bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Diversity-Generating Retroelements for Regulatory Pathway Tuning in Cyanobacteria
Authors: Vallota-Eastman Alec , Arrington Eleanor C. , Meeken Siobhan , Roux Simon , Dasari Krishna , Rosen Sydney , Miller Jeff F. , Valentine David L. , Paul Blair G. 
Published: May 2020

AbstractBackgroundCyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes.ResultsMembers of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria.ConclusionWe find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.
Rapid self-selecting and clone-free integration of transgenes into engineered CRISPR safe harbor locations inCaenorhabditis elegans
Authors: Stevenson Zachary C. , Moerdyk-Schauwecker Megan J. , Jamison Brennen , Phillips Patrick C. 
Published: May 2020

AbstractPrecision genome editing for model organisms has revolutionized functional analysis and validation of a wide variety of molecular systems. To date, the capacity to insert transgenes into the model nematodeCaenorhabditis eleganshas focused on utilizing either transposable elements or CRISPR-based safe harbor strategies. These methods require laborious screening processes that often result in false positives from heritable extrachromosomal arrays or rely on co-CRISPR markers to identify likely edited individuals. As a result, verification of transgene insertion requires anti-array selection screening methods or extensive PCR genotyping respectively. These approaches also rely on cloning plasmids for the addition of transgenes. Here, we present a novel safe harbor CRISPR-based integration strategy that utilizes engineered insertion locations containing a synthetic guide RNA target and a split-selection system to eliminate false positives from array formation, thereby providing integration-specific selection. This approach allows the experimenter to confirm an integration event has taken place without molecular validation or anti-array screening methods, and is capable of producing integrated transgenic lines in as little as five days post-injection. To further increase the speed of generating transgenic lines, we also utilized theC. elegansnative homology-based formation of extra-chromosomal arrays to assemble transgenesin-situ, removing the cloning step. We show that complete transgenes can be made and inserted into our split-selection safe harbor locations starting from PCR products, providing a clone-free and molecular-validation-free strategy for single-copy transgene integration. Overall, this combination of approaches provides an economical and rapid system for generating highly reproducible complex transgenics inC. elegans.
Characterization of Circular RNA Transcriptomes in Psoriasis and Atopic Dermatitis Reveals Disease-specific Expression Profiles
Authors: Moldovan Liviu Ionut , Tsoi Lam Alex , Weidinger Stephen , Gudjonsson Johann , Kjems Jørgen , Kristensen Lasse Sommer 
Published: May 2020

AbstractBackgroundAtopic dermatitis (AD) and psoriasis, two chronic inflammatory skin diseases, affect a large number of individuals worldwide, and are associated with various comorbidities. Circular RNA (circRNA) constitute a major class of non-coding RNAs that have been implicated in many human diseases, although their potential involvement in inflammatory skin diseases remains elusive.ObjectivesTo compare and contrast the circRNA expression landscapes in paired lesional and non-lesional skin from psoriasis and AD patients relative to skin from unaffected individuals. Moreover, to correlate circRNA expression to disease severity.MethodsWe analyzed high-depth RNA-seq data from paired lesional and non-lesional skin samples from 27 AD patients, 28 psoriasis patients, and 38 healthy controls. CircRNAs and their cognate linear transcripts were quantified using the circRNA detection algorithm, CIRI2.ResultsWe identified 39,286 unique circRNAs in total and found that psoriasis and AD lesional skin could be distinguished from non-lesional and healthy skin based on circRNA expression landscapes. In general, circRNAs were less abundant in lesional relative to non-lesional and healthy skin. Differential expression analyses revealed many significantly downregulated circRNAs, mainly in psoriasis lesional skin, and a strong correlation between psoriasis and AD-related circRNA expression changes was observed. A subset of circRNAs, including ciRS-7, was specifically dysregulated in psoriasis and show promise as biomarkers for discriminating AD from psoriasis.ConclusionPsoriasis and circRNA transcriptomes share expression features, including a global downregulation, but only psoriasis is characterized by several circRNAs being dysregulated independently of their cognate linear transcripts.
THE LOW-HARM SCORE FOR PREDICTING MORTALITY IN PATIENTS DIAGNOSED WITH COVID-19: A MULTICENTRIC VALIDATION STUDY
Authors: Soto-Mota Adrian , Marfil-Garza Braulio A. , Rodríguez Erick Martínez , Rodríguez José Omar Barreto , Romo Alicia Estela López , Minutti Paolo Alberti , Loya Juan Vicente Alejandre , Talavera Félix Emmanuel Pérez , Cervera Freddy José Ávila , Burciaga Adriana Velazquez , Aramburo Oscar Morado , Olguín Luis Alberto Piña , Soto-Rodríguez Adrian , Prado Andrés Castañeda , Doherty Patricio Santillán , Galindo Juan O Galindo , García Luis Alberto Guízar , Gordillo Daniel Hernández , Mejía Juan Gutiérrez 
Published: May 2020

ABSTRACT- ImportanceMany COVID-19 prognostic factors for disease severity have been identified and many scores have already been proposed to predict death and other outcomes. However, hospitals in developing countries often cannot measure some of the variables that have been reported as useful.- ObjectiveTo assess the sensitivity, specificity, and predictive values of the novel LOW-HARM score (Lymphopenia, Oxygen saturation, White blood cells, Hypertension, Age, Renal injury, and Myocardial injury).- DesignThe score was designed using data from already published cohorts of patients diagnosed with COVID-19. Afterwards, it was calculated it in 438 consecutive hospital admissions at twelve different institutions in ten different cities in Mexico.- SettingTwelve hospitals in ten different cities in Mexico.- ParticipantsData from 438 patients was collected. Data from 400 patients (200 deaths and 200 survivors) was included in the analysis.- ExposureAll patients had an infection with SARS-CoV-2 confirmed by PCR.- Main OutcomeThe sensitivity, specificity, and predictive values of different cut-offs of the LOW-HARM score to predict death.- ResultsMean scores at admission and their distributions were significantly lower in patients who were discharged compared to those who died during their hospitalization 10 (SD: 17) vs 70 (SD: 28). The overall AUC of the model was 95%. A cut-off > 65 points had a specificity of 98% and a positive predictive value of 96%. More than a third of the cases (36%) in the sample had a LOW-HARM score > 65 points.- Conclusions and relevanceThe LOW-HARM score measured at admission is highly specific and useful for predicting mortality. It is easy to calculate and can be updated with individual clinical progression.KEY POINTSQuestionIs it possible to predict mortality in patients diagnosed with COVID-19 using easy-to-access and easy-to-measure variables?FindingsThe LOW-HARM score (Lymphopenia, Oxygen saturation, White blood cells, Hypertension, Age, Renal injury, and Myocardial injury) is a one-hundred-point score that, when measured at admission, had an overall AUC of 95% for predicting mortality. A cut-off of ≥ 65 points had a specificity of 98% and a positive predictive value of 96%.MeaningThe LOW-HARM score measured at admission is highly specific and useful for predicting mortality in patients diagnosed with COVID-19. In our sample, more than a third of patients met the proposed cut-off.
Knowledge, attitude, practice and fear of COVID-19: A cross-cultural study
Authors: Ali Mohammad , Uddin Zakir , Banik Palash Chandra , Hegazy Fatma A. , Zaman Shamita , Ambia Abu Saleh Mohammed , Siddique Md. Kaoser Bin , Islam Rezoana , Khanam Fatema , Bahalul Sayed Mohammad , Sharker Md Ahiduzzaman , Hossain F M Akram , Ahsan Gias U 
Published: May 2020

AbstractBackgroundKnowledge, Attitude and Practice (KAP), and Fear toward COVID-19 are an important issue when designing public health approaches to control the spread of this highly contagious disease like COVID-19 during the global pandemic period. Studies with KAP and fear measures are limited only regional or country level, not yet with global or cross-cultural populations. The study is aimed to measure KAP and fear level towards COVID-19 and explore its cross-cultural variances in knowledge by socio-demographic factors among the general population of 8 different countries over 5 continents.MethodA cross-sectional online survey was conducted in April 2020 among 1296 participants using the Google form platform. Considering the social distancing formula and pandemic situation, we collect data using popular social media networks. Univariate and bivariate analyses were used to explore the collected data on KAP, fear, and sociodemographic factors.ResultOverall knowledge score was 9.7 (out of 12) and gender differences (female vs male: 9.8 vs 9.5) were significant (p=0.008) in the bivariate analysis. Knowledge score variances found significant in some regions by gender, marital status and education qualification. The highest and lowest mean knowledge scores were recorded in the Middle East (10.0) and Europe (9.3). Despite having a high fear score (22.5 out of 35), 78.35% of respondents were in a positive attitude and 81.7% in good practice level. Fear score rankings: Middle East (1st; 23.8), Europe (2nd; 23.2); Africa (3rd; 22.7); South Asia (4th; 22.1); Oceania (5th; 21.9); and North America (6th; 21.7). We didn’t find a correlation between fear and knowledge.LimitationDue to the nature of the online survey, aged and rural populations are under-representing (e.g. more than half of the responders are 16-29 age group).ConclusionKAP and fear variation exist among geographical regions. Gender, marital status and education qualification are factors in knowledge variances for some regions. KAP and fear measures can assist health education programs considering some sociodemographic factors and regions during an outbreak of highly contagious disease and, which can uplift a positive attitude and good practice.HighlightsCross-cultural KAP and fear toward COVID-19 are evaluatedRespondents from Europe scored less knowledge on COVID 19 but had more good knowledge levelAbout 80% participants had positive attitude and good practice behavior.Interestingly, Participants in Oceania avoided more crowded places whereas, in Europe worn more masks during outing as a measure of preventionParticipants in Middle East had the highest score in fear, and fear was independent of knowledge
The Potential Impact of Intensified Community Hand Hygiene Interventions on Respiratory tract Infections: A Modelling Study
Authors: Pham Thi Mui , Mo Yin , Cooper Ben S. 
Published: May 2020

AbstractIncreased hand hygiene amongst the general public has been widely promoted as one of the most important non-pharmaceutical interventions for reducing transmission during the ongoing COVID-19 pandemic and is likely to continue to play a key role in long-term efforts to suppress transmission before a vaccine can be deployed. For other respiratory tract infections community hand hygiene interventions are supported by evidence from randomised trials, but information on how effectiveness in reducing transmission scales with achieved changes in hand hygiene behaviour is lacking. This information is of critical importance when considering the potential value of substantially enhancing community hand hygiene frequency to help suppress COVID-19. Here, we developed a simple model-based framework for understanding the key determinants of the effectiveness of changes in hand hygiene behaviour in reducing transmission and use it to explore the potential impact of interventions aimed at achieving large-scale population-wide changes in hand hygiene behaviour. Our analyses show that the effect of hand hygiene is highly dependent on the duration of viral persistence on hands and that hand washing needs to be performed very frequently or immediately after hand contamination events in order to substantially reduce the probability of infection. Hand washing at a lower frequency, such as every 30 minutes or with a delay of 15 minutes after contamination events, may be adequate to reduce the probability of infection when viral survival on hands is longer, such as when hands are contaminated with mucus. Immediate hand washing after contamination is more effective than hand washing at fixed-time intervals even when the total number of hand washing events is similar. This event-prompted hand washing strategy is consistently more effective than fixed-time strategy regardless of hand contamination rates and should be highlighted in hand hygiene campaigns.
COVINet: A deep learning-based and interpretable prediction model for the county-wise trajectories of COVID-19 in the United States
Authors: Jiang Yukang , Tian Ting , Zhou Wenting , Zhang Yuting , Li Zhongfei , Wang Xueqin , Zhang Heping 
Published: May 2020

ABSTRACTThe cases of COVID-19 have been reported in the United States since January 2020. There were over 103 million confirmed cases and over one million deaths as of March 23, 2023. We propose a COVINet by combining the architecture of both Long Short-Term Memory and Gated Recurrent Unit and incorporating actionable covariates to offer high-accuracy prediction and explainable response. First, we train COVINet models for confirmed cases and total deaths with five input features, compare their Mean Absolute Errors (MAEs) and Mean Relative Errors (MREs) and benchmark COVINet against ten competing models from the United States CDC in the last four weeks before April 26, 2021. The results show that COVINet outperforms all competing models for MAEs and MREs when predicting total deaths. Then, we focus on the prediction for the most severe county in each of the top 10 hot-spot states using COVINet. The MREs are small for all predictions made in the last 7 or 30 days before March 23, 2023. Beyond predictive accuracy, COVINet offers high interpretability, enhancing the understanding of pandemic dynamics. This dual capability positions COVINet as a powerful tool for informing effective strategies in pandemic prevention and governmental decision-making.
Snx4-mediated nucleophagy targets transcription factors controllingATGgene expression
Authors: Hanley Sara E. , Willis Stephen D. , Cooper Katrina F. 
Published: May 2020

ABSTRACTAutophagy is controlled in part by the repression and activation of Autophagy-related (ATG) gene transcription. Here, we demonstrate that the conserved Cdk8 Kinase Module (CKM) of the mediator complex represses transcription of severalATGgenes. To relieve this repression following nitrogen starvation, Med13 is rapidly degraded via a novel selective autophagy mechanism. This pathway requires the core autophagy machinery but is independent of known nucleophagy systems. It requires the cytosolic filament nucleoporin Gle1, the sorting nexin Snx4-Atg20 heterodimer, and the scaffold protein Atg17. This suggests a model where Med13 traverses through the nuclear pore complex, passing from Gle1 to Snx4. Snx4 then transports Med13 to autophagosomes by binding to Atg17. This previously unidentified nucleophagy pathway also mediates the autophagic degradation of two transcriptional activators ofATGgenes (Rim15, Msn2) suggesting that this mechanism targets transcription factors that regulate ATG expression. This system provides a new level of selectivity, permitting the cell to fine-tune the autophagic response by controlling the turnover of both positive and negativeATGtranscription factors.
Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgG Combined Antibody Tests
Authors: Prazuck Thierry , Colin Mathilda , Giachè Susanna , Gubavu Camélia , Seve Aymeric , Rzepecki Vincent , Chevereau-Choquet Marie , Kiani Catherine , Rodot Victor , Lionnet Elsa , Courtellemont Laura , Guinard Jérôme , Pialoux Gilles , Hocqueloux Laurent 
Published: May 2020

AbstractBackgroundThe SARS-CoV-2 virus is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease). In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a real-life study to evaluate the performance of two RDTs, COVID-PRESTO® and COVID-DUO®, compared to the gold standard, RT-PCR.MethodsRT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orléans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated.ResultsAmong 381 patients with symptoms of COVID-19 who went to the hospital for a diagnostic, 143 patients were RT-PCR negative. Results of test with RDTs were all negative for these patients, indicating a specificity of 100% for both RDTs.In the RT-PCR positive subgroup (n=238), 133 patients were tested with COVID-PRESTO® and 129 patients were tested with COVID-DUO® (24 patients tested with both). The further the onset of symptoms was from the date of collection, the greater the sensitivity. The sensitivity of COVID-PRESTO® test ranged from 10.00% for patients having experienced their 1st symptoms from 0 to 5 days ago to 100% in patients where symptoms had occurred more than 15 days before the date of tests. For COVID-DUO® test, the sensitivity ranged from 35.71% [0-5 days] to 100% (> 15 days).ConclusionCOVID-PRESTO® and DUO® RDTs turned out to be very specific (none false positive) and to be sensitive enough after 15 days from onset of symptom. These easy to use IgG/IgM combined test kits are the first ones allowing a screening with capillary blood sample, by typing from a finger prick. These rapid tests are particularly interesting for screening in low resource settings.
Archiving experience: an exploration of the challenges of preserving virtual reality
Authors: Lischer-Katz Zack 
Published: May 2020

PurposeThis paper aims to explore the opportunities and challenges that immersive virtual reality (VR) technologies pose for archival theory and practice.Design/methodology/approachThis conceptual paper reviews research on VR adoption in information institutions and the preservation challenges of VR to identify ways in which VR has the potential to disrupt existing archival theory and practice.FindingsExisting archival approaches are found to be disrupted by the multi-layered structural characteristics of VR, the part–whole relationships between the technological elements of VR environments and the three-dimensional content they contain and the immersive, experiential nature of VR experiences. This paper argues that drawing on perspectives from phenomenology and digital materiality is helpful for addressing the preservation challenges of VR.Research limitations/implicationsThe findings extend conceptualizations of preservation by identifying gaps in existing preservation approaches to VR and stressing the importance of “experience” as a central element of archival practice and by emphasizing the embodied dimensions of interpreting archival records and the multiple scales of materiality that archival researchers and practitioners should consider to preserve VR.Practical implicationsThese findings provide guidance for digital curators and preservationists by outlining the current thinking on VR preservation and the impact of VR on digital preservation strategies.Originality/valueThis paper gives new insight into VR as an emerging area of concern to digital curation and preservation and expands archival thinking with new conceptualizations that disrupt existing paradigms.
Influence of maternal region of birth on neonatal outcomes of babies born small
Authors: Young Nicole E. , Davies‐Tuck Miranda , Malhotra Atul 
Published: May 2020

AbstractAimTo compare neonatal outcomes of small for gestational age (SGA) infants born to South Asian (SA)‐born women and Australian/New Zealand (ANZ)‐born women.MethodsRetrospective cohort study at a hospital network in Australia. Maternal and neonatal data were collected for infants born SGA between 2013 and 2017 to SA‐ or ANZ‐born women. Rates of perinatal mortality and neonatal morbidities were analysed between groups.ResultsA total of 1018 SA and 959 ANZ SGA infants were included. SA SGA babies were older (median [IQR] 39 [38‐40] weeks) and heavier (2590 [2310‐2780] grams) compared to ANZ SGA babies (38 [37‐40] weeks and 2480 [2059‐2740] grams; P < .001 for both). After adjustment for differences in demographics, SA SGA babies were 1.5 times more likely to develop hypothermia (CI: 1.16‐1.88, P = .001), but 60% less likely to be born with a major congenital malformation (CI: 0.24‐0.67, P = .001) and 36% less likely to need gavage feeding (CI: 0.43‐0.93, P = .02) compared to ANZ SGA babies.ConclusionSmall for gestational age babies of SA‐born women have different neonatal outcomes as compared to those born to ANZ‐born women. Further research into influence of maternal region of birth on placental function, organogenesis and body composition of SGA babies is warranted.