bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparison of the Time Spent in Emergency Departments by Older Adults With and Without Mental Health Needs
Authors: Goode Deborah , Slater Paul , Ryan Assumpta , Melby Vidar
Published: April 2021

Older adults present to emergency medical services with a multitude of clinical and functional needs due to polypharmacy and multipathology. Older adults with mental health needs require additional time for the more comprehensive assessment required as a result of their underlying mental health condition. This article compares the time spent in emergency departments by older adults who have a mental health need with those who do not. Information on how they access prehospital and inhospital care is examined alongside key factors that impact on time spent in emergency departments. Data were collected from hospital records of older adults presenting at emergency departments in 3 large Health and Social Care Trusts in the United Kingdom using a retrospective, secondary, official personal information database source over 1 year. A total sample of 74,766 attendance records of older adults older than 65 years were examined. adults who presented with or had a mental health condition in their diagnosis or history, which made up a subsample of 1,818 people, were found to have significant differences in the time spent in emergency departments and some notable differences in trends and admission patterns. They wait longer than the older person without mental health needs, are more likely to breach the 4-hr waiting time target, are admitted in higher numbers, and rely heavily on the ambulance service. Health and social care systems and services need to undergo transformations to ensure that all people who access services are treated fairly and effectively.
Vasospasm severity is associated with cerebral infarction after subarachnoid hemorrhage
Authors: Snider Samuel B , Migdady Ibrahim , LaRose Sarah L , Mckeown Morgan E , Regenhardt Robert W , Rosalind Lai Pui Man , Vaitkevicius Henrikas , Du Rose
Published: April 2021

Background

The presence of angiographic vasospasm after aneurysmal subarachnoid hemorrhage (aSAH) is associated with delayed-cerebral ischemia (DCI)-related cerebral infarction and worsened neurological outcome. Transcranial doppler (TCD) measurements of cerebral blood velocity are commonly used after aSAH to screen for vasospasm. We sought to determine whether time-varying TCD measured vasospasm severity is associated with cerebral infarction and to investigate the performance characteristics of different time/severity cutoffs for predicting cerebral infarction.

Methods

We used a retrospective, single-center cohort of consecutive adult aSAH patients with angiographic vasospasm and at least one TCD study. Our primary outcome was DCI-related cerebral infarction, defined as an infarction developing at least 2 days after any surgical intervention without an alternative cause. Time-varying TCD vasospasm severity was defined ordinally (absent, mild, moderate, severe) by the most abnormal vessel on each post-admission hospital day. Cox proportional-hazards models were used to examine associations between time-varying vasospasm severity and infarction. The optimal TCD-based time/severity thresholds for predicting infarction were then identified using the Youden J statistic.

Results

Of 218 aSAH patients with angiographic vasospasm, 27 (12%) developed DCI-related infarction. As compared to those without infarction, patients with infarction had higher modified Fisher scale (mFS) scores, and an earlier onset of more-severe vasospasm. Adjusted for mFS, vasospasm severity was associated with infarction (aHR 1.9, 95% CI: 1.3-2.6). A threshold of at least mild vasospasm severity on hospital day 4 had a negative predictive value of 92% for the development of infarction, but a positive predictive value of 25%.

Conclusions

In aSAH, TCD-measured vasospasm severity is associated with DCI-related infarction. In a single-center dataset, a TCD-based threshold for predicting infarction had a high negative predictive value, supporting its role as an early screening tool to identify at-risk patients.
A Multicenter Evaluation of Blood Purification with Seraph 100 Microbind Affinity Blood Filter for the Treatment of Severe COVID-19: A Preliminary Report
Authors: Chitty Stephen A. , Mobbs Sarah , Rifkin Brian S. , Stogner Steven W. , Lewis Michael S. , Betancourt Jaime , DellaVolpe Jeffrey , Abouzahr Fadi , Wilhelm Andrew M. , Szerlip Harold M. , Gaeta Robert M. , Rivera Ian , Oliver James D. , Olson Stephen W. , Debnath Subrata , Barnett Sean P. , Parikh Amay , Walter Robert J. , Nguyen Mai T. , Sullivan Breandan , Alcover Karl C. , Stewart Ian J. , Pratt Kathleen P. , Sharma Kumar , Chung Kevin K. ,   for the PURIFY INVESTIGATORS
Published: April 2021

Objective

The Seraph®100 Microbind Affinity Blood Filter® (Seraph 100) is an extracorporeal medical countermeasure that can remove many pathogens from blood, including the SARS-CoV-2 virus. The aim of this study was to evaluate safety and efficacy of Seraph 100 treatment for severe coronavirus disease 2019 (COVID-19).

Design

Multicenter retrospective observational cohort study.

Setting

Intensive care units across four of thirteen participating sites who have completed data extraction.

Patients

Critically ill COVID-19 patients treated with Seraph 100 under an Emergency Use Authorization (n=53) and historical control patients who met criteria for treatment (n=46).

Intervention

Extracorporeal treatment with the Seraph 100 filter.

Measurements and Main Results

At baseline, the median age was 61 years, 72.7% were male, and 59.6% required mechanical ventilation. The groups were matched in terms of sex, race/ethnicity, body mass index, APACHE II score, need for mechanical ventilation, and other COVID-19 treatments. However, patients in the Seraph 100 group were younger with a median age of 61 years (IQR 42-65) compared to controls who had a median age of 64 (IQR 56-68, p=0.036). The Seraph 100 group also had a lower median Charlson comorbidity index (2, IQR 0-3) compared to control patients (3, IQR 2-4, p=0.006). Mortality was lower in the Seraph 100 treated group compared to the historical controls (37.7% vs 67.4%, respectively, p=0.003). Multivariable logistic regression analysis yielded an odds ratio of 0.27 (95% confidence interval 0.09-0.79, p=0.016). Of the 53 patients treated with Seraph 100, only 1 patient experienced a serious adverse event (transient hypotension at the start of the treatment which required a brief period of vasopressor support).

Conclusions

These data suggest that broad spectrum, pathogen agnostic, extracorporeal blood purification technologies can be safely and effectively deployed to meet new pathogen threats as an adjunct to standard treatments while awaiting the development of directed pharmacologic therapies and/or vaccines.
Systematic review of the association between ABO blood type and COVID-19 incidence and mortality
Authors: Bai Yuqing , Yan Zhou , Murray Eleanor J
Published: April 2021

A large proportion of COVID-19 research has been focused on identifying markers of high-risk individuals. However, this research often fails to consider basic epidemiologic concepts to prevent bias in the design, selection, and analysis of observational data. One suspected marker of risk that has been repeatedly assessed is ABO blood type. Given the ease of measuring this biomarker, it is an appealing target for identifying high-risk individuals. However, this same ease of measurement makes associational research on ABO blood type and COVID prone to a range of common epidemiologic errors. We conducted a systematic review of studies assessing correlations between ABO blood type and COVID incidence, hospitalization, and mortality to determine the quality of evidence these studies provide and whether the overall evidence suggests ABO blood type could provide a useful indicator of COVID risk. We conclude that most existing studies are low quality and suffer from major methodological flaws. The few higher-quality studies which do exist find no association between ABO blood type and COVID outcomes. We conclude that there is no evidence to support the use of ABO blood type as a marker for COVID risk or severity.

Key Points

There is no sufficient evidence to conclude a biological relationship between ABO blood types and COVID-19 infection or severity.

Biases of existing research could be avoided by careful study design.
Shut Down Schools, Knock Down the Virus? No Causal Effect of School Closures on the Spread of COVID-19
Authors: Fukumoto Kentaro , McClean Charles T. , Nakagawa Kuninori
Published: April 2021

As COVID-19 spread in 2020, most countries shut down schools in the hopes of slowing the pandemic. Yet, studies have not reached a consensus about the effectiveness of these policies partly because they lack rigorous causal inference. Our study aims to estimate the causal effects of school closures on the number of confirmed cases. To do so, we apply matching methods to municipal-level data in Japan. We do not find that school closures caused a reduction in the spread of the coronavirus. Our results suggest that policies on school closures should be reexamined given the potential negative consequences for children and parents.
Dual Adhesive Unipolar Polysaccharides Synthesized by Overlapping Biosynthetic Pathways inAgrobacterium tumefaciens
Authors: Onyeziri Maureen C. , Natarajan Ramya , Hardy Gail G. , Xu Jing , Reynolds Ian P. , Kim Jinwoo , Merritt Peter M. , Danhorn Thomas , Hibbing Michael E. , Weisberg Alexandra J. , Chang Jeff H. , Fuqua Clay
Published: April 2021

Agrobacterium tumefaciens, is a member of the Alphaproteobacteria that pathogenizes plants, and associates with biotic and abiotic surfaces via a single cellular pole.A. tumefaciensproduces the unipolar polysaccharide (UPP) at the site of surface contact. UPP production is normally surface-contact inducible, but elevated levels of the second messenger cyclic diguanylate monophosphate (cdGMP) bypass this requirement. Multiple lines of evidence suggest that the UPP has a central polysaccharide component. Using anA. tumefaciensderivative with elevated cdGMP and mutationally disabled for other dispensable polysaccharides, a series of related genetic screens have identified a large number of genes involved in UPP biosynthesis, most of which are Wzx-Wzy-type polysaccharide biosynthetic components. Extensive analyses of UPP production in these mutants have revealed that the UPP is comprised of two genetically, chemically and spatially discrete forms of polysaccharide, and that each requires a specific Wzy-type polymerase. Other important biosynthetic, processing and regulatory functions for UPP production are also revealed, some of which are common to both polysaccharides, and a subset of which are specific to each species. Many of the UPP genes identified are conserved among diverse rhizobia, whereas others are more lineage specific.

Plain language summary

Bacteria attach to a wide variety of surfaces including host tissues, via externalized structures described as adhesins. We define a large set of genes involved in synthesis of a complex unipolar adhesin comprised of two distinct polysaccharides, that is required for surface attachment by the plant-associated pathogenAgrobacterium tumefaciens.
Sero-Prevalence and Risk Factor ofPeste Des Petits Ruminantsin Sheep and Goats of Ethiopia: Systematic Review and Meta-Analysis
Authors: Yizengaw Liuel , Molla Wassie , Temesgen Wudu
Published: April 2021

Background

Peste des petits ruminant (PPR) is the most common prevalent viral disease of sheep and goats that impacts productivity and international animal trade in the world and also in Ethiopia. Despite the huge economic consequences related toPPR, little is known about the sero-prevalence of this disease at the country levels. The objective of this systematic review and meta-analysis was to estimate a single-group summary for sero-prevalence ofPPRdisease in small ruminants of Ethiopia and assess the potential risk factor to contribute the sero-prevalence estimate.

Methodology

Article onPPRin sheep and goats were searched in PubMed, Web of Science, Google Scholar, reference lists and African online source of articles that had been conducted between 1994 to 2020 and using inclusion and exclusion criteria with restricted to those studies published in English language.

Results

A total of 13 published papers containing 46 district level studies were included for analyses. The single-group summary ofPPRdisease sero-prevalence in small ruminant was estimated to be 27.71% (95 % CI: 21.46 - 33.96). Overall, the estimated pooled sero-prevalence at country level in sheep was 33.56% (95% CI: 18.72–48.41) and in goats 25.14% (95% CI: 15.68–34.59). Significant heterogeneity (I2> 80%) was noted in all pooled estimates. The visual inspection of the funnel plot demonstrated the presence of possible publication bias which could be associated with the small number of studies and longtime interval.

Conclusions

This quantitative review showed that the pooled sero-prevalence to be high and regional prevalence estimates ofPPRpresented here will be useful in raising awareness and advocating the Governments to engage in initiativesPPRcontrol and prevention.
Automated Raman micro-spectroscopy of epithelial cells for the high-throughput classification
Authors: O’Dwyer Kevin , Domijan Katarina , Dignam Adam , Butler Marion , Hennelly Bryan M.
Published: April 2021

Raman micro-spectroscopy is a powerful technique for the identification and classification of cancer cells and tissues. In recent years, the application of Raman spectroscopy to detect bladder, cervical, and oral cytological samples has been reported to have an accuracy that is greater than standard pathology. However, despite being entirely non-invasive and relatively inexpensive, the slow recording time, and lack of reproducibility, have prevented the clinical adoption of the technology. Here we present an automated Raman cytology system that can facilitate high-throughput screening and improve reproducibility. The proposed system is designed to be integrated directly into the standard pathology clinic, taking into account their methodologies and consumables. The system employs image processing algorithms and integrated hardware/software architectures in order to achieve automation and is tested using the ThinPrep standard, including the use of glass slides, and a number of bladder cancer cell lines. The entire automation process is implemented using the open source Micro-Manager platform, and is made freely available. We believe this code can be readily integrated into existing commercial Raman micro-spectrometers.
Coagulation disorders in patients with severe hemophagocytic lymphohistiocytosis
Authors: Valade Sandrine , Joly Bérangère S. , Veyradier Agnès , Fadlallah Jehane , Zafrani Lara , Lemiale Virginie , Launois Amélie , Stepanian Alain , Galicier Lionel , Fieschi Claire , Mirouse Adrien , Tudesq Jean Jacques , Lepretre Anne-Claire , Azoulay Elie , Darmon Michael , Mariotte Eric
Published: April 2021

Background

Coagulation disorders are common in patients with hemophagocytic lymphohistiocytosis (HLH), associated with an increased risk of bleeding and death. We aim to investigate coagulation disorders and their outcome implications in critically ill patients with HLH.

Methods

We prospectively evaluated 47 critically ill patients with HLH (median age of 54 years [42-67]) between April 2015 and December 2018. Coagulation assessments were performed at day 1. Abnormal standard coagulation was defined as prothrombin time (PT) <50% and/or fibrinogen <2g/L. HLH aetiology was mostly ascribed to haematological malignancies (74% of patients).

Results

Coagulation disorders and severe bleeding events were frequent, occurring in 30 (64%) and 11 (23%) patients respectively. At day 1, median fibrinogen level was 2·65g/L [1.61-5.66]. Fibrinolytic activity was high as suggested by increased median levels of D-dimers, fibrin monomers, PAI-1 (plasminogen activator inhibitor) and tPA (tissue plasminogen activator). Forty-one (91%) patients had a decreased ADAMTS13 activity (A Disintegrin-like And Metalloproteinase with ThromboSpondin type 1 repeats, member 13). By multivariable analysis, the occurrence of a severe bleeding (OR 3.215 [1.194-8.653], p=0·021) and SOFA score (Sepsis-Related Organ Failure Assessment) at day 1 (OR 1.305 per point [1.146-1.485], p<0·001) were independently associated with hospital mortality. No early biological marker was associated with severe bleeding.

Conclusions

Hyperfibrinolysis may be the primary mechanism responsible for hypofibrinogenemia and may also participate in ADAMTS13 degradation. Targeting the plasmin system appears as a promising approach in severe HLH-related coagulation disorders.
Optimized Protocol for Cyanobacterial 16S rRNA Analysis in Danube Delta Lakes
Authors: Moza Maria Iasmina , Postolache Carmen
Published: April 2021

Molecular biology protocols have been more and more accessible to researchers for ecological investigations, however, these protocols always require optimization steps for the analysis of specific types of samples. The purpose of this study was to optimize a molecular protocol for the analysis of cyanobacterial 16S rRNA in Danube Delta shallows lakes. In this regard, several commercial DNA extraction kits were tested in comparison with potassium ethyl xanthogenate extraction method on different matrices. The obtained DNA was further used for 16S rRNA PCR optimization. Finally, an optimized protocol is proposed for the molecular analysis of cyanobacteria group in freshwater samples. The best DNA extraction method was the potassium xanthogenate extraction from dried cyanobacterial biomass. A dynamic in total genomic eDNA was observed, reflecting the seasonal difference in phytoplankton biomass from the studied lakes. The PCR protocol optimized by us can be successfully applied for the identification of a broad range of cyanobacterial genetic markers.
Memes: an R interface to the MEME Suite
Authors: Nystrom Spencer L. , McKay Daniel J.
Published: April 2021

Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we presentmemes, an R package which provides a seamless R interface to the MEME Suite.memesprovides a novel “data aware” interface to these tools, enabling rapid and complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools,memesleverages existing R/Bioconductor data structures to store the complex, multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally,memesprovides data visualization capabilities to facilitate communication of results.memesis available as a Bioconductor package athttps://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.
Computational investigation reveals that the mutant strains of SARS-CoV2 are highly infectious than wildtype
Authors: Kumar Rakesh , Kumar Rahul , Goel Harsh , Tanwar Pranay
Published: April 2021

Remarkable infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) is due to the rapid emergence of various strains, thus enable the virus to rule the world. Over the course of SARS-CoV2 pandemic, the scientific communities worldwide are responding to newly emerging genetic variants. However, the mechanism behind the persistent infection of these variants is still not known due to the paucity of study of these variants at molecular level. In this scenario, computational methods have immense utility in understanding the molecular and functional properties of different variants. Therefore, in this study various mutants (MTs) of SpikeS1 receptor binding domain (RBD) of highly infectious SARS-CoV2 strains were carried and elucidated the protein structure and dynamics using molecular dynamics (MD) approach. MD simulation study showed that all MTs exhibited stable structures with altered functional properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed through protein-protein docking and observed that MTs showed high binding affinities than WT. Hence, this study shed light on the molecular basis of infection caused by different variants of SARS-CoV2, which might play an important role in to cease the transmission and pathogenesis of virus and also implicate in rational designing of a specific drug.
PINAWeb: A web-based tool for the comparison of Protein-Protein Interaction Networks Aligners
Authors: Alcalá A. , Riera G. , García I. , Alberich R. , Llabrés M.
Published: April 2021

Motivation

Several protein-protein interaction networks (PPIN) aligners have been developed during the last 15 years. One of their goals is to help the functional annotation of proteins and the prediction of protein-protein interactions. A correct aligner must preserve the network’s topology as well as the biological coherence. However, this is a trade-off that is hard to achieve. In addition, most aligners require a considerable effort to use in practice and many researchers must choose an aligner without the opportunity to previously compare the performance of different aligners.

Results

We developed PINAWeb, a user-friendly web-based tool to obtain and compare the results produced by the aligners: AligNet, HubAlign, L-GRAAL, PINALOG and SPINAL. PPINs can be uploaded either from the STRING database or from a user database. The source code of PINAWeb is freely available on GitHub to enable researchers to add other aligners, network databases or alignment score metrics. In addition, PINAWeb provides a report with the analysis for every alignment in terms of topological and functional information scores, as well as the visualization of the alignments’ comparison (agreement/differences) when more than one aligner are considered.

Availability

https://bioinfo.uib.es/~recerca/PINAWeb
Protein Charge Neutralization is the Proximate Driver Dynamically Tuning a Nanoscale Bragg Reflector
Authors: Levenson Robert , Malady Brandon , Lee Tyler , Sabeh Yahya Al , Kohl Phillip , Li Youli , Morse Daniel E.
Published: April 2021

Reflectin is a cationic, block copolymeric protein that mediates the dynamic fine-tuning of color and brightness of light reflected from nanostructured Bragg reflectors in iridocyte skin cells of squids. In vivo, neuronally activated phosphorylation of reflectin triggers its assembly, driving osmotic dehydration of the membrane-bounded Bragg lamellae containing the protein to simultaneously shrink the lamellar thickness and spacing while increasing its refractive index contrast, thus tuning the wavelength and increasing the brightness of reflectance. In vitro, we show that reduction in repulsive net charge of the purified, recombinant reflectin – either (for the first time) by generalized anionic screening with salt, or by pH titration - drives a finely tuned, precisely calibrated increase in size of the resulting multimeric assemblies. The calculated effects of phosphorylation in vivo are consistent with these effects observed in vitro. X-ray scattering analyses confirm the sphericity, size and low polydispersity of the assemblies. Precise proportionality between assembly size and charge-neutralization is enabled by the demonstrated rapid dynamic arrest of multimer growth. The resulting stability of reflectin assemblies with time ensures reciprocally precise control of the particle number concentration, thereby encoding a precise calibration between the extent of neuronal signaling, osmotic pressure, and the resulting optical changes. The results presented here strongly suggest that it is charge neutralization, rather than any change in aromatic content, that is the proximate driver of assembly, fine-tuning a colligative property-based nanostructured biological machine. A physical mechanism is proposed.
Redefining thePTENPromoter: Identification of Two Upstream Transcription Start Regions
Authors: Grencewicz Dennis , Romigh Todd , Thacker Stetson , Abbas Ata , Jaini Ritika , Luse Donal , Eng Charis
Published: April 2021

Germline mutation ofPTENis causally observed in Cowden syndrome (CS) and is one of the most common genetic causes of autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are found to bePTEN-mutation negative. Reassessment ofPTENpromoter regulation may help explain abnormalPTENdosage, as only the minimal promoter and coding regions are currently included in diagnosticPTENmutation analysis. We reanalyzed the architecture of thePTENpromoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional TSRs at −2052 and −1907 basepairs from the start of PTEN, thus redefining thePTENpromoter and extending thePTEN5’UTR. The upstream TSRs described are active in cancer cell lines and human cancer and normal tissue. Further, these TSRs can produce novelPTENtranscripts due to the introduction of new splice sites. Evaluation of transcription factor binding specific to the upstream TSRs shows overrepresentation of TFs involved in inflammatory processes. Together, these data suggest that potentially clinically relevant promoter variants upstream of the known promoter may be overlooked in indivduals consideredPTENgermline mutation-negative and may also explain lack of PTEN expression in sporadic neoplasias withoutPTENsomatic structural defects.
Image-based Motion Artifact Reduction on Liver Dynamic Contrast Enhanced MRI
Authors: Wu Yunan , Liu Junchi , White Gregory M , Deng Jie
Published: April 2021

Liver MRI images often suffer degraded quality from ghosting or blurring artifact caused by patient respiratory or bulk motion. In this study, we developed a two-stage deep learning model to reduce motion artifact on dynamic contrast enhanced (DCE) liver MRIs. The stage-I network utilized a deep residual network with a densely connected multi-resolution block (DRN-DCMB) network to remove the majority of motion artifacts. The stage-II network applied the perceptual loss to preserve image structural features by updating the parameters of the stage-I network via backpropagation. The stage-I network was trained using small image patches simulated with five types of motion, i.e., rotational, sinusoidal, random, elastic deformation and through-plane, to mimic actual liver motion patterns. The stage-II network training used full-size images with the same types of motion as the stage-I network. The motion reduction deep learning model was testing using simulated motion images and images with real motion artifacts. The resulted images after two-stage processing demonstrated substantially reduced motion artifacts while preserved anatomic details without image blurriness. This model outperformed existing methods of motion reduction artifact on liver DCE-MRI.
The genetic population structure of Lake Tanganyika’sLatesspecies flock, an endemic radiation of pelagic top predators
Authors: Rick Jessica A. , Junker Julian , Kimirei Ismael A. , Sweke Emmanuel A. , Mosille Julieth B. , Dinkel Christian , Mwaiko Salome , Seehausen Ole , Wagner Catherine E.
Published: April 2021

Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemicLatesspecies of Lake Tanganyika(Lates stappersii, L. microlepis, L. mariaeandL. angustifrons)using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST= 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure withinL. mariae,with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis,andL. angustifrons).Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species—particularly that ofL. mariae—which may be important for conservation and management of this culturally and economically important clade of fish.
PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum
Authors: Zhou Yadi , Sukul Abhijit , Mishler-Elmore John W. , Faik Ahmed , Held Michael A.
Published: April 2021

Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. With the recent accumulation of RNA-seq data sets, the construction of RNA-seq-based GCNs has now become possible. Cereal crops, such asHordeum vulgare(barley) andSorghum bicolor(sorghum), are among the most important plants to humanity and contribute significantly to our food supply. However, co-expression network tools for these plants are outdated or lacking. In this study, we constructed global GCNs for barley and sorghum using 500 and 774 RNA-seq data sets, respectively. In addition, we curated the meta-information of these RNA-seq data sets and categorized them into four main tissue types, leaf, root, shoot, and flower/seed, and built tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus, offering an immersive environment for the exploration and visualization of gene expressions and co-expressions of barley and sorghum at the global and tissue-specific levels. PlantNexus is freely available athttps://plantnexus.ohio.edu/.
Blebs Promote Cell Survival by Assembling Oncogenic Signaling Hubs
Authors: Weems Andrew D. , Welf Erik S. , Driscoll Meghan K. , Zhou Felix , Mazloom-Farsibaf Hanieh , Chang Bo-Jui , Murali Vasanth S. , Gihana Gabriel M. , Weiss Byron G. , Chi Joseph , Rajendran Divya , Dean Kevin M. , Fiolka Reto , Danuser Gaudenz
Published: April 2021

Most human cells require anchorage for survival. Cell-substrate adhesion activates diverse signaling pathways, without which cells undergo anoikis – a form of programmed cell death1. Acquisition of anoikis resistance is a pivotal step in cancer disease progression, as metastasizing cancer cells often lose firm attachment to surrounding tissue2–5. In these poorly attached states, cells adopt rounded morphologies and form small hemispherical plasma membrane protrusions called blebs6–13. Bleb function has been thoroughly investigated in the context of amoeboid migration but is far less examined in other scenarios14–19. Here we show by quantitative subcellular 3D imaging and manipulation of cell morphological states that blebbing triggers the formation of plasma membrane-proximal signaling hubs that confer anoikis resistance. Specifically, we discovered in melanoma cells that blebbing generates plasma membrane contours, which recruit curvature-sensing septin proteins as scaffolds for constitutively active mutant NRAS and effectors. These signaling hubs activate ERK and PI3K – canonical promoters of pro-survival pathways. Inhibition of blebs or septins has little effect on the survival of well-adhered cells, but in detached cells causes NRAS mislocalization, reduced MAPK and PI3K activity, and ultimately, death. This unveils an unanticipated morphological requirement for mutant NRAS to operate as an effective oncoprotein. Moreover, we find that though some BRAF mutant melanoma do not rely on this survival pathway in a basal state, BRAF/MEK inhibition strongly sensitizes them to both bleb and septin inhibition. Importantly, we demonstrate that fibroblasts engineered to sustain blebbing acquire the same anoikis resistance as cancer cells even without harboring oncogenic mutations. These data define a role for blebs as potent signaling organelles capable of integrating myriad cellular information flows into concerted cellular responses, in this case granting robust anoikis resistance.
A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis
Authors: Capece Marina , Tessari Anna , Mills Joseph , Rampioni Vinciguerra Gian Luca , Lin Chenyu , McElwain Bryan K , Miles Wayne O. , Coppola Vincenzo , Palmieri Dario , Croce Carlo M.
Published: April 2021

The OsTIR1/auxin-inducible degron (AID) system allows “on demand” selective and reversible protein degradation upon exposure to the phytohormone auxin. In the current format, this technology does not allow to study the effect of acute protein depletion selectively in one phase of the cell cycle, as auxin similarly affects all the treated cells irrespectively of their proliferation status. Therefore, the AID system requires coupling with cell synchronization techniques, which can alter the basal biological status of the studied cell population. Here, we introduce a new AID system to Regulate OsTIR1 Levels based on the Cell Cycle Status (ROLECCS system), which induces proteolysis of both exogenously transfected and endogenous gene-edited targets in specific phases of the cell cycle. This new tool paves the way to studying the differential roles that target proteins may have in specific phases of the cell cycle.
Microglial ablation does not affect opioid-induced hyperalgesia in rodents
Authors: Liu Xin , Liu Bo-Long , Yang Qing , Zhou Xiangfu , Tang Shao-Jun
Published: April 2021

Opioids are the frontline analgesics in pain management. However, chronic use of opioid analgesics causes paradoxical pain that contributes to the decrease of their efficacy in pain control and the escalation of dose in long-term management of pain. The underling pathogenic mechanism is not well understood. Microglia have been commonly thought to play a critical role in the expression of opioid-induced hyperalgesia (OIH) in animal models. We performed microglial ablation experiments using either a genetic (CD11b-diphtheria toxin receptor transgenic mouse) or pharmacological (colony-stimulating factor 1 receptor inhibitor PLX5622) approaches. Surprisingly, ablating microglia using these specific and effective approaches did not cause detectable impairment in the expression of hyperalgesia induced by morphine. We confirmed this conclusion with behavioral test of mechanical and thermal hyperalgesia, in male and female mice, and with different species (mouse and rat). These findings raise caution about the widely assumed contribution of microglia to the development of OIH.
Holo-Hilbert Spectral-based Noise Removal Method for EEG High-Frequency Bands
Authors: Moradi Narges , LeVan Pierre , Akin Burak , Goodyear Bradley G. , Sotero Roberto C.
Published: April 2021

Simultaneous EEG-fMRI is a growing and promising field, as it has great potential to further our understanding of the spatiotemporal dynamics of brain function in health and disease. In particular, there is much interest in understanding the fMRI correlates of brain activity in the gamma band (>30 Hz), as these frequencies are thought to be associated with cognitive processes involving perception, attention, and memory, as well as with disorders such as schizophrenia and autism. However, progress in this area has been limited due to issues such as MR-induced artifacts in EEG recordings, which seem to be more problematic for gamma frequencies. This paper presents a noise removal method for the gamma band of EEG that is based on the Holo-Hilbert spectral analysis (HHSA), but with a new implementation strategy. HHSA uses a nested empirical mode decomposition (EMD) to identify amplitude and frequency modulations (AM and FM, respectively) by averaging over frequencies with high and significant powers. Our method examines gamma band by applying two layers of EMD to the FM and AM components, removing components with very low power based on the power-instantaneous frequency spectrum, and subsequently reconstructs the denoised gamma-band signal from the remaining components. Simulations demonstrate that our proposed method efficiently reduces artifacts while preserving the original gamma signal which is especially critical for simultaneous EEG/fMRI studies.
Microbiota-dependent inflammation promotes metabolic disorder via NF-κB-mediated inhibition of SREBP inDrosophilaadipocytes
Authors: Charroux Bernard , Royet Julien
Published: April 2021

Bacteria that colonize eukaryotic gut have profound influences on the physiology of their host. InDrosophila, many of these effects are mediated by the adipocytes that combine immune and metabolic functions. We show here that gut colonization by specific bacteria species stimulate lipogenesis in surrounding enterocytes but also in remote fat body cells and ovaries. This bacteria-dependent lipid production is mediated by SREBP and requires a functional insulin signaling. However, it is antagonized by microbiota-born peptidoglycan which by activating NF-κB signaling, cell-autonomously represses SREPP activation in adipocytes but not in enterocytes. We finally show that by reducing microbiota-derived PGN, the gut-produced PGRP-LB amidase balances host immune and metabolic responses of the fat body to gut-associated bacteria. In the absence of such modulation, uncontrolled immune pathway activation prevents lipid production by the fat body resulting in infection-dependent host death.

Bullets

Gut microbiota activates lipogenesis locally in enterocytes and remotely in adipocytes

Bacteria-dependent activation of SREBP in adipocytes is mediated by insulin signaling

Activation of lipid synthesis by microbiota is antagonized by NF-κB signaling triggered by gut-born peptidoglycan

By reducing peptidoglycan circulating levels, PGRP-LB maintains a balance between immune and metabolic response to microbiota
Imprinting on time-structured acoustic stimuli in ducklings
Authors: Monteiro Tiago , Hart Tom , Kacelnik Alex
Published: April 2021

Filial imprinting is a dedicated learning process that lacks explicit reinforcement. The phenomenon itself is narrowly heritably canalized, but its content, the representation of the parental object, reflects the circumstances of the newborn. Imprinting has recently been shown to be even more subtle and complex than previously envisaged, since ducklings and chicks are now known to select and represent for later generalization abstract conceptual properties of the objects they perceive as neonates, including movement pattern, heterogeneity, and inter-component relationships of same or different. Here we investigate whether day-old Mallard ducklings (Anas platyrhynchos) imprint on the temporal separation between duos of brief acoustic stimuli, and whether they generalize such timing information to novel sound types. Subjects did discriminate temporal structure when imprinted and tested on natural duck calls, but not when using white noise for imprinting or testing. Our data confirm that imprinting includes the establishment of neural representations of both primary percepts and abstract properties of candidate objects, meshing together genetically transmitted prior knowledge with selected perceptual input.
Accounting, inequality and COVID-19 in Australia
Authors: Andrew Jane , Baker Max , Guthrie James
Published: April 2021

Purpose

The authors explore the Australian Government's implementation of budgetary measures to manage the social and economic impacts of COVID-19, paying particular attention to how the country's history of inequality has shaped these actions, and the effect inequality may have on outcomes.

Design/methodology/approach

In this qualitative case study of public budgeting, the authors draw on the latest research into inequality to consider the implications of policy responses to COVID-19 in Australia. In particular, we examine the short-term introduction of what we term “people-focused” budgetary measures. These appeared contrary to the dominant neoliberalist approach to Australian welfare policymaking.

Findings

This paper foregrounds the relationship between budgeting, public policy and inequality and explores how decades of increasingly regressive tax systems and stagnating living wages have made both people, and the state, vulnerable to crises like COVID.

Social implications

There is still much to learn about the role of accounting in the shaping of growing economic inequality. In focusing on public budgeting within the context of COVID, the authors suggest ways accounting researchers can contribute to our understanding of economic inequality, both in terms of drivers and consequences. The authors hope to contribute to a growing body of accounting research that can influence social movements, political debates and policymaking, while also raising awareness of the consequences of wealth and income inequality.

Originality/value

The authors explore ways accounting scholars might help articulate a post-COVID future that avoids recreating the inequalities of the past and present.
Pandemic turned into pandemonium: the effect on supply chains and the role of accounting information
Authors: Velayutham Ajantha , Rahman Asheq Razaur , Narayan Anil , Wang Michael
Published: April 2021

Purpose

The purpose of this study is to examine the disruptive effects of COVID-19 on supply chains and question the role of accounting information in managing these supply chains in the face of such disruptive effects.

Design/methodology/approach

The study first explains the effects of COVID-19 on the supply chains of business entities. It then explains the role of accounting information in supply chain management, questions accounting information's ability to play such a role, and makes recommendations for better accounting disclosures and accounting research for supply chains of firms. To illustrate the salient points, a case study of Fisher and Paykel Healthcare is conducted. It identifies the risks and uncertainties of supply chains exposed by COVID-19 disruptions to businesses.

Findings

COVID-19 has affected Fisher and Paykel Healthcare from both the supply-side (upstream) and demand-side (downstream) perspectives. On the supply side, it has disrupted the supply of raw materials used in the manufacture of respiratory devices and the costs of importing such materials. On the demand side, it has disrupted market logistics and customer demand. This has subsequently affected production. Such disruptions can be overcome through the dissemination of appropriate accounting information for the different stages of the supply chain to the managers. Such accounting information can also be useful to external stakeholders for minimizing their risks.

Originality/value

The study attempts to create an awareness of the supply chain uncertainties faced by managers and stakeholders arising from exogenous shocks, such as a pandemic, and how these uncertainties can be mitigated by aligning accounting information flows with the supply chain activity flows. The observations made in this paper are at a conceptual level and, therefore, can be applied to any industry.
The street food experiences of the local-guided tour in the meal-sharing economy: the case of Bangkok
Authors: Cifci Ibrahim , Atsız Ozan , Gupta Vikas
Published: April 2021

Purpose

This study aims to understand the components of the street food experiences of the local-guided tour in the meal-sharing economy based on the online reviews of tourists who experienced a meal-sharing activity with a local guide in Bangkok.

Design/methodology/approach

Based on the qualitative approach, this study involved a content analysis of 384 narratives on Withlocals.

Findings

The study identified five components that embrace the street food experience: a local guide’s attributes, perceived food authenticity, local culture, perceived hygiene or cleanliness. Results also revealed that the Thai street foods are unique and authentic and can reach this experience level through a local guide.

Originality/value

Although the importance of international travellers' street food experiences and the popularity of the meal-sharing economy platforms are rapidly growing, there is no study which had combined both of these phenomena together to date. It is the first attempt to reveal the components of street food experiences in a meal-sharing platform.
Perceived authenticity of online-only brands (OOBs): a quali-quantitative study with online consumers
Authors: Jason Sit Kokho , Pino Giovanni , Pichierri Marco
Published: April 2021

Purpose

The present study examines the dimensions that are meaningful to define the perceived authenticity of online-only brands (OOBs) (i.e. retail brands that trade exclusively online) from a consumer's perspective. Past frameworks of perceived authenticity exist in the branding literature but consistently focus on contexts beyond e-commerce settings like OOBs.

Design/methodology/approach

We employed a mixed-method research design, consisting of quasi-qualitative and quantitative studies with online customers, to establish the dimensions meaningful for the perceived authenticity of OOBs. Our work has theory testing and building components.

Findings

We identify five dimensions that are meaningful to define consumers' perceived authenticity of OOBs. They are “honesty”, “connection”, “continuity”, “craftsmanship” and “accessibility”. Representing by multiple factors, “craftsmanship” serves as the most meaningful dimension followed by “accessibility”. Often being considered incompatible with perceived authenticity, we find accessibility particularly relevant to the context of OOBs. It describes the “convenient” and “affordable” aspects of OOBs, which typically serve as unique selling propositions.

Originality/value

Our work confirms the utility of established dimensions to define consumers' perceived authenticity of OOBs. This highlights that consumers hold some consistent authenticity image between non-online and online brands. Our work also reveals the accessibility dimension being neglected by the branding literature, suggesting a more up-to-date perspective is needed when studying consumers' perceived authenticity of OOBs.
Examining the influence of financial inclusion on financial well-being of marginalized street vendors: an empirical evidence from India
Authors: Nandru Prabhakar , Chendragiri Madhavaiah , Velayutham Arulmurugan
Published: April 2021

Purpose

The study attempts to explore the determinants of financial inclusion. Subsequently, it examines the effect of financial inclusion on financial well-being of marginalized street vendors in India.

Design/methodology/approach

The demand-side analysis of measuring financial inclusion with a sample of 371 marginalized street vendors is adopted. Both exploratory and descriptive research designs are employed in this study. The primary data collection is done by administering the structured interview schedule by using a convenience sampling technique. Confirmatory factor analysis (CFA) and structural equation modeling (SEM) are performed to describe the latent constructs and their hypothetical relationships with adequate empirical evidence.

Findings

Out of five dimensions of financial inclusion considered for the study, accessibility, availability, usage and affordability are found to be significant determinants of financial inclusion; however, the financial literacy dimension is found statistically insignificant. Further, the study results confirm that financial inclusion contributes substantially to the well-being of marginalized street vendors.

Research limitations/implications

The outcome of the study will facilitate all the stakeholders including policymakers and financial institutions to enact policy guidelines to ensure financial well-being of the marginalized street vendors through financial inclusion initiatives.

Originality/value

Financial well-being through financial inclusion is possible even without the effect of financial literacy from the unorganized sector perspective specifically marglianized street vendors. Thus, it adds new dimension to the existing literature on demand side analysis of measuring financial inclusion.