplexes, which aligned like a fraction of the semi-crystalline array. Further characterization using fluorescence analysis revealed that multimeric forms have a higher light-harvesting capability, but a lower thermal dissipation capability than the monomeric form, suggesting such a configurational conversion of PSII–LHCII supercomplexes possibly serves as a structural basis for the plants’ acclimation to environmental light.
Dynamics of primitive streak regression controls the fate of neuro-mesodermal progenitors in the chicken embryo
Authors: Guillot Charlene , Michaut Arthur , Rabe Brian , Pourquié Olivier
Published: May 2020

In classical descriptions of vertebrate development, the segregation of the three embryonic germ layers is completed by the end of gastrulation. Body formation then proceeds in a head to tail fashion by progressive deposition of lineage committed progenitors during regression of the Primitive Streak (PS) and tail bud (Pasteels, 1937b; Stern, 2004). Identification of Neuro-Mesodermal Progenitors (NMPs) contributing to both musculo-skeletal precursors (paraxial mesoderm) and spinal cord during axis formation by retrospective clonal analysis challenged these notions (Henrique et al., 2015; Tzouanacou et al., 2009). However, in amniotes such as mouse and chicken, the precise identity and localization of these cells has remained unclear despite a wealth of fate mapping analyses of the PS region. Here, we use lineage tracing in the chicken embryo to show that single cells located in the SOX2/T positive anterior PS region contribute to both neural and mesodermal lineages in the trunk and tail, but only express this bipotential fate with some delay. We demonstrate that posterior to anterior gradients of convergence speed and ingression along the PS gradually lead to exhaustion of all mesodermal precursor territories except for NMPs where limited ingression and increased proliferation maintain and amplify this pool of axial progenitors. As a result, most of the remaining mesodermal precursors from the PS in the tail bud are bipotential NMPs. Together, our results provide a novel understanding of the contribution of the PS and tail bud to the formation of the body of amniote embryos.
Small-molecule sensitization of RecBCD helicase-nuclease to a Chi hotspot-activated state
Authors: Karabulut Ahmet C. , Cirz Ryan T. , Smith Gerald R.
Published: May 2020

Coordination of multiple activities of complex enzymes is critical for life, including transcribing, replicating, and repairing DNA. Bacterial RecBCD helicase-nuclease must coordinate DNA unwinding and cutting to repair broken DNA. Starting at a DNA end, RecBCD unwinds DNA with its fast RecD helicase on the 5’-ended strand and its slower RecB helicase on the 3’-ended strand. At Chi hotspots (5’GCTGGTGG3’), RecB’s nuclease cuts the 3’-ended strand and loads RecA strand-exchange protein onto it. We report here that a small molecule NSAC1003, a sulfanyltriazolobenzimidazole, mimics Chi sites by sensitizing RecBCD to cut DNA at a Chi-independent position a certain percent of the DNA substrate’s length. This percent decreases with increasing NSAC1003 concentration. Our data indicate that NSAC1003 slows RecB and sensitizes it to cut DNA when the leading helicase RecD stops at the DNA distal end. Two previously described RecBCD mutants altered in the RecB ATP-binding site also have this property, but uninhibited wild-type RecBCD lacks it. Computation docks NSAC1003 into the ATP-binding site, suggesting that NSAC1003 acts directly on RecB. NSAC1003 will help elucidate the molecular mechanisms of RecBCD-Chi regulation and DNA repair. Similar studies could help elucidate other DNA enzymes whose activities are coordinated at chromosomal sites.
Susceptibility trends of zoliflodacin against multidrug-resistantNeisseria gonorrhoeaeclinical isolates in Nanjing, China (2014-2018)
Authors: Le Wenjing , Su Xiaohong , Lou Xiangdi , Li Xuechun , Gong Xiangdong , Wang Baoxi , Genco Caroline A. , Mueller John P. , Rice Peter A.
Published: May 2020

Previously, we reported potent activity of a novel spiropyrimidinetrione, zoliflodacin, againstN. gonorrhoeaeisolates from symptomatic men in Nanjing, China, collected in 2013. Here, we investigated trends of susceptibilities of zoliflodacin in 986 gonococcal isolates collected from men between 2014 and 2018.N. gonorrhoeaeisolates were tested for susceptibility to zoliflodacin and seven other antibiotics. Mutations ingyrA, gyrB, parCandparEgenes were determined by PCR and DNA sequencing. The MIC of zoliflodacin forN. gonorrhoeaeranged from ≤0.002 to 0.25 mg/L; the overall MIC50s and MIC90s were 0.06 mg/L and 0.125mg/L in 2018, increasing two-fold from 2014. However, the percent of isolates with lower zoliflodacin MICs declined in each year sequentially while the percent with higher MICs increased yearly (P≤0.00001). All isolates were susceptible to spectinomycin but resistant to ciprofloxacin (MIC ≥1 μg/ml); 21.2% (209/986) were resistant to azithromycin (≥1 μg/ml), 43.4% (428/986) were penicillinase-producing (PPNG), 26.9% (265/986) tetracycline-resistant (TRNG) and 19.4% (191/986) were multi-drug resistant (MDR) isolates. Among 143 isolates with higher zoliflodacin MICs (0.125-0.25 mg/L), all had quinolone resistance associated double or triple mutations ingyrA; 139/143 (97.2%) also had mutations inparC. There were no D429N/A and/or K450T mutations in GyrB identified in the 143 isolates with higher zoliflodacin MICs; a S467N mutation in GyrB was identified in one isolate. We report that zoliflodacin has excellentin vitroactivity against clinical gonococcal isolates, including those with high-level resistance to ciprofloxacin, azithromycin and extended spectrum cephalosporins.
Early Short Course Corticosteroids in Hospitalized Patients with COVID-19
Authors: Fadel Raef , Morrison Austin R. , Vahia Amit , Smith Zachary R. , Chaudhry Zohra , Bhargava Pallavi , Miller Joseph , Kenney Rachel M. , Alangaden George , Ramesh Mayur S. ,   Henry Ford COVID-19 Management Task Force
Published: May 2020

Background

There is no proven antiviral or immunomodulatory therapy for COVID-19. The disease progression associated with the pro-inflammatory host response prompted us to examine the role of early corticosteroid therapy in patients with moderate to severe COVID-19.

Methods

We conducted a single pre-test, single post-test quasi-experiment in a multi-center health system in Michigan from March 12 to March 27, 2020. Adult patients with confirmed moderate to severe COVID were included. A protocol was implemented on March 20, 2020 using early, short-course, methylprednisolone 0.5 to 1 mg/kg/day divided in 2 intravenous doses for 3 days. Outcomes of pre and post-corticosteroid groups were evaluated. A composite endpoint of escalation of care from ward to ICU, new requirement for mechanical ventilation, and mortality was the primary outcome measure. All patients had at least 14 days of follow-up.

Results

We analyzed 213 eligible subjects, 81 (38%) and 132 (62%) in pre-and post-corticosteroid groups, respectively. The composite endpoint occurred at a significantly lower rate in post-corticosteroid group compared to pre-corticosteroid group (34.9% vs. 54.3%, p=0.005). This treatment effect was observed within each individual component of the composite endpoint. Significant reduction in median hospital length of stay was observed in the post-corticosteroid group (8 vs. 5 days, p < 0.001). Multivariate regression analysis demonstrated an independent reduction in the composite endpoint at 14-days controlling for other factors (aOR: 0.45; 95% CI [0.25 – 0.81]).

Conclusion

An early short course of methylprednisolone in patients with moderate to severe COVID-19 reduced escalation of care and improved clinical outcomes.

In this multi-center quasi-experimental study of 213 patients, we demonstrate early short course of methylprednisolone in moderate to severe COVID-19 patients reduced the composite endpoint of escalation of care from ward to ICU, new requirement for mechanical ventilation, and mortality.
MALVIRUS: an integrated web application for viral variant calling
Authors: Ciccolella Simone , Denti Luca , Bonizzoni Paola , Vedova Gianluca Della , Pirola Yuri , Previtali Marco
Published: May 2020

Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in order to track the spread of the viral strains across the globe.

We present MALVIRUS, an easy-to-install and easy-to-use web application that assists users in two tasks:

computing a variant catalog consisting in a set of population SNP loci from the population sequences and

efficiently calling variants of the catalog from a read sample.

Tests on Illumina and Nanopore samples prove the efficiency and the effectiveness of MALVIRUS in genotyping SARS-CoV-2 strain samples with respect to GISAID data.
How strategy environment and wealth shape altruistic behaviour: Cooperation rules affecting wealth distribution in dynamic networks
Authors: Pathak Spandan , Verma Prateek , Ram Sumit K. , Sengupta Supratim
Published: May 2020

Societies rely on individual contributions to sustain public goods that benefit the entire community. Several mechanisms, that specify how individuals change their decisions based on past experiences, have been proposed to explain how altruists are not outcompeted by selfish counterparts. A key aspect of such strategy updates involves a comparison of an individual’s latest payoff with that of a random neighbour. In reality, both the economic and social milieu often shapes cooperative behaviour. We propose a new decision heuristic, where the propensity of an individual to cooperate depends on the local strategy environment in which she is embedded as well as her wealth relative to that of her neighbours. Our decision-making model allows cooperation to be sustained and also explains the results of recent experiments on social dilemmas in dynamic networks. Final cooperation levels depend only on the extent to which the strategy environment influences altruistic behaviour but are largely unaffected by network restructuring. However, the extent of wealth inequality in the community is affected by a subtle interplay between the environmental influence on a person’s decision to contribute and the likelihood of reshaping social ties, with wealth-inequality levels rising with increasing likelihood of network restructuring in some situations.
Type III interferons disrupt the lung epithelial barrier upon viral recognition
Authors: Broggi Achille , Ghosh Sreya , Sposito Benedetta , Spreafico Roberto , Balzarini Fabio , Lo Cascio Antonino , Clementi Nicola , De Santis Maria , Mancini Nicasio , Granucci Francesca , Zanoni Ivan
Published: May 2020

Lower respiratory tract infections are a leading cause of mortality driven by infectious agents. RNA viruses such as influenza virus, respiratory syncytial virus and the new pandemic coronavirus SARS-CoV-2 can be highly pathogenic. Clinical and experimental evidence indicate that most severe and lethal cases do not depend on the viral burden and are, instead, characterized by an aberrant immune response. In this work we assessed how the innate immune response contributes to the pathogenesis of RNA virus infections. We demonstrate that type III interferons produced by dendritic cells in the lung in response to viral recognition cause barrier damage and compromise the host tissue tolerance. In particular, type III interferons inhibit tissue repair and lung epithelial cell proliferation, causing susceptibility to lethal bacterial superinfections. Overall, our data give a strong mandate to rethink the pathophysiological roles of this group of interferons and their possible use in the clinical practice against endemic as well as emerging viral infections.
Reducing uncertainty in impact assessments for alien species
Authors: Clarke David A. , Palmer David J. , McGrannachan Chris , Burgess Treena I. , Chown Steven L. , Clarke Rohan H. , Kumschick Sabrina , Lach Lori , Leibhold Andrew M. , Roy Helen E. , Saunders Manu E. , Yeates David K. , Zalucki Myron P. , McGeoch Melodie A.
Published: May 2020

Impact assessment is a widely used and cost-effective tool for prioritising invasive alien species. With the number of alien and invasive alien species expected to increase, reliance on impact assessment tools for the identification of species that pose the greatest threats will continue to grow. Given the importance of such assessments for management and resource allocation, it is critical to understand the uncertainty involved and what effect this may have on the outcome. Using an uncertainty typology and insects as a model taxon, we identified and classified the sources and types of uncertainty when performing impact assessments on alien species. We assessed 100 alien insect species across two rounds of assessments with each species independently assessed by two assessors. Agreement between assessors was relatively low for all three EICAT components (mechanism, severity, confidence) after the first round. For the second round, we revised guidelines and gave assessors access to each other’s assessments which improved agreement by between 20-30%. Of the 12 potential reasons for assessment discrepancies identifieda priori, 11 occurred. The most frequent sources (andtypes) of uncertainty (i.e. differences between assessment outcomes for the same species) were: incomplete information searches (systematic error), unclear mechanism and/or extent of impact (subjective judgment due to a lack of knowledge), and limitations of the assessment framework (context dependence). In response to these findings, we identify actions to reduce uncertainty in the impact assessment process, particularly for assessing speciose taxa with diverse life histories such as Insecta. Evidence of environmental impact was available for most insect species, and (of the non-random original subset of species assessed) 14 or 29% of those with evidence were identified as high impact species (with either ‘Major’ or ‘Massive’ impact). Although uncertainty in risk assessment, including impact assessments, can never be eliminated, identifying and communicating its source and variety is a first step toward its reduction and a more reliable assessment outcome, regardless of the taxa being assessed.
Positive feedback induces switch between distributive and processive phosphorylation of Hog1
Authors: Mosbacher Maximilian , Lee Sung Sik , Peter Matthias , Claassen Manfred
Published: May 2020

Cellular decision making often builds on ultrasensitive MAPK pathways. The phosphorylation mechanism of MAP kinase has so far been described as either distributive or processive, with distributive mechanisms generating ultrasensitivity in theoretical analyses. However, thein vivomechanism of MAP kinase phosphorylation and its regulation by feedback loops remain unclear. We thus characterized the regulation of the MAP kinase Hog1 inSaccharomyces cerevisiae, which is transiently activated in response to hyperosmolarity. Specifically, we combined Hog1 activation data from different modalities and multiple conditions. We constructed ODE models with different pathway topologies, which were then assessedviaparameter estimation and model selection. Interestingly, our best fitting model switches between distributive and processive phosphorylation behavior via a positive feedback loop targeting the MAP kinase-kinase Pbs2. Simulations further suggest that this mixed mechanism is required not only for full sensitivity to stimuli, but also to ensure robustness to different perturbations.