bluuebunny/crossref_metadata_2025 huggingface dataset:
metaboprep: an R package for pre-analysis data description and processing
Authors: Hughes David A , Taylor Kurt , McBride Nancy , Lee Matthew A , Mason Dan , Lawlor Deborah A , Timpson Nicholas J , Corbin Laura J
Published: July 2021

Motivation

Metabolomics is an increasingly common part of health research and there is need for pre-analytical data processing. Researchers typically need to characterize the data and to exclude errors within the context of the intended analysis. While some pre-processing steps are common, there is currently a lack of standardization and reporting transparency for these procedures.

Results

Here we introduce metaboprep, a standardized data processing workflow to extract and characterize high quality metabolomics data sets. The package extracts data from pre-formed worksheets, provides summary statistics and enables the user to select samples and metabolites for their analysis based on a set of quality metrics. A report summarizing quality metrics and the influence of available batch variables on the data is generated for the purpose of open disclosure. Where possible, we provide users flexibility in defining their own selection thresholds.

Availability and implementation

metaboprep is an open-source R package available at https://github.com/MRCIEU/metaboprep

Contact

d.a.hughes@bristol.ac.uk or laura.corbin@bristol.ac.uk
A single cell transcriptome atlas reveals the heterogeneity of the healthy human cornea and identifies novel markers of the corneal limbus and stroma
Authors: Català Pere , Groen Nathalie , Dehnen Jasmin A. , Soares Eduardo , van Velthoven Arianne J.H. , Nuijts Rudy M.M.A. , Dickman Mor M. , LaPointe Vanessa L.S.
Published: July 2021

The cornea is the clear window that lets light into the eye. It is composed of five layers: epithelium, Bowman’s layer, stroma, Descemet’s membrane and endothelium. The maintenance of its structure and transparency are determined by the functions of the different cell types populating each layer. Attempts to regenerate corneal tissue and understand disease conditions requires knowledge of how cell profiles vary across this heterogeneous tissue. We performed a single cell transcriptomic profiling of 19,472 cells isolated from eight healthy donor corneas. Our analysis delineates the heterogeneity of the corneal layers by identifying cell populations and revealing cell states that contribute in preserving corneal homeostasis. We identified that the expression of CAV1, CXCL14, HOMER3 and CPVL were exclusive to the corneal epithelial limbal stem cell niche, CKS2, STMN1 and UBE2C were exclusively expressed in highly proliferative transit amplifying cells, and NNMT was exclusively expressed by stromal keratocytes. Overall, this research provides a basis to improve current primary cell expansion protocols, for future profiling of corneal disease states, to help guide pluripotent stem cells into different corneal lineages, and to understand how engineered substrates affect corneal cells to improve regenerative therapies.
Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF
Authors: Andreu Maria Jose , Alvarez-Franco Alba , Portela Marta , Gimenez-Llorente Daniel , Cuadrado Ana , Badia-Careaga Claudio , Tiana Maria , Losada Ana , Manzanares Miguel
Published: July 2021

The eukaryotic genome is tightly packed inside the nucleus, where it is organized in 3D at different scales. This structure is driven and maintained by different chromatin states and by architectural factors that bind DNA, such as the multi-zinc finger protein CTCF. Zygotic genome structure is established de novo after fertilization, but the impact of such structure on genome function during the first stages of mammalian development is still unclear. Here, we show that deletion of the Ctcf gene in mouse embryos impairs the correct establishment of chromatin structure, but initial lineage decisions take place and embryos are viable until the late blastocyst stage. Furthermore, we observe that maternal CTCF is not necessary for development. Transcriptomic analyses of mutant embryos show that the changes in metabolic and protein homeostasis programs that occur during the progression from the morula to the blastocyst depend on CTCF. Yet, these changes in gene expression do not correlate with disruption of chromatin structure, but mainly with proximal binding of CTCF to the promoter region of genes downregulated in mutants. Our results show that CTCF regulates both 3D genome organization and transcription during mouse preimplantation development, but mostly as independent processes.
Directional Cell Migration Guided by a Strain Gradient
Authors: Yang Feiyu , Chen Pengcheng , Xie Tianfa , Shao Yue , Li Bo , Sun Yubing
Published: July 2021

Strain gradients, a graded change in the percentage of the deformation across a continuous field by applying forces, widely exist in development and physiological activities. The directional movement of cells is essential for proper cell localization, and directional cell migration in responses to gradients of chemicals, rigidity, and density and topography of extracellular matrices have been well-established. However, it is unclear whether strain gradients imposed on cells are sufficient to drive directional cell migration. In this work, we develop a programmable uniaxial cell stretch device coupled with geometrical constraints to create controllable strain gradients on cells. We demonstrate that single rat embryonic fibroblasts respond to very small strain gradients. In a gradient level of ∼4% per mm, over 60% of the REFs prefer to migrate towards the lower strain side in both the static and the 0.1 Hz cyclic stretch conditions. We confirm that such responses to strain gradient are distinct from durotaxis or haptotaxis. Moreover, we discover that the directional migration of the cells is initiated by increased focal adhesion contact areas and higher rate of protrusion formation on the lower strain side of the cell. We further establish a 2D extended motor-clutch model to explain the molecular mechanism. Through our model, we find that the strain-introduced traction force determines integrin fibronectin pairs’ catch-release dynamics, which drives such directional migration. Together, our results establish strain gradient as a novel cue to regulate directional cell migration and may provide new insights into development and tissue repairs.
Fully resolved assembly of Cryptosporidium parvum
Authors: Menon Vipin K. , Okhuysen Pablo C. , Chappell Cynthia L. , Mahmoud Medhat , Mahmoud Medhat , Meng Qingchang , Doddapaneni Harsha , Vee Vanesa , Han Yi , Salvi Sejal , Bhamidipati Sravya , Kottapalli Kavya , Weissenberger George , Shen Hua , Ross Matthew C. , Hoffman Kristi L. , Cregeen Sara Javornik , Muzny Donna M. , Metcalf Ginger A. , Gibbs Richard A. , Petrosino Joseph F. , Sedlazeck Fritz J.
Published: July 2021

Background

Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. As such, it is important to understand the diversity and genomic makeup of this prevalent parasite to fight established infections and prohibit further transmission. The basis of every genomic study is a high quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies.

Findings

Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on two main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single copy BUSCO genes.

Conclusions

This high quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional and association studies.
Age-associated changes to neuronal dynamics involve a disruption of excitatory/inhibitory balance in C. elegans
Authors: Wirak Gregory S , Florman Jeremy , Alkema Mark J , Connor Christopher W , Gabel Christopher V
Published: July 2021

In the aging brain, many of the alterations underlying cognitive and behavioral decline remain opaque. C. elegans offers a powerful model for aging research, with a simple, well-studied nervous system to further our understanding of the cellular modifications and functional alterations accompanying senescence. We perform multi-neuronal functional imaging across the aged C. elegans nervous system, measuring an age-associated breakdown in system-wide functional organization. At single-cell resolution, we detect shifts in activity dynamics toward higher frequencies. In addition, we measure a specific loss of inhibitory signaling that occurs early in the aging process and alters the systems critical excitatory/inhibitory balance. These effects are recapitulated with mutation of the calcium channel subunit UNC-2/CaV2α,. We find that manipulation of inhibitory GABA signaling can partially ameliorate or accelerate the effects of aging. The effects of aging are also partially mitigated by disruption of the insulin signaling pathway, known to increase longevity, or by a reduction of caspase activation. Data from mammals are consistent with our findings, suggesting a conserved shift in the balance of excitatory/inhibitory signaling with age that leads to breakdown in global neuronal dynamics and functional decline.
Decoding Images from Multi-Region, High Resolution, Electrode Recordings In the Mouse Visual System
Authors: Fritz Chris
Published: July 2021

1

We hypothesize that deep networks are superior to linear decoders at recovering visual stimuli from neural activity. Using high-resolution, multielectrode Neuropixels recordings, we verify this is the case for a simple feed-forward deep neural network having just 7 layers. These results suggest that these feed-forward neural networks and perhaps more complex deep architectures will give superior performance in a visual brain-machine interface.
Epidemiological inference for emerging viruses using segregating sites
Authors: Park Yeongseon , Martin Michael , Koelle Katia
Published: July 2021

Epidemiological models are commonly fit to case data to estimate model parameters and to infer unobserved disease dynamics. Epidemiological models have also been fit to viral sequence data using phylodynamic inference approaches that rely on the reconstruction of viral phylogenies. However, especially early on in an expanding viral population, phylogenetic uncertainty can be substantial and methods that require integration over this uncertainty can be computationally intensive. Moreover, these approaches require estimation of parameters associated with models of sequence evolution in addition to the estimation of epidemiological parameters that are of primary interest. Here, we present an alternative approach to phylodynamic inference that can be used early on during the expansion of a viral lineage that circumvents the need for phylogenetic tree reconstruction. Our “tree-free” approach instead relies on quantifying the number of segregating sites observed in sets of sequences over time and using this trajectory of segregating sites to infer epidemiological parameters within a Sequential Monte Carlo (SMC) framework. Using forward simulations, we first show that epidemiological parameters and processes leave characteristic signatures in segregating site trajectories, demonstrating that these trajectories have the potential to be used for interfacing epidemiological models with sequence data. We then show that our proposed approach accurately recovers key epidemiological quantities such as the basic reproduction number and the timing of the index case from mock data simulated under a single-introduction scenario. Finally, we apply our approach to SARS-CoV-2 sequence data from France, estimating a reproductive number of approximately 2.5 to 2.7 under an epidemiological model structure that allows for multiple introductions, consistent with estimates from epidemiological surveillance data. Our findings indicate that “tree-free” statistical inference approaches that rely on simple population genetic summary statistics can be informative of epidemiological parameters and can be used for reconstructing infectious disease dynamics early on in an epidemic or during the expansion of a viral lineage.
MuscleNET: mapping electromyography to kinematic and dynamic biomechanical variables by machine learning
Authors: Nasr Ali , Bell Sydney , He Jiayuan , Whittaker Rachel L. , Jiang Ning , Dickerson Clark R. , McPhee John
Published: July 2021

Objective

This paper proposes machine learning models for mapping surface electromyography (sEMG) signals to regression of joint angle, joint velocity, joint acceleration, joint torque, and activation torque.

Approach

The regression models, collectively known as MuscleNET, take one of four forms: ANN (Forward Artificial Neural Network), RNN (Recurrent Neural Network), CNN (Convolutional Neural Network), and RCNN (Recurrent Convolutional Neural Network). Inspired by conventional biomechanical muscle models, delayed kinematic signals were used along with sEMG signals as the machine learning model’s input; specifically, the CNN and RCNN were modeled with novel configurations for these input conditions. The models’ inputs contain either raw or filtered sEMG signals, which allowed evaluation of the filtering capabilities of the models. The models were trained using human experimental data and evaluated with different individual data.

Main results

Results were compared in terms of regression error (using the root-mean-square) and model computation delay. The results indicate that the RNN (with filtered sEMG signals) and RCNN (with raw sEMG signals) models, both with delayed kinematic data, can extract underlying motor control information (such as joint activation torque or joint angle) from sEMG signals in pick-and-place tasks. The CNNs and RCNNs were able to filter raw sEMG signals.

Significance

All forms of MuscleNET were found to map sEMG signals within 2 ms, fast enough for real-time applications such as the control of exoskeletons or active prostheses. The RNN model with filtered sEMG and delayed kinematic signals is particularly appropriate for applications in musculoskeletal simulation and biomechatronic device control.
The characteristics of the HIV-1 Env glycoprotein contribute to viral pathogenesis
Authors: Pérez-Yanes Silvia , Pernas Maria , Marfil Silvia , Cabrera-Rodríguez Romina , Ortiz Raquel , Rovirosa Carla , Estévez-Herrera Judith , Olivares Isabel , Casado Concepción , Lopez-Galindez Cecilio , Blanco Julià , Valenzuela-Fernández Agustin
Published: July 2021

The understanding of HIV-1 pathogenesis and clinical progression is incomplete because of the variable contribution of host, immune and viral factors. The involvement of viral factors has been investigated in extreme clinical phenotypes from rapid progressors to long-term non-progressors (LTNPs). Among HIV-1 proteins, the envelope glycoprotein complex (Env) has concentrated many studies for its important role in the immune response and in the first steps of viral replication. In this study, we analyzed the contribution of 41 Envs from 24 patients with different clinical progression rates and viral loads (VLs), LTNP-Elite Controllers (LTNP-ECs); Viremic LTNPs (vLTNPs), and non-controller’s individuals contemporary to LTNPs or recent, named Old and Modern progressors. We analyzed the Env expression, the fusion and cell-to-cell transfer capacities as well as viral infectivity. The sequence and phylogenetic analysis of Envs were also performed. In every functional characteristic, the Envs from subjects with viral control (LTNP-ECs and vLTNPs) showed significant lower performance compared to those from the progressor individuals (Old and Modern). Regarding sequence analysis, the variable loops of the gp120 subunit of the Env (i.e., V2, V4 and mainly V5) of the progressor individuals showed longer and more glycosylated sequences than controller subjects. Therefore, HIV-1 Envs presenting poor viral functions and shorter sequences were associated with viremic control and the non-progressor clinical phenotype, whereas functional Envs were associated with the lack of virological control and progressor clinical phenotypes. These correlations support the central role of Env genotypic and phenotypic characteristics in the in vivo HIV-1 infection and pathogenesis.

IMPORTANCE

The role of the virus in the pathogenesis of HIV-1 infection has not been investigated in isolates from individuals with different progression rates. In this work, we studied the properties of the envelope glycoprotein complex (Env) in individuals with different progression rates to elucidate its role in pathogenesis. We estimated the Env expression, the CD4 binding, the fusion and cell-to-cell viral transfer capacities that affect the infectivity of the viral Envs in recombinant viruses. The Envs from individuals which control viral replication and lack clinical progression (LTNP-ECs and vLTNPs) showed lower functional capacities than from subjects with clinical progression (Old and Modern). The functional increase of the Envs characteristics was associated with an increase in viral infectivity and in increased length of variable loops and the number of glycosylation sites of the Env (gp120/SU). These results support the concept that viral characteristics contribute to viral infection and pathogenesis.
Genome-Wide Association Meta-Analysis Using a Recessive Model Illuminates Genetic Architecture of Type 2 Diabetes
Authors: O’Connor Mark J. , Huerta-Chagoya Alicia , Cortés-Sánchez Paula , Bonàs-Guarch Silvía , Guindo-Martínez Marta , Cole Joanne B. , Torrents David , Veerapen Kumar , Grarup Niels , Kurki Mitja , Rundsten Carsten F. , Pedersen Oluf , Brandslund Ivan , Linneberg Allan , Hansen Torben , Leong Aaron , Florez Jose C. , Mercader Josep M.
Published: July 2021

Objective

Most genome-wide association studies (GWAS) of complex traits are performed using models with additive allelic effects. Hundreds of loci associated with type 2 diabetes have been identified using this approach. Additive models, however, can miss loci with recessive effects, thereby leaving potentially important genes undiscovered.

Research Design and Methods

We conducted the largest GWAS meta-analysis using a recessive model for type 2 diabetes. Our discovery sample included 33,139 cases and 279,507 controls from seven European-ancestry cohorts including the UK Biobank. We then used two additional cohorts, FinnGen and a Danish cohort, for replication. For the most significant recessive signal, we conducted a phenome-wide association study across hundreds of traits to make inferences about the pathophysiology underlying the increased risk seen in homozygous carriers.

Results

We identified 51 loci associated with type 2 diabetes, including five variants with recessive effects undetected by prior additive analyses. Two of the five had minor allele frequency less than 5% and were each associated with more than doubled risk. We replicated three of the variants, including one of the low-frequency variants, rs115018790, which had an odds ratio in homozygous carriers of 2.56 (95% CI 2.05-3.19, P=1×10−16) and a stronger effect in men than in women (interaction P=7×10−7). Colocalization analysis linked this signal to reduced expression of the nearby PELO gene, and the signal was associated with multiple diabetes-related traits, with homozygous carriers showing a 10% decrease in LDL and a 20% increase in triglycerides.

Conclusions

Our results demonstrate that recessive models, when compared to GWAS using the additive approach, can identify novel loci, including large-effect variants with pathophysiological consequences relevant to type 2 diabetes.
Heparin for Moderately Ill Patients with Covid-19
Authors: Sholzberg Michelle , Tang Grace H. , Rahhal Hassan , AlHamzah Musaad , Kreuziger Lisa Baumann , Ní Áinle Fionnuala , Alomran Faris , Alayed Khalid , Alsheef Mohammed , AlSumait Fahad , Pompilio Carlos Eduardo , Sperlich Catherine , Tangri Sabrena , Tang Terence , Jaksa Peter , Suryanarayan Deepa , Almarshoodi Mozah , Castellucci Lana , James Paula D. , Lillicrap David , Carrier Marc , Beckett Andrew , Colovos Christos , Jayakar Jai , Arsenault Marie-Pier , Wu Cynthia , Doyon Karine , Andreou E. Roseann , Dounaevskaia Vera , Tseng Eric K. , Lim Gloria , Fralick Michael , Middeldorp Saskia , Lee Agnes Y.Y. , Zuo Fei , da Costa Bruno R. , Thorpe Kevin E. , Negri Elnara Márcia , Cushman Mary , Jüni Peter ,   the RAPID Trial investigators
Published: July 2021

Background

Heparin, in addition to its anticoagulant properties, has anti-inflammatory and potential anti-viral effects, and may improve endothelial function in patients with Covid-19. Early initiation of therapeutic heparin could decrease the thrombo-inflammatory process, and reduce the risk of critical illness or death.

Methods

We randomly assigned moderately ill hospitalized ward patients admitted for Covid-19 with elevated D-dimer level to therapeutic or prophylactic heparin. The primary outcome was a composite of death, invasive mechanical ventilation, non-invasive mechanical ventilation or ICU admission. Safety outcomes included major bleeding. Analysis was by intention-to-treat.

Results

At 28 days, the primary composite outcome occurred in 37 of 228 patients (16.2%) assigned to therapeutic heparin, and 52 of 237 patients (21.9%) assigned to prophylactic heparin (odds ratio, 0.69; 95% confidence interval [CI], 0.43 to 1.10; p=0.12). Four patients (1.8%) assigned to therapeutic heparin died compared with 18 patients (7.6%) assigned to prophylactic heparin (odds ratio, 0.22; 95%-CI, 0.07 to 0.65). The composite of all-cause mortality or any mechanical ventilation occurred in 23 (10.1%) in the therapeutic heparin group and 38 (16.0%) in the prophylactic heparin group (odds ratio, 0.59; 95%-CI, 0.34 to 1.02). Major bleeding occurred in 2 patients (0.9%) with therapeutic heparin and 4 patients (1.7%) with prophylactic heparin (odds ratio, 0.52; 95%-CI, 0.09 to 2.85).

Conclusions

In moderately ill ward patients with Covid-19 and elevated D-dimer level, therapeutic heparin did not significantly reduce the primary outcome but decreased the odds of death at 28 days.

Trial registration numbers: NCT04362085; NCT04444700
Automated lung sound analysis using the LungPass platform: A sensitive and specific tool for identifying lower respiratory tract involvement in COVID-19
Authors: Lapteva Elena A. , Kharevich Olga N. , Khatsko Victoria V. , Voronova Natalia A. , Chamko Maksim V. , Bezruchko Irina V. , Katibnikova Elena I. , Loban Elena I. , Mouawie Mostafa M. , Binetskaya Helena , Aleshkevich Sergey , Karankevich Aleksey , Dubinetski Vitaly , Vestbo Jørgen , Mathioudakis Alexander G.
Published: July 2021

Background

Lower respiratory tract (LRT) involvement, observed in about 20% of patients suffering from coronavirus disease 2019 (COVID-19) is associated with a more severe clinical course, adverse outcomes and long-term sequelae. Early identification of LRT involvement could facilitated targeted and timely interventions that could alter the short- and long-term disease outcomes. The LungPass is an automated lung sound analysis platform developed using neural network technology and previously trained. We hypothesised that the LungPass could be used as a screening tool for LRT involvement in patients with COVID-19.

Methods

In a prospective observational study involving 282 individuals with presenting in the emergency department with a strong clinical suspicion of COVID-19 and imaging findings consistent with COVID-19 LRT involvement (25.5% had concomitant hypoxia), and 32 healthy controls, we assessed the sensitivity and specificity of the LungPass in identifying LRT involvement in COVID-19. We also compared the auscultatory findings of the LungPass compared to a chest physician using a traditional, high-quality stethoscope.

Results

Among individuals with COVID-19 LRT involvement, the LungPass identified crackles in at least one auscultation site in 93.6% and in two or more points in 84%. Moreover, the LungPass identified any abnormal lung sound (crackles or wheeze) in at least one auscultation site in 98.6% and in at least two points in 94% of the participants. The respective percentages for the respiratory physicians were lower.

Considering the presence of any added abnormal sound (crackles or wheeze) in at least two auscultation points as evidence of LRT involvement, LungPass demonstrated a sensitivity of 98.6% (95% confidence intervals [CI]: 96.4%-99.6%) and a specificity of 96.9% (95% CI: 83.8%-99.9%) in identifying COVID-19 LRT involvement.

Conclusion

This exploratory study suggests the LungPass is a sensitive and specific platform for identifying LRT involvement due to COVID-19, even before the development of hypoxia.
REACT-1 round 13 interim report: acceleration of SARS-CoV-2 Delta epidemic in the community in England during late June and early July 2021
Authors: Riley Steven , Eales Oliver , Haw David , Wang Haowei , Walters Caroline E. , Ainslie Kylie E. C. , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Barclay Wendy , Cooke Graham , Ward Helen , Darzi Ara , Elliott Paul
Published: July 2021

Background

Despite high levels of vaccination in the adult population, cases of COVID-19 have risen exponentially in England since the start of May 2021 driven by the Delta variant. However, with far fewer hospitalisations and deaths per case during the recent growth in cases compared with 2020, it is intended that all remaining social distancing legislation in England will be removed from 19 July 2021.

Methods

We report interim results from round 13 of the REal-time Assessment of Community Transmission-1 (REACT-1) study in which a cross-sectional sample of the population of England was asked to provide a throat and nose swab for RT-PCR and to answer a questionnaire. Data collection for this report (round 13 interim) was from 24 June to 5 July 2021.

Results

In round 13 interim, we found 237 positives from 47,729 swabs giving a weighted prevalence of 0.59% (0.51%, 0.68%) which was approximately four-fold higher compared with round 12 at 0.15% (0.12%, 0.18%). This resulted from continued exponential growth in prevalence with an average doubling time of 15 (13, 17) days between round 12 and round 13. However, during the recent period of round 13 interim only, we observed a shorter doubling time of 6.1 (4.0, 12) days with a corresponding R number of 1.87 (1.40, 2.45). There were substantial increases in all age groups under the age of 75 years, and especially at younger ages, with the highest prevalence in 13 to 17 year olds at 1.33% (0.97%, 1.82%) and in 18 to 24 years olds at 1.40% (0.89%, 2.18%). Infections have increased in all regions with the largest increase in London where prevalence increased more than eight-fold from 0.13% (0.08%, 0.20%) in round 12 to 1.08% (0.79%, 1.47%) in round 13 interim. Overall, prevalence was over 3 times higher in the unvaccinated compared with those reporting two doses of vaccine in both round 12 and round 13 interim, although there was a similar proportional increase in prevalence in vaccinated and unvaccinated individuals between the two rounds.

Discussion

We are entering a critical period with a number of important competing processes: continued vaccination rollout to the whole adult population in England, increased natural immunity through infection, reduced social mixing of children during school holidays, increased proportion of mixing occurring outdoors during summer, the intended full opening of hospitality and entertainment and cessation of mandated social distancing and mask wearing. Surveillance programmes are essential during this next phase of the epidemic to provide clear evidence to the government and the public on the levels and trends in prevalence of infections and their relationship to vaccine coverage, hospitalisations, deaths and Long COVID.
Intracellular phase separation of globular proteins facilitated by short cationic peptides
Authors: Yeong Vivian , Wang Jou-wen , Horn Justin M. , Obermeyer Allie C.
Published: July 2021

Phase separation provides intracellular organization and underlies a variety of cellular processes. These biomolecular condensates exhibit distinct physical and material properties. Current strategies for engineering condensate formation include using intrinsically disordered domains and altering protein surface charge by chemical supercharging or site-specific mutagenesis. We add to this toolbox by designing short, highly charged peptide tags that provide several key advantages for engineering protein phase separation. Herein, we report the use of short cationic peptide tags for sequestration of proteins of interest into bacterial condensates. Using a panel of GFP variants, we demonstrate how cationic tag and globular domain charge contribute to intracellular phase separation in E. coli and observe that the tag can affect condensate disassembly at a given net charge near the phase separation boundary. We showcase the broad applicability of these tags by appending them onto enzymes and demonstrating that the sequestered enzymes remain catalytically active.

Abstract Figure
Local CpG density affects the trajectory of age-associated epigenetic changes
Authors: Higham Jonathan , Zhang Qian , Walker Rosie M. , Harris Sarah E. , Howard David M. , Hawkins Emma L. , Sandu Anca-Larisa , Steele J. Douglas , Waiter Gordon D. , Murray Alison D. , Evans Kathryn L. , McIntosh Andrew M. , Visscher Peter M. , Deary Ian J. , Cox Simon R. , Sproul Duncan
Published: July 2021

DNA methylation is an epigenetic mark associated with gene repression and genome stability. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Rates of aging inferred from these clocks correlate with human health. However, the molecular mechanisms underpinning age-associated DNA methylation changes are unknown. Local DNA sequence plays a strong role in programming DNA methylation levels at individual loci independently of age, but its influence on age-associated DNA methylation changes is unknown. We analysed longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs in the genome. We show that changes in methylation with age are especially apparent at 8,322 low CpG density loci. Using SNP data from the same individuals we demonstrate that DNA methylation trajectories are affected by local sequence polymorphisms at 1,487 loci with low CpG density. More generally, we find that local CpG density is a strong determinant of a CpG’s methylation trajectory and that CpGs located in low CpG density regions are particularly prone to change. Overall, our results demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.
Rapid evolution of the functionally conserved gap genegiantinDrosophila
Authors: Chang Wenhan , Matute Daniel R. , Kreitman Martin
Published: July 2021

Developmental processes in multicellular organisms, and the outcomes they produce, are often evolutionarily conserved. Yet phylogenetic conservation of developmental outcomes is not reflected in functional preservation of the genes regulating these processes, a phenomenon referred to as developmental system drift (1, 2). Little is known about the evolutionary forces producing change in the molecular details of regulatory genes and their networks while preserving development outcomes. Here we address this void in knowledge by systematically swapping theDrosophila melanogastercoding and noncoding regions of the essential gap gene,giant, a key regulator of embryonic pattern formation, with orthologous sequences drawn from both closely and distantly related species within the genus. Employing sensitized genetic complementation assays, the loss of a transgene’s ability to restore viability occurs across phylogeny at every interspecific level of comparison and includes both coding and noncoding changes. Epistasis is present as well — both between coding and noncoding sequences and, in a dramatic example of change-of-sign epistasis, between the only two coding substitutions separating two very closely related species. A continuous process of functional divergence hidden under conserved phylotypic developmental outcomes requires reconsideration of the prevailing view that the essential genes in conserved regulatory networks are protected from the driving forces of evolutionary change.
In Silico Defined SARS-CoV2 Epitopes May Not Predict Immunogenicity to COVID19
Authors: Pan Ke , Chiu Yulun , Chen Michelle , Wang Junmei , Lai Ivy , Singh Shailbala , Shaw Rebecca , Yee Cassian
Published: July 2021

SARS-CoV-2 infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally, if not more important than humoral responses in mediating recovery and immune-protection. One of the major challenges in developing T cell-based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticatedin silicomethods to predict putative epitopes deduced from binding affinities and consensus data. Our studies find that, in contrast to current dogma, ‘immunodominant’ SARS-CoV-2 peptides defined by suchin silicomethods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes.
Tactile motor attention induces sensory attenuation for sounds
Authors: Fritz Clara , Flick Mayra , Zimmermann Eckart
Published: July 2021

Sensory events appear reduced in intensity when we actively produce them. Here, we investigated sensory attenuation in a virtual reality setup that allowed us to manipulate the time of tactile feedback when pressing a virtual button. We asked whether tactile motor attention might shift to the tactile location that makes contact with the button. In experiment one, we found that a tactile impulse was perceived as more intense when button pressing. In a second experiment, participants pushed a button and estimated the intensity of sounds. We found sensory attenuation for sounds only when tactile feedback was provided at the time the movement goal was reached. These data indicate that attentional prioritization for the tactile modality during a goal-directed hand movement might lead to a transient reduction in sensitivity in other modalities, resulting in sensory attenuation for sounds.
Stress relaxation amplitude of hydrogels determines migration, proliferation, and morphology of cells in 3-D
Authors: Hazur Jonas , Endrizzi Nadine , Schubert Dirk W. , Boccaccini Aldo R. , Fabry Ben
Published: July 2021

The viscoelastic behavior of hydrogel matrices sensitively influences the cell behavior in 3D culture and biofabricated tissue model systems. Previous reports have demonstrated that cells tend to adhere, spread, migrate and proliferate better in hydrogels with pronounced stress relaxation. However, it is currently unknown if cells respond more sensitively to the amplitude of stress relaxation, or to the relaxation time constant. To test this, we compare the behavior of fibroblasts cultured for up to 10 days in alginate and oxidized alginate hydrogels with similar Young’s moduli but diverging stress relaxation behavior. We find that fibroblasts elongate, migrate and proliferate better in hydrogels that display a higher stress relaxation amplitude. By contrast, the cells’ response to the relaxation time constant was less pronounced and less consistent. Together, these data suggest that it is foremost the stress relaxation amplitude of the matrix that determines the ability of cells to locally penetrate and remodel the matrix, which subsequently leads to better spreading, faster migration, and higher cell proliferation. We conclude that the stress relaxation amplitude is a central design parameter for optimizing cell behavior in 3-D hydrogels.
Centriole distal-end proteins CP110 and Cep97 influence centriole cartwheel growth at the proximal-end
Authors: Aydogan Mustafa G. , Hankins Laura E. , Steinacker Thomas L. , Mofatteh Mohammad , Saurya Saroj , Wainman Alan , Wong Siu-Shing , Lu Xin , Zhou Felix Y. , Raff Jordan W.
Published: July 2021

Centrioles are composed of a central cartwheel tethered to nine-fold symmetric microtubule (MT) blades. The centriole cartwheel and MTs are thought to grow from opposite ends of these organelles, so it is unclear how they coordinate their assembly. We previously showed that an oscillation of Polo-like kinase 4 (Plk4) helps to initiate and time the growth of the cartwheel at the proximal end. Here, we show that CP110 and Cep97 form a complex close to the distal-end of the centriole MTs whose levels rise and fall as the new centriole MTs grow, entrained by the core Cdk/Cyclin oscillator that drives the nuclear divisions in these embryos. These CP110/Cep97 dynamics, however, do not appear to time the period of centriole MT growth directly. Instead, we find that changing the levels of CP110/Cep97 alters the Plk4 oscillation and the growth of the cartwheel at the proximal end. These findings reveal an unexpected crosstalk between factors normally concentrated at opposite ends of the growing centrioles, which may help to coordinate centriole growth.
Evaluation of intranasal nafamostat or camostat for SARS-CoV-2 chemoprophylaxis in Syrian golden hamsters
Authors: Neary M , Box H , Sharp J , Tatham L , Curley P , Herriott J , Kijak E , Arshad U , Hobson JJ , Rajoli RKR , Pertinez H , Valentijn A , Dhaliwal K , McCaughan F , Rannard SP , Kipar A , Stewart JP , Owen A
Published: July 2021

Successful development of a chemoprophylaxis against SARS-CoV-2 could provide a tool for infection prevention implementable alongside vaccination programmes. Camostat and nafamostat are serine protease inhibitors that inhibit SARS-CoV-2 viral entry in vitro but have not been characterised for chemoprophylaxis in animal models. Clinically, nafamostat is limited to intravenous delivery and while camostat is orally available, both drugs have extremely short plasma half-lives. This study sought to determine whether intranasal dosing at 5 mg/kg twice daily was able to prevent airborne transmission of SARS-CoV-2 from infected to uninfected Syrian golden hamsters. SARS-CoV-2 viral RNA was above the limits of quantification in both saline- and camostat-treated hamsters 5 days after cohabitation with a SARS-CoV-2 inoculated hamster. However, intranasal nafamostat-treated hamsters remained RNA negative for the full 7 days of cohabitation. Changes in body weight over the course of the experiment were supportive of a lack of clinical symptomology in nafamostat-treated but not saline- or camostat-treated animals. These data are strongly supportive of the utility of intranasally delivered nafamostat for prevention of SARS-CoV-2 infection and further studies are underway to confirm absence of pulmonary infection and pathological changes.
Cytoplasmic Switch of ARS2 Isoforms Promotes Nonsense-Mediated mRNA Decay and Arsenic Sensitivity
Authors: Mesa-Perez Monica , Hamilton Phineas T. , Miranda-Rodriguez Alex , Brodie Nicholas , O’Sullivan Connor , Christie Jennifer , Ryan Bridget C. , Chow Robert L. , Goodlett David , Nelson Christopher J. , Howard Perry L.
Published: July 2021

The life of RNA polymerase II (RNAPII) transcripts is shaped by the dynamic formation of mutually exclusive ribonucleoprotein complexes (RNPs) that direct transcript biogenesis and turnover. A key regulator of RNA metabolism in the nucleus is the scaffold protein ARS2 (arsenic resistance protein 2), bound to the cap binding complex (CBC). We report here that alternative splicing of ARS2’s intron 5, generates cytoplasmic isoforms that lack 270 amino acids from the N-terminal of the protein and are functionally distinct from nuclear ARS2. Switching of ARS2 isoforms within the CBC in the cytoplasm has dramatic functional consequences, changing ARS2 from a NMD inhibitor to a NMD promoter that enhances the binding of UPF1 to NCBP1, ERF1 and DHX34, favouring SURF complex formation, SMG7 recruitment and transcript degradation. ARS2 isoform exchange is also relevant during arsenic stress, where cytoplasmic ARS2 promotes a global response to arsenic in a CBC-independent manner. We propose that ARS2 isoform switching promotes the proper recruitment of RNP complexes during NMD and the cellular response to arsenic stress. The existence of non-redundant ARS2 isoforms is relevant for cell homeostasis, stress response, and cancer treatment.
Glycocalyx engineering with heparan sulfate mimetics attenuates Wnt activity during adipogenesis to promote glucose uptake and metabolism
Authors: Trieger Greg W. , Pessentheiner Ariane R. , Purcell Sean C. , Green Courtney R. , DeForest Natalie , Willert Karl , Majithia Amit R. , Metallo Christian M. , Godula Kamil , Gordts Philip L. S. M.
Published: July 2021

Adipose tissue (AT) plays a crucial role in maintaining me tabolic homeostasis by storing lipids and glucose from circulation as intracellular fat. As peripheral tissues like AT become insulin resistant, decompensation of blood glucose levels occurs causing type 2 diabetes (T2D). Currently, glycocalyx modulating as a pharmacological treatment strategy to improve glucose homeostasis in T2D patients is underexplored. Here, we show a novel role for cell surface heparan sulfate (HS) in establishing glucose uptake capacity and metabolic utilization in differentiated adipocytes. Using a combination of chemical and genetic interventions, we identified that HS modulates this metabolic phenotype by attenuating levels of Wnt signaling during adipogenesis. By engineering the glycocalyx of preadipocytes with exogenous synthetic HS mimetics, we were able to enhance glucose clearance capacity after differentiation through modulation of Wnt ligand availability. These findings establish the cellular glycocalyx as a possible new target for therapeutic intervention in T2D patients by enhancing glucose clearance capacity independent of insulin secretion.

SIGNIFICANCE

Metabolic disorders associated with the Western-style diet, such as type 2 diabetes, are among the main drivers of mortality in the US and globally, with more than 380 million people currently affected by this disease worldwide. However, treatment options for type 2 diabetes are currently limited to management of caloric uptake and expenditure, with none able to reverse the condition long-term. The ability to reprogram adipose tissues to improve their overall capacity to clear glucose may provide one such opportunity. Here we provide evidence that glycocalyx remodeling in pre-adipocytes with heparan sulfate mimetics will alter their differentiation program by modulating Wnt signaling to produce adipocytes with increased glucose uptake and utilization.
Crystal structures of three N-acylhydrazone isomers
Authors: Purandara H. , Foro Sabine , Thimme Gowda B.
Published: July 2021

The crystal structures of three isomers of (E)-4-chloro-N-{2-[2-(chlorobenzylidene)hydrazinyl]-2-oxoethyl}benzenesulfonamide, namely, (E)-4-chloro-N-{2-[2-(2-chlorobenzylidene)hydrazinyl]-2-oxoethyl}benzenesulfonamide (I), (E)-4-chloro-N-{2-[2-(3-chlorobenzylidene)hydrazinyl]-2-oxoethyl}benzenesulfonamide (II) and (E)-4-chloro-N-{2-[2-(4-chlorobenzylidene)hydrazinyl]-2-oxoethyl}benzenesulfonamide (III), with the general formula C15H13Cl2N3O3S are described, with the chloro group in ortho, meta and para positions in the benzylidene benzene ring. All the three isomeric compounds crystallize in the centrosymmetric triclinic P\overline{1} space group with one molecule each in the asymmetric unit and two molecules in the unit cell. The dihedral angles between the two phenyl rings are 11.09 (14), 53.79 (18) and 72.37 (11)° in (I), (II) and (III), respectively. The central part of the molecule (–C—N—N=C–) is almost linear with C—N—N—C torsion angles of 179.1 (2), −169.5 (3) and 178.5 (2)° for (I), (II) and (III), respectively. In all the three crystals, the molecules form inversion dimers with R
2
2(8) ring motifs, which are further augmented by C—H...O interactions.
Bis(pyridine-2-carboxylato-κ2
N,O)copper(II)]–benzene-1,3,5-tricarboxylic acid–water (1/2/2)
Authors: Zhang Wenkai , Zhang Bingguang , Sun Qiaozhen
Published: July 2021

In the title complex, [Cu(C6H4O2N)2]·2C9H6O6·2H2O, the Cu2+ ion lies on a center of inversion and coordinates with symmetry related pyridine nitrogen and carboxyl oxygen atoms from two pyridine-2-carboxylic acid anions, giving rise to a square-planar coordination geometry. There are weak axial bonds between Cu and an O atom of a symmetry-related trimesic acid moieties [Cu...O = 2.837 (2) Å] The Cu...O weak interactions and hydrogen bonds stabilize the whole structure.
Ethanol(nitrato)[tris(4-cyano-3-phenyl-1H-pyrazol-1-yl)hydroborato]nickel(II)
Authors: Salerno Elvin V. , Kadel Lava R. , Eichhorn David M.
Published: July 2021

The synthesis and structure is reported of TpPh,4CNNi(NO3)(EtOH) or [Ni(C30H19BN9)(NO3)(C2H6O)], the first half-sandwich complex of a cyanoscorpionate ligand. The pseudooctahedral coordination sphere of the NiII ion is comprised of a tridentate tris(4-cyano-3-phenylpyrazolyl)borate ligand, a bidentate nitrate ligand and a neutral ethanol ligand. The phenyl substituents on the TpPh,4CN ligand are relatively parallel to the planes of the ethanol and nitrate ligands. An intermolecular hydrogen-bonding interaction is evident between the ethanol OH group and the pyrazole CN substituent. The ethanol ligand was modeled with a 0.572 (13)/0.428 (13) disorder of the methyl C atom.
Analysis of operational and financial performance of ports: an integrated fuzzy DEMATEL-TOPSIS approach
Authors: Gayathri C. , Kamala V. , Gajanand M.S. , Yamini S.
Published: July 2021

Purpose

Ports handle a significant portion of international cargo, so the performance of ports plays a major role in the economic development of a country. This paper aims to study how port performance depends on various interdependent factors and how it requires a holistic approach, which accounts for all the necessary criteria that contribute to the overall efficiency and performance.

Design/methodology/approach

An integrated fuzzy DEMATEL-TOPSIS approach with an objective to evaluate the operational capability and financial performance of the ports is proposed. A case study is presented with an analysis of the major South Indian ports to assess port operational performance and evaluate various financial ratios to assess financial performance.

Findings

Through a review of the literature and based on the inputs from experts, six criteria affecting the operational performance and six financial criteria were identified. The debt coverage ratios turned out to be the most important, while the liquidity ratios were the least important. The six operational criteria have almost similar importance. The final results indicate a consistent overall performance by the Ennore Port, except during one financial year.

Practical implications

The proposed solution approach helps to identify and concentrate on the criteria that affect port performance. It will also help to evaluate and understand the dynamics involved in the performance of ports.

Originality/value

This work highlights the key measurable operational and financial criteria that affect the efficiency of ports. The integrated fuzzy DEMATEL-TOPSIS approach provides a better way to evaluate and benchmark port performance.