bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smartphone-based Sickle Cell Disease Detection and Monitoring for Point-of-Care Settings
Authors: Ilyas Shazia , Sher Mazhar , Du E , Asghar Waseem 
Published: May 2020

AbstractSickle cell disease (SCD) is a worldwide hematological disorder causing painful episodes, anemia, organ damage, stroke, and even deaths. It is more common in sub-Saharan Africa and other resource-limited countries. Conventional laboratory-based diagnostic methods for SCD are time-consuming, complex, and cannot be performed at point-of-care (POC) and home settings. Optical microscope-based classification and counting demands a significant amount of time, extensive setup, and cost along with the skilled human labor to distinguish the normal red blood cells (RBCs) from sickled cells. There is an unmet need to develop a POC and home-based test to diagnose and monitor SCD and reduce mortality in resource-limited settings. An early-stage and timely diagnosis of SCD can help in the effective management of the disease. In this article, we utilized a smartphone-based image acquisition method for capturing RBC images from the SCD patients in normoxia and hypoxia conditions. A computer algorithm is developed to differentiate RBCs from the patient’s blood before and after cell sickling. Using the developed smartphone-based technique, we obtained similar percentage of sickle cells in blood samples as analyzed by conventional method (standard microscope). The developed method of testing demonstrates the potential utility of the smartphone-based test for reducing the overall cost of screening and management for SCD, thus increasing the practicality of smartphone-based screening technique for SCD in low-resource settings. Our setup does not require any special storage requirements and is particularly useful in assessing the severity of the SCD. This is the characteristic advantage of our technique as compared to other hemoglobin-based POC diagnostic techniques.
Learning-induced plasticity in the barrel cortex is disrupted by inhibition of layer 4 somatostatin-containing interneurons
Authors: Dobrzanski G , Lukomska A , Zakrzewska R , Posluszny A , Kanigowski D , Urban-Ciecko J , Liguz-Lecznar M , Kossut M 
Published: May 2020

ABSTRACTLearning-related plasticity in the cerebral cortex is linked to the action of disinhibitory circuits of interneurons. Pavlovian conditioning, in which stimulation of the vibrissae is used as conditioned stimulus, induces plastic enlargement of the cortical functional representation of vibrissae activated during conditioning, visualized with [14C]-2-deoxyglucose (2DG). Using layer-specific, cell-selective DREADD transductions, we examined the involvement of somatostatin- (SOM-INs) and vasoactive intestinal peptide (VIP-INs)-containing interneurons in the development of learning-related plastic changes. We injected DREADD-expressing vectors into layer IV (L4) barrels or layer II/III (L2/3) areas corresponding to activated vibrissae. The activity of interneurons was modulated during training, and 2DG maps were obtained 24 h later. In mice with L4 but not L2/3 SOM-INs suppressed during conditioning, the plastic change of whisker representation and the conditioned reaction were absent. No effect of inhibiting VIP-INs was found. We report that the activity of L4 SOM-INs is indispensable for learning-induced plastic change.
Protease Activity Profiling Via Programmable Phage Display
Authors: Román-Meléndez Gabriel D. , Venkataraman Thiagarajan , Monaco Daniel R. , Larman H. Benjamin 
Published: May 2020

AbstractEndopeptidases catalyze the internal cleavage of proteins, playing pivotal roles in protein turnover, substrate maturation and the activation of signaling cascades. A broad range of biological functions in health and disease are controlled by proteases, yet assays to characterize their activities at proteomic scale do not yet exist. To address this unmet need, we have developed SEPARATE (SensingEndoPeptidaseActivity viaRelease and recapture using flAnkingTagEpitopes), which uses monovalent phage display of the entire human proteome at 90-aa peptide resolution. We demonstrate that SEPARATE is compatible with several human proteases from distinct catalytic classes, including Caspase-1, ADAM17, and Thrombin. Both well-characterized and newly identified substrates of these enzymes were detected in the assay. SEPARATE was used to discover a non-canonical Caspase-1 substrate, the E3 ubiquitin ligase HUWE1, a key mediator of apoptotic cell death. SEPARATE is a novel methodology to enable efficient, unbiased assessment of endopeptidase activity using a phage-displayed proteome.
Children’s Hospital Los Angeles COVID-19 Analysis Research Database (CARD) - A Resource for Rapid SARS-CoV-2 Genome Identification Using Interactive Online Phylogenetic Tools
Authors: Shen Lishuang , Maglinte Dennis , Ostrow Dejerianne , Pandey Utsav , Bootwalla Moiz , Ryutov Alex , Govindarajan Ananthanarayanan , Ruble David , Han Jennifer , Triche Timothy J. , Bard Jennifer Dien , Biegel Jaclyn A. , Judkins Alexander R. , Gai Xiaowu 
Published: May 2020

AbstractEffective response to the Coronavirus Disease 2019 (COVID-19) pandemic requires genomic resources and bioinformatics tools for genomic epidemiology and surveillance studies that involve characterizing full-length viral genomes, identifying origins of infections, determining the relatedness of viral infections, performing phylogenetic analyses, and monitoring the continuous evolution of the SARS-CoV-2 viral genomes. The Children’s Hospital, Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) (https://covid19.cpmbiodev.net/) is a comprehensive genomic resource that provides access to full-length SARS-CoV-2 viral genomes and associated meta-data for over 30,000 (as of May 20, 2020) isolates collected from global sequencing repositories and the sequencing performed at the Center for Personalized Medicine (CPM) at CHLA. Reference phylogenetic trees of global and USA viral isolates were constructed and are periodically updated using selected high quality SARS-CoV-2 genome sequences. These provide the baseline and analytical context for identifying the origin of a viral infection, as well as the relatedness of SARS-CoV-2 genomes of interest. A web-based and interactive Phylogenetic Tree Browser supports flexible tree manipulation and advanced analysis based on keyword search while highlighting time series animation, as well as subtree export for graphical representation or offline exploration. A Virus Genome Tracker accepts complete or partial SARS-CoV-2 genome sequence, compares it against all available sequences in the database (>30,000 at time of writing), detects and annotates the variants, and places the new viral isolate within the global or USA phylogenetic contexts based upon variant profiles and haplotype comparisons, in a few seconds. The generated analysis can potentially aid in genomic surveillance to trace the transmission of any new infection. Using CHLA CARD, we demonstrate the identification of a candidate outbreak point where 13 of 31 CHLA internal isolates may have originated. We also discovered multiple indels of unknown clinical significance in the orf3a gene, and revealed a number of USA-specific variants and haplotypes.
Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition inEscherichia coli
Authors: Gerken Henri , Vuong Phu , Soparkar Ketaki , Misra Rajeev 
Published: May 2020

ABSTRACTEscherichia colisecretes high-affinity Fe3+chelators to solubilize and transport chelated Fe3+via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+acts as a repressor. Work carried out in this paper shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of theompCandompFporin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance (EPR) spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR onfeoBexpression is sufficient to overcome the negative effect of activated Fur onfeoB. In atonBmutant, which lacks functional ferric transport systems, deletion ofompRseverely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion ofompCandompFis not viable. These data, together with the observation of de-repression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutantenvZalleles on iron regulon.IMPORTANCEThe work presented here solved a long-standing paradox of the negative effects of certain missense alleles ofenvZ, which codes for kinase of the EnvZ/OmpR two component system, on the expression of ferric uptake genes. The data revealed that the constitutiveenvZalleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit thefeooperon due to the positive effect of activated EnvZ/OmpR. The data also revealed importance of porins in iron homeostasis.
A new microcirculation culture method with a self-organized capillary network
Authors: Sugihara Kei , Yamaguchi Yoshimi , Usui Shiori , Nashimoto Yuji , Hanada Sanshiro , Kiyokawa Etsuko , Uemura Akiyoshi , Yokokawa Ryuji , Nishiyama Koichi , Miura Takashi 
Published: May 2020

AbstractA lack of microcirculation has been one of the most significant obstacles for three-dimensional culture systems of organoids and embryonic tissues. Here, we developed a simple and reliable method to implement a perfusable capillary network in vitro. The method employed the self-organization of endothelial cells to generate a capillary network and a static pressure difference for culture medium circulation, which can be easily introduced to standard biological laboratories and enables long-term cultivation of vascular structures. Using this culture system, we perfused the lumen of the self-organized capillary network and observed a flow-induced vascular remodeling process, cell shape changes, and collective cell migration. We also observed an increase in cell proliferation around the synthetic vasculature induced by flow, indicating functional perfusion of the culture medium. We also reconstructed extravasation of tumor and inflammatory cells, and circulation inside spheroids including endothelial cells and human lung fibroblasts. In conclusion, this system is a promising tool to elucidate the mechanisms of various biological processes related to vascular flow.
A putative new SARS-CoV protein, 3a*, encoded in an ORF overlapping ORF3a
Authors: Firth Andrew E. 
Published: May 2020

ABSTRACTIdentification of the full complement of genes in SARS-CoV-2 is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high throughput experimental approaches – such as ribosome profiling – cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV and related viruses (subgenusSarbecovirus), and correlating with the conserved presence of an open reading frame and plausible translation mechanism, we identified a putative new gene, ORF3a*, overlapping ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3a* is indeed translated during infection. ORF3a* is conserved across the subgenusSarbecovirus, and encodes a 40–41 amino acid predicted transmembrane protein.
A novel RNA virus,Macrobrachium rosenbergiiGolda virus (MrGV), linked to mass mortalities of the larval giant freshwater prawn in Bangladesh
Authors: Hooper Chantelle , Debnath Partho P. , Biswas Sukumar , van Aerle Ronny , Bateman Kelly S. , Basak Siddhawartha K. , Rahman Muhammad M. , Mohan Chadag V. , Rakibul Islam H.M. , Ross Stuart , Stentiford Grant D. , Currie David , Bass David 
Published: May 2020

1AbstractMass mortalities of the larval stage of the giant freshwater prawn,Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producingM. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing.De novovirus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in theNidoviralesorder. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread inM. rosenbergiihatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of MrGV suggest that it is likely to be a new species within theNidoviralesorder. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.
Potential antiviral options against SARS-CoV-2 infection
Authors: Ianevski Aleksandr , Yao Rouan , Fenstad Mona Høysæter , Biza Svetlana , Zusinaite Eva , Reisberg Tuuli , Lysvand Hilde , Løseth Kirsti , Landsem Veslemøy Malm , Malmring Janne Fossum , Oksenych Valentyn , Erlandsen Sten Even , Aas Per Arne , Hagen Lars , Pettersen Caroline H. , Tenson Tanel , Afset Jan Egil , Nordbø Svein Arne , Bjørås Magnar , Kainov Denis E. 
Published: May 2020

AbstractAs of June 2020, the number of people infected with severe acute respiratory coronavirus 2 (SARS-CoV-2) continues to skyrocket, with more than 6,5 million cases worldwide. Both the World Health Organization (WHO) and United Nations (UN) has highlighted the need for better control of SARS-CoV-2 infections. However, developing novel virus-specific vaccines, monoclonal antibodies and antiviral drugs against SARS-CoV-2 can be time-consuming and costly. Convalescent sera and safe-in-man broad-spectrum antivirals (BSAAs) are readily available treatment options. Here we developed a neutralization assay using SARS-CoV-2 strain and Vero-E6 cells. We identified most potent sera from recovered patients for treatment of SARS-CoV-2-infected patients. We also screened 136 safe-in-man broad-spectrum antivirals against SARS-CoV-2 infection in Vero-E6 cells and identified nelfinavir, salinomycin, amodiaquine, obatoclax, emetine and homoharringtonine. We found that combinations of virus-directed nelfinavir along with host-directed amodiaquine exhibited the highest synergy. Finally, we developed a website to disseminate the knowledge on available and emerging treatments of COVID-19.
3D long-term recurrent convolutional networks for human sub-assembly recognition in human-robot collaboration
Authors: Wen Xianhe , Chen Heping 
Published: May 2020

Purpose
Human assembly process recognition in human–robot collaboration (HRC) has been studied recently. However, most research works do not cover high-precision and long-timespan sub-assembly recognition. Hence this paper aims to deal with this problem.

Design/methodology/approach
To deal with the above-mentioned problem, the authors propose a 3D long-term recurrent convolutional networks (LRCN) by combining 3D convolutional neural networks (CNN) with long short-term memory (LSTM). 3D CNN behaves well in human action recognition. But when it comes to human sub-assembly recognition, the accuracy of 3D CNN is very low and the number of model parameters is huge, which limits its application in human sub-assembly recognition. Meanwhile, LSTM has the incomparable superiority of long-time memory and time dimensionality compression ability. Hence, by combining 3D CNN with LSTM, the new approach can greatly improve the recognition accuracy and reduce the number of model parameters.

Findings
Experiments were performed to validate the proposed method and preferable results have been obtained, where the recognition accuracy increases from 82% to 99%, recall ratio increases from 95% to 100% and the number of model parameters is reduced more than 8 times.

Originality/value
The authors focus on a new problem of high-precision and long-timespan sub-assembly recognition in the area of human assembly process recognition. Then, the 3D LRCN method is a new method with high-precision and long-timespan recognition ability for human sub-assembly recognition compared to 3D CNN method. It is extraordinarily valuable for the robot in HRC. It can help the robot understand what the sub-assembly human cooperator has done in HRC.
Farmers' preferences and willingness to pay for microcredit in Benin: results from in-the-field choice experiments in Benin
Authors: Ogouvide Tchekpo Fortune , Adegbola Ygue Patrice , Zossou Roch Cedrique , Zannou Afio , Biaou Gauthier 
Published: May 2020

PurposeThis document analyses farmers' preferences and willingness to pay (CAP) for microcredit, in order to facilitate their access in rural areas.Design/methodology/approachData are based on a discrete choice experiment with 400 randomly selected farmers from 20 villages of the 7 Benin agricultural development hubs (ADHs). The preference choice modelling was performed using mixed logit (MXL) and latent class logit (LCL) models. Farmers' willingness to pay for each preferred attribute was estimated. The endogenous attribute attendance (EAA) model was also used to capture attribute non-attendance (ANA) phenomenon.FindingsThe results indicate that, on average, farmers prefer individual loans, low interest rates, in kind + cash loans, cash loans, disbursement before planting and loans with at least 10-month duration. These preferences vary according to farmers' classes. Farmers are willing to pay higher or lower interest rates depending on attribute importance. The estimate of the EAA model indicates that, when taking the ANA phenomenon into consideration, people will show stronger attitudes regarding WTP for important factors.Research limitations/implicationsBased on these results from Benin, microfinance institutions (MFIs) in developing countries can, based on the interest rates currently charged, attract more farmers as customers, reviewing the combination of the levels of the attributes associated with the nature of the loan, the type of loan (individual or collective), the disbursement period of funds, the waiting period of the loan and the loan duration. However, the study only considered production credit, ignoring equipment or investment credit.Practical implicationsThe document provides information on the key factors that can facilitate producers' access to MFI products and services.Social implicationsFacilitating small farmers' access to financial service will contribute to poverty reduction.Originality/valueThis research contributes to the knowledge of the attributes and attribute levels favoured by farmers when choosing financial products and the amounts they agree to pay for these attributes. The implementation of the results would facilitate small producers' access to financial services; thus contributing to poverty reduction.
The geographical and income differences in the determinants of African sovereign credit ratings
Authors: Botha Ilse , Pretorius Marinda 
Published: May 2020

PurposeThe importance of obtaining a sovereign credit rating from an agency is still underrated in Africa. Literature on the determinants of sovereign credit ratings in Africa is scarce. The purpose of this research is to determine what the determinants are for sovereign credit ratings in Africa and whether these determinants differ between regions and income groups.Design/methodology/approachA sample of 19 African countries' determinants of sovereign credit ratings are compared between 2007 and 2014 using a panel-ordered probit approach.FindingsThe findings indicated that the determinants of sovereign credit ratings differ between African regions and income groups. The developmental indicators were the most significant determinants across all income groups and regions. The results affirm that the identified determinants in the literature are not as applicable to African sovereigns, and that developmental variables and different income groups and regions are important determinants to consider for sovereign credit ratings in Africa.Originality/valueThe results affirm that the identified determinants in the literature are not as applicable to African sovereigns, and that developmental variables and different income groups and regions are important determinants to consider for sovereign credit ratings in Africa. Rating agencies follow the same rating assignment process for developed and developing countries, which means investors will have to supplement the allocated credit rating with additional information. Africa can attract more investment if African countries obtain formal, accurate sovereign credit ratings, which take the characteristics of the continent into consideration.
Significance of Basal ganglia calcification in Down's syndrome
Authors: Thoms Lesley , Idowu Adelola , Nehra Arjun , Biswas Asit 
Published: May 2020

Purpose
There is high incidence of dementia in individuals with Down’s syndrome. Much of the emphasis has been on Alzheimer’s disease as being most prevalent; however, it is apparent that other dementia types are also likely, to which this patient cohort may be predisposed. Specifically, this paper aims to highlight the potential for subcortical dementias in Down’s syndrome, suggesting a role for broader cognitive screening in aging individuals.

Design/methodology/approach
This paper describes a case of a female with Down’s syndrome and mild intellectual disability who presented with early signs of distinctive cognitive impairment and radiological calcification of the basal ganglia.

Findings
An active 42-year-old lady, who was mostly independent of activities of daily living and in part-time employment, presented with a three-year history of progressive cognitive deficit, characteristic of subcortical decline. She had no personal or known family history of mental illness, epilepsy or dementia. Routine blood tests showed chronic renal impairment, mild hypocalcaemia and vitamin D deficiency, managed by her GP. CT scan showed only bilateral basal ganglia calcification.

Originality/value
There is a widespread appreciation for the link between Down’s syndrome and Alzheimer’s disease but lesser consideration of the possibility of subcortical dementias. Given the differential nature and presentation of the two dementias, this case report highlights a need for clinicians to consider both to effectively manage these patients in the longer-term. Screening is discussed as a potential means of achieving this.