bluuebunny/crossref_metadata_2025 huggingface dataset:
Causes and Circumstances of Death in Portopulmonary Hypertension
Authors: Sahay Sandeep , Al Abdi Sami , Melillo Celia , Newman Jennie , Dweik Raed A. , Heresi Gustavo A. , Tonelli Adriano R.
Published: June 2021

Background.

The causes and circumstances surrounding death are poorly studied in patients with portopulmonary hypertension (PoPH). We sought to determine the specific reasons for dying and characteristics surrounding this process in patients with PoPH.

Methods.

All deaths of patients with PoPH followed in the Cleveland Clinic Pulmonary Vascular Program were prospectively reviewed by the pulmonary hypertension team between 1996 and 2020.

Results.

A total of 69 patients with PoPH (age 56.0 ± 8.9 y), with 49% females, were included. Causes of death were available in 52 (75%) patients, of these PoPH either directly or indirectly contributed to death in 13 of 52 (25%) of patients, meanwhile 39 of 52 (75%) of the patients died because of progressive liver disease and its related complications. Decompensated liver disease was the leading cause of death in this cohort 20 of 52 (38%), whereas 19 of 52 (37%) died because of conditions associated with liver disease. About half, 36 of 69 (52%) of patients died in a healthcare environment and 23 of 36 (64%) during a hospitalization at Cleveland Clinic. A total of 59 of 69 (74%) of patients received pulmonary arterial hypertension (PAH)-specific therapies. Six patients died after liver transplantation (in 3 death was related to PAH-related complications). Most of the patients in this cohort of PoPH patients were considered unsuitable for liver transplantation for a variety of reasons. Advanced healthcare directives were available in only 28% of patients.

Conclusions.

Most patients with PoPH died because of complications of their liver disease. PAH directly or indirectly contributed to death in a third of them. A quarter of them did not receive PAH-specific therapy before their death.
Karnofsky Performance Score—Failure to Thrive as a Frailty Proxy?
Authors: Stedman Margaret R. , Watford Daniel J. , Chertow Glenn M. , Tan Jane C.
Published: June 2021

Background.

Among patients listed for kidney transplantation, the Karnofsky Performance Status (KPS) Scale has been used as a proxy for frailty and proposed as a predictor of long-term posttransplant outcomes. The KPS is required by the Organ Procurement and Transplantation Network for all transplants; however, the interrater reliability of KPS reporting in kidney transplant candidates has not been well investigated, and there is concern regarding limitations of using KPS that may influence transplant eligibility.

Methods.

We performed an observational study using existing Scientific Registry of Transplant Recipients data from 2006 to 2020 to examine the variability, reliability, and trends in the KPS among patients on the kidney transplant waitlist.

Results.

Our analysis included 8197 kidney transplant candidates with >1 KPS in a 3-mo period. We observed 2–7 scores per patient with an average score of 78.9 (SD = 12, 95% confidence interval, 78.8-79.1). We found substantial variability in KPS reporting, in which 27% of the patients had scores that varied widely with 20–80 points in difference. Interrater reliability in the 10-point scale was poor (30%). When using a condensed 4-category scale (disabled, requires assistance, capable of self-care, normal activity), 38% of patients experienced at least a 1-category shift in their score.

Conclusions.

The lack of reliability in KPS reporting raises concerns when applying the KPS as a proxy for frailty and a metric to be considered when evaluating candidacy for kidney transplantation.
Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen
Authors: Dawson Daniel , Rasmussen David , Peng Xinxia , Lanzas Cristina
Published: June 2021

Indirect (environmental) and direct (host–host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.
Mandibular morphology, task specialization and bite mechanics in
Pheidole
ants (Hymenoptera: Formicidae)
Authors: Klunk Cristian L. , Argenta Marco A. , Casadei-Ferreira Alexandre , Economo Evan P. , Pie Marcio R.
Published: June 2021

Ants show remarkable ecological and evolutionary success due to their social life history and division of labour among colony members. In some lineages, the worker force became subdivided into morphologically distinct individuals (i.e. minor versus major workers), allowing for the differential performance of particular roles in the colony. However, the functional and ecological significance of these morphological differences are not well understood. Here, we applied finite element analysis (FEA) to explore the biomechanical differences between major and minor ant worker mandibles. Analyses were carried out on mandibles of two
Pheidole
species, a dimorphic ant genus. We tested whether major mandibles evolved to minimize stress when compared to minors using combinations of the apical tooth and masticatory margin bites under strike and pressure conditions. Majors performed better in pressure conditions yet, contrary to our expectations, minors performed better in strike bite scenarios. Moreover, we demonstrated that even small morphological differences in ant mandibles might lead to substantial differences in biomechanical responses to bite loading. These results also underscore the potential of FEA to uncover biomechanical consequences of morphological differences within and between ant workers.
Stability of trusses by graphic statics
Authors: McRobie Allan , Millar Cameron , Baker William F.
Published: June 2021

This paper presents a graphical method for determining the linearized stiffness and stability of prestressed trusses consisting of rigid bars connected at pinned joints and which possess kinematic freedoms. Key to the construction are the rectangular areas which combine the reciprocal form and force diagrams in the unified Maxwell–Minkowski diagram. The area of each such rectangle is the product of the bar tension and the bar length, and this corresponds to the rotational stiffness of the bar that arises due to the axial force that it carries. The prestress stability of any kinematic freedom may then be assessed using a weighted sum of these areas. The method is generalized to describe the out-of-plane stability of two-dimensional trusses, and to describe three-dimensional trusses in general. The paper also gives a graphical representation of the ‘product forces’ that were introduced by Pellegrino and Calladine to describe the prestress stability of trusses.
A novel concept for low-cost non-electronic detection of overloading in the foot during activities of daily living
Authors: Chatzistergos Panagiotis E. , Chockalingam Nachiappan
Published: June 2021

Identifying areas in the sole of the foot which are routinely overloaded during daily living is extremely important for the management of the diabetic foot. This work showcases the feasibility of reliably detecting overloading using a low-cost non-electronic technique. This technique uses thin-wall structures that change their properties differently when they are repeatedly loaded above or below a tuneable threshold. Flexible hexagonal thin-wall structures were produced using three-dimensional printing, and their mechanical behaviour was assessed before and after repetitive loading at different magnitudes. These structures had an elastic mechanical behaviour until a critical pressure (Pcrit= 252 kPa ± 17 kPa) beyond which they buckled. Assessing changes in stiffness after simulated use enabled the accurate detection of whether a sample was loaded above or belowPcrit(sensitivity = 100%, specificity = 100%), with the overloaded samples becoming significantly softer. No specificPcritvalue was targeted in this study. However, finite-element modelling showed thatPcritcan be easily raised or lowered, through simple geometrical modifications, to become aligned with established thresholds for overloading (e.g. 200 kPa) or to assess overloading thresholds on a patient-specific basis. Although further research is needed, the results of this study indicate that clinically relevant overloading could indeed be reliably detected without the use of complex electronic in-shoe sensors.
Crystal structure of the C-terminal domain of envelope protein VP37 from white spot syndrome virus reveals sulphate binding sites responsible for heparin binding
Authors: Somsoros Wasusit , Sangawa Takeshi , Takebe Katsuki , Attarataya Jakrada , Wongprasert Kanokpan , Senapin Saengchan , Rattanarojpong Triwit , Suzuki Mamoru , Khunrae Pongsak
Published: June 2021

White spot syndrome virus (WSSV) is the most virulent pathogen causing high mortality and economic loss in shrimp aquaculture and various crustaceans. Therefore, the understanding of molecular mechanisms of WSSV infection is important to develop effective therapeutics to control the spread of this viral disease. In a previous study, we found that VP37 could bind with shrimp haemocytes through the interaction between its C-terminal domain and heparin-like molecules on the shrimp cells, and this interaction can also be inhibited by sulphated galactan. In this study, we present the crystal structure of C-terminal domain of VP37 from WSSV at a resolution of 2.51 Å. The crystal structure contains an eight-stranded β-barrel fold with an antiparallel arrangement and reveals a trimeric assembly. Moreover, there are two sulphate binding sites found in the position corresponding to R213 and K257. In order to determine whether these sulphate binding sites are involved in binding of VP37 to heparin, mutagenesis was performed to replace these residues with alanine (R213A and K257A), and the Surface Plasmon Resonance (SPR) system was used to study the interaction of each mutated VP37 with heparin. The results showed that mutants R213A and K257A exhibited a significant loss in heparin binding activity. These findings indicated that the sites of R213 and K257 on the C-terminal domain of envelope protein VP37 are essential for binding to sulphate molecules of heparin. This study provides further insight into the structure of C-terminal domain of VP37 and it is anticipated that the structure of VP37 might be used as a guideline for development of antivirus agent targeting on the VP37 protein.
Namilumab or infliximab compared to standard of care in hospitalised patients with COVID-19 (CATALYST): a phase 2 randomised adaptive trial
Authors: Fisher Benjamin A. , Veenith Tonny , Slade Daniel , Gaskell Charlotte , Rowland Matthew , Whitehouse Tony , Scriven James , Parekh Dhruv , Balasubramaniam Madhu S. , Cooke Graham , Morley Nick , Gabriel Zoe , Wise Matthew P. , Porter Joanna , McShane Helen , Ho Ling-Pei , Newsome Philip N. , Rowe Anna , Sharpe Rowena , Thickett David R. , Bion Julian , Gates Simon , Richards Duncan , Kearns Pamela
Published: June 2021

Background

Dysregulated inflammation is associated with poor outcomes in Coronavirus disease 2019 (COVID-19). We assessed the efficacy of namilumab, a granulocyte-macrophage colony-stimulating factor inhibitor and infliximab, a tumour necrosis factor inhibitor in hospitalised patients with COVID-19 in order to prioritise agents for phase 3 trials.

Methods

In this randomised, multi-arm, parallel group, open label, adaptive phase 2 proof-of-concept trial (CATALYST) we recruited hospitalised patients ≥ 16 years with COVID-19 pneumonia and C-reactive protein (CRP) ≥ 40mg/L in nine UK hospitals. Participants were randomly allocated with equal probability to usual care, or usual care plus a single 150mg intravenous dose of namilumab (150mg) or infliximab (5mg/kg). Randomisation was stratified for ward versus ICU. The primary endpoint was improvement in inflammation in intervention arms compared to control as measured by CRP over time, analysed using Bayesian multi-level models. ISRCTN registry number 40580903.

Findings

Between 15thJune 2020 and 18thFebruary 2021 we randomised 146 participants: 54 to usual care, 57 to namilumab and 35 to infliximab. The probabilities that namilumab and infliximab were superior to usual care in reducing CRP over time were 97% and 15% respectively. Consistent effects were seen in ward and ICU patients and aligned with clinical outcomes, such that the probability of discharge (WHO levels 1-3) at day 28 was 47% and 64% for ICU and ward patients on usual care, versus 66% and 77% for patients treated with namilumab. 134 adverse events occurred in 30/55 (54.5%) namilumab patients compared to 145 in 29/54 (53.7%) usual care patients. 102 events occurred in 20/29 (69.0%) infliximab patients versus 112 events in 17/34 (50.0%) usual care patients.

Interpretation

Namilumab, but not infliximab, demonstrated proof-of-concept evidence for reduction in inflammation in hospitalised patients with COVID-19 pneumonia which was consistent with secondary clinical outcomes. Namilumab should be prioritised for further investigation in COVID-19.

Funding

Medical Research Council.
A Chinese host genetic study discovered type I interferons and causality of cholesterol levels and WBC counts on COVID-19 severity
Authors: Zhu Huanhuan , Zheng Fang , Li Linxuan , Jin Yan , Luo Yuxue , Li Zhen , Zeng JingYu , Tang Ling , Li Zilong , Xia Ningyu , Liu Panhong , Han Dan , Shan Ying , Zhu Xiaoying , Liu Siyang , Xie Rong , Chen Yilin , Liu Wen , Liu Longqi , Xu Xun , Wang Jian , Yang Huanming , Shen Xia , Jin Xin , Cheng Fanjun
Published: June 2021

As of early May 2021, the ongoing pandemic COVID-19 has caused over 160 million of infections and over 3 million deaths worldwide. Many risk factors, such as age, gender, and comorbidities, have been studied to explain the variable symptoms of infected patients. However, these effects may not fully account for the diversity in disease severity. Here, we present a comprehensive analysis of a broad range of patients’ laboratory and clinical assessments to investigate the genetic contributions to COVID-19 severity. By performing GWAS analysis, we discovered several concrete associations for laboratory features. Based on these findings, we performed Mendelian randomization (MR) analysis to investigate the causality of laboratory traits on disease severity. From the MR study, we identified two causal traits, cholesterol levels and WBC counts. The functional gene related to cholesterol levels is ApoE and people with particular ApoE genotype are more likely to have higher cholesterol levels, facilitating the process that SARS-CoV-2 binds on its receptor ACE2 and aggravating COVID-19 disease. The functional gene related to WBC counts is MHC system that plays a central role in the immune system. The host immune response to the SARS-CoV-2 infection greatly affects the patients’ severity status and clinical outcome. Additionally, our gene-based and GSEA analysis revealed interferon pathways, including type I interferon receptor binding, regulation of IFNA signaling, and SARS coronavirus and innate immunity. We hope that our work will make a contribution in studying the genetic mechanisms of disease illness and serve as useful reference for the clinical diagnosis and treatment of COVID-19.
COVID-19 infections in day care centres in Germany: Social and organisational determinants of infections in children and staff in the second and third wave of the pandemic
Authors: Neuberger Franz , Grgic Mariana , Diefenbacher Svenja , Spensberger Florian , Lehfeld Ann-Sophie , Buchholz Udo , Haas Walter , Kalicki Bernhard , Kuger Susanne
Published: June 2021

Background

During the SARS-CoV-2 pandemic, German early childhood education and care (ECEC) centres organised childrens attendance variably (i.e., reduced opening hours, emergency support for few children only or full close-down). Further, protection and hygiene measures like fixed children/staff groups, ventilation and surface disinfection were introduced among ECEC centres. To inform or modify public health measures in ECEC, we investigate the occurrence of SARS-CoV-2 infections among children and staff of ECEC centres in light of social determinants (socioeconomic status of the children) and recommended structural and hygiene measures. We focus on the question if the relevant factors differ between the 2nd (when no variant of concern (VOC) circulated) and the 3rd wave (when VOC B.1.1.7 (Alpha) predominated).

Methods

Based on panel data from a weekly online survey of ECEC centre managers (calendar week 36/2020 to 22/2021, ongoing) including approx. 8500 centres, we estimate the number of SARS-CoV-2 infections in children and staff using random-effect-within-between (REWB) panel models for count data in the 2nd and 3rd wave.

Results

Centres with a high proportion of children with low socioeconomic status (SES) have a higher risk of infections in staff and children. Strict contact restrictions between groups like fixed group assignments among children and fixed staff assignments to groups prevent infections. Both effects tend to be stronger in the 3rd wave.

Contribution

ECEC centres with a large proportion of children from a low SES background and lack of using fixed child/staff cohorts experience higher COVID-19 rates. Centres should be supported in maintaining recommended measures over the long run. Preventive measures such as vaccination of staff should be prioritised in centres with large proportions of low SES children.
Inverse planning for radiofrequency ablation in cancer therapy using multiple damage models
Authors: Kulkarni-Thaker Shefali , Aleman Dionne , Fenster Aaron
Published: June 2021

Radiofrequency ablation (RFA) offers localized and minimally invasive treatment of small-to-medium sized inoperable tumors. In RFA, tissue is ablated with high temperatures obtained from electrodes (needles) inserted percutaneously or via an open surgery into the target. RFA treatments are generally not planned in a systematic way, and do not account for nearby organs-at-risk (OARs), potentially leading to sub-optimal treatments and inconsistent treatment quality. We therefore develop a mathematical framework to design RFA treatment plans that provide complete ablation while minimizing healthy tissue damage. Borrowing techniques from radiosurgery inverse planning, we design a two-stage approach where we first identify needle positions and orientations, called needle orientation optimization, and then compute the treatment time for optimal thermal dose delivery, called thermal dose optimization. Several different damage models are used to determine both target and OAR damage. We present numerical results on three clinical case studies. Our findings indicate a need for high source voltage for short tip length (conducting portion of the needle) or fewer needles, and low source voltage for long tip length or more needles to achieve full coverage. Further, more needles yields a larger ablation volume and consequently more OAR damage. Finally, the choice of damage model impacts the source voltage, tip length, and needle quantity.
A novel RT-LAMP workflow for rapid salivary diagnostics of COVID-19 and effects of age, gender and time from symptom onset
Authors: Kobayashi Gerson Shigeru , Brito Luciano Abreu , de Paula Moreira Danielle , Suzuki Angela May , Hsia Gabriella Shih Ping , Pimentel Lylyan Fragoso , de Paiva Ana Paula Barreto , Dias Carolina Regoli , Lourenço Naila Cristina Vilaça , Oliveira Beatriz Araujo , Manuli Erika Regina , Corral Marcelo Andreetta , Cavaçana Natale , Neto Miguel Mitne , Sales Maria Mirtes , Aquila Luiz Phellipe Dell’ , Filho Alvaro Razuk , Parrillo Eduardo Fagundes , Mendes-Corrêa Maria Cássia , Sabino Ester Cerdeira , Costa Silvia Figueiredo , Leal Fabio Eudes , Sgro Germán Gustavo , Farah Chuck Shaker , Zatz Mayana , Passos-Bueno Maria Rita
Published: June 2021

Objectives

Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP workflow for viral detection in saliva, and to provide more information regarding its potential in COVID-19 diagnostics.

Methods

Clinical and contrived specimens were used to screen/optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate clinical performance (n = 90) and to characterize saliva based on age, gender and time from onset of symptoms (n = 49).

Results

The devised workflow achieved 93.2% sensitivity, 97% specificity, and 0.895 Kappa for salivas containing >102 copies/μL. Further analyses in saliva showed peak viral load in the first days of symptoms and lower viral loads in females, particularly among young individuals (<38 years). NOP RT-PCR data did not yield relevant associations.

Conclusions

This novel saliva RT-LAMP workflow can be applied to point-of-care testing. This work reinforces that saliva better correlates with transmission dynamics than NOP specimens, and reveals gender differences that may reflect higher transmission by males. To maximize detection, testing should be done immediately after symptom onset, especially in females.

HIGHLIGHTS

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Development of DGS, a dithiothreitol/guanidine-based solution for stabilization of the viral genome that increases sensitivity for SARS-CoV-2 detection in saliva;

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Rapid, cost-effective RT-LAMP assay workflow for viral detection in saliva without need of RNA extraction;

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Insights into the differences in viral load between saliva and naso-oropharyngeal specimens, and correlation with age, gender and time from symptom onset;
Percolation across households in mechanistic models of non-pharmaceutical interventions in SARS-CoV-2 disease dynamics
Authors: Franco Caroline , Ferreira Leonardo Souto , Sudbrack Vítor , Borges Marcelo Eduardo , Poloni Silas , Inácio Prado Paulo , White Lisa J , Águas Ricardo , André Kraenkel Roberto , Coutinho Renato Mendes
Published: June 2021

Since the emergence of the novel coronavirus disease, mathematical modelling has become an important tool for planning strategies to combat the pandemic by supporting decision-making and public policies, as well as allowing an assessment of the effect of different intervention scenarios. A proliferation of compartmental models was observed in the mathematical modelling community, aiming to understand and make predictions regarding the spread of COVID-19. Such approach has its own advantages and challenges: while compartmental models are suitable to simulate large populations, the underlying well-mixed population assumption might be problematic when considering non-pharmaceutical interventions (NPIs) which strongly affect the connectivity between individuals in the population. Here we propose a correction to an extended age-structured SEIR framework with dynamic transmission modelled using contact matrices for different settings in Brazil. By assuming that the mitigation strategies for COVID-19 affect the connections between different households, network percolation theory predicts that the connectivity across all households decreases drastically above a certain threshold of removed connections. We incorporated this emergent effect at population level by modulating the home contact matrices through a percolation correction function, with the few remaining parameters fitted to to hospitalisation and mortality data from the city of São Paulo. We found significant support for the model with implemented percolation effect using the Akaike Information Criteria (AIC). Besides better agreement to data, this improvement also allows for a more reliable assessment of the impact of NPIs on the epidemiological dynamics.
Breakthrough infection with SARS-CoV-2 and its predictors among healthcare workers in a medical college and hospital complex in Delhi, India
Authors: Sharma Pragya , Mishra Suruchi , Basu Saurav , Tanwar Neha , Kumar Rajesh
Published: June 2021

Introduction

The study objective was to determine the breakthrough infection rate of Covid-19 (SARS-CoV-2) infection in those vaccinated with either BBV152 or AZD1222 (ChAdOx1-S) vaccine among healthcare workers (HCWs).

Methods

A cross-sectional analysis was conducted a medical college and hospital complex in Delhi, India through telephonic interviews among HCWs who had received at-least one dose of a Covid-19 vaccine during January to March’ 2021. Breakthrough infections were operationally defined as occurrence of Covid-19 infection ≥14 days after administration of two doses of either Covid-19 vaccine.

Results

We enrolled 325 HCWs with mean (SD) age of 29.1 (9.9) years including 211 (64.9%) males. Two seventy nine (85.8%) HCWs were fully vaccinated while 46 (14.2%) were partially vaccinated. There were 168 (51.7%) BBV152 and 157 (48.3%) AZD1222 (ChAdOx1-S) recipients.

A total of 37 (11.3%, 95% C.I. 8.3, 15.3) breakthrough infections were observed in the HCWs. The median (IQR) time until incidence of Covid-19 breakthrough infection since receiving second dose of either Covid-19 vaccine was 47 (28.5, 55) days. Additionally, 20 (6.1%) non-breakthrough Covid-19 infections were recorded in the HCWs post vaccination with either a single dose of a Covid-19 vaccine or both doses but prior to a period of 14 days since administration of the second dose.

Most breakthrough infection cases (94.4%) were mild and did not require supplemental oxygen therapy. HCWs without a history of natural Covid-19 infection and recovery prior to vaccination were 3.8 times more at risk to contract a Covid-19 infection or reinfection in spite of vaccination with at-least one dose of either Covid-19 vaccine.

Conclusion

Nearly one in nine HCWs experienced a Covid-19 breakthrough infection in the present study.
Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291–1329 CE) indicates the first known case of late-onset Pompe disease
Authors: Iadarola Barbara , Lavezzari Denise , Modi Alessandra , Esposti Chiara Degli , Beltrami Cristina , Rossato Marzia , Zaro Valentina , Napione Ettore , Latella Leonardo , Lari Martina , Caramelli David , Salviati Alessandro , Delledonne Massimo
Published: June 2021

Mummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard “clinical exome analysis” conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder.
Shotgun Immunoproteomic Approach for the Discovery of Linear B Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei
Authors: D’haeseleer Patrik , Collette Nicole M. , Lao Victoria , Segelke Brent W. , Branda Steven S. , Franco Magdalena
Published: June 2021

Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of peptide epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Identification of linear epitopes is currently an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B cell epitopes and development of vaccines to counter emerging biological threats.
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research
Authors: Scott Benjamin M. , Lacasse Vincent , Blom Ditte G. , Tonner Peter D. , Blom Nikolaj S.
Published: June 2021

Background

The coronavirus nonstructural protein 5 (Nsp5) is a cysteine protease required for processing the viral polyprotein and is therefore crucial for viral replication. Nsp5 from several coronaviruses have also been found to cleave host proteins, disrupting molecular pathways involved in innate immunity. Nsp5 from the recently emerged SARS-CoV-2 virus interacts with and can cleave human proteins, which may be relevant to the pathogenesis of COVID-19. Based on the continuing global pandemic, and emerging understanding of coronavirus Nsp5-human protein interactions, we set out to predict what human proteins are cleaved by the coronavirus Nsp5 protease using a bioinformatics approach.

Results

Using a previously developed neural network trained on coronavirus Nsp5 cleavage sites (NetCorona), we made predictions of Nsp5 cleavage sites in all human proteins. Structures of human proteins in the Protein Data Bank containing a predicted Nsp5 cleavage site were then examined, generating a list of 92 human proteins with a highly predicted and accessible cleavage site. Of those, 48 are expected to be found in the same cellular compartment as Nsp5. Analysis of this targeted list of proteins revealed molecular pathways susceptible to Nsp5 cleavage and therefore relevant to coronavirus infection, including pathways involved in mRNA processing, cytokine response, cytoskeleton organization, and apoptosis.

Conclusions

This study combines predictions of Nsp5 cleavage sites in human proteins with protein structure information and protein network analysis. We predicted cleavage sites in proteins recently shown to be cleaved in vitro by SARS-CoV-2 Nsp5, and we discuss how other potentially cleaved proteins may be relevant to coronavirus mediated immune dysregulation. The data presented here will assist in the design of more targeted experiments, to determine the role of coronavirus Nsp5 cleavage of host proteins, which is relevant to understanding the molecular pathology of SARS-CoV-2 infection.
Thin-film freeze-drying of a Norovirus vaccine candidate
Authors: Xu Haiyue , Bhowmik Tuhin , Gong Kevin , Anh Huynh Thu Ngoc , Williams Robert O. , Cui Zhengrong
Published: June 2021

A bivalent Norovirus vaccine candidate has been developed that contains Norovirus strain GI.1 Norwalk-virus like particles (VLP) and strain GII.4 Consensus VLP adsorbed onto aluminum (oxy)hydroxide. In the present study, we tested the feasibility of converting the vaccine from a liquid suspension into dry powder by thin-film freeze-drying (TFFD). With the proper amount of trehalose and/or sucrose as cryoprotectant, TFFD can be applied to transform the Norovirus vaccine candidate into dry powders without causing antigen loss or particle aggregation, while maintaining the potency of the antigens within a specified acceptable range. In an accelerated stability study, the potency of the antigens was also maintained in the specified acceptable range after the dry powders were stored for eight weeks at 40°C, 75% relative humidity. The dry powder Norovirus vaccine offers the potential to eliminate the cold chain requirement for transport and/or storage of the vaccine.
Metabolomics of lung microdissections reveals region- and sex-specific metabolic effects of acute naphthalene exposure in mice
Authors: Stevens Nathanial C. , Edwards Patricia C. , Tran Lisa M. , Ding Xinxin , Van Winkle Laura S. , Fiehn Oliver
Published: June 2021

Naphthalene is a ubiquitous environmental contaminant produced by combustion of fossil fuels and is a primary constituent of both mainstream and side stream tobacco smoke. Naphthalene elicits region-specific toxicity in airway club cells through cytochrome P450 (P450)-mediated bioactivation, resulting in depletion of glutathione and subsequent cytotoxicity. While effects of naphthalene in mice have been extensively studied, few experiments have characterized global metabolomic changes in the lung. In individual lung regions, we found metabolomic changes in microdissected mouse lung conducting airways and parenchyma obtained from animals sacrificed 2, 6, and 24 hours following naphthalene treatment. Data on 577 unique identified metabolites were acquired by accurate mass spectrometry-based assays focusing on lipidomics and non-targeted metabolomics of hydrophilic compounds. Statistical analyses revealed distinct metabolite profiles between the two major lung regions. In addition, the number and magnitude of statistically significant exposure-induced changes in metabolite abundance were different between lung airways and parenchyma for unsaturated lysophosphatidylcholines (LPCs), dipeptides, purines, pyrimidines, and amino acids. Importantly, temporal changes were found to be highly distinct for male and female mice, with males exhibiting predominant treatment-specific changes only at two hours post-exposure. In females, metabolomic changes persisted until six hours post-naphthalene treatment, which may explain the previously characterized higher susceptibility of female mice to naphthalene toxicity. In both males and females, treatment-specific changes corresponding to lung remodeling, oxidative stress response, and DNA damage were observed, which may provide insights into potential mechanisms contributing to the previously reported effects of naphthalene exposure in the lung.
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
Authors: Umer Husen M. , Zhu Yafeng , Pfeuffer Julianus , Sachsenberg Timo , Lehtiö Janne , Branca Rui , Perez-Riverol Yasset
Published: June 2021

We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512).

Availability

The software is freely available. pypgatk: (https://github.com/bigbio/py-pgatk/), and pgdb: (https://github.com/nf-core/pgdb)

Contact

Yasset Perez-Riverol (yperez@ebi.ac.uk), Rui Branca (rui.mamede-branca@ki.se)

Supplementary information

Supplementary data are available online.
Optimization of Phosphate Limited Autoinduction Broth for 2-Stage Heterologous Protein Expression in E. coli
Authors: Menacho-Melgar Romel , Hennigan Jennifer N. , Lynch Michael D.
Published: June 2021

Autoinducible, 2-stage protein expression leveraging phosphate inducible promoters has been recently shown to enable not only high protein titers but also consistent performance across scales from screening systems (microtiter plates) to instrumented bioreactors. However, to date small scale production using microtiter plates and shake flasks rely on a complex autoinduction broth (AB) that requires making numerous media components, not all amenable to autoclaving. In this report, we develop a simpler media formulation (AB-2) with just a few autoclavable components. We show that AB-2 is robust to small changes in its composition and performs equally, if not better, than AB across different scales. AB-2 will facilitate adoption of phosphate limited 2-stage protein expression protocols.
Populus ERF85 balances xylem cell expansion and secondary cell wall formation in hybrid aspen
Authors: Seyfferth Carolin , Wessels Bernard A. , Vahala Jorma , Kangasjärvi Jaakko , Delhomme Nicolas , Hvidsten Torgeir R. , Tuominen Hannele , Lundberg-Felten Judith
Published: June 2021

Secondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identify a novel role for the ethylene induced Populus ETHYLENE RESPONSE FACTOR ERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of ERF85 is high in phloem and cambium cells and during expansion of xylem cells, while it is low in maturing xylem tissue. Extending ERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation and growth. Expression of genes associated with plant vascular development and biosynthesis of SCW chemical components such as xylan and lignin, was downregulated in the transgenic trees. Our results suggest that ERF85 activates genes related with xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of ERF85 during wood development together with the observed phenotypes in response to ectopic ERF85 expression suggests that ERF85 functions as a switch between different phases of xylem differentiation during wood formation.
Genetic and phylogenetic uncoupling of structure and function in human transmodal cortex
Authors: Valk Sofie L. , Xu Ting , Paquola Casey , Park Bo-yong , Bethlehem Richard A.I. , Vos de Wael Reinder , Royer Jessica , Masouleh Shahrzad Kharabian , Bayrak Şeyma , Kochunov Peter , Yeo B.T. Thomas , Margulies Daniel , Smallw Jonathan , Eickhoff Simon B. , Bernhardt Boris C.
Published: June 2021

Brain structure scaffolds intrinsic function, supporting cognition and ultimately behavioral flexibility. However, it remains unclear how a static, genetically controlled architecture supports flexible cognition and behavior. Here, we synthesize genetic, phylogenetic and cognitive analyses to understand how the macroscale organization of structure-function coupling across the cortex can inform its role in cognition. In humans, structure-function coupling was highest in regions of unimodal cortex and lowest in transmodal cortex, a pattern that was mirrored by a reduced alignment with heritable connectivity profiles. Structure-function uncoupling in non-human primates had a similar spatial distribution, but we observed an increased coupling between structure and function in association regions in macaques relative to humans. Meta-analysis suggested regions with the least genetic control (low heritable correspondence and different across primates) are linked to social cognition and autobiographical memory. Our findings establish the genetic and evolutionary uncoupling of structure and function in different transmodal systems may support the emergence of complex, culturally embedded forms of cognition.
Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya
Published: June 2021

Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein-protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were then performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. The top hub genes such as MYC, EGFR, LNX1, YBX1, HSP90AA1, ESR1, FN1, TK1, ANLN and SMAD9 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Receiver operating characteristic curve (ROC) analysis and RT-PCR confirmed that these genes were significantly associated with T1DM. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the advancement and progression of T1DM, and certain genes might be used as candidate target molecules to diagnose, monitor and treat T1DM.
Genomics analysis of hexanoic acid exposure in Drosophila species
Authors: Drum Z.A. , Lanno S.M. , Gregory S.M. , Shimshak S.J. , Ahamed M. , Barr W. , Bekele B. , Biester A. , Castro C. , Connolly L. , DelGaudio N. , Humphrey W. , Karimi H. , Karolczak S. , Lawrence T. , McCracken A. , Miller-Medzon N. , Murphy L. , Park C. , Park S. , Qiu C. , Serra K. , Snyder G. , Strauss A. , Tang S. , Vyzas C. , Coolon Joseph D.
Published: June 2021

Drosophila sechellia is a dietary specialist endemic to the Seychelles islands that has evolved to consume the fruit of Morinda citrifolia. When ripe, the fruit of M. citrifolia contains octanoic acid and hexanoic acid, two medium chain fatty acid volatiles that deter and are toxic to generalist insects. D. sechellia has evolved resistance to these volatiles allowing it to feed almost exclusively on this host plant. The genetic basis of octanoic acid resistance has been the focus of multiple recent studies, but the mechanisms that govern hexanoic acid resistance in D. sechellia remain unknown. To understand how D. sechellia has evolved to specialize on M. citrifolia fruit and avoid the toxic effects of hexanoic acid, we exposed adult D. sechellia, D. melanogaster and D. simulans to hexanoic acid and performed RNA sequencing comparing their transcriptional responses to identify D. sechellia specific responses. Our analysis identified many more genes responding transcriptionally to hexanoic acid in the susceptible generalist species than in the specialist D. sechellia. Interrogation of the sets of differentially expressed genes showed that generalists regulated the expression of many genes involved in metabolism and detoxification whereas the specialist primarily downregulated genes involved in the innate immunity. Using these data we have identified interesting candidate genes that may be critically important in aspects of adaptation to their food source that contains high concentrations of HA. Understanding how gene expression evolves during dietary specialization is crucial for our understanding of how ecological communities are built and how evolution shapes trophic interactions.
Parallel and non-parallel divergence within polymorphic populations of brook stickleback,Culaea inconstans(Actinopterygii: Gasterosteidae)
Authors: Willerth Kaitlyn , Franks Emily , Mee Jonathan A.
Published: June 2021

Studying parallel evolution allows us to draw conclusions about the repeatability of adaptive evolution. Whereas populations likely experience similar selective pressures in similar environments, it is not clear if this will always result in parallel divergence of ecologically relevant traits. Our study investigates the extent of parallelism associated with the evolution of pelvic spine reduction in brook stickleback populations. We find that populations with parallel divergence in pelvic spine morphology do not exhibit parallel divergence in head and body morphology but do exhibit parallel divergence in diet. In addition, we compare these patterns associated with pelvic reduction in brook stickleback to well-studied patterns of divergence between spined and unspined threespine stickleback. Whereas spine reduction is associated with littoral habitats and a benthic diet in threespine stickleback, spine reduction in brook stickleback is associated with a planktonic diet. Hence, we find that pelvic spine divergence is associated with largely non-parallel ecological consequences across species.