bluuebunny/crossref_metadata_2025 huggingface dataset:
Pretransplant Hypoalbuminemia As A Predictor of Medical Arterial Calcification During Waiting List Pre‐Kidney Transplant Period: A Propensity Score Weighting Analysis
Authors: Tantisattamo Ekamol , Leelaviwat Natnicha , Lopimpisuth Chawit , Saowapa Sakditad , Polpichai Natchaya , Vutthikraivit Possawat
Published: April 2020

Introduction

Medial arterial calcification (MAC) is common in advanced chronic kidney disease and end‐stage renal disease. Whether serum albumin as a surrogate marker of inadequate dialysis is associated with MAC is unknown.

Methods

Since breast arterial calcification is exclusively medial, mammogram was used to identify MAC. Renal transplant recipients (RTR) with MG during pretransplant period was divided into 2 groups: pretransplant normoalbuminemia and hypoalbuminemia (serum albumin <4 g/dL). Baseline characteristics including potential confounders were balanced by propensity score weighting(PSW). Association between serum albumin status and MAC during pretransplant period is examined by multiple logistic regression.

Results

Of 51 RTR, mean age±SD was 57±10.5 years old and the majority were white 28 (54%) followed by African American 18 (35%) and others 5 (9%) patients. Five patients never been on dialysis and 34 patients had dialysis (29 with hemodialysis and 5 with peritoneal dialysis) with a median time of dialysis prior to kidney transplantation was 3.79 years (0.72 to 20.38 years). Among 34 patients with hypoalbuminemia, 16 patients had MAC; whereas only 4 out of 17 patients in normoalbuminemia had MAC (47.06% vs. 23.53%, p 0.135). Mean serum albumin were 3.3±0.6 and 4.2±0.2 g/dL in hypoalbuminemic and normoalbuminemic groups, respectively (p <0.001). Baseline characteristics and potential confounders including age, race, cause of kidney diseases, dialysis modalities, pretransplant obesity status, diabetes, corrected calcium, and phosphorus were balanced by using PSW with generalized boosted modeling (Figure
and
). Hypoalbuminemic group had 3.09 times higher the odds of having MAC compared to normoalbuminemic group, but the association was not significant (OR 3.09; 95%CI 0.62 to 15.41). By using multiple logistic regression with adjustment for co‐variated used in the PSW, the magnitude of the association became significant with a 75.55 times greater the odds of MAC in hypoalbuminemic group compared to normoalbuminemic group (OR 75.55; 95%CI 1.42 to 4013.69).

Conclusions

Not only being one of the surrogate markers of malnutrition and inadequate dialysis, hypoalbuminemia is also associated with MAC in well‐matched study population using PSW. Since MAC is associated with higher mortality in RTR, hypoalbuminemia during pretransplantation should be corrected to improve posttransplant outcomes.

Love plot estimating propensity score weights using generalized boosted modeling with balancing covariates

Figure 1

Histogram estimating propensity score weights using generalized boosted modeling with balancing covariates

Figure 2
Integrating hands‐on model building with graded online discussions to learn DNA structure‐function relationships in an upper level General Biochemistry course for majors
Authors: Hite Kristopher Charles
Published: April 2020

An active‐learning DNA structure/function exercise was undertaken in a 4000‐level majors biochemistry course. During the fourth in‐person class period of the spring 2020 semester majors enrolled in a three‐credit General Biochemistry course were asked to build a physical model of DNA consisting of one turn of the helix including 10 base‐pairs. Students were told to self‐associate into groups of six and each group was then instructed to build a specific base‐pair: 5 groups were assigned GC, 5 were assigned AT. Students were further instructed to divide the labor by partnerships, one to build a purine base, another to build the complementary pyrimidine, and the third to build the sugar‐phosphate. The class was provided with large bundles of six different brightly colored pipe‐cleaners, a bamboo skewer to use as an in‐plane scaffold for the base‐pairs, a large ring stand, and 10 perpendicular rod clamps. They were then given 10 minutes to build their respective base‐pairs then the last five minutes to work together as a class to assemble a single model. The instructor and many students photographed the model and uploaded image files to the online learning platform accompanied by the following prompt.

“How much information can we obtain from the admittedly incomplete model we built in class today? Examine the photograph and see if you can decipher the sequence on the two strands. We know adenine is yellow, thymine is purple, guanine is orange, and cytosine is blue. If this sequence were part of a gene which amino acids might they encode? What information would help us answer these questions more precisely? Feel free to share any photos you took during class in replies to this post. You may opt‐out of any one of the next three weekly graded discussions by building your own improved, more beautiful model using the same starting materials for equal credit.”

This exercise incorporates multiple active‐learning techniques simultaneously including elements of “think‐pair‐share” during the initial partnership phase, small group work during the assembly of the mononucleotides, and large group cooperation during final assembly of the model. The online follow‐up discussion and optional model‐refinement assignment allow individualized student‐driven engagement with the structure of DNA and how it works to store genetic information.

Support or Funding Information

Department of Biochemistry College of Agriculture and Life Sciences at Virginia Polytechnic and State University (Virginia Tech)

A single turn of the DNA double‐helix: a physical model cooperatively created by students in a 4000 level General Biochemistry course as part of an active‐learning exercise. Model built with large ring stand, 10 perpendicular rod clamps, brighlty‐colored pipe‐cleaners, bamboo skewers, and small plastic beads.

Figure 1
Predation risks of signalling and searching: bats prefer moving katydids
Authors: Geipel Inga , Kernan Ciara E. , Litterer Amber S. , Carter Gerald G. , Page Rachel A. , ter Hofstede Hannah M.
Published: April 2020

Males signalling their attractiveness to females are at risk from predators that exploit mating signals to detect and locate prey. Signalling, however, is not the only risky activity in sexual interactions: mate searching can incur risk as well. Male Neotropical pseudophylline katydids produce both acoustic and vibrational signals (tremulations). Females reply to male signals with tremulations of their own, and both sexes walk to find one another. We asked if movement increases predation risk, and whether tremulation or walking was more attractive to predators. We offered the Neotropical gleaning batMicronycteris microtisa series of two-choice tests, presenting the bats with katydid models that were motionless or moved in a way to mimic either tremulating or walking. We found that prey movements do put prey at risk. AlthoughM. microtiscan detect motionless prey on leaves, they preferred moving prey. Our study shows that movement can put searching or signalling prey in danger, potentially explaining why silent female katydids are frequently consumed by gleaning bats.
James Petiver's 1717
Papilionum Britanniae
: an analysis of the first comprehensive account of British butterflies (Lepidoptera: Papilionoidea)
Authors: Vane-Wright Richard I.
Published: April 2020

Although the contributions of James Petiver to the early development of systematic natural history are widely acknowledged, he is often criticized for scientific, curatorial and even social shortcomings. This rather dubious reputation is at odds with his standing among entomologists as ‘the father of British butterflies’. Shortly before his death in 1718, Petiver published a densely packed eight-page pamphlet entitled
Papilionum Britanniae
. Analysis of this work, which at first sight makes an apparently exaggerated claim of accounting for ‘above eighty English butterflies’, reveals that Petiver was an original, perceptive and truly systematic entomologist, in several important respects ahead of his time.
Modelling and forecasting art movements with CGANs
Authors: Lisi Edoardo , Malekzadeh Mohammad , Haddadi Hamed , Lau F. Din-Houn , Flaxman Seth
Published: April 2020

Conditional generative adversarial networks (CGANs) are a recent and popular method for generating samples from a probability distribution conditioned on latent information. The latent information often comes in the form of a discrete label from a small set. We propose a novel method for training CGANs which allows us to condition on a sequence of continuous latent distributions
f
(1)
, …,
f

(
K
)

. This training allows CGANs to generate samples from a sequence of distributions. We apply our method to paintings from a sequence of artistic movements, where each movement is considered to be its own distribution. Exploiting the temporal aspect of the data, a vector autoregressive (VAR) model is fitted to the means of the latent distributions that we learn, and used for one-step-ahead forecasting, to predict the latent distribution of a future art movement
f

(
K
+1)

. Realizations from this distribution can be used by the CGAN to generate ‘future’ paintings. In experiments, this novel methodology generates accurate predictions of the evolution of art. The training set consists of a large dataset of past paintings. While there is no agreement on exactly what current art period we find ourselves in, we test on plausible candidate sets of present art, and show that the mean distance to our predictions is small.
Effects of trading networks on the risk of bovine tuberculosis incidents on cattle farms in Great Britain
Authors: Fielding Helen R. , McKinley Trevelyan J. , Delahay Richard J. , Silk Matthew J. , McDonald Robbie A.
Published: April 2020

Trading animals between farms and via markets can provide a conduit for spread of infections. By studying trading networks, we might better understand the dynamics of livestock diseases. We constructed ingoing contact chains of cattle farms in Great Britain that were linked by trading, to elucidate potential pathways for the transmission of infection and to evaluate their effect on the risk of a farm experiencing a bovine tuberculosis (bTB) incident. Our findings are consistent with variation in bTB risk associated with region, herd size, disease risk area and history of previous bTB incidents on the root farm and nearby farms. However, we also identified effects of both direct and indirect trading patterns, such that connections to more farms in the England High-Risk Area up to three movements away from the root farm increased the odds of a bTB incident, while connections with more farms in the England Low-Risk Area up to eight movements away decreased the odds. Relative to other risk factors for bTB, trading behaviours are arguably more amenable to change, and consideration of risks associated with indirect trading, as well direct trading, might therefore offer an additional approach to bTB control in Great Britain.
Experimental study of shear and hydraulic bonding strength between casing and cement under complex temperature and pressure conditions
Authors: Yang Huanqiang , Fu Qi , Wu Jiang , Qu Lulu , Xiong Dong , Liu Yang
Published: April 2020

The cement sheath plays a vital role in preventing gas channelling. It is important to understand the interfacial bonding between the casing and cement sheath when the downhole temperature and pressure change. This paper demonstrates the results of an experimental study to investigate the effect of high temperature and high pressure and their variations on the cement sheath interfacial bonding strength (CSIBS). An experimental device was developed that is used to test the shear and hydraulic bonding strength with the method of uniaxial compression and gas channelling. The results show that both temperature and pressure have a significant influence on the CSIBS. As the curing temperature increases with a constant curing time or as the curing time increases with a constant curing temperature, the CSIBS first increases and then converges to a stable value. The casing roughness has a crucial effect on the shear bonding strength but little effect on the hydraulic bonding strength. Though the CSIBS decreases obviously with the decrease in temperature, it undergoes little change when the temperature first increases and then recovers to the initial value. When the internal casing pressure decreases to a certain value or first increases to a certain value followed by recovery to the initial state, the hydraulic bonding strength tends to be 0 MPa, which means that the interface undergoes debonding between the casing and cement.
Bleaching-driven reef community shifts drive pulses of increased reef sediment generation
Authors: Perry Chris T. , Morgan Kyle M. , Lange Ines D. , Yarlett Robert T.
Published: April 2020

The ecological impacts of coral bleaching on reef communities are well documented, but resultant impacts upon reef-derived sediment supply are poorly quantified. This is an important knowledge gap because these biogenic sediments underpin shoreline and reef island maintenance. Here, we explore the impacts of the 2016 bleaching event on sediment generation by two dominant sediment producers (parrotfish and
Halimeda
spp.) on southern Maldivian reefs. Our data identifies two pulses of increased sediment generation in the 3 years since bleaching. The first occurred within approximately six months after bleaching as parrotfish biomass and resultant erosion rates increased, probably in response to enhanced food availability. The second pulse occurred 1 to 3 years post-bleaching, after further increases in parrotfish biomass and a major (approx. fourfold) increase in
Halimeda
spp. abundance. Total estimated sediment generation from these two producers increased from approximately 0.5 kg CaCO
3
m
−2
yr
−1
(pre-bleaching; 2016) to approximately 3.7 kg CaCO
3
m
−2
yr
−1
(post-bleaching; 2019), highlighting the strong links between reef ecology and sediment generation. However, the relevance of this sediment for shoreline maintenance probably diverges with each producer group, with parrotfish-derived sediment a more appropriate size fraction to potentially contribute to local island shorelines.
Trajectory construction of Dirac evolution
Authors: Holland Peter
Published: April 2020

We extend our programme of representing the quantum state through exact stand-alone trajectory models to the Dirac equation. We show that the free Dirac equation in the angular coordinate representation is a continuity equation for which the real and imaginary parts of the wave function, angular versions of Majorana spinors, define conserved densities. We hence deduce an exact formula for the propagation of the Dirac spinor derived from the self-contained first-order dynamics of two sets of trajectories in 3-space together with a mass-dependent evolution operator. The Lorentz covariance of the trajectory equations is established by invoking the ‘relativity of the trajectory label'. We show how these results extend to the inclusion of external potentials. We further show that the angular version of Dirac's equation implies continuity equations for currents with non-negative densities, for which the Dirac current defines the mean flow. This provides an alternative trajectory construction of free evolution. Finally, we examine the polar representation of the Dirac equation, which also implies a non-negative conserved density but does not map into a stand-alone trajectory theory. It reveals how the quantum potential is tacit in the Dirac equation.
Magnetic reconnection in partially ionized plasmas
Authors: Ni Lei , Ji Hantao , Murphy Nicholas A. , Jara-Almonte Jonathan
Published: April 2020

Magnetic reconnection has been intensively studied in fully ionized plasmas. However, plasmas are often partially ionized in astrophysical environments. The interactions between the neutral particles and ionized plasmas might strongly affect the reconnection mechanisms. We review magnetic reconnection in partially ionized plasmas in different environments from theoretical, numerical, observational and experimental points of view. We focus on mechanisms which make magnetic reconnection fast enough to compare with observations, especially on the reconnection events in the low solar atmosphere. The heating mechanisms and the related observational evidence of the reconnection process in the partially ionized low solar atmosphere are also discussed. We describe magnetic reconnection in weakly ionized astrophysical environments, including the interstellar medium and protostellar discs. We present recent achievements about fast reconnection in laboratory experiments for partially ionized plasmas.
Social norms and cultural diversity in the development of third-party punishment
Authors: House Bailey R. , Kanngiesser Patricia , Barrett H. Clark , Yilmaz Süheyla , Smith Andrew Marcus , Sebastian-Enesco Carla , Erut Alejandro , Silk Joan B.
Published: April 2020

Human cooperation is probably supported by our tendency to punish selfishness in others. Social norms play an important role in motivating third-party punishment (TPP), and also in explaining societal differences in prosocial behaviour. However, there has been little work directly linking social norms to the development of TPP across societies. In this study, we explored the impact of normative information on the development of TPP in 603 children aged 4–14, across six diverse societies. Children began to perform TPP during middle childhood, and the developmental trajectories of this behaviour were similar across societies. We also found that social norms began to influence the likelihood of performing TPP during middle childhood in some of these societies. Norms specifying the punishment of selfishness were generally more influential than norms specifying the punishment of prosocial behaviour. These findings support the view that TPP of selfishness is important in all societies, and its development is shaped by a shared psychology for responding to normative information. Yet, the results also highlight the important role that children's prior knowledge of local norms may play in explaining societal variation in the development of both TPP and prosociality.
Negative associations between parasite avoidance, resistance and tolerance predict host health in salmonid fish populations
Authors: Klemme Ines , Hyvärinen Pekka , Karvonen Anssi
Published: April 2020

Genetic variation in defence against parasite infections is fundamental for host–parasite evolution. The overall level of defence of a host individual or population includes mechanisms that reduce parasite exposure (avoidance), establishment (resistance) or pathogenicity (tolerance). However, how these traits operate and evolve in concert is not well understood. Here, we investigated genetic variation in and associations between avoidance, resistance and tolerance in a natural host–parasite system. Replicated populations of Atlantic salmon (Salmo salar) and sea trout (an anadromous form of brown trout,Salmo trutta) were raised under common garden conditions and infected with the eye flukeDiplostomum pseudospathaceum. We demonstrate significant genetic variation in the defence traits across host populations and negative associations between the traits, with the most resistant populations showing the weakest avoidance and the lowest infection tolerance. These results are suggestive of trade-offs between different components of defence and possibly underlie the genetic variation in defence traits observed in the wild. Because the three defence mechanisms affect host–parasite evolution in profoundly different ways, we emphasize the importance of studying these traits in concert.
Epidemiological and Genomic Analysis of SARS-CoV-2 in Ten Patients from a Mid-sized City outside of Hubei, China
Authors: Chen Jinkun , Hilt Evann E. , Wu Huan , Jiang Zhuojing , Zhang QinChao , Wang JiLing , Wang Yifang , Li Fan , Li Ziqin , Tang Jialiang , Yang Shangxin
Published: April 2020

A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing COVID-19 pandemic. In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from ten patients in Shaoxing, a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020). We obtained viral genomes with > 99% coverage and a mean depth of 296X demonstrating that viral genomic analysis is feasible via metagenomics sequencing directly on nasopharyngeal samples with SARS-CoV-2 Real-time PCR Ct values less than 28. We found that a cluster of 4 patients with travel history to Hubei shared the exact same virus with patients from Wuhan, Taiwan, Belgium and Australia, highlighting how quickly this virus spread to the globe. The virus from another cluster of two family members living together without travel history but with a sick contact of a confirmed case from another city outside of Hubei accumulated significantly more mutations (9 SNPs vs average 4 SNPs), suggesting a complex and dynamic nature of this outbreak. We also found 70% patients in this study had the S genotype, consistent with an early study showing a higher prevalence of genotype out of Hubei than that inside Hubei. We calculated an average mutation rate of 1.37×10−3 nucleotide substitution per site per year, which is similar to that of other coronaviruses. Our findings add to the growing knowledge of the epidemiological and genomic characteristics of SARS-CoV-2 that are important for guiding outbreak containment and vaccine development. The moderate mutation rate of this virus also lends hope that development of an effective, long-lasting vaccine may be possible.
Impact of non-pharmaceutical interventions on documented cases of COVID-19
Authors: Banholzer Nicolas , van Weenen Eva , Kratzwald Bernhard , Seeliger Arne , Tschernutter Daniel , Bottrighi Pierluigi , Cenedese Alberto , Salles Joan Puig , Vach Werner , Feuerriegel Stefan
Published: April 2020

Background

The novel coronavirus (SARS-CoV-2) has rapidly evolved into a global epidemic. To control its spread, countries have implemented non-pharmaceutical interventions (NPIs), such as school or border closures, while others have even enforced complete lockdowns. Here we study the impact of NPIs in reducing documented cases of COVID-19. Documented case numbers are selected because they are essential for decision-makers in the area of health-policy when monitoring and evaluating current control mechanisms.

Methods

We empirically estimate the relative reduction in the number of new cases attributed to each NPI. A cross-country analysis is performed using documented cases through April 15, 2020 from n = 20 countries (i.e., the United States, Canada, Australia, the EU-15 countries, Norway, and Switzerland).

Results

As of April 15, venue closures were associated with a reduction in the number of new cases by 36 % (95% credible interval [CrI] 20–48 %), closely followed by gathering bans (34 %; 95% CrI 21–45 %), border closures (31 %; 95% CrI 19–42 %), and work bans on non-essential business activities (31 %; 95% CrI 16–44 %). Event bans lead to a slightly less pronounced reduction (23 %; 95% CrI 8–35 %). School closures (8 %; 95% CrI 0–23 %) and lockdowns (5 %; 95% CrI 0–14 %) appeared to be the least effective among the NPIs considered in this analysis.

Conclusions

With this cross-country analysis, we provide early estimates regarding the impact of different NPIs for controlling the COVID-19 epidemic. These findings are relevant for evaluating current health-policies.
Diagnosis and Prediction Model for COVID-19 Patient’s Response to Treatment based on Convolutional Neural Networks and Whale Optimization Algorithm Using CT Images
Authors: Elghamrawy Sally , Hassanien Aboul Ella
Published: April 2020

The outbreak of coronavirus diseases (COVID-19) has rabidly spread all over the world. The World Health Organization (WHO) has announced that coronavirus COVID-19 is an international pandemic. The Real-Time Reverse transcription-polymerase Chain Reaction (RT-PCR) has a low positive and sensitivity rate in the early stage of COVID-19. As a result, the Computed Tomography (CT) imaging is used for diagnosing. COVID-19 has different key signs on a CT scan differ from other viral pneumonia. These signs include ground-glass opacities, consolidations, and crazy paving. In this paper, an Artificial Intelli-gence-inspired Model for COVID-19 Diagnosis and Prediction for Patient Response to Treatment (AIMDP) is proposed. AIMDP model has two main functions reflected in two proposed modules, namely, the Diagnosis Module (DM) and Prediction Module (PM). The Diagnosis Module (DM) is proposed for early and accurately detecting the patients with COVID-19 and distinguish it from other viral pneumonias using COVID-19 signs obtained from CT scans. The DM model, uses Convolutional Neural Networks (CNNs) as a Deep learning technique for segmentation, can process hundreds of CT images in seconds to speed up diagnosis of COVID-19 and contribute in its containment. In addition, some countries haven’t the ability to provide all patients with the treatment and intensive care services, so it will be mandatory to give treatment to only responding patients. In this context, the Prediction Module (PM) is proposed for predicting the ability of the patient to respond to treatment based on different factors e.g. age, infection stage, respiratory failure, multi-organ failure and the treatment regimens. PM implement the Whale Optimization Algorithm for selecting the most relevant patient’s features. The experimental results show promising performance for the proposed diagnosing and prediction modules, using a dataset with hundreds of real data and CT images.
Susceptibility and Sustainability of India against CoVid19: a multivariate approach
Authors: Ray Soumi , Roy Mitu
Published: April 2020

Purpose

We are currently in the middle of a global crisis. Covid19 pandemic has suddenly threatened the existence of human life. Till date, as no medicine or vaccine is discovered, the best way to fight against this pandemic is prevention. The impact of different environmental, social, economic and health parameters is unknown and under research. It is important to identify the factors which can weaken the virus, and the nations which are more vulnerable to this virus.

Materials and Methods

Data of weather, vaccination trends, life expectancy, lung disease, number of infected people in the pre-lockdown and post-lockdown period of highly infected nations are collected. These are extracted from authentic online resources and published reports. Analysis is done to find the possible impact of each parameter on CoVid19.

Results

CoVid19 has no linear correlation with any of the selected parameters, though few parameters have depicted non-linear relationship in the graphs. Further investigations have shown better result for some parameters. A combination of the parameters results in a better correlation with infection rate.

Conclusions

Though depending on the study outcome, the impact of CoVid19 in India can be predicted, the required lockdown period cannot be calculated due to data limitation.
FALSE-NEGATIVE RESULTS OF INITIAL RT-PCR ASSAYS FOR COVID-19: A SYSTEMATIC REVIEW
Authors: Arevalo-Rodriguez Ingrid , Buitrago-Garcia Diana , Simancas-Racines Daniel , Zambrano-Achig Paula , Campo Rosa Del , Ciapponi Agustín , Sued Omar , Martínez-García Laura , Rutjes Anne , Low Nicola , Bossuyt Patrick M. , Perez-Molina Jose A , Zamora Javier
Published: April 2020

Background

A false-negative case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) infection is defined as a person with suspected infection and an initial negative result by reverse transcription-polymerase chain reaction (RT-PCR) test, with a positive result on a subsequent test. False-negative cases have important implications for isolation and risk of transmission of infected people and for the management of coronavirus disease 2019 (COVID-19). We aimed to review and critically appraise evidence about the rate of RT-PCR false-negatives at initial testing for COVID-19.

Methods

We searched MEDLINE, EMBASE, LILACS, as well as COVID-19 repositories including the EPPI-Centre living systematic map of evidence about COVID-19 and the Coronavirus Open Access Project living evidence database. Two authors independently screened and selected studies according to the eligibility criteria and collected data from the included studies. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the proportion of false-negative test results with the corresponding 95% CI using a multilevel mixed-effect logistic regression model. The certainty of the evidence about false- negative cases was rated using the GRADE approach for tests and strategies. All information in this article is current up to July 17, 2020.

Results

We included 34 studies enrolling 12,057 COVID-19 confirmed cases. All studies were affected by several risks of bias and applicability concerns. The pooled estimate of false-negative proportion was highly affected by unexplained heterogeneity (tau-squared= 1.39; 90% prediction interval from 0.02 to 0.54). The certainty of the evidence was judged as very low, due to the risk of bias, indirectness, and inconsistency issues.

Conclusions

There is a substantial and largely unexplained heterogeneity in the proportion of false-negative RT-PCR results. The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability. Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-CoV-2 infection given that up to 54% of COVID-19 patients may have an initial false-negative RT-PCR (certainty of evidence: very low). An update of this review when additional studies become available is warranted.

Systematic review registration

Protocol available on the OSF website:https://osf.io/gp38w/
Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency
Authors: Ghosh Arindam , Som Anup
Published: April 2020

Pluripotent stem cells (PSCs) have been observed to occur in two distinct states — naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layersin vitrobut differ in their potential to generate germline chimerain vivo.Understanding the molecular mechanisms that govern these two states of pluripotency in human can open up a plethora of opportunities for studying early embryonic development and in biomedical applications. In this work, we use weighted gene co-expression network (WGCN) approach to identify the key molecular makers and their interactions that define the two distinct pluripotency states. Signed-hybrid WGCN was reconstructed from transcriptomic data (RNA-seq) of naive and primed state pluripotent samples. Our analysis revealed two sets of genes that are involved in establishment and maintenance of naive (4791 genes) and primed (5066 genes) states. The naive state genes were found to be enriched for biological processes and pathways related to metabolic processes while primed state genes were associated with system development. Further, we identified the top 10% genes by intra-modular connectivity as hubs and the hub transcription factors for each group, thus providing a three-tier list of genes associated with naive and primed states of pluripotency in human.

HIGHLIGHTS

Weighted gene co-expression network analysis (WGCNA) identified 4791 and 5066 genes to be involved in naive and primed states of human pluripotency respectively.

Functional and pathway enrichment analysis revealed the naive genes were mostly related to metabolic processes and primed genes to system development.

The top 10% genes based on intra-modular connectivity from each group were defined as hubs.

Identified 52 and 33 transcription factors among the naive and primed module hubs respectively.

The transcription factors might play a switch on-off mechanism in induction of the two pluripotent states.
Histopathology and Ultrastructural Findings of Fatal COVID-19 Infections
Authors: Bradley Benjamin T. , Maioli Heather , Johnston Robert , Chaudhry Irfan , Fink Susan L. , Xu Haodong , Najafian Behzad , Marshall Desiree , Lacy J. Matthew , Williams Timothy , Yarid Nicole
Published: April 2020

Background

SARS-CoV-2 is the cause of an ongoing pandemic with a projected 100,000 to 240,000 U.S. deaths. To date, documentation of histopathologic features in fatal cases of COVID-19 has been limited due to small sample size and incomplete organ sampling.

Methods

Post-mortem examinations were performed on 12 fatal COVID-19 cases in Washington State during February-March 2020. Clinical and laboratory data were reviewed. Tissue examination of all major organs was performed by light microscopy and electron microscopy. The presence of viral RNA in sampled tissues was tested by RT-PCR.

Results

All 12 patients were older with significant preexisting comorbidities. The major pulmonary finding was diffuse alveolar damage in the acute and/or organizing phases with virus identified in type I and II pneumocytes by electron microscopy. The kidney demonstrated viral particles in the tubular epithelium, endothelium, and podocytes without significant inflammation. Viral particles were also observed in the trachea and large intestines. SARS-CoV-2 RNA was detected in the cardiac tissue of a patient with lymphocytic myocarditis. RT-PCR also detected viral RNA in the subcarinal lymph nodes, liver, spleen, and large intestines.

Conclusion

SARS-CoV-2 represents the third novel coronavirus to cause widespread human disease since 2002. Similar to SARS and MERS, the primary pathology was diffuse alveolar damage with virus located in the pneumocytes. However, other major organs including the heart and kidneys may be susceptible to viral replication and damage leading to increased mortality in those with disseminated disease. Understanding the pathology of SARS-CoV-2 will be essential to design effective therapies.
Connectivity establishes spatial readout of visual looming in a glomerulus lacking retinotopy
Authors: Morimoto Mai M. , Nern Aljoscha , Zhao Arthur , Rogers Edward M. , Wong Allan M. , Isaacson Mathew D. , Bock Davi D. , Rubin Gerald M. , Reiser Michael B.
Published: April 2020

Visual systems can exploit spatial correlations in the visual scene by using retinotopy, the organizing principle by which neighboring cells encode neighboring spatial locations. However, retinotopy is often lost, such as when visual pathways are integrated with other sensory modalities. How is spatial information processed in the absence of retinotopy? Here, we focused on visual looming responsive LC6 cells in Drosophila, a population whose dendrites collectively tile the visual field, but whose axons form a single glomerulus—a structure lacking retinotopic organization—in the central brain. We identified multiple glomerulus neurons and found that they respond to looming in different portions of the visual field, unexpectedly preserving spatial information. Through EM reconstruction of all LC6 synaptic inputs to the glomerulus, we found that LC6 and downstream cell types form circuits within the glomerulus that establish spatial readout of visual features and contralateral suppression—mechanisms that transform visual information for behavioral control.
JARID2 and AEBP2 regulate PRC2 activity in the presence of H2A ubiquitination or other histone modifications
Authors: Kasinath Vignesh , Beck Curtis , Sauer Paul , Poepsel Simon , Kosmatka Jennifer , Faini Marco , Toso Dan , Aebersold Ruedi , Nogales Eva
Published: April 2020

The Polycomb repressive complexes PRC1 and PRC2 functionally interact to coordinate cell type identity by the epigenetic regulation of gene expression. It has been proposed that PRC2 is recruited to genomic loci via the recognition of PRC1-mediated mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub1), but the mechanism of this process remains poorly understood. Here, we report the cryo-EM structure of human PRC2 with cofactors JARID2 and AEBP2 bound to a nucleosome substrate containing H2AK119ub1. We find that JARID2 and AEBP2 each interact with one of the two ubiquitin molecules in the nucleosome. A ubiquitin-interaction motif (UIM) in JARID2 is sandwiched between ubiquitin and the histone H2A-H2B acidic patch. Simultaneously, the tandem zinc-fingers of AEBP2 interact with the second ubiquitin and the histone H2A-H2B surface on the opposite side of the nucleosome. JARID2 plays a dual role in the H2AK119ub1 dependent stimulation of PRC2 through interactions with both EED via its K116 trimethylation and with the H2AK119-ubiquitin. AEBP2, on the other hand, appears to primarily serve as a scaffold contributing to the interaction between PRC2 and the H2AK119ub1 nucleosome. Our structure also provides a detailed visualization of the EZH2-nucleosome interface, revealing a segment of EZH2 (named “bridge helix”) that is stabilized as it bridges the EZH2(SET) domain, the H3 tail and the nucleosomal DNA. In addition to the role played by AEBP2 and JARID2 in PRC2 regulation by H2AK119ub1 recognition, we also observe that the presence of these cofactors partially overcomes the inhibitory effect that H3K4- and H3K36-trimethylation have on core PRC2. Together, our results reveal the central role played by cofactors JARID2 and AEBP2 in orchestrating the crosstalk between histone post-translational modifications and PRC2 methyltransferase activity.
Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics
Authors: Meirelles Lucas A. , Perry Elena K. , Bergkessel Megan , Newman Dianne K.
Published: April 2020

As antibiotic-resistant infections become increasingly prevalent worldwide, understanding the factors that lead to antimicrobial treatment failure is essential to optimizing the use of existing drugs. Opportunistic human pathogens in particular typically exhibit high levels of intrinsic antibiotic resistance and tolerance1, leading to chronic infections that can be nearly impossible to eradicate2. We asked whether the recalcitrance of these organisms to antibiotic treatment could be driven in part by their evolutionary history as environmental microbes, which frequently produce or encounter natural antibiotics3,4. Using the opportunistic pathogenPseudomonas aeruginosaas a model, we demonstrate that the self-produced natural antibiotic pyocyanin (PYO) activates bacterial defenses that confer collateral tolerance to certain synthetic antibiotics, including in a clinically-relevant growth medium. Non-PYO-producing opportunistic pathogens isolated from lung infections similarly display increased antibiotic tolerance when they are co-cultured with PYO-producingP. aeruginosa. Furthermore, we show that beyond promoting bacterial survival in the presence of antibiotics, PYO can increase the apparent rate of mutation to antibiotic resistance by up to two orders of magnitude. Our work thus suggests that bacterial production of natural antibiotics in infections could play an important role in modulating not only the immediate efficacy of clinical antibiotics, but also the rate at which antibiotic resistance arises in multispecies bacterial communities.
Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices
Authors: Walker Joseph F. , Shen Xing-Xing , Rokas Antonis , Smith Stephen A. , Moyroud Edwige
Published: April 2020

The genomic data revolution has enabled biologists to develop innovative ways to infer key episodes in the history of life. Whether genome-scale data will eventually resolve all branches of the Tree of Life remains uncertain. However, through novel means of interrogating data, some explanations for why evolutionary relationships remain recalcitrant are emerging. Here, we provide four biological and analytical factors that explain why certain genes may exhibit “outlier” behavior, namely, rate of molecular evolution, alignment length, misidentified orthology, and errors in modeling. Using empirical and simulated data we show how excluding genes based on their likelihood or inferring processes from the topology they support in a supermatrix can mislead biological inference of conflict. We next show alignment length accounts for the high influence of two genes reported in empirical datasets. Finally, we also reiterate the impact misidentified orthology and short alignments have on likelihoods in large scale phylogenetics. We suggest that researchers should systematically investigate and describe the source of influential genes, as opposed to discarding them as outliers. Disentangling whether analytical or biological factors are the source of outliers will help uncover new patterns and processes that are shaping the Tree of Life.
Phylodynamics of SARS-CoV-2 transmission in Spain
Authors: Díez-Fuertes Francisco , Iglesias-Caballero María , Monzón Sara , Jiménez Pilar , Varona Sarai , Cuesta Isabel , Zaballos Ángel , Thomson Michael M , Jiménez Mercedes , García Pérez Javier , Pozo Francisco , Pérez-Olmeda Mayte , Alcamí José , Casas Inmaculada
Published: April 2020

Objectives

SARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe.

Methods

Maximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2.

Results

Phylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai.

Conclusions

Multiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.
Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells
Authors: Eisele A.S. , Cosgrove J. , Magniez A. , Tubeuf E. , Bento S. Tenreira , Conrad C. , Cayrac F. , Tak T. , Lyne A.M. , Urbanus J. , Perié L.
Published: April 2020

The cytokine erythropoietin (EPO) is a potent inducer of erythrocyte development and one of the most prescribed biopharmaceuticals. The action of EPO on erythroid progenitor cells is well established, but its direct action on hematopoietic stem and progenitor cells (HSPCs) is still debated. Here, using cellular barcoding, we traced the differentiation of hundreds of single murine HSPCs, afterex vivoEPO-exposure and transplantation, in five different hematopoietic cell lineages, and observed the transient occurrence of high-output Myeloid-Erythroid-megaKaryocyte (MEK)-biased and Myeloid-B-cell-Dendritic cell (MBDC)-biased clones. Single-cell RNA sequencing (ScRNAseq) analysis ofex vivoEPO-exposed HSPCs revealed that EPO induced the upregulation of erythroid associated genes in a subset of HSPCs, overlapping with multipotent progenitor (MPP) 1 and MPP2. Transplantation of Barcoded EPO-exposed-MPP2 confirmed their enrichment in Myeloid-Erythroid-biased clones. Collectively, our data show that EPO does act directly on MPP independent of the niche, and modulates fate by remodeling the clonal composition of the MPP pool.
Effects of species traits and abiotic factors during the stages of plant invasions
Authors: Vedder Daniel , Leidinger Ludwig , Cabral Juliano Sarmento
Published: April 2020

The success of species invasions depends on multiple factors acting over the four invasion stages transport, colonisation, establishment, and landscape spread. Each of these stages is influenced simultaneously by particular species traits and abiotic factors. While the importance of many of these determinants has already been investigated in relative isolation, they are rarely studied in combination and even then mostly ignore the final phase, i.e., landscape spread.

Here we address this shortcoming by exploring the effect of both species traits and abiotic factors on the success of invasions using an individual-based mechanistic model, and relate those factors to the stages of invasion. This approach enables us to explicitly control abiotic factors (temperature as surrogate for productivity, disturbance and propagule pressure) as well as to monitor whole-community trait distributions of environmental adaptation, mass and dispersal abilities. We simulated introductions of plant individuals to an oceanic island to assess which abiotic factors and species traits contribute to invasion success.

We found that the most influential factors were higher propagule pressure and a particular set of traits. This invasion trait syndrome was characterized by a relative similarity in functional traits of invasive species to natives, while invasives had on average higher environmental tolerances, higher body mass and increased dispersal abilities, i.e., were more generalist and dispersive.

Our results highlight the importance in management practice of reducing the import of alien species, especially from similar habitats.
Biodiversity loss underlies the dilution effect of biodiversity
Authors: Halliday Fletcher W. , Rohr Jason R. , Laine Anna-Liisa
Published: April 2020

The dilution effect predicts increasing biodiversity to reduce the risk of infection, but the generality of this effect remains unresolved. Because biodiversity loss generates predictable changes in host community competence, we hypothesized that biodiversity loss might drive the dilution effect. We tested this hypothesis by reanalyzing four previously published meta-analyses that came to contradictory conclusions regarding generality of the dilution effect. In the context of biodiversity loss, our analyses revealed a unifying pattern: dilution effects were inconsistently observed for natural biodiversity gradients, but were commonly observed for biodiversity gradients generated by disturbances causing losses of native biodiversity. Incorporating biodiversity loss into tests of generality of the dilution effect further indicated that scale-dependency may strengthen the dilution effect only when biodiversity gradients are driven by biodiversity loss. Together, these results help to resolve one of the most contentious issues in disease ecology: the generality of the dilution effect.